title: HUVEC rep1


title: 3N_rep2

status: Public on Jul 02 2019

type: SRA

city: Illkirch

first: Hinrich

last: Gronemeyer

address: 1 rue Laurent Fries

department: Functional genomics and cancer

country: France

institute: IGBMC

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_3

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
QC of fastq files were performed using FASTQC, Alignment was performed using Hisat2 using human genome build hg19
Raw read counts were performed using SummarizedExperiment (R package)
Differetial expression was assessed using DEseq2 (R package)
Genome_build: hg19
Supplementary_files_format_and_content: DEseq2 output file having differential expressed genes

molecule: total RNA

organism: Homo sapiens

source_name: Prostate tissue

extract_protocol:
Total RNA was isolated from fresh frozen prostate cancer tissue along with matched normal using Trizol (Invitrogen), rRNA was removed using Ribo minus Gold kit
Strand specific total RNA libraries were prepared using Illumina guidelines

tag: tissue

value: Normal

value: Frozen tissue

tag: replicate

value: Biological Replicate 2


title: PE-M_rep4

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

country: USA

institute: University of Wisconsin-Madison

description: Freshly isolated unpassaged (P0) human umbilical vein endothelial cells (HUVECs)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
STAR (Dobin et al. 2013), a splice-junction aware RNASeq alignment algorithm, was used to map reads to version GRCh38.p10 of the human genome (Ensembl). Mapped reads were counted in each sample using RSEM (RNASeq by Expectation Maximization), as described in Li and Dewey (2011).
Genome_build: Gh38.P10
Supplementary_files_format_and_content: tab-delimited text files include RSEM values for each Sample .

source_name: HUVECs

extract_protocol:
Total RNA samples were isolated from P0-HUVECs using an RNeasy Mini Kit (Qiagen, Valencia, CA). The concentration and quality of each RNA sample were assessed using NanoDrop™ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100-bioanalyzer (Agilent Technologies, Santa Clara, CA). Only RNA samples with high RNA integrity number (>8.5) were utilized in this study.
RNA libraries (one library per cell preparation) are generated using the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, California, USA) following the manufacturer’s instruction. In brief, 300ng total RNA of each sample is fragmented using divalent cations under elevated temperature, and purified. Double-stranded complementary DNAs (cDNAs) are synthesized using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers. The cDNAs are ligated to Illumina adapters and amplified in a Linker Mediated PCR reaction (LM-PCR) for 9 cycles using PhusionTM DNA Polymerase and Illumina's PE genomic DNA primer set followed by purification (Agencourt AMPure XP beads, Qiagen).

tag: diagnosis

value: Preeclampsia

tag: fetal sex

value: M

tag: gestational weeks


title: PE-M_rep6


title: PE-M_rep3


title: 1T_rep1

description:
Differential analysis using two biological replicates of tumor tissue against two biological replicates of normal tissue
DESeq2_out_1

value: Tumor

value: Biological Replicate 1


title: PE-M_rep2


title: PE-M_rep1


title: PE-F_rep5

value: F


title: 1N_rep1


title: PE-F_rep2


title: PE-F_rep1


title: PE-F_rep4


title: PE-F_rep3


title: NT-M_rep8

value: Normotensive


title: NT-M_rep5


title: NT-M_rep6


title: NT-M_rep3


title: NT-M_rep4


title: NT-F_rep5


title: NT-F_rep8


title: NT-M_rep1


title: NT-F_rep7


title: NT-M_rep2


title: NT-F_rep3


title: NT-F_rep6


title: NT-F_rep2


title: PE-M_rep5


title: NT-F_rep4


title: NT-F_rep1


title: NT-M_rep7


title: control_351_15.3_left

city: Haifa

first: Philippa

last: Melamed

address: Technion City

country: Israel

institute: Technion-Israel Institute of Technology

data_processing:
FASTQ for quality control, mapping by TopHat
HTSeq-count for read counting
normalization of raw counts and differential expression by DESeq2 in R platform
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: normalized counts for each gene in each sample: excel file

organism: Mus musculus

source_name: ovary

extract_protocol:
TRIzol extraction, Clean & Concentrator (Zymo) purification
CEL-Seq preparation protocol
each sample was barcoded using a pool of 3 different CEL-Seq primers to create technical repeats for each sample in order to reduce technical variability due to differences in barcode efficiency

treatment_protocol: mice were treated with 3% DSS in their drinking water for 7 d

tag: strain

tag: treatment

value: control


title: control_345_15.4_left


title: control_387_16.9_left


title: control_352_15.3_right


title: control_334_13.5_right


title: control_388_16.9_right


title: control_333_13.5_left


title: Ctl 3

type: RNA

city: Honolulu

first: Yiqiang

last: Zhang

state: HI

address: 651 Ilalo St BSB-311D

department: Anatomy, Biochemistry and Physiology

institute: University of Hawaii Manoa

description: Cardiomyocytes from adult bi-transgenic mouse

hyb_protocol: The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols.

scan_protocol: The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings.

data_processing: Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Partek Genomic Suite

label: Biotin

source_name: Adult mouse cardiomyocytes (Ctl)

label_protocol: Affymetrix Biotin Labeling kit

growth_protocol: Freshly isolated cardiomyocytes or cardiac progenitor cells derived from continuous/prolonged culture of adult cardioymocytes

extract_protocol: single-cell direct cDNA synthesis and amplification; NuGEN Pico kit

tag: cell type

value: adult mouse cardiomyocytes


title: control_303_11.4_left


title: control_304_11.4_right


title: control_328_13.4_right


title: retina_sham operated_rep2

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
Gene expression in retina of sham operated rat
CTR2
raw data file: ONC2-CTR2_US83000181_252828212643_S01_GE2_1200_Jun14_1_2.txt

hyb_protocol: 825 ng of Cy3 labeled RNA from the right retina of a rat subjected to optic nerve crush (ONC) and 825 ng Cy5-labeled RNA from the right retina of a sham operated (CTR) rat were co-hybridized with each microarray for 17h at 65°C.

scan_protocol: After washing the chip was scanned with an Agilent G2539A dual laser scanner at 5μm pixel size/20-bit.

data_processing:
The scanned images were analyzed with Feature Extraction Software v. 11.1.19.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers  or with foreground fluorescence less than twice their background in any of the 8 profiled samples were excluded. Data were normalized by an in-house developed, iterative method that alternates intra- and inter-array normalization to the median of the background-subtracted fluorescence of the valid spots in each channel separately, until the overall maximum error of estimate reaches less than 5%.
Normalized (to the median of valid spots in the respective (green or red) channel) background subtracted signal intensity. Although the RNA samples were hybridized on two-color microarrays, data were processed and are presented as resulted from analysis with one-color microarray.

organism: Rattus norvegicus

source_name: retina_sham operated

label_protocol: Total RNA was reverse transcribed in the presence of cyanine Cy3- or Cy5-dUTP and the incorporation of the fluorescent tags was determined with  a NanoDrop ND-2000 Spectrophotometer (http://www.nanodrop.com) .

extract_protocol: Total RNA was extracted using Qiagen RNeasy minikit (www.Qiagen.com) following the manufacturer's recommendations), concentration determined with a NanoDrop ND-2000 Spectrophotometer (http://www.nanodrop.com) and purity with Agilent RNA 6000 Nano kit in an Agilent 2100 Bioanalyzer (www.agilent.com).

treatment_protocol: 8w old female rats were deeply anesthetized by intraperitoneal injection of a mixture of xylazine (10 mg/kg body weight) and ketamine (60 mg/kg body weight). Under a stereoscopic microscope, the right optic nerve was accessed through an incision made in the superior orbital rim, and the conjunctiva was dissected with forceps towards the back of the eye to expose the retrobulbar portion of the optic nerve. The lesion was done by crushing the optic nerve for 10 s at 3 mm from the optic disc, using a pair of watchmaker’s forceps. Sham operated rats underwent the same procedure, except that the forceps was not closed. Animals were euthanized two weeks after the procedure.

value: Lister Hooded

tag: Sex

value: female

tag: age

value: 8 weeks

value: retina

value: sham operated


title: retina_optic nerve crush_rep3

description:
Gene expression in retina of rat with crushed optic nerve
ONC3
raw data file: ONC3-CTR3_US83000181_252828212643_S01_GE2_1200_Jun14_1_3.txt

source_name: retina_optic nerve crush

value: optic nerve crush


title: retina_optic nerve crush_rep2

description:
Gene expression in retina of rat with crushed optic nerve
ONC2
raw data file: ONC2-CTR2_US83000181_252828212643_S01_GE2_1200_Jun14_1_2.txt


title: CPC 2

description: cardiac progenitor cells derived from dedifferentiated/proliferative bi-transgenic mouse cardiomyocytes

source_name: mouse cardiac progenitor cells (CPC)

value: cardiac progenitor cells


title: retina_sham operated_rep4

description:
Gene expression in retina of sham operated rat
CTR4
raw data file: ONC4-CTR4_US83000181_252828212643_S01_GE2_1200_Jun14_1_4.txt


title: retina_optic nerve crush_rep4

description:
Gene expression in retina of rat with crushed optic nerve
ONC4
raw data file: ONC4-CTR4_US83000181_252828212643_S01_GE2_1200_Jun14_1_4.txt


title: retina_sham operated_rep3

description:
Gene expression in retina of sham operated rat
CTR3
raw data file: ONC3-CTR3_US83000181_252828212643_S01_GE2_1200_Jun14_1_3.txt


title: control_327_13.4_left


title: CPC 3


title: DSS_393_16.3_left

value: DSS


title: DSS_394_16.3_right


title: control_249_10.5_left


title: control_274_10.6_right


title: control_273_10.6_left


title: Ctl 1


title: macc1_2

city: Berlin

first: Mathias

last: Dahlmann

address: Robert-Rössle-Str. 10

department: Experimental and Clinical Research Center

country: Germany

institute: Charité University Medicine

description: Gene expression in cell line with ectopic MACC1 overexpression

hyb_protocol: 1.65 ug of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a Agilent Human Gene Expression Microarray Slide (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on a GenePix 4000B Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using protocol GE1-v5_91_0806 and grid 014850_D_20060807.

source_name: SW480/MACC1 replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.9 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 spectrophotometer.

growth_protocol: Cells were grown in RPMI-1640 medium (PAA Laboratories) containing 10% fetal bovine serum (FBS; PAA) and were cultured in a humidified atmosphere with 5% CO2.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen), following the manufacturer's recommendations, including on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples with a RIN of >9.0 were used for the expression analysis

value: colon adenocarcinoma

tag: cell line


title: macc1_1

source_name: SW480/MACC1 replicate 1


title: control_2

description: Gene expression in cell line with vector control

source_name: SW480/vector replicate 2


title: control_346_15.4_right


title: CPC 1


title: retina_optic nerve crush_rep1

description:
Gene expression in retina of rat with crushed optic nerve
ONC1
raw data file: ONC1-CTR1_US83000181_252828212643_S01_GE2_1200_Jun14_1_1.txt


title: control_1

source_name: SW480/vector replicate 1


title: retina_sham operated_rep1

description:
Gene expression in retina of sham operated rat
CTR1
raw data file: ONC1-CTR1_US83000181_252828212643_S01_GE2_1200_Jun14_1_1.txt


title: Ctl 2


title: control_250_10.5_right


title: DSS_339_15.1_left


title: DSS_321_13.2_left


title: DSS_340_15.1_right


title: DSS_298_11.1_right


title: DSS_322_13.2_right


title: DSS_297_11.1_left


title: DSS_292_11.2_right


title: DSS_291_11.2_left


title: Heart/Ventricle: MI_rep2

data_processing:
Standard Protocol recommended in 10X Genomics protocol for single-nucleus RNA seq.
Pre-mRNA transcriptome integrated with the four transgenes (Cre transcript within the MerCreMer fusion gene, BFP, RFP, and GFP) was built using cellranger mkref command according to 10x Genomics’ recommendation.
Mouse GRCm38.93 fasta and transcript annotations were downloaded from Ensembl, including a subset of “gene” types such as protein coding, lincRNA, antisense. Transgenes were added to both as new contigs in the fasta file and as genes/transcripts, and subsequently a mouse pre-transcriptome reference was generated by writing a new annotation file. Cellranger count was used to obtain gene-level summaries.
Genome_build: Mm10 pretranscriptome integrated with 4 transgenes.
Supplementary_files_format_and_content: Gene_barcode_matrices

source_name: Heart/Ventricle

extract_protocol:
Total ventricular nuclei were isolated and purified using modified protocol including ioxitanol gradient/layer for nuclei enrichment.
10X Chromium Single Cell VDJ and 5' Barcoding and Library Construction (only gene expression option used)

treatment_protocol: Myocardial infarction was created by ligation of the left anterior descending artery in adult triple-transgenic mice treated with tamoxifen chow for two weeks followed by at least 2 weeks recovery period.

tag: cells

value: total ventricular nuclei

tag: molecule subtype

value: single-nucleus RNA


title: Heart/Ventricle: MI_rep1


title: DSS_255_10.4_left


title: Heart/Ventricle: Ctl


title: DSS_256_10.4_right


title: Sf1_rep2_NET-prism

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

description: nascent RNA

data_processing:
Library strategy: NET-Seq
All the NET-prism fastq files were processed using custom Python scripts to remove PCR duplicates and reads arising from RT bias (mm10 genome). Reads mapping exactly to the last nucleotide of each intron and exon (Splicing intermediates) were further removed from the analysis. The final NET-prism BAM files were converted to bigwig (1 bp bin), separated by strand, and normalized to x1 sequencing depth using Deeptools (v 2.4) with an “–Offset 1” in order to record the position of the 5’ end of the sequencing read which corresponds to the 3’ end of the nascent RNA. NET-seq/prism tags sharing the same or opposite orientation with the TSS were assigned as ‘sense’ and ‘anti-sense’ tags, respectively.
Genome_build: mm10

source_name: mESCs

growth_protocol: The E14 cell line (mESCs) was cultured at 37 °C, 7.5% CO2, on 0.1% gelatin coated plates, in DMEM + GlutaMax™ (Gibco) with 15% fetal bovine serum (Gibco), MEM non- essential amino acids (Gibco), penicillin/streptomycin (Gibco), 550 µM 2-mercaptoethanol (Gibco), and 10 ng/ml of leukaemia inhibitory factor (LIF) (eBioscience).

extract_protocol:
108 ES cells were used for each IP. It is important to split cells down to five batches of 2x107 each when performing nuclei extraction. All extraction steps are performed on ice to avoid degradation of the nascent RNA. 2x107 were treated with 200 μl of cytoplasmic lysis buffer (0.15% (vol/vol) NP-40, 10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25 µM α-amanitin (Epichem), 10 U RNasin Ribonuclease inhibitor (Promega) and 1× protease inhibitor mix (Thermo)) for 5 min on ice. Lysate was layered on 500 μl of sucrose buffer (10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25% (wt/vol) sucrose, 25 µM α-amanitin, 20 U RNasin Ribonuclease inhibitor and 1× protease inhibitor mix) and spun down for 5 min at 16,000g (4ºC). Supernatant was carefully removed and nuclei were resuspended in 100 μl of DNase digestion buffer ( 1x DNase buffer (NEB), 25 µM α-amanitin, 20 U RNasin Ribonuclease inhibitor and 1× protease inhibitor mix) and further treated with 100 U of DNase I (NEB) for 20 min on ice. It is important for nuclei to be fully resuspended in the DNase digestion buffer. Non resuspended nuclei are an indication of harsh cytoplasmic lysis conditions – In this case reduce the volume of cytoplasmic lysis buffer.
Chromatin-solubilised nuclei were spun down at 6,000g (4ºC) for 2 min and supernatant was carefully removed. Nuclei were further treated with 200 μl of nuclei lysis buffer (1% (vol/vol) NP-40, 20 mM HEPES (pH 7.5), 125 mM NaCl, 50 mM urea, 0.2 mM EDTA, 0.625 mM DTT, 25 µM α-amanitin, 20 U RNasin Ribonuclease inhibitor and 1× protease inhibitor mix) for 5 min on ice. Nuclei lysate was spun down at 18,500g (4ºC) for 2 min and supernatant from five different batches was combined.
X1 Phophatase inhibitor mix (Thermo) was implemented on all the above extraction steps for batches intended for Pol II S2ph and Pol II S5ph immunoprecipitations.
Combined supernatants from the previous step were incubated in a final 1/10 dilution in IP buffer for 2 hours at 4ºC. Beads were washed 4 times with 1 ml of IP buffer and 700 μl of Qiazol (Qiagen) was directly added to the beads, followed by 140 μl of Chloroform. Samples were spun down and supernatant was ethanol precipitated (0.3M NaOAc, 2 μl Glycoblue). Concentration and size of nascent RNA was assessed by Nanodrop and TapeStation 2200, respectively. An IP from 108 ES cells usually yields ~200-1000 ng of nascent RNA. Assessment of RNA size is important in order to evaluate the fragmentation time during the library preparation.

value: E14 cell line

tag: chip antibody


title: Control 4

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data. FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread 1.22.3.
Read counts were summarized by Entrez Gene ID using featureCounts and NCBI annotation in Rsubread.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons), gene symbol and the number of reads mapping to that gene.

source_name: femoral cortical bone

extract_protocol:
Femora were collected, ends removed and marrow flushed out prior to snap freezing in liquid nitrogen. The cortical bone was homogenized in QIAzol lysis reagent at 4 degrees C using a Polytron PTA 20S homogenised. RNA was extracted using a Rneasy Lipid Tissue Mini kit (Qiagen) according to manufacturer's instructions.
mRNA reverse transcription cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: background strain

tag: genotype

tag: parent cross


title: DSS_262_10.3_right


title: Ssrp1_sequential_IP_NET-prism

description: nascent RNA

value: Total Pol II (ab817 - Abcam), Ssrp1 (Biolegends)


title: Control 3


title: Ephrin B2 deficient 3


title: Sf1_rep1_NET-prism

description: nascent RNA


title: Control 2


title: Ephrin B2 deficient 1


title: Control 1


title: Ephrin B2 deficient 2


title: Mediator_rep1_NET-prism

description: nascent RNA

data_processing:
Library strategy: NET-Seq
All the NET-prism fastq files were processed using custom Python scripts to remove PCR duplicates and reads arising from RT bias (mm10 genome). Reads mapping exactly to the last nucleotide of each intron and exon (Splicing intermediates) were further removed from the analysis. The final NET-prism BAM files were converted to bigwig (1 bp bin), separated by strand, and normalized to x1 sequencing depth using Deeptools (v 2.4) with an “–Offset 1” in order to record the position of the 5’ end of the sequencing read which corresponds to the 3’ end of the nascent RNA. NET-seq/prism tags sharing the same or opposite orientation with the TSS were assigned as ‘sense’ and ‘anti-sense’ tags, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph and bw

extract_protocol:
The E14 cell line (mESCs) was cultured at 37 °C, 7.5% CO2, on 0.1% gelatin coated plates, in DMEM + GlutaMax™ (Gibco) with 15% fetal bovine serum (Gibco), MEM non- essential amino acids (Gibco), penicillin/streptomycin (Gibco), 550 µM 2-mercaptoethanol (Gibco), and 10 ng/ml of leukaemia inhibitory factor (LIF) (eBioscience). 108 ES cells were used for each IP. It is important to split cells down to five batches of 2x107 each when performing nuclei extraction. All extraction steps are performed on ice to avoid degradation of the nascent RNA. 2x107 were treated with 200 μl of cytoplasmic lysis buffer (0.15% (vol/vol) NP-40, 10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25 µM α-amanitin (Epichem), 10 U RNasin Ribonuclease inhibitor (Promega) and 1× protease inhibitor mix (Thermo)) for 5 min on ice. Lysate was layered on 500 μl of sucrose buffer (10 mM Tris-HCl (pH 7.0), 150 mM NaCl, 25% (wt/vol) sucrose, 25 µM α-amanitin, 20 U RNasin Ribonuclease inhibitor and 1× protease inhibitor mix) and spun down for 5 min at 16,000g (4ºC). Supernatant was carefully removed and nuclei were resuspended in 100 μl of DNase digestion buffer ( 1x DNase buffer (NEB), 25 µM α-amanitin, 20 U RNasin Ribonuclease inhibitor and 1× protease inhibitor mix) and further treated with 100 U of DNase I (NEB) for 20 min on ice. It is important for nuclei to be fully resuspended in the DNase digestion buffer. Non resuspended nuclei are an indication of harsh cytoplasmic lysis conditions – In this case reduce the volume of cytoplasmic lysis buffer.   Chromatin-solubilised nuclei were spun down at 6,000g (4ºC) for 2 min and supernatant was carefully removed. Nuclei were further treated with 200 μl of nuclei lysis buffer (1% (vol/vol) NP-40, 20 mM HEPES (pH 7.5), 125 mM NaCl, 50 mM urea, 0.2 mM EDTA, 0.625 mM DTT, 25 µM α-amanitin, 20 U RNasin Ribonuclease inhibitor and 1× protease inhibitor mix) for 5 min on ice. Nuclei lysate was spun down at 18,500g (4ºC) for 2 min and supernatant from five different batches was combined.   X1 Phophatase inhibitor mix (Thermo) was implemented on all the above extraction steps for batches intended for Pol II S2ph and Pol II S5ph immunoprecipitations.  Combined supernatants from the previous step were incubated in a final 1/10 dilution in IP buffer for 2 hours at 4ºC. Beads were washed 4 times with 1 ml of IP buffer and 700 μl of Qiazol (Qiagen) was directly added to the beads, followed by 140 μl of Chloroform. Samples were spun down and supernatant was ethanol precipitated (0.3M NaOAc, 2 μl Glycoblue). Concentration and size of nascent RNA was assessed by Nanodrop and TapeStation 2200, respectively. An IP from 108 ES cells usually yields ~200-1000 ng of nascent RNA. Assessment of RNA size is important in order to evaluate the fragmentation time during the library preparation.
Combined supernatants from the previous step were incubated in a final 1/10 dilution in IP buffer for 2 hours at 4ºC. Beads were washed 4 times with 1 ml of IP buffer and 700 μl of Qiazol (Qiagen) was directly added to the beads, followed by 140 μl of Chloroform. Samples were spun down and supernatant was ethanol precipitated (0.3M NaOAc, 2 μl Glycoblue). Concentration and size of nascent RNA was assessed by Nanodrop and TapeStation 2200, respectively. An IP from 108 ES cells usually yields ~200-1000 ng of nascent RNA. Assessment of RNA size is important in order to evaluate the fragmentation time during the library preparation.

value: Med14 (Invitrogen)


title: TFIID_rep2_NET-prism

description: nascent RNA

value: TFIID (Santa Cruz)


title: Mediator_rep2_NET-prism

description: nascent RNA


title: TFIID_rep1_NET-prism

description: nascent RNA


title: Ssrp1_rep2_NET-prism

description: nascent RNA

value: Ssrp1 (Biolegends)


title: DSS_261_10.3_left


title: PolS5_rep2_NET-prism

description: nascent RNA

value: Pol II S5ph (ab5408 – Abcam)


title: Spt6_rep1_NET-prism

description: nascent RNA

value: Spt6 (Cell Signalling)


title: Ssrp1_rep1_NET-prism

description: nascent RNA


title: Spt6_rep2_NET-prism

description: nascent RNA


title: PolS2_rep2_NET-prism

description: nascent RNA

value: Pol II S2ph (Cat No:61083 – Active Motif)


title: PolS5_rep1_NET-prism

description: nascent RNA


title: PolS2_rep1_NET-prism

description: nascent RNA


title: TG CD25 Low rep 3

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.80

source_name: regulatory T cells from spleen and lymph nodes (inguinal, cervical and brachial)

extract_protocol:
T regs were isolated from splenocyes and lymph nodes of Atg5+/+ DC and Atg5-/- DC mice by CD4+ enrichment and FACS sorting to isolate CD4+ CD62L+ CD25 High or CD4+ CD62L+ CD25 Low  populations.  Total RNA was extracted using RNeasy Mini Kit. SMARTer™ Ultra Low RNA kit (Clontech) was used for the reverse transcription and cDNA amplification. 10 ng of total RNA was used as input for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: regulatory T cells (CD4+ CD62L+ CD25 Low)

value: Atg5 flox/flox CD11c Cre +/-


title: TG CD25 Low rep 2


title: WT CD25 Low rep 3

value: Atg5 flox/flox CD11c Cre -/-


title: TG CD25 Low rep 1


title: TG CD25 High rep 2

value: regulatory T cells (CD4+ CD62L+ CD25 High)


title: TG CD25 High rep 3


title: WT CD25 Low rep 1


title: WT CD25 Low rep 2


title: WT CD25 High rep 2


title: WT CD25 High rep 3


title: WT CD25 High rep 1


title: RNA_YBX1_RIP

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description: YBX1 RIP in T24 cell

data_processing:
Library strategy: RNA-BisSeq
Raw Reads were stripped of adaptor sequence and removed low quality bases using Trimmomatic, clean reads were aligned to the hg19 genome assembly using using meRanGh from meRanTK.
The m5C sites were called using meRanCall from meRanTK (FDR < 0.01).
The YBX1 binding regions (peaks) were identified by using the MACS2. The cutoff threshold for P value < 0.01 was set.
Genome_build: hg19
Supplementary_files_format_and_content: txt, YBX1 binging cpeaks

source_name: T24 cell line

extract_protocol:
Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis.
Flag-YBX1 overexpressed T24 cells pellets were resuspended with 2 volume of lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 400 U/ml RNase inhibitor), and incubated at 4 °C for 30 min with rotation. Then the lysate was centrifuged at 15 000 g for 20 min. Before incubating the lysate with Flag beads, 100ul were taken as input. The anti-Flag M2 magnetic beads (Sigma, 10 μl per mg lysate) were washed with NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U/ml RNase inhibitor) four times. Cell lysate was mixed with M2 beads and incubated at 4 °C for 4 h with rotation. The beads were washed two times with 1 ml ice-cold NT2 buffer. Then the beads were subject to Micrococal nuclease (NEB) digestion (1:1 000 000 dilution) for 8 min at 37 °C. The beads were cooled on ice immediately for 5 min and washed two times with 1 ml ice-cold 1× PNK+EGTA buffer (50 mM Tris-HCl pH 7.5, 20 mM EDTA, 0.05% NP-40, 200 U/ml RNase inhibitor) and two times with 1 ml ice-cold 1× PK buffer (50 mM NaCl, 100 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.2% SDS, 200 U/ml RNase inhibitor). Then the beads were digested with 200 μl pre-heated (20 min at 50 °C) Proteinase K and RNAs were extracted with an equal volume of Acid-Phenol: Chloroform, pH 4.5 (Ambion). The RNAs were subjected to rRNA removal and Bisseq. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length.

value: T24 cell line


title: T3800-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3800

data_processing:
Reads were mapped to the hg19 genome with hisat2.
The number of reads mapped to each Ensembl gene was counted using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: txt, Reads count for each gene in each sample.

molecule: polyA RNA

source_name: human Bladder Tissue

extract_protocol:
Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-Seq library construction.
RNA-Seq libraries was directly constructed by using KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length.

value: 50 year

tag: tissue

value: Bladder cancer tumor tissue


title: RNA_input

description: Input sample for YBX1 RIP in T24 cell


title: YBX1_RIP_BS

description: RNA-BisSeq for YBX1 RIP sample

source_name: T25 cell line


title: T3750-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3750

value: 54 year


title: T3740-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3740

value: 69 year


title: T3660-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3660

value: 79 year


title: T3635-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3635

value: 82 year


title: T3560-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3560

value: 56 year


title: T3403-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3403

value: 44 year


title: T3451-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3451

value: 48 year


title: T3515-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3515

value: 74 year


title: T3357-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3357


title: T3371-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3371

value: 80 year


title: TG CD25 High rep 1


title: T3614-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3614


title: T3282-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3282

value: 52 year


title: T3138-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3138

value: 64 year


title: T3143-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3143

value: 67 year


title: T3196-T

description: RNAseq for tumor tissue of Bladder cancer of individual 3196

value: 77 year


title: T2347-T

description: RNAseq for tumor tissue of Bladder cancer of individual 2347

value: 51 year


title: T2644-T

description: RNAseq for tumor tissue of Bladder cancer of individual 2644

value: 58 year


title: T2297-T

description: RNAseq for tumor tissue of Bladder cancer of individual 2297

value: 73 year


title: T2759-T

description: RNAseq for tumor tissue of Bladder cancer of individual 2759

value: 61 year

value: Bladder cancer tumor tissue


title: T2771-T

description: RNAseq for tumor tissue of Bladder cancer of individual 2771

value: 71 year


title: T2224-T

description: RNAseq for tumor tissue of Bladder cancer of individual 2224

value: 62 year


title: T1495-T

description: RNAseq for tumor tissue of Bladder cancer of individual 1495

value: 65 year


title: T2804-T

description: RNAseq for tumor tissue of Bladder cancer of individual 2804

value: 59 year


title: T2226-T

description: RNAseq for tumor tissue of Bladder cancer of individual 2226

value: 76 year


title: T0565-T

description: RNAseq for tumor tissue of Bladder cancer of individual 0565

value: 46 year


title: T0982-T

description: RNAseq for tumor tissue of Bladder cancer of individual 0982

value: 56 year


title: T1067-T

description: RNAseq for tumor tissue of Bladder cancer of individual 1067

value: 70 year


title: T1037-T

description: RNAseq for tumor tissue of Bladder cancer of individual 1037


title: T0531-T

description: RNAseq for tumor tissue of Bladder cancer of individual 0531

value: 55 year


title: T0474-T

description: RNAseq for tumor tissue of Bladder cancer of individual 0474

value: 72 year


title: T0555-T

description: RNAseq for tumor tissue of Bladder cancer of individual 0555

value: 74 year


title: T1664-T

description: RNAseq for tumor tissue of Bladder cancer of individual 1664

value: 78 year


title: T0156-T

description: RNAseq for tumor tissue of Bladder cancer of individual 0156

value: 57 year


title: T0453-T

description: RNAseq for tumor tissue of Bladder cancer of individual 0453

value: 50 year


title: T0466-T

description: RNAseq for tumor tissue of Bladder cancer of individual 0466


title: N3800-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3800

value: Paracancerous tissue of bladder cancer


title: N3740-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3740

value: 69 year


title: N3635-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3635

value: 82 year


title: N3451-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3451

value: 48 year


title: N3111-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3111

value: 43 year


title: N3467-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3467


title: N3138-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3138

value: 64 year


title: N2804-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 2804

value: 60 year


title: N3522-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3522


title: N2297-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 2297

value: 73 year


title: N2759-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 2759

value: 61 year


title: N2347-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 2347

value: 51 year


title: N2688-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 2688

value: 62 year


title: N1495-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 1495

value: 65 year


title: N2224-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 2224


title: N1691-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 1691

value: 71 year


title: N1664-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 1664


title: N1067-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 1067

value: 68 year


title: N0897-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 0897


title: N0565-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 0565

value: 46 year


title: N0531-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 0531

value: 55 year


title: N1037-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 1037

value: 72 year


title: N0474-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 0474

value: Paracancerous tissue of bladder cancer


title: N0555-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 0555

value: 77 year


title: N0156-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 0156

value: 57 year


title: N3143-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 3143

value: 67 year


title: siNSUN2-BS

description: RNA-BisSeq of siNSUN2 in T24 cell

data_processing:
Library strategy: RNA-BisSeq
Raw Reads were stripped of adaptor sequence and removed low quality bases using Trimmomatic, clean reads were aligned to the hg19 genome assembly using using meRanGh from meRanTK.
The m5C sites were called using meRanCall from meRanTK (FDR < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: txt, m5C sites in control and NSUN2 knockdown samples

extract_protocol:
Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-BisSeq library construction.
For RNA-BisSeq, bisulfite-treated mRNAs were first subjected to reverse transcription with ACT hexamers and Superscript II Reverse Transcriptase (Invitrogen), and the following processes were carried out with KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length.

value: T24 cell line


title: N0453-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 0453


title: T3800-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3800

data_processing:
Library strategy: RNA-BisSeq
Raw Reads were stripped of adaptor sequence and removed low quality bases using Trimmomatic, clean reads were aligned to the hg19 genome assembly using using meRanGh from meRanTK.
The m5C sites were called using meRanCall from meRanTK (FDR < 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: All m5C sites and levels in each sample.

value: 50 year

value: Bladder cancer tumor tissue


title: T3750-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3750

value: 54 year


title: T3740-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3740

value: 69 year


title: siControl-BS

description: RNA-BisSeq of siControl in T24 cell


title: T3635-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3635

value: 82 year


title: T3660-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3660

value: 79 year


title: T3357-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3357

value: 44 year


title: T3451-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3451

value: 48 year


title: T3403-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3403


title: T3614-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3614


title: N1063-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 1063

value: 64 year


title: T3515-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3515

value: 74 year


title: T3371-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3371

value: 80 year


title: T3560-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3560

value: 56 year


title: N0466-T

description: RNAseq for paracancerous tissue of bladder cancer of individual 0466

value: 55 year

value: Paracancerous tissue of bladder cancer


title: T3282-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3282

value: 52 year


title: T2759-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 2759

value: 61 year


title: T2771-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 2771

value: 71 year


title: T2804-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 2804

value: 59 year


title: T3138-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3138

value: Bladder cancer tumor tissue


title: T3143-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3143

value: 67 year


title: T2644-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 2644

value: 58 year


title: T2347-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 2347

value: 51 year


title: T2297-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 2297

value: 73 year


title: T1664-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 1664

value: 78 year


title: T1037-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 1037


title: T1495-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 1495

value: 65 year


title: T1067-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 1067

value: 70 year


title: T0565-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 0565

value: 46 year


title: T0531-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 0531


title: T0474-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 0474

value: 72 year


title: T0555-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 0555

value: 74 year


title: T3196-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 3196

value: 77 year


title: T0453-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 0453

value: 50 year


title: N3740-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3740

value: 69 year

value: Paracancerous tissue of bladder cancer


title: N3522-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3522


title: N3800-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3800


title: N3635-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3635

value: 82 year


title: N3467-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3467

value: 59 year


title: N3451-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3451

value: 48 year


title: T0156-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 0156

value: 57 year

value: Bladder cancer tumor tissue


title: N3143-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3143

value: 67 year


title: N3111-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3111

value: 43 year


title: N2688-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 2688

value: 62 year


title: N3138-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 3138

value: 64 year


title: N2804-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 2804

value: 60 year


title: T2226-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 2226

value: 76 year


title: N2759-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 2759

value: 61 year


title: T2224-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 2224


title: N2297-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 2297

value: 73 year


title: T0982-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 0982

value: 56 year


title: N2224-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 2224


title: N2347-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 2347

value: 51 year


title: N1495-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 1495

value: 65 year


title: N1691-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 1691

value: 71 year

value: Paracancerous tissue of bladder cancer


title: N1067-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 1067

value: 68 year


title: T0466-BS

description: RNA-BisSeq for tumor tissue of Bladder cancer of individual 0466

value: 55 year


title: N0897-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 0897

value: 69 year


title: N0565-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 0565

value: 46 year


title: N1037-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 1037

value: 72 year


title: N1664-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 1664

value: 78 year


title: N0555-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 0555

value: 77 year


title: N0531-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 0531


title: N0474-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 0474


title: N0466-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 0466


title: N0156-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 0156

value: 57 year


title: N0453-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 0453


title: siNSUN2-T_rep2

description: RNAseq of siNSUN2  replicate 2 in T24 cell

data_processing:
Reads were mapped to the hg19 genome with hisat2.
The number of reads mapped to each Ensembl gene was counted using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: txt, Reads count for each sample.

value: T24 cell line


title: siControl-T_rep2

description: RNAseq of siControl  replicate 2 in T24 cell


title: siNSUN2-T_rep1

description: RNAseq of siNSUN2  replicate 1 in T24 cell


title: 863-3H

city: Zurich

first: Eva

last: Koch

address: Winterthurerstrasse 190

department: IEU

institute: University of Zurich

data_processing:
reads were mapped against the reference genome(ftp://ftp.ensemblgenomes.org/pub/release30/metazoa/gtf/tribolium_castaneum/Tribolium_castaneum.Tcas3.30.gtf.gz) with STAR v.2.5  (adaptors were trimmed and  the first 10 bases were hard trimmed, minimum average quality Q10, minimum tail quality 10, minimum read length 20).
Number of reads per gene were counted with FeatureCounts (gtfFeatureType: exon, featureLevel: gene, allowMultiOverlap=TRUE, minFeatureOverlap=10, minMapQuality=10)
Genome_build: Tcas3.30
Supplementary_files_format_and_content: tab-delimited text files: raw read counts data for each sample

organism: Tribolium castaneum

source_name: females, whole body

growth_protocol: Beetles were kept in 24h dark on organic wheat flour mixed with 10% organic baker's yeast. Flour and yeast were sterilized by heating them for 12h at 80°C before use. RNA was extracted from the whole body of reproducing females at the age of eight weeks.

extract_protocol:
RNA Mini Prep kit (Zimo Research, California, USA)
LEXOGEN mRNA-Seq Library Kit (LEXOGEN GmbH, Vienne, Austria)

treatment_protocol: We used four different climatic conditions. A control condition (33°C, 70% relative humidity) , in which the beetles had lived for more than 20 generations, and three stressful treatments: Dry, Hot, Hot-Dry. The conditions in the treatments were: Hot: 37°C and 70% r. h., Dry: 33°C and 30% r. h., Hot-Dry: 37°C and 30% r. h.

tag: environment

value: Hot

value: female


title: 863-4HD

value: Hot-Dry


title: siControl-T_rep1

description: RNAseq of siControl  replicate 1 in T24 cell


title: 863-4CT

value: Control


title: 863-4D

value: Dry


title: 863-2HD


title: 863-3D


title: 863-2H


title: 863-3CT


title: 863-2D


title: 863-2CT


title: N1063-BS

description: RNA-BisSeq for paracancerous tissue of bladder cancer of individual 1063

value: 64 year


title: 863-1H


title: 863-1D


title: 799-4H


title: 799-4CT


title: 799-3HD


title: 799-3H


title: 799-3D


title: 799-3CT


title: 799-2H


title: 799-2HD


title: 799-2D


title: 863-3HD


title: 799-1HD


title: 799-1D


title: 710-4CT


title: 799-1CT


title: 710-4HD


title: 710-4D


title: 710-4H


title: 710-3HD


title: 710-3H


title: 710-3CT


title: 863-1CT


title: 710-2HD


title: 710-3D


title: 710-2H


title: 799-4D


title: 710-2D


title: 710-2CT


title: 710-1HD


title: 710-1H


title: 638-4CT


title: 710-1D


title: 638-3H


title: 638-4HD


title: 710-1CT


title: 799-1H


title: 638-4H


title: 799-2CT


title: 638-3HD


title: 638-2HD


title: 638-3CT


title: 638-1H


title: 638-1HD


title: 638-1CT


title: 496-3HD


title: 496-4H


title: 496-3D


title: 638-3D


title: 496-3CT


title: 496-4D


title: 638-2CT


title: 496-3H


title: 638-1D


title: 496-2HD


title: 638-4D


title: 496-4CT


title: 496-2D


title: 496-1D


title: 432-4H


title: 432-4HD


title: 496-1CT


title: 638-2H


title: 432-4D


title: 432-4CT


title: 432-3HD


title: 432-3D


title: 432-2HD


title: 432-2H


title: 432-2D


title: 432-1HD


title: 638-2D


title: 432-2CT


title: 432-1H


title: 432-1CT


title: 348-4H


title: 348-4CT


title: 432-1D


title: 496-1H


title: 348-4HD


title: 348-4D


title: 348-3D


title: 496-2CT


title: 348-3HD


title: 348-2HD


title: 348-3CT


title: 348-2H


title: 348-2D


title: 348-2CT


title: 496-1HD


title: 432-3H


title: 348-1D


title: 432-3CT


title: 348-1HD


title: 293-4H


title: 293-4D


title: 293-3CT


title: 293-3D


title: 293-3H


title: 293-4CT


title: 293-1HD


title: 293-2D


title: 293-1D


title: 245-4D


title: 245-4CT


title: 245-2HD


title: 245-3D


title: 496-2H


title: 245-2H


title: 245-3CT


title: 348-1CT


title: 245-1H


title: 245-2D


title: 245-2CT


title: 245-1HD


title: 293-4HD


title: 245-3H


title: 245-1D


title: 245-1CT


title: 348-1H


title: 1077-4HD


title: 1077-4H


title: 1077-4D


title: 293-2H


title: 293-1CT


title: 293-2HD


title: 245-4H


title: 1077-4CT


title: 1077-3H


title: 245-3HD


title: 1077-3CT


title: 1077-3D


title: 1077-3HD


title: 1077-2HD


title: 1077-2H


title: 1077-1D


title: 1077-1HD


title: 1077-1CT


title: 1077-2D


title: 103-4D


title: 103-4H


title: 103-4HD


title: 103-4CT


title: 103-3HD


title: 103-3D


title: 103-3H


title: 1077-1H


title: 103-2HD


title: 103-3CT


title: 103-2H


title: 103-2D


title: 103-1H


title: 103-2CT


title: 103-1HD


title: 103-1D


title: 1005-4HD


title: 103-1CT


title: 1005-4H


title: 1077-2CT


title: MDBK-GFP

city: Haikou

first: Feng

last: Pang

address: Renmin Road 58

institute: Hainan University

data_processing:
Single-end sequencing on Illumina HiSeq 2500
Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N);
Removing reads containing adapters
Removing reads shorter than 18nt (not include adapters).
genome build: GCA_000003055.3
Differentially expressed miRNAs were identified with fold change ≥2 and P value <0.05.
Supplementary_files_format_and_content: MDBK-GFP-E5 vs MDBK-GFP miRNA differential expression

organism: Bos taurus

source_name: MDBK cells expressing GFP

extract_protocol:
Ambion mirVana miRNA Isolation Kit (Thermo Fisher Scientific)
TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)

value: Kidney

value: MDBK

value: epithelial cells


title: MDBK-GFP-E5

data_processing:
Single-end sequencing on Illumina HiSeq 2500
Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N);
Removing reads containing adapters
Removing reads shorter than 18nt (not include adapters).
Differentially expressed miRNAs were identified with fold change ≥2 and P value <0.05.
genome build: GCA_000003055.3
Supplementary_files_format_and_content: MDBK-GFP-E5 vs MDBK-GFP miRNA differential expression

source_name: MDBK cells expressing BPV-13 E5


title: shHAT1C5_H3K9Ac

city: Palo Alto

first: Michael

last: Snyder

state: CA

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

library_source: genomic

data_processing:
adapter trimming (cutadapt)
alignment to hg19 (bowtie2)
deduplication (Picard tools)
sort and filter (samtools)
peak calling (MACS2)
differential peak calls (DiffBind)
genome-wide normalization (align2rawsignal)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig of ChIP-seq signal track

molecule: genomic DNA

source_name: hTert-HME1 cell line

growth_protocol: Mammary epithelial growth media (Lonza)

extract_protocol:
1% formaldehyde crosslinking, quench with glycine, chromtin extraction with nuclei isolation, disruption with RIPA, then sonication, clarification.  Chromatin immunoprecipitation was performed with anti-H3K9Ac antibody (Abcam ab4441) and protein A/G agarose.
end-repair, adapter ligation, PCR

value: anti-H3K9Ac antibody (Abcam ab4441)


title: 17EP11_S16

city: Minneapolis

first: Ying

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
Raw, QC-ed short reads were cleaned via trimmomatic81 using set parameters (ILLUMINACLIP:all_illumina_adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:70).
The preprocessed reads were directly input into MiXCR82 for TCR profiling with default setting (https://mixcr.readthedocs.io/en/latest/rnaseq.html)
KnownTRB clonetypes in rhesus monkeys was used as reference.
The resulted TRB clonetypes were further filtered using customized threshold with a clone fraction of ≥ 0.5%.
Data from Rocket is presented in the manuscript.

organism: Macaca mulatta

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted from frozen PBLs using Rneasy Plus Universal (Qiagen) and first strand cDNA was created from the poly A tailed fraction of total RNA
SMART™ Approach for Full-Length cDNA Library Construction
Enriched VDJ Enriched VDJ amplicons from each sample were uniquely dual-indexed by PCR for multiplexing compatibility during sequencing

treatment_protocol: Frozen XXX  aliqouts were thawed and rested overnight in XX  media with X% FBS prior to antibody staining and XX the next day. No XX were added

tag: time period

value: Base line


title: 17EP16_S20


title: 17EP15_S18


title: 17EP10_S14

value: Base Line


title: shHAT1B6_H3K9Ac


title: 1005-4CT


title: shHAT1A7_H3K9Ac


title: 1005-3H


title: 1005-3HD


title: shCon5_H3K9Ac

value: control


title: shCon3_H3K9Ac


title: 1005-3D


title: shCon2_H3K9Ac


title: 1005-3CT


title: ACM_rep3

description:
ACM3
replicate 3

hyb_protocol: Standard Illumina BeadChip Hyb protocol / Whole-Genome Gene Expression Direct Hybridization

scan_protocol: Standard Illumina iScan protocol.

data_processing:
Feature extraction using GenomeStudio V2011, with Gene Expression module.
Normalized Averaged signal, exported GenomeStudio -Gene Expression module

source_name: cardiomyocytes from adult ventricle

label_protocol: Standard Illumina BeadChip Labeling protocol

growth_protocol: Primary cardiomyocytes (fetal-ECM, adult- ACM, or hypertrophic- TAC).

extract_protocol: Rneasy Protocol (Qiagen kit) with Dnase I treatment step.

value: CD1 background

tag: developmental stage

value: adult

value: cardiomyocytes from adult ventricle

tag: disease state


title: ACM_rep1

description:
ACM1
replicate 1

tag: strain


title: 1005-4D


title: TAC_rep3

description:
TAC3
replicate 3

source_name: cardiomyocytes from the ventricle of hypertrophic heart

tag: time

value: 7 day post-op

value: hypertrophic heart


title: ECM-rep2

description:
ECM2
replicate 2

source_name: cardiomyocytes from fetal ventricle

tag: cell type

value: cardiomyocytes from fetal ventricle


title: TAC_rep2

description:
TAC2
replicate 2

value: cardiomyocytes from the ventricle of hypertrophic heart


title: TAC_rep1

description:
TAC1
replicate 1


title: ACM_rep2

description:
ACM2
replicate 2


title: shHAT1_C5_h4k5ac_ChIP-seq

data_processing:
adapter trimming with cutadapt/1.8.1 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -O 5 -m 30 -q 15
alignment with bowtie2 -q --phred33 -X 2000 --fr -p 8 -x hg19
samtools/1.2 view -Sb
samtools/1.2 sort  -@ 8 -m 2G
picard-tools/1.92 Mark duplicates
samtools/1.2 filter out unmapped reads and filter out mitochondrial reads (samtools view -b -f 1 -F 12 -L)
phantompeakqualtools/run_spp_nodups.R
macs2/2.1.0 callpeak -q 0.01 --nomodel --extsize 53
align2rawsignal -of="bg" -n=5 -l=105 -k=epanechnikov -w 150 -f=0 -mm=30
bedGraphToBigWig
Aligned bam files were used for differential peak calling with R version 3.3.1 and  DiffBind using parameters summits=250, and deseq2 linear modeling.
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs, diffbind.csv

growth_protocol: Mammary Epithelial Growth Medium (Lonza)

extract_protocol:
1% formaldehyde crosslinking, followed by isolation of nuclei, lysis in RIPA buffer, then sonication with Branson and Bioruptor Pico, clarification of extract, then immunoprecipitation with specific antibodies
Illumina Truseq

tag: treatment

tag: replicate

value: h4k5ac -- Millipore cat# 07-327


title: 1005-2HD

value: Hot-Dry

tag: Sex

value: female


title: 1005-2H

value: Hot


title: shHAT1_A7_h4k5ac_ChIP-seq

tag: cell line


title: Toll10b + myrAkt 4

city: Charlottesville

first: Miyuki

last: Suzawa

state: VA

address: 1340 Jefferson Park Ave 5015 Pinn Hall

department: Pharmacology

institute: University of Virginia

data_processing:
Transcript-level quantitation with Salmon
Gene level summarization with txImport
Normalization with DESeq2
Differential expression with DESeq2
Genome_build: BDGP6 (dm6) annotation of the fly transcriptome from Ensemble

organism: Drosophila melanogaster

source_name: Mid-third inster larval fat body

growth_protocol: Drosophila melanogaster fat body in mid third inster larvae

extract_protocol:
Total RNA from fat bodies was purified by Direct-zol RNA Microprep kit (Zymo Research)
Ovation RNA-Seq System for Drosophila (NuGEN) was used to generate the cDNA library for sequencing on an Illumina HiSeq 4000

treatment_protocol: Transgenes encoding RFP, GFP, Toll10b, or myrAkt were driven in mid third instar larval fat body for 12 h at 30 ˚C using a temperature-sensitive Tub-GAL80ts transgene in combination with r4-GAL4

value: w; Tub-GAL80ts/UAS-Toll10b ; r4-GAL4/UAS-myrAkt

value: fat body


title: Toll10b + myrAkt 2


title: Toll10b + myrAkt 3


title: shHAT1_B6_h4k5ac_ChIP-seq


title: yap-1(ys38)_embryos_rep2

city: Seoul

first: Junho

last: Lee

address: Gwanak-ro 1

department: Department of Biological Sciences

country: South Korea

institute: Seoul National University

hyb_protocol: the standard Affymetrix protocol

scan_protocol: the standard Affymetrix protocol

data_processing: The chip data were analyzed using the Microarray Suite version 5.0 (MAS 5.0) with global scaling performed as the normalization method using Genplex ver.3.0

organism: Caenorhabditis elegans

source_name: yap-1(ys38), whole embryos

label_protocol: the standard Affymetrix protocol

growth_protocol: Worms were maintained by the standard method. To collect embryos of N2 and yap-1(ys38), gravid adults from 10 plates of 10cm NGM were bleached

extract_protocol: Total RNA was extracted by the freezing-thawing method using Trizol according to the manufacturer's instructions.

value: embryos


title: ECM-rep1

description:
ECM1
replicate 1


title: yap-1(ys38)_embryos_rep3


title: Toll10b + myrAkt 1


title: yap-1(ys38)_embryos_rep1

source_name: yap-1(ys38, whole embryos


title: wildtype_embryos_rep3

source_name: WT, whole embryos


title: wildtype_embryos_rep1


title: myrAkt 4

value: w; Tub-GAL80ts/UAS-RFP ; r4-GAL4/UAS-myrAkt

value: RFP/myrAkt


title: shCon5_h4k5ac_ChIP-seq

value: shControl


title: 1005-2D

value: Dry


title: wildtype_embryos_rep2

description: The results of N2-2 were significantly different from those of the other two replicates, therefore were excluded from our analysis.


title: myrAkt 3


title: 1005-2CT

value: Control


title: myrAkt 2


title: shCon3_h4k5ac_ChIP-seq


title: 1005-1H


title: 1005-1HD


title: shHAT1_C5_h4k12ac_ChIP-seq

value: h4k12ac -- abcam cat# ab46983


title: shCon2_h4k5ac_ChIP-seq


title: myrAkt 1


title: Toll10b 3

value: w; Tub-GAL80ts/UAS-Toll10b ; r4-GAL4/UAS-GFP


title: Toll10b 1


title: Toll10b 4


title: shHAT1_B6_h4k12ac_ChIP-seq


title: Toll10b 2


title: 1005-1D


title: ctrl 4

value: w; Tub-GAL80ts/UAS-RFP ; r4-GAL4/UAS-GFP

value: RFP/GFP


title: shHAT1_A7_h4k12ac_ChIP-seq


title: ctrl 2


title: ctrl 1


title: 1005-1CT


title: shCon3_h4k12ac_ChIP-seq


title: shCon5_h4k12ac_ChIP-seq


title: shCon2_h4k12ac_ChIP-seq


title: ctrl 3


title: Rbap46_ChIP-seq_2

value: untreated

value: Rbap46 -- cell signaling cat# 6882


title: HAT1_ChIP-seq_2

value: HAT1 -- abcam cat# ab194296


title: Rbap46_ChIP-seq_1


title: HAT1_ChIP-seq_1


title: Huh7.5.1 HCC cells_PBS treated (48h), biological rep2

first: Jun-Nian

last: Zhou

address: 27# Taiping Road

institute: Institute of Health Service and Transfusion Medicine

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Huh7.5.1_PBS (48 hours) as controls

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The cells were maintained in DMEM (Sigma) containing 10% FBS (ExCell Biology, Shanghai, China) at 37°C with 5% CO2.

extract_protocol: Total cellular RNA was isolated from the cells using an RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol.

treatment_protocol: The cells were washed with PBS after removed medium, and the TriZol was added into the cell monolayer, gently mixed with the tips, and immmediately freezed with liquid N2, followed by stored in the -80 oC freezer.

value: Hepatocellular carcinoma (HCC) cell line

tag: treated with

value: PBS (48 hours) as controls


title: input_2

description: input.bigwig

tag: chip antibody


title: Huh7.5.1 HCC cells_PBS treated (48h), biological rep1


title: Huh7.5.1 HCC cells_arsenic trioxide treated (48h), biological rep1

source_name: Huh7.5.1_3.6 μM arsenic trioxide (48 hours)

value: 3.6 μM arsenic trioxide (48 hours)


title: TREM1 knockout Microglia biological replicate 6

city: Stanford

first: Katrin

middle: I

last: Andreasson

state: California

address: 1201 Welch Rd, MSLS P250

department: Neurology and neurological sciences

description: Gene expression data from Microglia of ischemic hemisphere in TREM1 Knockout mouse brain at day 2 post 45min MCAo

hyb_protocol: 3.0 μg of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array at 60 rpm for 16 h at 45°C in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing: The Affymetric Clariom S microarrays were analyzed with RMA to detect the gene-level differential expression using the Affymetrix Transcriptome Anaylsis Console (TAC) 4.0 Software using default parameters. The significant genes (FDR<0.05) were ranked by fold-change with a cutoff of 2.  TAC4.0 software output does not include data for  ~6000 internal control probe sets, thus the sample tables include data for ~22K Clariom S probe sets that assay gene expression.

label: biotin

source_name: Microglia from ischemic hemisphere of TREM1 Knockout mice

label_protocol: Microarray was performed at the Protein and Nucleic Acid (PAN) Facility at the Stanford University. The RNA integrity was examined on a bioanalyzer (Agilent). High-quality RNA (RNA integrity number >7.5) was used for expression microarray analysis. 0.6-0.8 ng of total RNA was used to generate double strand cDNA. 6.6 μg of ds cDNA were fragmented and labeled with biotin according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher).

extract_protocol: RNA from neutrophils, macrophages and microglia from TREM1 -/- and +/+ ischemic hemispheres was extracted with Qiagen RNeasy Micro kit according to the manufacturer’s instructions.

treatment_protocol: 8-10 week-old male C57BL/6 mice, of genotype TREM1+/+ and TREM1-/-, underwent MCAo for 45min followed by reperfusion (MCA0-RP). 48 hours after the reperfusion, mice were transcardially perfused with cold heparinized 0.9% NaCl and ischemic hemispheres were homogenized manually to filter through 70µm cell strainer. All cells in the homogenate were then purified by myelin depletion with Miltenyi Myelin removal kit according to the manufacturer’s instructions. After cell staining with CD45, CD11b and Ly6g,  neutrophils (CD45Hi, CD11b+, Ly6G+), macrophages (CD45Hi, CD11b+, Ly6G-) and microglia (CD45Lo, CD11b+, Ly6G+) were sorted  and RNA isolated for Affymetrix Clariom HT microarray analysis.

value: TREM1 Knockout

tag: gender

value: male

value: brain

value: microglia

tag: age

value: 8-10 weeks


title: Huh7.5.1 HCC cells_arsenic trioxide treated (48h), biological rep2


title: TREM1 knockout Microglia biological replicate 4

tag: genotype


title: TREM1 knockout Microglia biological replicate 5

tag: tissue


title: SMMC-7721 HCC cells_PBS treated (48h), biological rep2

source_name: SMMC-7721_PBS (48 hours) as controls


title: SMMC-7721 HCC cells_arsenic trioxide treated (48h), biological rep2

source_name: SMMC-7721_3.6 μM arsenic trioxide (48 hours)


title: SMMC-7721 HCC cells_arsenic trioxide treated (48h), biological rep1


title: input_1

description: input.bigwig


title: SMMC-7721 HCC cells_PBS treated (48h), biological rep1


title: mRNA_RectalCancer_rep87

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

country: Japan

institute: Japanese Foundation For Cancer Research

hyb_protocol: After fragmentation, RNA was hybridized withAffymetrix Hybridization,Wash, and Stain Kit on Affymetrix PrimeView Human Gene Expression Array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA-dabg using Affymetrix Expression Console software.

source_name: Rectal cancer tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Micro Kit following manufacturer's instruction.

value: rectal cancer

value: M

tag: batch

value: Batch 2


title: TREM1 knockout Microglia biological replicate 3


title: WT Microglia biological replicate 6

description: Gene expression data from microglia of ischemic hemisphere in WT mouse brain at day 2 post 45min MCAo

source_name: Microglia from ischemic hemisphere of WT mice

value: WT


title: TREM1 knockout Microglia biological replicate 2


title: mRNA_RectalCancer_rep90


title: mRNA_RectalCancer_rep91


title: mRNA_RectalCancer_rep89


title: mRNA_RectalCancer_rep88


title: WT Microglia biological replicate 5


title: TREM1 knockout Microglia biological replicate 1


title: mRNA_RectalCancer_rep86

value: F


title: SW480-NC

city: Hangzhou

first: Jingjing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Road

department: pathology

institute: Zhejiang University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to HG19 whole genome using Hisat2 (v2.0.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Ballgown software.
Genome_build: HG19

source_name: colorectal cancer cells

growth_protocol: SW480-NC and SW480-STC2 cells were cultured in RPMI 1640 medium with 10% fetal bovine serum in the atmosphere of 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from cells by using RNeasy Mini Kit (Qiagen). cDNA samples were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina).
Sequencing was performed on the Illumina HiSeq platform 2500 platform (Illumina) using standard Illumina protocols.

value: negative control


title: SW480-STC2

value: STC2 overexpression


title: mRNA_RectalCancer_rep85


title: mRNA_RectalCancer_rep84


title: WT Microglia biological replicate 4


title: siB2-1_bih_C

data_processing:
Alignment with tophat version 2.0.11 using gencode hg19 GTF gencode.v19.annotation.gtf
Reads counted with summarizeOverlaps function from GenomicAlignments R package (Bioconductor)
DESeq2 workflow was followed: DESeqDataSet was used to make a dds object using the design formula: ~media + replicate + siRNA_type
data was rlog transformed, followed by limma removeBatchEffect command to remove batch effect associated with A replicates
estimateSizeFactors command was used to normalize for sequencing depth.  This resulted in the 20160215_normMatrix.csv file
Genome_build: hg19
Supplementary_files_format_and_content: supplementary file: 20160215_normMatrix.csv has normalized, transformed read counts for each ensemble gene per sample

source_name: hTert-HME1 cell line

growth_protocol: Mammary Epithelial Growth Medium (Lonza) at 37degC with 5% CO2

extract_protocol:
AllPrep (Qiagen) followed by RiboZero (Illumina)
Script-seq v2 (Illumina)

treatment_protocol: siRNA transfection with RNAiMAX (Invitrogen)

value: hTert-HME1 cell line

tag: sirna

tag: media

value: -EGF

tag: passages

tag: biological replicate

value: C


title: mRNA_RectalCancer_rep83


title: WT Microglia biological replicate 3

tag: strain


title: mRNA_RectalCancer_rep82


title: sscon2_bih_C

description: RNAconEGFC


title: mRNA_RectalCancer_rep81


title: WT Microglia biological replicate 1

tag: cell type


title: mRNA_RectalCancer_rep79


title: mRNA_RectalCancer_rep78


title: mRNA_RectalCancer_rep77


title: mRNA_RectalCancer_rep76


title: mRNA_RectalCancer_rep80


title: siB2-1_comp_C

value: +EGF (complete)


title: sscon2_comp_C

description: RNAconCompC


title: siB2-1_bih_B

value: B


title: WT Microglia biological replicate 2


title: siB2-1_comp_B


title: TREM1 knockout Macrophage biological replicate 6

description: Gene expression data from Macrophage of ischemic hemisphere in TREM1 Knockout mouse brain at day 2 post 45min MCAo

source_name: Macrophage from ischemic hemisphere of TREM1 Knockout mice

value: TREM1 Knockout

value: macrophage


title: mRNA_RectalCancer_rep74


title: sscon2_comp_B

description: RNAconCompB


title: TREM1 knockout Macrophage biological replicate 5

value: male

value: brain


title: TREM1 knockout Macrophage biological replicate 4

value: 8-10 weeks


title: mRNA_RectalCancer_rep75

value: rectal cancer


title: mRNA_RectalCancer_rep70

value: M


title: mRNA_RectalCancer_rep71

value: Batch 2


title: mRNA_RectalCancer_rep68


title: TREM1 knockout Macrophage biological replicate 3


title: mRNA_RectalCancer_rep69


title: TREM1 knockout Macrophage biological replicate 2


title: siB2-1_comp_A

value: A


title: mRNA_RectalCancer_rep73

value: F


title: mRNA_RectalCancer_rep67


title: mRNA_RectalCancer_rep72


title: mRNA_RectalCancer_rep66


title: mRNA_RectalCancer_rep63


title: siB2-1_bih_A


title: sscon2_bih_A

description: RNAconEGFA


title: WT Macrophage biological replicate 2

description: Gene expression data from macrophage of ischemic hemisphere in WT mouse brain at day 2 post 45min MCAo

source_name: Macrophage from ischemic hemisphere of WT mice

value: WT


title: TREM1 knockout Macrophage biological replicate 1


title: mRNA_RectalCancer_rep65

description: 9C971 has a duplicate to bridge batches 1 and 2.


title: mRNA_RectalCancer_rep61


title: mRNA_RectalCancer_rep58


title: sscon2_comp_A

description: RNAconCompA


title: siB2-1_bih_C

description: accessible chromatin

data_processing:
Adapter trimming with Cutadapt version 1.8.1
Alignment with bowtie version 1.1.1
Picard-tools version 1.92 MarkDuplicates to remove duplicates, then mitochondrial reads were filtered
MACS2 callpeak function to create narrowpeak files, which were merged
Signal track created with align2rawsignal, then signal exported to cagt file with Extractsignal program
Genome_build: hg19
Supplementary_files_format_and_content: cagt file: mean signal over merged peaks

extract_protocol:
AllPrep (Qiagen)
ATAC-seq per Buenrostro et al. Nature Methods 2013


title: TREM1 knockout neutrophil biological replicate 5

description: Gene expression data from neutrophil of ischemic hemisphere in TREM1 Knockout mouse brain at day 2 post 45min MCAo

source_name: Neutrophil from ischemic hemisphere of TREM1 Knockout mice

value: neutrophil


title: mRNA_RectalCancer_rep60


title: siB2-1_comp_C

description: accessible chromatin

value: hTert-HME1 cell line


title: sscon2_bih_C

description: accessible chromatin

value: -EGF


title: TREM1 knockout neutrophil biological replicate 4


title: mRNA_RectalCancer_rep57


title: WT Macrophage biological replicate 1


title: WT Macrophage biological replicate 3


title: mRNA_RectalCancer_rep55


title: mRNA_RectalCancer_rep64


title: mRNA_RectalCancer_rep56


title: mRNA_RectalCancer_rep62


title: mRNA_RectalCancer_rep59


title: TREM1 knockout neutrophil biological replicate 2


title: mRNA_RectalCancer_rep53


title: mRNA_RectalCancer_rep50

value: Batch 1


title: sscon2_comp_C

description: accessible chromatin

value: +EGF (complete)

value: C


title: mRNA_RectalCancer_rep52


title: siB2-1_bih_B

description: accessible chromatin

value: B


title: sscon2_bih_B

description: accessible chromatin


title: mRNA_RectalCancer_rep48


title: siB2-1_comp_B

description: accessible chromatin


title: sscon2_comp_B

description: accessible chromatin


title: siB2-1_bih_A

description: accessible chromatin


title: WT neutrophil biological replicate 2

description: Gene expression data from neutrophil of ischemic hemisphere in WT mouse brain at day 2 post 45min MCAo

source_name: Neutrophil from ischemic hemisphere of WT mice


title: WT neutrophil biological replicate 4


title: mRNA_RectalCancer_rep51


title: mRNA_RectalCancer_rep54


title: ATAC-Seq DCyc-like ZT16 rep1 rep2

city: College Station

first: Christine

last: Merlin

address: 3258 TAMU

department: Biology

institute: Texas A&M University

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings. Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
Adapter sequence was removed using fastx clipper (hannonlab.cshl.edu/fastx_toolkit/) with options "-Q33 -n -v". Clipped reads were mapped to the monarch genome (v3; (Zhan and Reppert 2013)) using Bowtie2 (Langmead and Salzberg 2012) with parameters "--phred33 –local”. Unmapped reads and mapped reads with low mapping quality of less than 10 were discarded after sorting using SAMtools version 0.1.19 (Li, Handsaker et al. 2009). Mapped reads of high quality were adjusted such that those aligned to the + strand and the – strand were shifted by +4 bp and by –5 bp, respectively, as described in (Buenrostro, Wu et al. 2015).
ATAC-seq peaks were called using MACS2 (Zhang, Liu et al. 2008) with parameters "-q 0.01 --nomodel --shift -100 --extsize 200 --keep-dup all", using reads from naked DNA as control. For each genotype and time point, consensus peaks between biological replicates were generated by merging peaks with overlapping start and end coordinates using HOMER (Heinz et al, 2010). Pairwise comparison of the biological replicates were performed by quantifying in each replicate the density of reads contained within consensus peaks using HOMER. To compare replicates from all genotypes and time points to one another, peaks from all libraries were merged in a set of 37,642 consensus peaks, read densities were quantified in each sample, and correlation was determined using the Pearson correlation coefficient (Eisen, Spellman et al. 198. Given that high level of reproducibility was found between biological replicates, ATAC-seq peaks from replicate libraries of WT, Clk KO and DCyc-like mutant at ZT04 and ZT16 were merged by calling peaks on both replicates at the same time using MACS2 with the same parameters as before. The number of peaks called ranged from 13,555 to 23,222 and were used for subsequent analysis.
Locations of ATAC-seq peaks with respect to genomic features were determined for each condition using merged peaks from biological replicates. Although a few number of peaks could not be annotated because they were present in scaffolds containing no annotated genes, majority of the peaks were assigned (in order of priority) as one of the following: (1) promoter-TSS if present within –1kb to +100bp of the transcription start site (TSS), (2) TTS if within -100bp to +1kb of the transcription termination site (TTS), (3) exon if within any exon, (4) intron if within any intron, or (5) intergenic. Differential peak analysis between conditions was performed on sets of merged peaks using HOMER and DESeq2 (Love, Huber et al. 2014) package in R with default FDR cutoff of < 0.05 and log2 fold-change of > 1 and < ‒1. To visualize ATAC-seq peaks, bigWig files normalized to 10 million reads were generated from bam files and visualized using the Integrative Genomics Viewer (IGV; (Robinson et al, 2011; Thorvaldsdóttir et al, 2013)).
Occupied transcription factor (TF) DNA binding sites within open chromatin regions associated to clock-controlled genes were identified in the ATAC-seq peaks of brains of WT ZT04 and WT ZT16 using the Wellington TF footprinting algorithm of pyDNase (Piper, Elze et al. 2013) with a p-value < 10-10 and false discovery rate (FDR) < 0.01. Footprints common to both time points or specific to either one were identified using the intersect command of bedtools (Quinlan and Hall, 2010) with options -wao. Footprints from each group were further analyzed in WT, Clk KO and DCyc-like mutant at ZT04 and ZT16 using the "dnase_to_treeview.py" script in pyDNase to generate CSV files containing Tn5 integration counts from the center of the footprints flanked by 100 bp on either sides. Heat maps were then generated in Java Treeview (Saldanha 2004 using the CSV files as input. To determine the effect of clock disruption on time-of-day dependent footprints, average profiles were generated using a modified dnase_average_profile.py script in pyDNase to obtain raw Tn5 integration counts from positive and negative strands of the 200 bp regions and averaging them for each bp. Data smoothing was applied using 3-bp rolling averages.
Motif analysis
Genome_build: Monarch genome (assembly v3)
Supplementary_files_format_and_content: bigWig files containing the alignment

organism: Danaus plexippus

source_name: 3 brains per rep

growth_protocol: Monarch butterflies were raised in the laboratory on semi-artificial diet under 15 hours light, 9 hours dark (LD, 15:9) conditions in Percival incubators at 25ºC and 70% humidity, as previously described (Markert, Zhang et al. 2016). Adult were housed in glassine envelopes in the same lighting and temperature conditions, and were manually fed a 25% honey solution daily.

extract_protocol:
Brains free of eye photoreceptors were dissected in ice-cold ringer’s solution and resuspended twice in 600 μl of NP-40 lysis buffer (10mM Tris-HCl at pH 7.5, 10mM NaCl, 3 mM MgCl2, and 0.1% NP-40). Crude nuclei were prepared by homogenizing the brains in a 2 ml, ice-cold, Dounce homogenizer with two strokes of a loose-fitting pestle.
Nuclei was directly subjected to transposition by Tn5 transposase for 30 min at 37°C using the Nextera DNA Library Preparation Kit (Illumina), and the tagmented DNA was then purified using a Zymo DNA Clean & ConcentratorTM-5 Kit, all according to a previously published protocol (Buenrostro et al, 2015). To generate a control naked DNA library, 1ng of genomic DNA extracted with phenol/chloroform was also subjected to transposition by Tn5 transposase and the tagmented DNA was purified following the same procedures. Barcoded libraries were PCR amplified, each using a common custom primer and a unique custom Nextera barcoded primer, as in (Buenrostro et al, 2015). For each library, after an initial round of five PCR cycles, the optimal number of PCR cycles to stop amplification prior to saturation was estimated by real-time quantitative PCR. Five to ten additional PCR cycles were then performed bringing the total number to 10 (for control DNA) to 15 cycles, and the libraries were purified using a Qiagen MinElute PCR purification kit. Libraries quality and size distribution was assessed on a Bioanalyzer, libraries were quantified by real-time quantitative PCR and mixed in equimolar ratios before sequencing on a single lane of using 50bp single end reads on an Hi-seq 2500 (Illumina).

treatment_protocol: Adult monarchs were entrained for a minimum of 7 days after eclosion in 15:9 LD cycles at 25ºC.

tag: time

value: Brain

value: DCyc-like mutant

value: female


title: ATAC-Seq Control DNA

source_name: 6 brains

value: control

value: wild-type

value: female and male


title: mRNA_RectalCancer_rep47

value: rectal cancer

value: M


title: mRNA_RectalCancer_rep49


title: WT neutrophil biological replicate 1

value: male

value: brain

value: 8-10 weeks


title: sscon2_bih_A

description: accessible chromatin

value: hTert-HME1 cell line

value: A


title: mRNA_RectalCancer_rep44

value: Batch 1


title: mRNA_RectalCancer_rep43


title: ATAC-Seq DCyc-like ZT04 rep1 rep2


title: mRNA_RectalCancer_rep41


title: mRNA_RectalCancer_rep45


title: TREM1 knockout neutrophil biological replicate 1

value: TREM1 Knockout

value: neutrophil


title: mRNA_RectalCancer_rep46


title: mRNA_RectalCancer_rep40


title: mRNA_RectalCancer_rep36


title: mRNA_RectalCancer_rep38

value: F


title: mRNA_RectalCancer_rep39


title: mRNA_RectalCancer_rep35


title: WT neutrophil biological replicate 3

value: WT


title: ATAC-Seq WT ZT16 rep1 rep2

value: Brain


title: 525216c

city: Hershey

first: Raquel

last: Buj

state: PA

address: 500 University Drive

department: Physiology

institute: Penn State College of Medicine

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using TopHat (v.2.0.9)
Differential expression analysis was done using Cuffdiff tool which is available by Cufflinks (v.2.0.2) as described in  (Lynch et al., 2015).
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample and differential expression analysis for Senescnece-bypass Vs Senescence

growth_protocol: IMR90 were cultured according to the ATCC in low oxygen (2% O2) in DMEM (4.5 g/L glucose, corning cat#10017CV) with 10% FBS supplemented with L-glutamine, non-essential amino acids, sodium pyruvate, and sodium bicarbonate. Experiments were performed on population doubling #30.

extract_protocol:
Total RNA was extracted from cells with Trizol (Life Technologies) and DNAse treated with RNeasy Mini Kit (Qiagen, cat#74104) following the manufacturer’s instructions.
The cDNA libraries were prepared using KAPA Stranded RNA-Seq Kits with RiboErase (Kapa Biosystems)
Next generation sequencing was performed in The Penn State College of Medicine Genome Sciences and Bioinformatics Core facility  using a HiSeq 2500 sequencer (Illumina).

treatment_protocol: IMR90 cells were infected with pLKO.1 GFP or pLKO.1-shRRM2, and 24 hours later cells were infected with pLKO.1 GFP vector or pLKO.1-shp16. Cells were selected with puromycin (3ug/mL) for 7 days.

tag: shRNA

value: pLKO.1 shRRM2 + pLKO.1 shp16

tag: group

value: Senescence-bypass


title: mRNA_RectalCancer_rep33

tag: Sex


title: sscon2_comp_A

description: accessible chromatin

value: +EGF (complete)


title: ATAC-Seq ClkKO ZT04 rep1 rep2

value: Clk KO

value: female


title: mRNA_RectalCancer_rep34

value: rectal cancer

value: M


title: ATAC-Seq WT ZT04 rep1 rep2

value: wild-type

value: female and male


title: siB2-1_comp_A

description: accessible chromatin

value: hTert-HME1 cell line


title: 525216b

tag: cell line


title: 525216a


title: mRNA_RectalCancer_rep37


title: RNA-Seq ClkKO ZT22 rep2

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.38 and RTA 1.18.61 software with default parameter settings. Sequencer .bcl basecall files were formatted into .fastq files using CASAVA_v1.8.2 script configureBclToFastq.pl.
Reads were mapped to the monarch genome (assembly v3; (Zhan and Reppert 2013)) using TopHat2 (Kim, Pertea et al. 2013) with parameters "--read-realign-edit-dist 2 -g 1 --b2-sensitive”.
Expression levels of transcripts were quantified using Cufflinks (Trapnell, Williams et al. 2010, Trapnell, Roberts et al. 2012).
A modified Fourier transformation was used (Wijnen, Naef et al. 2005) to identify cycling transcripts meeting the following criteria: (1) three or more reads per kilo base per million mapped reads (RPKM) in at least one time point, (2) F24 (24-hr spectral power) > 0.45, (3) p-value of the F24, as described in (Menet, Rodriguez et al. 2012) < 0.05 (i.e., experimental pF24-value is within the top 5% of the 10,000 pF24-values calculated from randomized permutation), and (3) amplitude (maximal/minimal experimental values) > 1.3.
Heat maps were produced using heatmap.2 in gplots package for R. Gene ontology and KEGG pathway enrichment analysis were performed using Metascape (metascape.org).
Genome_build: Monarch genome (assembly v3)
Supplementary_files_format_and_content: Output from cufflinks in generic FPKM Tracking Format saved as plain text files containing the estimated gene-level expression values.

source_name: 3 brains

extract_protocol:
Brains free of eye photoreceptors were dissected in 0.5X RNA later (Ambion) to prevent RNA degradation, and stored at -80ºC until use. Total RNA was extracted using an RNeasy Mini kit (Qiagen).
PolyA+ RNA was isolated from 2 μg of total RNA with NEBNext Oligo d(T) magnetic beads (New England Biolabs), and multiplexed libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos (New England Biolabs) and amplified with 12 PCR cycles, following the manufacturer’s recommendations. Libraries quality and size distribution was verified on a Bioanalyzer, libraries were quantified by real-time quantitative PCR, and 16 multiplexed libraries were mixed in equimolar ratios and sequenced on a Hi-seq 2500 (Illumina) using 50bp single end reads.


title: ATAC-Seq ClkKO ZT16 rep1 rep2


title: mRNA_RectalCancer_rep42


title: RNA-Seq ClkKO ZT22 rep1

value: male


title: mRNA_RectalCancer_rep29

value: Batch 1


title: 525587b

value: pLKO.1 shRRM2

value: Senescence


title: mRNA_RectalCancer_rep31


title: mRNA_RectalCancer_rep26


title: mRNA_RectalCancer_rep24


title: mRNA_RectalCancer_rep28


title: mRNA_RectalCancer_rep25


title: RNA-Seq ClkKO ZT16 rep2


title: RNA-Seq ClkKO ZT16 rep1


title: 587587c

description: pLKO.1 empty vector

value: pLKO.1 empty vector

value: Control


title: 587587b

description: pLKO.1 empty vector


title: mRNA_RectalCancer_rep32

value: F


title: 525587c


title: mRNA_RectalCancer_rep30


title: mRNA_RectalCancer_rep23


title: RNA-Seq ClkKO ZT10 rep2

value: Brain


title: mRNA_RectalCancer_rep22


title: 587587a

description: pLKO.1 empty vector


title: RNA-Seq ClkKO ZT04 rep2


title: TREM1 knockout neutrophil biological replicate 3

value: TREM1 Knockout

value: brain

value: neutrophil

value: 8-10 weeks


title: mRNA_RectalCancer_rep21

value: rectal cancer


title: GFP3

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

data_processing:
Unaligned bam files were converted to FastQ files using Bedtools 2.17.
Original 100bp reads were trimmed down to 50bp with trimmomatic 0.33.
FastQ files were aligned against the dm6 genome using STAR 2.3.0e, using default options.
Aligned reads were imported in R using RSamtools to perform further quality control steps. Only reads with MapQ>0 (aligning to 10 sites or less) were kept for downstream procedures.
To obtain per-sample expression estimates we used the summarizeOverlaps function from the GenomicAlignments package, using the IntersectionNotEmpty mode and single end strand specific options.
Counts were used to perform a differential expression analysis using the DESeq2 package, previously removing genes without reads in any of the analyzed samples, and using the default options.
Output results were filtered to consider differentially expressed genes with |FC|>2 and Benjamini-Hochberg adjusted pvalue < 0.05.
FastQC v011 was used to perform a quality control overview of FastQ files and aligned BAM files.
Binary tracks in BigWig format were generated with the rtracklayer package, both for individual and pooled samples by group.
The log2FC information was used to rank all genes in the genome with nreads>0 and a a Gene Set Enrichment Analysis was performed with Gene Ontology, GOSLIM and KEGG collections.
Genome_build: dm6
Supplementary_files_format_and_content: DESeq2 Differentially expressed genes in RAS vs GFP including chromosomal location information (space, start, end), gene information (width, FBgn, strand, description, symbol, entrez_id, genename), sample and group counts, and DESeq2 differential expression results (log2Foldchange, stat, pvalue, BH-adj pvalue), and null hypothesis rejection column (-1: down, 0: notDE, 1: up)

source_name: wing imaginal disc

growth_protocol: Ap>Gal4, myrT,RasV12; TubGal80ts and Ap>Gal4, myrT,GFP-i; TubGal80ts flies where allowe to grow for 6 days at 18ºC and the shifted at 29ºC for three days prior to the dissection of the wondering L3 larvae wing imaginal dics. The followin stocks wew used Ap>Gal4 (RRID:BDSC_3041), UAS-myrT (RRID:BDSC_32222) and UAS-RasV12 (RRID:BDSC_64196)

extract_protocol:
150.000 cells were collected in Lysis Buffer (20 mM DTT, 10 mM Tris.HCl ph 7.4, 0.5% SDS, 1 μg/μl proteinase K), incubated for 15 min at 65oC and stored at -80ºC. RNA was extracted using RNA Clean XP bead suspension (Agencourt Bioscience), digested with DNAse-I, cleaned-up by a 2nd pull-down and eluted in water.
Library preparation was perfomed using the kit Quant Seq 3' mRNA-Seq Library Prerp for Illumina (Lexogen) following the manufacture's instructions
3' mRNA sequencing in a 100 nucleotides Single Read lane

treatment_protocol: Drosophila wing imaginal discs disgregated with trypsin and the FACS sorted to select the dorsal transgene expressing cells.

value: wing imaginal disc

value: GFP-i

tag: replicate


title: mRNA_RectalCancer_rep19

value: M


title: RNA-Seq ClkKO ZT04 rep1

value: Clk KO


title: RNA-Seq ClkKO ZT10 rep1

value: male


title: mRNA_RectalCancer_rep18

value: Batch 1


title: RNA-Seq Cry2KO ZT22 rep2

value: Cry2 KO

value: female


title: mRNA_RectalCancer_rep16


title: mRNA_RectalCancer_rep17


title: mRNA_RectalCancer_rep20


title: GFP1


title: RNA-Seq Cry2KO ZT22 rep1


title: 525587a

value: pLKO.1 shRRM2

value: Senescence


title: RAS3

value: RasV12 expressing


title: mRNA_RectalCancer_rep27


title: mRNA_RectalCancer_rep15


title: GFP2


title: mRNA_RectalCancer_rep13


title: mRNA_RectalCancer_rep10


title: mRNA_RectalCancer_rep12


title: mRNA_RectalCancer_rep11


title: mRNA_RectalCancer_rep14


title: RAS2


title: mRNA_RectalCancer_rep7