title: WtLeaf4

city: xinxiang

first: kangning

last: wei

state: henan

address: jianshe road

institute: Henan Normal University

description: small RNA

data_processing:
Getting rid of low quality reads(number of bases with quality less than 10 ≥ 4, number of bases with quality less than 13 ≥ 6 at the same time.)
Getting rid of reads which proportion of N (N is unable to determine the base information) is greater than 10
Getting rid of reads with 5' primer contaminants and reads without the insert fragments
Getting rid of reads without 3' primer
Getting rid of reads with poly A
Getting rid of reads shorter than 18nt
Supplementary_files_format_and_content: sequences and count values

organism: Triticum aestivum

source_name: leaf

growth_protocol: The wheat were grown in natural environment,Henan Normal University,Xinxiang ,Henan, China

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Small RNA libraries were prepared by following the BGISEQ's protocol.

tag: cultivar

value: winter wheat Shimai 22

tag: growth/developmental stage

value: jointing stage

value: leaf

value: wild type


title: CV_S6

status: Public on Oct 01 2019

type: RNA

city: Jouy en Josas, France

first: Unai

middle: Escribano

last: Vazquez

state: --- Sélectionner ---

address: Domaine de Vilvert Bat 440

department: MICALIS

country: France

institute: INRA

description: CV

data_processing:
The normalization and all the data analysis were performed according to the GenEx software (Multid Analyses).
For the normalization the Global normalization method of the expression of all genes was applied.
The GenNex software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The deltadeltaCt values are not available.
Fold Change worksheet reports relative quantification of the expiremental group (CEC, Nissle or CV) to the control group (Ax: axenic/germfree), where Ax group has been used as a calibrator on the DeltadeltaCt calculation.

label: FAM

molecule: total RNA

organism: Mus musculus

source_name: Colonic mucosa

label_protocol: Gene expression analysis was performed with a customized TaqMan OpenArray Real-time PCR System (Life Technologies). The cDNA (10 μl) was mixed with the TaqMan OpenArray Real-Time PCR Master Mix and loaded onto the cards using the AccuFill™ System. The cards were cycled in an OpenArray NT Cycler System (Applied Biosystems).

extract_protocol: RNA isolation was carried out using the Ambion mirVana Kit (Life Technologies) according to the manufacturer’s recommendations. The RNA quality of all samples was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) with an average RNA integrity number superior to 9 on a scale of 0 to 10.

tag: colonisation  status

value: CV

tag: group type

value: conventional

tag: colonisation days


title: XEN-PG rep1

type: SRA

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

description: eXtraEmbryonic  eNdoderm stem (XEN) cells from primitive endoderm of in vitro parthenogenetic (PG) blastocyst

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped to the pig reference genome (Sscrofa11.1) using HISAT21 (version 2.0.4) with parameters “hisat2 --sensitive --no-discordant --no-mixed -I 1 -X 1000” and to the reference cDNA sequence using Bowtie22 with parameters “bowtie2 -q  --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200”.
Then the expression levels of each gene were calculated by the fragments per kilobase of exons per million fragments mapped (FPKM) using RSEM3 with parameters “rsem-calculate-expression --paired-end -p 8” based on the result of Bowtie2.
The final expression matrix was subjected to hierarchical clustering using R software.
Development stage (PE, PrE, TE, VE and EPI)-specific genes were selected to do the subsequent analyses. They were mapped to the final expression matrix to do the PCA and heatmap analysis with R software.
FPKMs of 13,825 protein coding genes detected by RNA-seq
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each sample

molecule: polyA RNA

organism: Sus scrofa

source_name: Embryonic cells

growth_protocol: Embryonic explants and XEN cells were cultured on a feeder layer of early passage (n=3) CF-1 mouse embryonic fibroblasts (MEF) cells mitotically inactivated by treatment with mitomycin-C (3 hr, 10 μg/mL). A day before seeding the embryos or XEN cells, the feeders were plated in MEF medium (high-glucose Dulbecco's modified Eagle medium, DMEM (Gibco, Grand Island, NY) supplemented with 10% (v/v) FBS (HyClone, Logan, UT)) on 0.1% (v/v) gelatin-coated four-well plates (Nunclon) at a density of 3-5 × 105 cells per cm2. At least 2 hr before the start of the experiment, the MEF medium was aspirated and replaced with ‘standard ES medium’ which included DMEM/ Nutrient Mixture Ham's F12 (DMEM/F-12, Gibco) supplemented with 15% ES-qualified fetal calf serum (FCS, HyClone), 1 mM sodium pyruvate, 2 mM L-glutamine, 100 units/mL penicillin-streptomycin, 0.1 mM 2-β-mercaptoethanol, 1% non-essential amino acids (NEAA) (all from Gibco), with various combination of growth factors; 10 ng/mL human recombinant leukemia inhibitory factor (hrLIF; Milipore, Bedford, MA) and 10 ng/mL human recombinant basic fibroblast growth factor (hrbFGF; R&D Systems, Minneapolis, MN). Other media combinations that were tested include RPMI 1640 or N2B27 serum free medium (1:1 ratio of DMEM/F12 and Neurobasal medium plus N2 and B27) (all from Gibco), with a com bination of LIF and/or bFGF, or 25 ng/mL human recombinant fibroblast growth factor 4 (hrFGF4; R&D Systems) and 1 μg/mL heparin. Following initial plating, attachment and outgrowth development, the medium was refreshed on d 3, followed by media exchange every 2 days. After 7-8 days of culture, the primary outgrowths were mechanically dissociated into small clumps, and transferred onto fresh feeders for passaging. The pXEN cells were cultured at 38.5°C in 5% O2 and 5% CO2, with the culture medium being refreshed every other day and passaged at 1:20 every 7-8 days. Cells were passaged as clumps by gentle pipetting following 10 min digestion with Accutase (Gibco).

extract_protocol:
For isolation of genomic DNA (gDNA) from cells and tissues, the QIAamp mini DNA Kit (Qiagen) was used according to the manufacturers’ instructions. Total RNA was isolated using Trizol plus RNeasy mini kit (Qiagen) and mRNA from individual blastocysts was extracted using the Dynabeads mRNA Direct Kit (Dynal Asa, Oslo, Norway).
Synthesis of cDNA was performed using a High Capacity cDNA Reverse transcription kit (Applied Biosystems; ABI, Foster City, CA) according to the manufacturers’ instructions. The QIAseq FX Single Cell RNA Library kit (Qiagen) was used for Illumina library preparation and transcriptomics analysis.

treatment_protocol: The pXEN cells were differentiated by means of embryoid body (EB) formation and treatment with small molecules and factors as previously described [#ref]. pXEN cells were dissociated as clumps, washed, and resuspended in medium (DMEM/F12 plus 15% FBS) as hanging drops on the lid of a 60mm dish, and cultured for 5 days, during which time spheroids were formed. To direct pXEN cells differentiation into either visceral endoderm (VE) or parietal endoderm (PE), accutase-dissociated single cells (2 x 105 cells per cm2) were seeded onto a laminin- or fibronectin-coated 6 well plate in N2B27 medium supplemented with the respective differentiation factors and/or chemicals. For example, for differentiation into VE, the cells were treated with CHIR99021(10 μM, stem cell biotech) and BMP4 (50 ng/mL, R&D) for activating Wnt/β-catenin pathway; for differentiation into PE, Folskolin (50 μM) and dbcAMP (1 mM) for activating the cyclic adenosine monophosphate (cAMP) signaling pathway were utilized; as per previous publications [#ref]. Differentiation medium was replaced every two days, and cells were processed for analysis on day 12.

tag: sample type


title: PXB E077 IFN α

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

country: Japan

institute: University of Fukui

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

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

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

organism: Homo sapiens

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

growth_protocol: A monolayer of primary human hepatocytes derived from chimeric mice with human liver was obtained from PhoenixBio Co., Lid (Hiroshima, Japan) and grown in BioCoatTM Collagen I white plate (Corning Life Science, Tewksburry, MA, USA). Hepatocytes were cultured in dHCGM medium consisting of Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, St Lois, MO, USA) with 10% FBS, 20 mM HEPES (Life Technologies/Gibco), 44 mM NaHCO3 (WAKO, Osaka, Japan), 100 U/ml penicillin G, 100 μg/ml streptomycin, 15 μg/ml L-proline (WAKO), 0.25 μg/ml Insulin (Sigma-Aldrich), 50 nM dexamethasone (Sigma-Aldrich), 5 ng/ml epidermal growth factor (Sigma-Aldrich), 0.1 mM L-ascorbic acid 2-phosphate (WAKO), and 2% dimethyl sulfoxide (Sigma-Aldrich).

extract_protocol: RNAs were extracted with TRIZol reagent (Thermo Fisher Scientific) and cDNA was synthesized with High Capacity RNA-to-cDNA Kit (Applied Biosystems, Foster City CA, USA), following the manufacturer’s instructions.

treatment_protocol: HBV for in vitro viral infection was obtained from the culture medium of HepG2 transfected with HBV plasmids. HBV DNA was isolated using SMITEST EX-R&D (MBL; Medical & Biological laboratories Co., LTD, Nagano, Japan) according to the manufacture’s protocol, and the amount of HBV DNA was determined by real-time PCR. PXB cells were infected with the collected HBV at same equivalents in the presence of 4% polyethylene glycol 8000 (PEG8000, Sigma-Aldrich). PXB cells were harvested after 22 days after the infection. IFN-γ (Recombinant Human IFN-γ; PeproTech, Rocky Hill, NJ, USA) or IFN-α (SUMIFERON; Dainippon Pharmaceutical Co. Ltd., Osaka, Japan) were added to each medium of PXB cells at 1 x 10^4 ng/ml and 1 x 10^5 IU/ml, respectively, at the time of medium change from day 4 after the infection.

tag: tissue

value: primary human hepatocytes

tag: treatment

value: HBV infection, IFN α


title: MCF10A cells, hG1a1

city: Graz

first: Wolfgang

last: Schreibmayer

state: Styria

address: Neue Stiftingtalstrasse 6/D04

department: Biophysics

country: Austria

institute: Medical University of Graz

data_processing:
Mapping to human Transcriptome reference (AmpliSeq_Transcriptome_21K.v1, Thermo Fisher) by TMAP
Count reads per Transcript
Write Excel xls
Supplementary_files_format_and_content: Count reads per Transcript

source_name: benign mammary epithelial cell line MCF10A

extract_protocol:
Cells were grown to 70% - 80% confluence, harvested by trypsinization and spun at 750 rpm for 3 minutes. RNA was isolated from cell-pellet using QIA shredder spin column and RNeasy Mini Kit according to manufacturer’s protocol.
10 ng of isolated RNA was heat inactivated for 10 min at 80 °C followed by cDNA Synthesis using the SuperScript ® VILO™ cDNA Synthesis Kit. DNA library was generated using the Ion AmpliSeq™Transcriptome Human Gene Expression Kit according to manufacturers’ instructions. Sequencing was performed on Ion S5 XL benchtop sequencer (Thermo Fisher Scientific) to a length of 200 base pairs. On average 8 million reads were sequenced per sample.

tag: cell line

tag: genotype

value: stably overexpressing KCNJ3 gene product (GIRK1)


title: krill fished at 06:00, DD, biological replicate 3 (DD06-C1)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

description: Gene expression profiling of Antarctic krill in DD condition (DD06-C1)

hyb_protocol: 1.65 μg of labeled cRNA were used in each reaction and the hybridization was carried out at 65°C for 17 hours in an hybridization oven rotator (Agilent Technologies, Palo Alto, CA). The arrays were washed by Agilent Gene expression washing buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Inter-array normalization of expression levels was performed with quantile to correct possible experimental distortions. A normalization function was applied to the expression data of all experiments and then values of spot replicates within arrays were averaged. Furthermore, Feature Extraction Software provided spot quality measures to evaluate the quality and the reliability of the hybridization. In particular, flag glsFound (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as not available (NA). So, in order to make more robust and unbiased statistical analyses, probes with a high proportion of null values were removed from the dataset. 26% of null was used as threshold in the filtering process, obtaining a total of 38,231 available krill transcripts.

organism: Euphausia superba

label_protocol: 800 ng of total RNA were labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labeled with Cy3-dCTP. Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE).

extract_protocol: For each sampling, five-seven animals were collected, and total RNA was extracted with TRIzol (Thermo Fisher) reagent according to the manufacter's instructions. All RNA samples were checked for quality by capillary electrophoresis (RNA 6000 Nano LabChip, Agilent Bioanalyzer 2100, Agilent Technologies).

treatment_protocol: Maintenance of krill and specimens collection were identical to what was described by Teschke et al. (2011). Briefly, two experimental tanks were exposed to a light:dark (LD) regime of 16 hours light and 8 hours darkness and constant darkness (DD) respectively. Prior to the collection of samples, all specimens, in both experimental tanks, were exposed for a period of 3–4 weeks to these conditions to provide a successful acclimatisation to the aquarium conditions. Krill were sampled at regular intervals (every three hours) over a full 24 hour cycle.

value: Head (including brain and compound eyes)


title: PXB E077 Nashi

source_name: primary human hepatocytes derived from chimeric mice with human liver

value: HBV infection, untreated


title: AEP knockdown cell 1

city: Shanghai

first: Zhaoyuan

last: Fang

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

description:
AEP knockdown cell 1
U87_KD_1

hyb_protocol: Agilent standard procedures and instructions

scan_protocol: Feature Extraction software, Agilent Technologies

data_processing: The raw signal data were processed, log transformed and quantile normalized (limma package).

source_name: AEP knockdown cells

extract_protocol:
Total RNA was isolated from 3 control and 3 AEP RNAi U87 cell lines.
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 , Life technologies, Carlsbad, CA, US) & TAKARA RNAiso Plus#9109 following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: AEP knockdown


title: krill fished at 06:00, DD, biological replicate 2 (DD06-B1)

description: Gene expression profiling of Antarctic krill in DD condition (DD06-B1)


title: PXB Kansen Nashi

value: uninfected, untreated


title: krill fished at 09:00, DD, biological replicate 1 (DD09-A)

description: Gene expression profiling of Antarctic krill in DD condition (DD09-A)


title: krill fished at 09:00, DD, biological replicate 2 (DD09-B)

description: Gene expression profiling of Antarctic krill in DD condition (DD09-B)


title: CV_S2

description: CV


title: WtLeaf3

description: small RNA

treatment_protocol: no treatment

value: spring greenup stage


title: XEN-VI rep3

description: eXtraEmbryonic  eNdoderm stem (XEN) cells from primitive endoderm of an in vivo blastocyst


title: PXB E077 IFN γ

value: HBV infection, IFN γ


title: XEN-PG rep2

value: eXtraEmbryonic  eNdoderm stem (XEN) cells from primitive endoderm of in vitro parthenogenetic (PG) blastocyst


title: MCF10A cells, eGFP2

value: benign mammary epithelial cell line MCF10A

value: stably overexpressing eGFP (control)


title: XEN-VI rep2

value: eXtraEmbryonic  eNdoderm stem (XEN) cells from primitive endoderm of an in vivo blastocyst


title: WtLeaf2

description: small RNA

value: winter wheat Shimai 22

value: winter dormancy stage

value: leaf


title: CV_S3

description: CV

value: CV

value: conventional


title: MCF10A cells, eGFP1


title: WtLeaf1

description: small RNA

value: winter wheat collected at three leaf stage

value: wild type


title: XEN-VI rep1


title: krill fished at 06:00, DD, biological replicate 1 (DD06-A1)

description: Gene expression profiling of Antarctic krill in DD condition (DD06-A1)

value: Head (including brain and compound eyes)


title: CV_S1

description: CV


title: MCF10A cells, wt2

value: wt


title: CART_HA_CD8_Naive_Day7_HAbulk

city: PALO ALTO

first: Hima

last: Anbunathan

state: CA

address: 265 Campus Drive

country: USA

institute: Stanford University

description: processed data file: Processed_TPMs.csv

data_processing:
Expression levels of genes were quantified using Kallisto 0.44.0 , with Gencode v27 reference transcriptome , and hg38 as the reference human genome
TPMs were summed for transcript-level quantification
Genome_build: hg38
Supplementary_files_format_and_content: TPM

source_name: CAR T CELLS

extract_protocol:
For T cell subset-specific RNA-seq, T cells were isolated from healthy donor buffy coats. Before activation, naïve and central memory CD4+ or CD8+ subsets were isolated using a BD FACSAria cell sorter (Stem Cell FACS Core, Stanford University School of Medicine) using the following markers: Naïve (CD45RA+CD45RO-, CD62L+, CCR7+, CD95-, and CD122-), Central Memory (CD45RA-CD45RO+, CD62L+, CCR7+). Sorted starting populations were activated, transduced, and cultured as described above. On days 7, 10, and 14 of culture, CAR+ CD4+ and CD8+ cells were sorted, and RNA was isolated using Qiagen mRNEasy kit.
Samples library prep and sequencing was performed by BGI America (Cambridge, MA)

tag: cell type

tag: compartment

value: Naive

tag: timepoint


title: CART_HA_CD8_Naive_Day14_HAbulk

description: processed data file: Processed_TPMs.csv


title: CART_HA_CD8_Naive_Day10_HAbulk

description: processed data file: Processed_TPMs.csv


title: CEC_S8

description: CEC

value: E. coli CEC

value: mono-associated


title: lamb6_supplemented_D56

type: genomic

city: Saint Genes Champanelle

first: Evelyne

last: Forano

state: France

address: INRA Centre ARA

department: UMR MEDIS

description: rumen microbiota of young lambs

hyb_protocol: DNA hybridization (1 microgram for each DNA) was performed at 65°C during 24 h following the Agilent protocol “Oligonucleotide Array-Based CGH for gDNA Analysis”.

scan_protocol: microarray slides were scanned using an Agilent G2505B microarray scanner (Agilent Technologies, Santa Clara, CA, United States) with a resolution of 5 microns and the XDR mode (Extended Dynamic Range) set up at 10 and 100% PhotoMultiplier Tubes (PMT) gain.

data_processing: Fluorescence intensities of oligonucleotide spots were extracted from the scanned images using the Feature Extraction software (V11.0, Agilent Technologies, Santa Clara, CA, United States). Data were processed with dedicated scripts based on C++ and Delphi languages. For each probe, median intensity value of the three replicates was conserved and used as the probe signal value. The signal-to-noise ratio (SNR), similar to the detection threshold response and corresponding to the probe signal value divided by the local background intensity value, was calculated for each probe. Results for 25- and 54-mer probes were treated independently and for each probe type, a gene was considered as detected when 65% of probes were positive. The SNR value of a detected gene was then calculated by the mean of the SNR of all 25- or 54-mer probes targeting this gene.

molecule: genomic DNA

organism: Microbiota

label_protocol: DNA(2 microgrammes) was labeled using the ULS aRNA Labeling Kit and Cy3 cyanine (Kreatech Diagnostics, Amsterdam, Netherlands) following the manufacturer’s recommendations.

extract_protocol: DNA was extracted from 250 mg of rumen  content following Yu and Morrison procedure (Yu and Morrison 2004). DNA yield and quality were determined after Nanodrop 1000 spectrophotometric quantification. DNA extracts were stored at -20°C until analysis.

tag: host

value: Ovis aries

value: rumen

value: feed supplement


title: CART_HA_CD8_CM_Day7_HAbulk

description: processed data file: Processed_TPMs.csv

value: Central memory


title: lamb5_supplemented_D56

description: rumen microbiota of young lambs


title: CART_HA_CD8_CM_Day14_HAbulk

description: processed data file: Processed_TPMs.csv


title: CEC_S6

description: CEC


title: CEC_S5

description: CEC


title: CEC_S7

description: CEC


title: lamb3_control_D56

description: rumen microbiota of young lambs

value: control


title: lamb2_control_D56

description: rumen microbiota of young lambs


title: lamb4_supplemented_D56

description: rumen microbiota of young lambs


title: CART_HA_CD8_CM_Day10_HAbulk

description: processed data file: Processed_TPMs.csv


title: CEC_S9

description: CEC


title: CEC_S3

description: CEC


title: lamb1_control_D56

description: rumen microbiota of young lambs


title: MCF10A cells, wt1

value: benign mammary epithelial cell line MCF10A


title: CEC_S2

description: CEC


title: AGO2_3 (small RNA)

city: Halle

first: Claus

last: Weinholdt

address: Von-Seckendorff-Platz 1

department: Institute of Computer Science

country: Germany

institute: Martin Luther University Halle-Wittenberg

data_processing:
adapter trimming by cutadapt
quality filtering by sickle  -q 20 -l 15
mapping by bowtie-1.1.2 (-n 3 --best --strata) to combined reference of the tobacco genome (Ntab-BX_AWOK-SS.fa) and the TBSV sequence (TBSV.fa)
sambamba -view -f TBSV
input of mapped reads by Rsamtools
mapped reads were partitioned into six sets depending on the read-lengths (21, 22, or 24 nucleotides) and the mapped strand (positive or negative), and the starting positions of the mapped reads were counted as peak expression
Reads were stored in 5’ to 3’ orientation in the Sequence Alignment Map (SAM) format, so the first (last) nucleotide was counted for reads mapped onto the positive (negative) strand
Genome_build: Ntab-BX_AWOK-SS.fa (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/sierro_et_al_2014/assembly/Ntab-BX_AWOK-SS.fa.gz)  + TBSV.fa
Supplementary_files_format_and_content: semicolon-delimited text files include raw peak counts for each Sample.

organism: Nicotiana tabacum

source_name: TBSV incubated cells with subsequent AGO2-IP

growth_protocol: Nicotiana tabacum BY-2 cells were grown in Murashige-Skoog liquid medium at 23°C.

extract_protocol:
RNA was isolated from DCL assays or AGO/RISC immunoprecipitations by treatment with proteinase K followed by Phenol/Chloroform extraction and ethanol precipitation
RNA libraries were prepared using illumina protocolls.

treatment_protocol: BY-2 protoplasts were generated by treatment with Cellulase RS and Pectolyase Y-23. Evacuolated BY-2 protoplasts were obtained by percoll gradient centrifugation and extracts (BYL) were prepared by disrupting cells using a dounce homogenizer.

tag: lysate

value: BY2 lysate (BYL)

value: exposed TBSV dsRNA to the BYL

tag: rip antibody

value: anti-FLAG

tag: sequencing input

value: RNA of TBSV dsRNA-incubated extract with subsequent AGO2-IP


title: PP6C

description: PP

data_processing:
The normalization and all the data analysis were performed according to the GenEx software (Multid Analyses).
For the normalization the Global normalization method of the expression of all genes was applied.
The GenNex software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The deltadeltaCt values are not available.

label_protocol: Gene expression analysis was performed with  TaqMan OpenArray Mouse Inflammation Panel Real-time PCR System (Life Technologies). The cDNA (10 μl) was mixed with the TaqMan OpenArray Real-Time PCR Master Mix and loaded onto the cards using the AccuFill™ System. The cards were cycled in an OpenArray NT Cycler System (Applied Biosystems).

tag: intrarectal treatment

value: PBS

tag: oral treatment

tag: experimental group

value: Healthy control


title: PP5C

description: PP


title: CEC_S10

description: CEC

tag: colonisation  status

tag: group type


title: CART_HA_CD4_Naive_Day10_HAbulk

description: processed data file: Processed_TPMs.csv


title: CEC_S4

description: CEC

tag: colonisation days


title: CART_HA_CD4_Naive_Day7_HAbulk

description: processed data file: Processed_TPMs.csv


title: CEC_S1

description: CEC


title: AGO2_1 (small RNA)

tag: cultivar


title: CART_HA_CD4_CM_Day14_HAbulk

description: processed data file: Processed_TPMs.csv


title: Ax_S33

description: Ax

value: germfree


title: AGO1_2 (small RNA)

source_name: TBSV incubated cells with subsequent AGO1-IP

tag: treatment

value: RNA of TBSV dsRNA-incubated extract with subsequent AGO1-IP


title: N7C

description: Nissle

value: DNBS

value: Nissle

value: Nissle treated


title: CART_HA_CD4_Naive_Day14_HAbulk

description: processed data file: Processed_TPMs.csv

value: Naive


title: CART_HA_CD4_CM_Day10_HAbulk

description: processed data file: Processed_TPMs.csv


title: PP3C

description: PP


title: Ax_S32

description: Ax


title: CART_CD19_CD8_Naive_Day7_HAbulk

description: processed data file: Processed_TPMs.csv


title: N4C

description: Nissle


title: DCL_3 (small RNA)

source_name: TBSV incubated cells

value: RNA of TBSV dsRNA-incubated extract


title: Ax_S31

description: Ax


title: DCL_2 (small RNA)


title: CART_CD19_CD8_Naive_Day14_HAbulk

description: processed data file: Processed_TPMs.csv


title: Ax_S30

description: Ax


title: AGO1_1 (small RNA)


title: N1C

description: Nissle


title: AGO2_2 (small RNA)


title: CART_HA_CD4_CM_Day7_HAbulk

description: processed data file: Processed_TPMs.csv


title: Ax_S22

description: Ax


title: CART_CD19_CD8_Naive_Day10_HAbulk

description: processed data file: Processed_TPMs.csv


title: XEN-PG rep3

tag: sample type

value: eXtraEmbryonic  eNdoderm stem (XEN) cells from primitive endoderm of in vitro parthenogenetic (PG) blastocyst


title: PP4C

description: PP


title: DP5C

description: DP

value: Sick control


title: DCL_1 (small RNA)


title: CART_CD19_CD8_CM_Day7_HAbulk

description: processed data file: Processed_TPMs.csv

value: Central memory


title: N5C

description: Nissle


title: CART_CD19_CD8_CM_Day14_HAbulk

description: processed data file: Processed_TPMs.csv


title: Ax_S21

description: Ax

value: control


title: Bcdim2_Bsseq

city: Beijing

first: Chang

last: He

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Resources

institute: Institute of Botany, the Chinese Academy of Sciences

description: incubated on PDB liquid media

library_source: genomic

data_processing:
Sequencing was performed using the HighSeq4000.
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were analyzed by BGI programs.
After filtering, the clean data was then mapped to the reference genome by BSMAP.
Methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine, which was also equal the mC/C ratio at each reference cytosine.
Genome_build: Botrytis cinerea B05.10 RefSeq Genome
Supplementary_files_format_and_content: Bedgraph files include the identification results of DNA methylation for each locus.

organism: Botrytis cinerea

source_name: genomic DNA from Bcdim2 mutant

growth_protocol: The four samples were incubated with PDB liquid media for 24 hours.

extract_protocol:
Genomic DNA was extracted with CTAB reagent from 24 hours old mycelium.
library constructing, the DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of approximately 250 bp, followed by the blunt-ending, dA addition to 3'-end, finally, adaptor ligation (in this case of methylated adaptors to protect from bisulfite conversion), essentially according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. At last, Sequencing was performed using the HighSeq4000 or other Illumina platforms.
Whole Genome Bisulfite Sequencing

treatment_protocol: On rocking shaker at 22 oC.

tag: strain

value: Bcdim2 mutant

tag: growth stage

value: mycelium

tag: incubation time

value: 24 hours


title: Bcdim2rid2_Bsseq

description: incubated on PDB liquid media

source_name: genomic DNA from Bcrid2dim2 mutant

value: Bcdim2rid2 mutant


title: DP3C

description: DP

value: PBS


title: Ax_S20

description: Ax


title: CART_CD19_CD8_CM_Day10_HAbulk

description: processed data file: Processed_TPMs.csv

tag: cell type

tag: compartment

tag: timepoint


title: Ax_S12

description: Ax


title: Bcrid2_Bsseq

description: incubated on PDB liquid media

source_name: genomic DNA from Bcrid2 mutant

value: Bcrid2 mutant


title: DP2C

description: DP


title: Ax_S11

description: Ax

value: germfree


title: B05.10_BSseq

description: incubated on PDB liquid media

source_name: genomic DNA from B05.10 strain


title: CART_CD19_CD4_Naive_Day14_HAbulk

description: processed data file: Processed_TPMs.csv


title: Ax_S10

description: Ax


title: CART_CD19_CD4_Naive_Day10_HAbulk

description: processed data file: Processed_TPMs.csv


title: LA-SOL_37_2 [AC-21_S7]

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

data_processing:
Adequate sequencing quality was confirmed using FastQC version 0.11.5 (Andrews, 2010).
First, these reads were trimmed using cutadapt version 1.11.
To remove the “QuantSEQ FWD” adaptor sequence the trimmed reads were mapped to the genome of L. theobromae LA-SOL3 using the STAR aligning software v 2.5.3a42.
The RSEM software, version v1.2.31, was used to generate count tables.
Genome_build: L. theobroma (SUB3910116,PRJNA449280)
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample

organism: Lasiodiplodia theobromae

extract_protocol:
The mycelium of each replicate (three replicates per condition) was ground in liquid nitrogen and total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma), according to the manufacturer’s instructions. Samples were incubated for 15 min with the DNase I digestion set (RNase-Free DNase Set, Qiagen). Integrity and quality analysis were done on a 2100 Bioanalyzer RNA (Agilent Technologies).
Illumina mRNA sequencing libraries were made from 500 ng total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to manufacturer's protocol. Fourteen PCR cycles were used during the enrichment PCR. The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in an Illumina Nextseq 500 high throughput flow cell, generating single-end 75bp reads.

tag: temperature

value: 37 ºC

tag: age

value: 4 days

tag: tissue

value: Mycelium


title: LA-SOL_37_3 [AC-23_S8]


title: C6C

description: CEC

tag: intrarectal treatment

value: DNBS

tag: oral treatment

value: CEC

value: CEC treated


title: MPs5vm

city: Nanjing

first: Gu

last: Weiqing

address: Xianlin

institute: Nanjing University

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below:(1) Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10 (SLIDINGWINDOW:  4:10) (2) Remove trailing low quality or N bases (below quality 3) (TRAILING:3) (3) Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence, the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30, removed non-overlapping portions (ILLUMINACLIP: adapter.fa:  2: 30: 7) (4) Drop reads below the 26 bases long (5) Discard those reads that can not form paired
The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the clean reads.
Cell Ranger uses an aligner called STAR, which peforms splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non-exonic loci, the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts, looking for compatibility. A read that is compatible with the exons of an annotated transcript, and aligned to the same strand, is considered mapped to the transcriptome. If the read is compatible with a single gene annotation, it is considered uniquely (confidently) mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting.
Cell Ranger takes as input the expected number of recovered cells, N (see -- expect-cells). Let m be a robust estimate of the maximum total UMI counts, taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group (library) and, if the reference contains multiple genomes, for each genome.
Genome_build: Danio_rerio_Ensemble_91
Supplementary_files_format_and_content: gene-cell expression matrix

organism: Danio rerio

source_name: intestinal cells

extract_protocol:
The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument(10x Genomics, USA) to generate single cell Gel bead in Emulsion (GEMs).
ScRNA-seq libraries were prepared using the GemCode Single-Cell 3’ Gel Bead, Chip and Library Kits (10x Genomics, USA) as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.

treatment_protocol: Exposure solutions were prepared by adding 100 nm, 5 μm or 200 μm PS-MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles (no filtering systems were used in the tanks). After 21-d exposure, zebrafish were collected and intestine were rapidly extracted on ice.

value: Intestinal single cell suspension

tag: exposed pollutants

value: 5μm PS-MPs


title: MPs200vm

value: 200μm PS-MPs


title: CART_CD19_CD4_Naive_Day7_HAbulk

description: processed data file: Processed_TPMs.csv

value: Naive


title: C8C

description: CEC

tag: experimental group


title: DP4C

description: DP

value: Sick control


title: C2C

description: CEC


title: MPs100nm

value: 100nm PS-MPs


title: LA-SOL_37_1 [AC-19_S6]


title: CART_CD19_CD4_CM_Day7_HAbulk

description: processed data file: Processed_TPMs.csv

value: Central memory


title: CART_CD19_CD4_CM_Day14_HAbulk

description: processed data file: Processed_TPMs.csv


title: C1C

description: CEC


title: CK


title: LA-SOL_25_3 [AC-17_S5]

value: 25 ºC


title: PP6I

description: PP

source_name: Ileal mucosa

value: PBS

value: Healthy control


title: PP5I

description: PP


title: CART_CD19_CD4_CM_Day10_HAbulk

description: processed data file: Processed_TPMs.csv


title: E2_Rapamycin+Rasagiline

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

description:
RNA-Seq
E2_Rapamycin+Rasagiline

data_processing:
Illumina Casava1.7 software used for basecalling
The RNA sequencing reads were trimmed for adaptors, masked for low-complexity or low-quality sequence, and subsequently mapped to the rat genome (rn6) using STAR (version 2.4.0f1)
The SAM/BAM files were further processed using the SAMtools (version 0.1.18) and read count quantitations were obtained using BEDTools multicov (version 2.25.0).
Normalization of read counts and differential expression analysis between genotypes was carried out using the DESeq2 R package in Bioconductor (release 2.13).
Genome_build: rn6
Supplementary_files_format_and_content: TPM

organism: Rattus norvegicus

source_name: ELT3-V3 leiomyoma cells

extract_protocol:
Total RNA from tumors was extracted using TRIzol (Thermo Fisher) and RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

tag: barcode

value: CTTGTA

value: Tumor

tag: source

value: Subcutaneous xenograft


title: LA-SOL_25_2 [AC-15_S4]

value: 4 days

value: Mycelium


title: A3_Rapamycin+Rasagiline

description:
RNA-Seq
A3_Rapamycin+Rasagiline

value: GGCTAC


title: LA-SOL_25_1 [AC-13_S3]


title: E3_Rapamycin+Clorgyline

description:
RNA-Seq
E3_Rapamycin+Clorgyline

value: GATCAG


title: PP4I

description: PP


title: PP3I

description: PP


title: C2_Rapamycin

description:
RNA-Seq
C2_Rapamycin

value: GCCAAT


title: B1_Rapamycin

description:
RNA-Seq
B1_Rapamycin

value: ACAGTG


title: PP1bI

description: PP


title: MPs200vm.1

data_processing:
Single-end reads was assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence.
Quality filtering on the raw reads were performed under specific filtering conditions to obtain the high-quality clean reads according to the Cutadapt (V1.9.1, http://cutadapt.readthedocs.io/en/stable/) quality controlled process.
The reads were compared with the reference database (Silva database, https://www.arb-silva.de/) using UCHIME algorithm (UCHIME Algorithm, http://www.drive5.com/usearch/manual/uchime_algo.html) to detect chimera sequences, and then the chimera sequences were removed. Then the Clean Reads finally obtained.
Sequences analysis were performed by Uparse software (Uparse v7.0.1001，http://drive5.com/uparse/). Sequences with ≥97% similarity were assigned to the same OTUs. Representative sequence for each OTU was screened for further annotation.
Genome_build: none
Supplementary_files_format_and_content: tables of relative abundance after homogenization

source_name: Intestinal contents

extract_protocol:
The contents of the separated intestine are extruded. Total DNA in the intestinal contents was isolated with DNeasy Blood & Tissue Kit (QIAGEN,Germany). DNA concentration was measured using a NanoDrop spectrophotometer (NanoDrop One,Thermo, USA). After DNA quality analysis by electrophoresis, the extracted DNA was amplified using primers(Forward primer:5’-CCTAYGGGRBGCASCAG-3’; Reverse primer: 5’-GGACTACNNGGGTATCTAAT-3’) to target the V3-V4 regions of the bacterial 16S rRNA gene.
The obtained PCR products were purified by GeneJET Gel Extraction Kit (Thermofisher, USA) and applied to construct the sequencing library. The library was sequenced on an Ion S5TM XL platform.

treatment_protocol: Exposure solutions were prepared by adding 100nm, 5μm or 200μm PS-MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles (no filtering systems were used in the tanks). After 21-d exposure, zebrafish were collected and intestine were rapidly extracted on ice.

value: 200vm PS-MPs

value: intestine


title: MPs5vm.3

value: 5vm PS-MPs


title: MPs200vm.2


title: N5I

description: Nissle

value: DNBS

value: Nissle


title: MPs200vm.3


title: N4I

description: Nissle


title: H1_Control

description:
RNA-Seq
H1_Control

value: TGACCA


title: N2I

description: Nissle

value: Nissle treated


title: MPs5vm.2


title: E1_Control

description:
RNA-Seq
E1_Control

value: CGATGT


title: MPs5vm.1


title: N1I

description: Nissle


title: D5_Rapamycin+Clorgyline

description:
RNA-Seq
D5_Rapamycin+Clorgyline

value: CAGATC


title: CV_S4

description: CV

source_name: Colonic mucosa

tag: colonisation  status

value: CV

tag: group type

value: conventional

tag: colonisation days


title: p1703_4_Donor 2  FH

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Clariom D microarray.

scan_protocol: Arrays were scanned on a GeneChip 3000 scanner.

data_processing: Basic Affymetrix chip and Experimental Quality Analyses were performed using the Expression Console Software v1.4.1.46. Probe summarization and Data Normalization was done using RMA.

label: biotin

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manua, Affymetrix).

growth_protocol: PBMCs from peripheral blood were isolated by density gradient centrifugation over LymphoPrep, followed by positive selection of monocytes with CD14 magnetic microbeads

extract_protocol: RNA was extracted using Qiagen RNEasy kit as per the manufacturers instructions.

treatment_protocol: Monocytes were incubated for 48 h with 150 μg/ml  factor H or medium only at 2.5 mln cells in 2.5 ml RPMI medium

tag: treatment

value: Factor H

tag: donor

value: Donor 2

value: blood

value: monocyte


title: MPs100nm.3

value: 100nm PS-MPs


title: p1703_8_Donor 4  FH

value: Donor 4

tag: cell type


title: p1703_7_Donor 4 ctrl

value: Control


title: p1703_6_Donor 3  FH

value: Donor 3


title: TC

first: Kuipu

last: Zhang

address: 130  Meilong Rd.

department: State  Key  Laboratory  of  Bioreactor  Engineering

institute: East  China  University  of  Science and Technology

description: IonXpressRNA(42)_007_R_2015_03_25_20_33_15_sn247770157_NOV-71-HLL_Auto_sn247770157_NOV-71-HLL_103

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 Streptomyces albus J1074 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCF_000827005.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Streptomyces albus

source_name: high-yield of salinomycin mutant

growth_protocol: S. albus S12, and their derivatives were grown on ISP4 agar plates (BD, USA) for sporulation. For shaking flask fermentation, a 100 μL of the spore suspension was inoculated into a 250 mL ﬂask containing 30 mL fresh medium (4.0% glucose, 3.0% soy ﬂour, 1.0% yeast extract, 0.2% calcium carbonate) and further incubated for 26-32 h as a seed culture. Then, a 3 mL of the seed culture was transferred into a 30 mL fermentation medium (0.8% germ powder, 0.5% soybean powder, 0.2% potassium chloride, 0.10% sodium chloride, 0.16% urea, 0.2% tartaric acid, 0.01% magnesium sulfate, 0.01% dibasic potassium phosphate, 0.5% calcium carbonate, 15% soybean oil, pH 6.6–6.9) on a rotary shaker at 250 rpm and 33 °C for 7 days.

extract_protocol:
RNA samples from the mutant strain TK, Tet30Chl25 and the parental strain S12 were analyzed in fermentation medium at five day points, and then were frozen directly in liquid nitrogen and stored at −80 °C. The extraction and quality detection of transcriptional samples were performed by Sangon Biotech Co., Ltd. (Shanghai, P.R. China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: culture condition

value: fermentation medium for 5 days

tag: salinomycin yield

value: High


title: DP5I

description: DP

value: DNBS

value: PBS

value: Sick control


title: TK

description: IonXpressRNA(4)_008_R_2015_03_25_20_33_15_sn247770157_NOV-71-HLL_Auto_sn247770157_NOV-71-HLL_103

source_name: low-yield of salinomycin mutant

value: TK

value: Low


title: p1703_3_Donor 2 ctrl


title: p1703_9_Donor 5 ctrl

value: Donor 5


title: MPs100nm.2

tag: age

value: intestine


title: N3I

description: Nissle

value: Nissle

value: Healthy control


title: S12

description: IonXpressRNA(53)_006_R_2015_03_25_20_33_15_sn247770157_NOV-71-HLL_Auto_sn247770157_NOV-71-HLL_103

source_name: parental strain

value: middle


title: MPs100nm.1

tag: tissue


title: DP4I

description: DP

tag: intrarectal treatment


title: DP3I

description: DP

tag: oral treatment


title: CK.3

tag: exposed pollutants


title: p1703_12_Donor 6  FH

value: Factor H

value: Donor 6

value: blood

value: monocyte


title: DP2I

description: DP

tag: experimental group


title: DP1I

description: DP


title: CV_S10

description: CV

data_processing:
The normalization and all the data analysis were performed according to the GenEx software (Multid Analyses).
For the normalization the Global normalization method of the expression of all genes was applied.
The GenNex software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. The deltadeltaCt values are not available.
Fold Change worksheet reports relative quantification of the expiremental group (CEC, Nissle or CV) to the control group (Ax: axenic/germfree), where Ax group has been used as a calibrator on the DeltadeltaCt calculation.

value: CV

value: conventional


title: CK.2


title: C8I

description: CEC

value: CEC

value: CEC treated


title: p1703_2_Donor 1  FH

value: Donor 1


title: Cells were given a radiation dose of 18 Gy at 6 frequencies

city: Urumqi

first: Zhang

last: Zegao

state: Xinjiang

address: 91 Tianchi Route

department: the Second Department of Radiation Oncology

institute: People’s Hospital of Xinjiang Uyghur Autonomous Region

description: Gene expression data from human esophageal cancer cells

hyb_protocol: Samples were then hybridized to microarrays at 45°C for 16–18 hours using the Affymetrix Clariom S Assay (human; Cat No 902926; Thermo Fisher Scientific). After hybridization, phycoerythrin streptavidin was used to clean and stain the microarrays on an Affymetrix Fluidics Station 450.

scan_protocol: The Affymetrix GeneChip Command Console was then used to scan the microarrays.

data_processing: The Robust Multichip Analysis (RMA) algorithm was used for data analysis, with global scales and default analyzers as normalization methods.

source_name: Human esophageal cancer cell line, Eco13

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in DMEM containing 10% fetal bovine serum at 37°C in a constant-temperature cell incubator with 5% CO2 and were seeded in a Corning 25 cm2 gas permeable cell culture flask at a density of 1 × 106 cells/mL.

extract_protocol: Cells (1 × 106) in T and C were lysed 48 h after radiation ceased, to extract total RNA using TRIzol (Life Technologies, Carlsbad, CA, USA).

treatment_protocol: The liquid level of the culture medium was kept at 0.5 cm, and the light-limiting barrel was kept close to the liquid surface. The source skin distance was 95 cm. A 6-Mev electron beam was administered using an Elekta Linear Accelerator at a dose rate of 500 cGy/min.

tag: cell line


title: p1703_1_Donor 1 ctrl

value: Control


title: p1703_5_Donor 3 ctrl

value: Donor 3


title: RTK17.1_O2-limited_N-sufficient (NH4+) [RTK171100816]

city: Christchurch

first: Carlo

middle: Robert

last: Carere

address: University of Canterbury, Private Bag 4800,, Deliver to Carlo Carere, Link Building, room A311

department: Chemical and Process Engineering

country: New Zealand

institute: University of Canterbury

data_processing:
An average of 7,988,451 raw untrimmed reads were obtained for each of the five conditions sampled. These reads were then analysed using the Artificial Intelligence RNA-Seq pipeline (Sequentia Biotech, Barcelona, Spain), which were reduced to an average of 7,287,318 following quality filtering and trimming.
Retained paired-end reads (100 bp) were then mapped to the genome of Methylacidiphilum infernorum strain V4 (GCA_000019665.1)(Hou et al., 2008) using the ‘different genotype’ setting. An average of 80.01 % reads were mapped to genes within the reference genome.
Following this, differential gene expression profiles and accompanying statistical analysis was performed using the edgeR (Robinson et al., 2010) tool available within the Artificial Intelligence RNA-Seq pipeline. Expression values are given as FPKM (Fragments per Kilobase Million; Table S1)(Mortazavi et al., 2008).
Genome_build: Methylacidiphilum infernorum strain V4 (GCA_000019665.1)
Supplementary_files_format_and_content: rawcounts with genome coordanates; fpkm data

organism: Candidatus Methylacidiphilum infernorum

source_name: RTK17.1_O2-limited_N-sufficient (NH4+)

growth_protocol: Chemostat cultivation was performed to investigate H2 metabolism on the growth and intracellular glycogen production with respect to unbalanced growth conditions (O2 and nitrogen limitation). Cultures were continuously incubated at pH 2.5, 50 °C with stirring (800 rpm). The reactor was constantly maintained at a volume of 0.5 l with V4 mineral medium (Carere et al., 2017), prepared with or without NH4Cl (0.4 g l-1) addition (as necessary), and supplied at a constant flow rate of 10 ml h−1 (D=0.02 h−1). Custom gas mixtures were supplied to the chemostat at a rate of 10 ml min−1 and contained approximately (v/v) 3 % CH4 and 26 % CO2 for all experiments; O2 at (v/v) 14.1 % and 3.5 %, respectively for O2-replete and -limiting conditions, and H2 at 0.4 % (v/v). The balance of all gas mixtures was made up with N2.

extract_protocol:
isolation of mRNA was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer's protocol. Following total RNA extraction, ribosomal RNAs were removed using the Ribo-Zero rRNA removal kit (bacteria) and the quality of the remaining RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent).
Ribo-Zero User Guide, TruSeq Stranded Total RNA prep

treatment_protocol: Cell culture samples for transcriptome sequencing were harvested (10 ml) from steady-state chemostat experiments, pelleted by centrifugation at 5,000 x g (15 min, 4 °C), suspended in 1 ml RNAlater Stabilisation solution (ThermoFisher Scientific) and then stored at -80 °C until required for further analysis, as per the manufacturer’s recommended protocols.

tag: sample type

value: Microbial biomass, chemostat (steady-state)

tag: oxygen

tag: nitrogen

value: N-sufficient (NH4+)


title: p1703_10_Donor 5  FH

value: Donor 5


title: keratinocytes_si-Circ_rep3

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

institute: Karolinska Institutet

description: MT6_si_circ_50nM-4_(Clariom_S_Human).CEL

hyb_protocol: The samples were hybridized to a Clariom S Human Array Plate according to standard Affymetrix GeneTitan protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneTitan Scanner.

data_processing: Generated CEL files were analyzed using Transcriptome Analysis Console (TAC) v. 4.0.1 and the RMA method

source_name: keratinocytes transfected with si-hsa_circ_0084443

label_protocol: Total RNA was labeled using the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s (Affymetrix) instructions.

growth_protocol: Human epidermal keratinocytes (HEKa) were cultured in EpiLife medium (Gibco™) supplemented with Human Keratinocyte Growth Supplement (Cascade Biologics) and 1% penicillin streptomycin (Gibco™) at 37°C in 5% CO2.

extract_protocol: 24 hours after transfection, the total RNA was extracted with Trizol reagent.

treatment_protocol: The third passage keratinocytes at 60-70% confluence were transfected with 50 nM si-hsa_circ_0084443 or si Control (Eurofins Genomics) using Lipofectamine 2000 (Invitrogen).

value: skin

value: Human primary epidermal keratinocytes (HEKa)

tag: transfected with

value: 50 nM si-hsa_circ_0084443 for 24hrs


title: p1703_11_Donor 6 ctrl

tag: treatment


title: Cells were cultured normally


title: RTK17.1_O2-excess_N-sufficient (NH4+) [RTK171270616]

source_name: RTK17.1_O2-excess_N-sufficient (NH4+)


title: RTK17.1_O2-excess_N-sufficient (NH4+) [RTK171120716]


title: C5I

city: Jouy en Josas, France

first: Unai

last: Vazquez

address: Domaine de Vilvert Bat 440

institute: INRA

description: CEC

extract_protocol: RNA isolation was carried out using the Ambion mirVana Kit (Life Technologies) according to the manufacturer’s recommendations. The RNA quality of all samples was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) with an average RNA integrity number superior to 9 on a scale of 0 to 10.

value: DNBS


title: C7I

description: CEC


title: Strain hTM72 transfect with siatg5/7

city: Durham

first: Paloma

middle: B

last: Liton

state: NC

address: DUMC Box 3802

institute: Duke University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data analysis was performed using the Partek Flow and Partek Genome Suite statistical analysis software (Partek Incorporated).

source_name: Strain hTM72 transfect with siatg5/7

label_protocol: standard Affymetrix protocol

growth_protocol: Human TM cells were isolated from dissected TM tissue from discarded corneal rims after surgical corneal transplantation at Duke University Eye Center and cultured as described earlier (Liton et al., 2008)

extract_protocol: At 72 h post-transfection, cells were washed with cold PBS and fixed in RNAlater (Qiagen). Total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA), following the manufacturer's protocol, and treated in-column with DNase I. RNA concentration and quality were determined using the Agilent 2100 Bioanalyzer. Total RNA (5 µg) from human TM primary cultures with transient silenced autophagy and controls were independently hybridized to human Clariom D microarrays (ThermoFisher) following the manufacturer's instructions at the Duke Microarray Core Facility.

treatment_protocol: primary human TM cells were plated on 24-well plate, with 60-80% confluence, in 0.5 mL of the growth media.  After 24 h, the cells were transfected with either 5 pmol of siRNA against ATG5 (siAtg5, sc-41445) and ATG7 (siAtg7, sc-41447) or 5 pmol of non-targeting siRNA (siNC, sc-37007) using Lipofectamin® RNAiMAX Reagent, according to the manufacturer’s instructions.

value: trabecular meshwork cell


title: CK.1

value: intestine


title: C3I

description: CEC


title: C1I

description: CEC


title: RTK17.1_O2-limited_N-limited (N2) [RTK171121216]

source_name: RTK17.1_O2-limited_N-limited (N2)

value: N-limited (N2)


title: RTK17.1_O2-limited_N-limited (N2) [RTK171060317]


title: HCT116 bait 5 HiSeq1

status: Public on Sep 30 2019

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

description: Sample name: NW047.NW28HRPB009bio11_MID03

data_processing:
Library strategy: 3C-seq
Sequence reads were mapped using bwa 0.7.12-r1039 to a reference genome composed of PhiX, BDGP5 (Drosophila), K12 (E. coli) and human (hg19). Alignments with mapping quality greater than 10 of the read 2 were used to determine the probe position. An extension region (region from the probe’s end to the first restriction site) was used to discriminate valid from mis-annealing events. The total number of alignments in the read 1 with the proper probe extension in the second read was reported by restriction fragment. Next, the number of distinct transposon integration sites was also reported to remove PCR duplicates.
Genome_build: hg19/BDGP5/PhiX/K12
Supplementary_files_format_and_content: Tab-delimited text files.

organism:
Drosophila melanogaster
Homo sapiens

source_name: HCT116, bait 5, HiSeq

growth_protocol: Human colon cancer cells (HCT116) were maintained in McCoy’s 5A modified medium (Life Technologies, 16600-082) supplemented with 10% Fetal Bovine Serum (FBS), penicillin (Life Technologies) and streptomycin (Life technologies). Normal colon cells (HCEC, ScienCell, 2950) were maintained in Colonic Epithelial Cell Medium (ScienCell, 2951). Both cells were cultured under 5% CO2 circumstance at 37 C.

extract_protocol:
Chromosome Conformation Capture (3C) was performed as described before with slight modification. Briefly, 1 million of the cells were fixed with 1% monomeric formaldehyde for 10 min at RT and excess amount of the formaldehyde was captured by 0.125 M Glycine. Then, cells were collected and suspended in 10 ml of nuclear isolation buffer (0.2% NP-40, 10 mM Tris-cl, pH 7.5, 10 mM NaCl, x1 Proteinase inhibitor (Roche, 04693116001)) and incubated for 10 min on ice. Isolated nuclei were precipitated and washed with 1 ml of Buffer 2 (New England Biolabs, B7002S). Next, nuclei were re-suspended in 500 ul of x1.2 buffer 2. Un-crosslinked fraction was removed by adding 5 ul of 10% SDS and incubated for 1 hr at 37 °C. Then, excess amount of SDS was captured by TritonX-100. The chromatin DNA was fragmented by the incubation at 37 °C for overnight with HindIII (1 U/ul, New England Biolabs, R0104T). As a spiking control, same amount of chromatin was isolated from Drosophila S2 cells with same method and mixed with chromatin for analysis. After the inactivation of the enzyme, the solution was transferred to 50 ml tube containing 7 ml of ligation buffer (50 mM Tris-cl, pH 7.5, 10 mM MgCl2, 1% Triton X-100) and incubated for 1 hr at 37 °C. Then, 70 ul of 100 mM ATP, 70 ul of 1 M DTT and 2000 U of T4 DNA ligase were added. Then, the solution was incubated at 16 °C for overnight followed by for 1 hr at RT. Crosslink was reversed with conventional methods. Finally, DNA was collected by ethanol precipitation followed by the purification with MSB Spin PCRapace (Stratec, 1020220200) and Zymo Clean & Concentrator-5 (Zymo Research, D4013). The digestion efficiency was estimated by qPCR. The quality of 3C DNA was visualized on 1% agarose gel.
3C DNA was tagmented and adapter DNA which equipped with T7 RNA polymerase promoter was incorporated by limited cycle PCR using either Nextera or Nextera XT DNA sample prep kit (Illumina, FC-121-1031, FC-131-1024). The resulting product was amplified by in vitro transcription (Maxiscript T7 kit, Life Technology, AM1312M). The template DNA was fragmented by Turbo DNase I (Life Technology, AM2239) prior to the RNA purification by RNeasy (Qiagen, 74104). For primer annealing, 1 ug of template RNA with 0.2uM of bait-specific primer was denatured at 75 °C for 3 min and then mixed with x2 buffer of Platinum Quantitative RT-PCR ThermoScript One-Step System (Life Technology, 11731-015) and 0.5U/ul of SUPERase In RNase inhibitor (Life Technology, AM2694). The solution was incubated at 4 °C for 44-48 hrs. Then, following the incubation at 65 °C for 5 min, the primer was extended by adding Thermoscript Plus/Platinum Taq mix at 60 °C for 30 min. After the inactivation of reverse transcriptase, bait-interactor chimeric DNA was enriched by PCR with Illumina P5 and bait-specific primer. At last, Illumina P7 sequence was incorporated with Nextera DNA sample prep kit by following manufacturer's instruction.

treatment_protocol: For Flavopiridol treatment, cells were incubated with 2 mM Flavopiridol (Sigma Aldrich, F3055) at growing condition for 6 hrs.

value: human colorectal carcinoma cell line

tag: spiking control

value: Drosophila S2 cell chromatin

tag: probes


title: keratinocytes_si-Ctrl_rep1

description: MT1_si_ctrl_50nM-2_(Clariom_S_Human).CEL

source_name: keratinocytes transfected with si-control

tag: cell type

value: 50 nM si-Control for 24hrs


title: AGS_circCTNNB1

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of circ-CTNNB1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: AGS stably transfected with circ-CTNNB1

growth_protocol: Human gastric cancer cell line AGS was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

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

treatment_protocol: The circ-CTNNB1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of puromycin.

value: gastric cancer

value: AGS

tag: genotype

value: circ-CTNNB1 overexpression

tag: passages


title: HCT116 bait 5 HiSeq2

description: Sample name: NW047.NW28HRPB009bio12_MID07


title: keratinocytes_si-Circ_rep1

description: MT4_si_circ_50nM-1_(Clariom_S_Human).CEL


title: Strain hTM67 transfect with siatg5/7

source_name: Strain hTM67 transfect with siatg5/7


title: keratinocytes_si-Circ_rep2

description: MT5_si_circ_50nM-3_(Clariom_S_Human).CEL


title: keratinocytes_si-Ctrl_rep2

description: MT2_si_ctrl_50nM-3_(Clariom_S_Human).CEL


title: Strain hTM64 transfect with siNC

source_name: Strain hTM64 transfect with siNC


title: keratinocytes_si-Ctrl_rep3

description: MT3_si_ctrl_50nM-4_(Clariom_S_Human).CEL


title: Strain hTM72 transfect with siNC

source_name: Strain hTM72 transfect with siNC


title: Strain hTM67 transfect with siNC

source_name: Strain hTM67 transfect with siNC


title: Strain hTM64 transfect with siatg5/7

source_name: Strain hTM64 transfect with siatg5/7


title: SK04_CD47--_2_exosome_miRNA

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols. For microRNAs, 1 microgram of total RNAs was labeled with Affymetrix FlashTag kit using normal affymetrix procedure for labeling, hybridization, staining and scanning.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

source_name: CD47- serum exosome

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: WT (JK) and CD47- (JINB8) T cells (25x106) were cultured using HITES medium (90% Ham's F-12, 10% RPMI 1640 medium, 5 mM HEPES, 2 mM glutamine, 0.1% BSA, 5 μg/ml insulin, 5 ng/ml sodium selenite, 5 μg/ml transferrin (Thermo Fisher Scientific, Waltham, MA), 200 nM hydrocortisone Sigma Aldrich, St. Louis, MO) for 24-48 h at 37°C. The cells were harvested by centrifugation at 1300 RPM for 5 minutes. Cell pellets were washed with 1X PBS for 5 minutes and used for total RNA extraction. Cell supernatants were collected into new tubes and centrifuged at 395xg (1300 RPM) for 5 minutes. Cell supernatants were collected into new tubes and centrifuged for 10 minutes at 2103xg using using Thermo Sorvall Legend XTR (3000 RPM). The supernatants were concentrated using Centrcon-YM-10 filters to 500 µl. The EVs were precipitated using the Exo-quick kit (SBI System Bioscience, Palo Alto, CA) or Exo-spin™ kit (Cell Guidance Systems, St. Louis, MO ) according to the manufacturer’s instructions. The precipitated EVs were used for isolating total RNA and/or miRNA for real time PCR analysis.

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

value: serum

tag: diet

value: ND

tag: cell compartment

value: exosome


title: SK04_CD47--_1_exosome_miRNA

tag: tissue


title: SK06_JINB-exosome3_miRNA

source_name: JinB8 exosome

value: T lymphocyte


title: SK01_WT-3_exosome_miRNA

source_name: WT serum exosome


title: SK04_JINB-exosome1_miRNA


title: SK02_JK-exosome2_miRNA

source_name: JK exosome

value: JK


title: SK01_WT-2_exosome_miRNA


title: SK03_JK-exosome3_miRNA


title: SK01_JK-exosome1_miRNA


title: SK01_WT-1_exosome_miRNA


title: SK04_CD47--_3_exosome_miRNA


title: Increta2

city: San Francisco

first: M.

middle: Yvonne

last: Kim

address: 3rd st.

institute: UC San Francisco

hyb_protocol: Sample processing and hybridization was performed by the UCSF Gladstone Institute.

data_processing: Affymetrix CEL files were processed and annotated using the Oligo software package. Raw values were normalized via the Robust Multi-Array Average (RMA) algorithm.

source_name: cytotrophoblast

growth_protocol: The University of California San Francisco Institutional Review Board (Committee on Human Research) approved this study. Written informed consent was obtained from all donors. Women with preexisting medical conditions such as thyroid insufficiency, chronic hypertension, or diabetes mellitus were excluded from the case and the control groups. Other exclusion criteria included premature rupture of membranes and/or fetal anomaly. Cases were identified based on prenatal imaging—ultrasound or MRI—consistent with an invasive placenta. Intra-operatively, findings were consistent with PAS as the placenta did not separate after delivery. Final confirmation of this diagnosis was made by a gynecologic pathologist. Gestational age-matched control samples were obtained from women who had a preterm birth (PTB), diagnosed according to the criteria recommended by Herron et al., including regular uterine contractions at >20 or <37 weeks of gestation, which are 5-8 min apart and accompanied by 1 of the following events: progressive changes in the cervix, cervical dilation ≥ 2 cm, and/or cervical effacement ≥ 80%. Patients with evidence of inflammation were excluded on the basis of the following criteria: maternal fever >100.4F, uterine tenderness, fetal tachycardia (fetal heart rate >160 beats per min), and/or (placental) histologic criteria compatible with inflammation.

extract_protocol: Total RNA was isolated using the Trizol reagent according to the manufacturer’s directions. The RNA concentration was determined via a Nanodrop spectrophotometer (Thermo Scientific) and quality was assessed using an Agilent 2100 Bioanalyzer. Only samples with a RNA integrity number (RIN) greater than 7 were used in subsequent analyses. We used Affymetrix Human Gene 2.0 ST arrays to profile the global gene expression patterns of CTBs isolated from gestational age matched PAS cases (n=6) vs. placentas from pregnancies that ended in PTB (n=3).

treatment_protocol: CTB isolation steps include extensive washing of the chorionic villi, sequential digestion with collagenase/trypsin and isolation via Percoll density gradient centrifugation. The first three times these preparations were made, CTB purity was confirmed by immunostaining for the TB marker cytokeratin 7, which showed at least a 90% purity.

value: placenta

value: cytotrophoblast

tag: diagnosis

value: Placental Accreta Spectrum (PAS)


title: Accreta2

scan_protocol: Sample processing and hybridization was performed by the UCSF Gladstone Institute.


title: Percreta3

label_protocol: Sample processing and hybridization was performed by the UCSF Gladstone Institute.


title: Accreta1


title: Increta1


title: SK05_JINB-exosome2_miRNA


title: HEK293 rep-3

city: indianapolis

first: Rudong

last: Li

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

description: RNA, PCR product

data_processing:
Illumina adapters removed using cutadapt (v1.9.1)
Alignment of transcripts to the reference sequence was performed using STAR (v2.5.3a)
Counts of aligned reads were enumerated based on R Bioconductor GenomeAlignment (Lawrence M et al., PLoS Comput Biol 2013, doi:10.1371/journal.pcbi.1003118)
Genome_build: The reference sequence is (a part of) the Exontrap plasmid (466 nt in total) that is supposed to generate RNA products.
Supplementary_files_format_and_content: tab-delimited text files including the read counts for spliced and aberrant (or unspliced) transcripts

source_name: Cell line

growth_protocol: Transfected HeLa, HEK293 and HepG2 cells with the Exontrap plasmids were seeded at a density of 0.9 x 10e5 in 24-well plates. Each plate contained 5 replicates per cell line. Twenty-four hours after cell plating, 500 ng of the library pool was complexed with 1.5 μL of Lipofectamine 3000 Reagent (Thermo Fisher Scientific, Waltham MA) in 50 μL of Opti-MEM media as per the manufacturer’s instructions, before adding the transfection mixture to each well. Cell culture and transfection reagents were used without antibiotics.

extract_protocol:
Cells were lysed in situ 48 hours after transfection and total RNA was isolated using miRNeasy mini kit with the optional DNase digestion step (Qiagen, Germantown MD) following the manufacturer’s protocol.
Using 285-400 ng RNA, cDNA was synthesized with QuantiTect Reverse Transcription kit (Qiagen, Germantown MD) following the manufacturer’s protocol. cDNA was PCR amplified using barcoded primers. 2 μL cDNA were amplified in a 50 μL volume containing 2X Invitrogen Platinum SuperFi PCR Master Mix (Thermo Fisher Scientific, Waltham MA) using 1 μM (final concentration) barcoded primers. The sequencing library was created by end-polishing the barcoded PCR products, followed by adapter ligation and amplification, according to instructions of Illumina (Illumina, Inc., San Diego, CA).


title: HEK293 rep-5

description: RNA, PCR product


title: HepG2 rep-5

description: RNA, PCR product


title: HEK293 rep-4

description: RNA, PCR product


title: HepG2 rep-1

description: RNA, PCR product


title: HepG2 rep-4

description: RNA, PCR product


title: HepG2 rep-2

description: RNA, PCR product


title: HepG2 rep-3

description: RNA, PCR product


title: PTL3

value: preterm birth (used as control)


title: Percreta2


title: HEK293 rep-2

description: RNA, PCR product


title: HeLa rep-5

description: RNA, PCR product

value: HeLa


title: HEK293 rep-1

description: RNA, PCR product


title: HeLa rep-1

description: RNA, PCR product


title: PTL2


title: HeLa rep-2

description: RNA, PCR product


title: HeLa rep-3

description: RNA, PCR product


title: PTL1


title: H9_SmallRNA_ManNAz-enrich

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

institute: Stanford University

data_processing:
unique, not-depth-normalized RT stops from each dataset
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig, containing unique, not-depth-normalized RT stops from each dataset

source_name: H9 embryonic stem cells

extract_protocol: RNA was extracted with TRIzol, purified with a Zymo silica-based column. Excess proteins were digested with Proteinase K and RNA again cleaned up with a Zymo column. Biotin was conjugated to total RNA with DBCO-biotin and cleaned up with a Zymo column. Small RNAs were fractionated using sucrose density gradient.

treatment_protocol: All cells were treated with 100 uM Ac4-ManNAz for 24 hours prior to RNA collection.

value: ManNAz enriched small RNAs


title: H9_SmallRNA_Input

value: Input small RNAs


title: HeLa_SmallRNA_ManNAz-enrich

source_name: HeLa cells


title: HeLa_SmallRNA_Input


title: HeLa rep-4

description: RNA, PCR product


title: REC-1_300nM_Day7

city: Hachioji

first: Yuki

last: Kagiyama

address: Horinouchi 1432-1

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
Avadis NGS Version 2.1 software was used for analysis.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Avadis NGS Version 2.1.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM using Avadis NGS

source_name: MCL cell

growth_protocol: RPMI1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted from up to 5 x 106 cells using the ISOGEN II reagent (Nippongene).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the three MCL cell lines (Mino, JeKo-1 and REC-1) were treated with vehicle control, 300 nM, or 1000 nM OR-S1 for 5 days and 7 days

tag: or-s1 concentration

tag: day

value: Day 7

value: Mantle cell lymphoma


title: REC-1_1000nM_Day7

tag: cell line


title: REC-1_1000nM_Day5

value: Day 5


title: REC-1_0nM

value: 0 nM

value: Day 0


title: JeKo-1_1000nM_Day7


title: JeKo-1_1000nM_Day5


title: Mino_300nM_Day7

value: Mino


title: Mino_1000nM_Day7


title: Mino_0nM


title: Mino_1000nM_Day5


title: JeKo-1_0nM


title: JeKo-1_300nM_Day7


title: Mino_300nM_Day5


title: scDT1_Unaffect_Lot4

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

description:
We analyzed single-cells, which were sorted to 384-wells in total.
README_InstructionsForDemultiplexing.txt

data_processing:
(Bulk RNA-seq) Quality control of fastq files was carried out by cutadapt (v1.2.1) and PRINSEQ (v0.19.2). For mapping the reads to a reference genome, we used TopHat (v2.0.13).
(Bulk RNA-seq) Data assambling and comparision of expression lebel were performed by using Cufflinks (v2.2.1). For clustering analyses, we used cummeRbund.
(Quartz-Seq2) BCL files generated by Illumina NextSeq500 were converted to fastq files by bcl2fastq2 (v2.17.1.14) with demultiplexing pool barcodes.
(Quartz-Seq2) Data for Quartz-Seq2 was processed according to previous study [Sasagawa et al. Genome Biology, 2018, 19:29].
Genome_build: (Bulk RNA-seq) GRCh37.primary_assembly.genome.fa
Genome_build: (Quartz-Seq2) GRCh38.primary_assembly.genome.fa
Supplementary_files_format_and_content: tab-delimited text files include fpkm or UMI counts for each gene for each sample/cell

source_name: Single-cells from cerebral organoid

growth_protocol: For neural stem/progenitor cells: iPS cells were dissociated into single cells using Accumax and transferred to PrimeSurface 96U plates at a density of 9,000 cells/well. The cells were cultured for 8 days in DFK5 medium supplemented with 10uM SB431542 and 100 nM LDN-193189. The medium was also supplemented with 30 uM Y-27632 for the first 4 days. On day 8, embryoid bodies (EBs) were transferred onto 6-well culture plates coated with Matrigel Basement Membrane Matrix Growth Factor Reduced at a density of 48 EBs/well in DFN2 medium consisting of DMEM/F12+Gluta MAX, 1 x N2 Supplement, 1 x  MEM NEAA, 100 uM 2-ME, 0.5 x penicillin/streptomycin and 100nM LDN-193189. Medium was replaced every 3 days until day 24.

extract_protocol:
For bulk RNA-seq, total RNA was isolated using the TRIzol reagent and a PureLink RNA Micro Kit according to the manufacturer’s instructions. For single-cell RNA-seq using Quartz-Seq2, we used the set of v3.1 RT primers corresponds to one set of the 384-well PCR plate with lysis buffer, the wells of which have unique barcodes for Quartz-Seq2. Single cells were isolated in the 384-well PCR plate with 1 µL of lysis buffer (0.1111 µM respective RT primers, 0.12 mM dNTP mix, 0.3% NP-40, 1 unit/µL RNasin plus) containing ERCC spike mix I. We analyzed the single-cells with Quartz-Seq2.
For bulk RNA-seq, libraries were prepared from the purified RNA by using a TruSeq RNA Sample Preparation Kit v2  The length of libraries was 316-429 bp, including adaptor sequences.For single-cell RNA-seq, we performed Quartz-Seq2 according to previous study [Sasagawa et al. Genome Biology, 2018, 19:29].

value: iPS cell-derived cerebral organoids

tag: individual

value: DT1_U (Unaffected)

tag: clone #

tag: passage # of ipsc

tag: cultured period

value: 35 days

tag: method name

value: Single-cell RNA-seq using Quartz-Seq2 (v3.1, RT6.25)


title: scDT1_Unaffect_Lot3


title: scDT1_Unaffect_Lot1


title: scDT1_Affect_Lot3

value: DT1_A (Affected)


title: scDT1_Unaffect_Lot2


title: scDT1_Affect_Lot4


title: scDT1_Affect_Lot1


title: JeKo-1_300nM_Day5


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, CS_882_2

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCM38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalization of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Genome_build: GRCM38
Supplementary_files_format_and_content: tab-delimited text files include RSEM expected read count values for each sample

source_name: Hematopoitic stem and progenitor cells

extract_protocol:
LKS+ Scl:Cdx2 BM of secondary transplant leukemic mice was sorted
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500 Sequencer High Output mode (1 × 75 bp).

value: mCherry+ Lineage low cKit+ Sca1+

tag: strain

value: bone marrow

tag: disease stage

value: Acute T cell leukemia

value: Scl-CreERT x Cdx2


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, CS_252_2

tag: cell type


title: REC-1_300nM_Day5


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, CS_882_1

tag: genotype


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, CS_472_2

value: Acute myeloid/erythro-myeloid leukemia


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, CS_472_3


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, CS_252_1


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, S_315_2

value: Healthy

value: Scl-CreERT


title: mCherry+ LKS+ BM cells, HighDose5

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
mCherry+ LKS+ BM of Scl:Cdx2 leukemic mice was sorted after one treatment cycle of Azacitidine or vehicle
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500 Sequencer High Output mode (1 × 75 bp).

tag: treatment

value: prolonged low dose Azacitidine

value: Acute myeloid leukemia


title: mCherry+ LKS+ BM cells, HighDose4


title: mCherry+ LKS+ BM cells, LowDose4

value: short-intermittent high dose Azacitidine


title: mCherry+ LKS+ BM cells, LowDose5


title: mCherry+ LKS+ BM cells, LowDose3


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, S_315_1


title: mCherry+ LKS+ BM cells, V21

value: Vehicle


title: mCherry+ LKS+ BM cells, V12


title: scDT1_Affect_Lot2


title: mCherry+ LKS+ BM cells, V11


title: Lineage low cKit+ Sca1+ cells, CSF_1452

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCM38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Genome_build: GRCM38
Supplementary_files_format_and_content: tab-delimited text files include RSEM expected read count values for each sample

extract_protocol:
BM LKS+ from  Scl-CreERT, Scl-CreERTxCdx2, Scl-CreERT x FLT3 ITD/+ and Scl-CreERT x Cdx2 x FLT3 ITD/+ mice four weeks after tamoxifen induction
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500 Sequencer High Output mode (1 × 75 bp).

value: Lineage low cKit+ Sca1+

tag: time point

value: 4 weeks post tamoxifen

value: Scl-CreERT x Cdx2 x FLT3 ITD/+


title: Lineage low cKit+ Sca1+ cells, CSF_1449


title: Lineage low cKit+ Sca1+ cells, CSF_1627


title: Lineage low cKit+ Sca1+ cells, CS_1489


title: Lineage low cKit+ Sca1+ cells, CS_1488


title: Lineage low cKit+ Sca1+ cells, CS_1386


title: Lineage low cKit+ Sca1+ cells, SF_1536

value: Scl-CreERT x FLT3 ITD/+


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, S_1275_3


title: Input DNA rep-3

description: DNA plasmid

library_source: other

molecule: other

organism: synthetic construct

source_name: Input DNA

tag: sample type

value: Exontrap plasmid used for transfection


title: BM LKS+ CD45.2+ (mCherry+ for Scl:Cdx2) cells, S_1275_1

tag: tissue


title: Lineage low cKit+ Sca1+ cells, S_1490


title: Input DNA rep-4

description: DNA plasmid


title: Lineage low cKit+ Sca1+ cells, S_1494


title: mCherry+ LKS+ BM cells, HighDose3


title: RORaf/fDSS-rep.1

city: Seoul

first: Dongha

address: 599 Gwanak-ro

country: South Korea

institute: Seoul National University

description: After dissection, distal colons were separately excised, and placed in Petri dishes containing cold Phosphate-Buffered Saline (PBS). Blood vessels and associated fat were removed, the intestine was opened longitudinally and vigorously washed on ice in PBS with 1mM DTT to remove mucus. Colons were then cut into small pieces and placed in fresh PBS with 5 mM, and shaken at 150 rpm for 15 min. The supernatant was transferred into a fresh tube, centrifuged (500 g, 5 min at 4°C) and washed with ice-cold PBS twice. The pellet was immediately processed for subsequent analysis.

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly and the transcriptome using STAR (v2.5.3a) with GENCODE M16 annotation.
RSEM (v1.3.0) was used to calculate the expected read counts, FPKM and TMP for each sample from the corresponding bam files.
The read counts were processed using DESeq2 (v1.18.1) to identify differentailly expressed genes.
The TPM values were extracted and used for following downstream analyses such as hierarchical clustering, K-mean clustering, and GSEA.
Genome_build: mm10

source_name: IEC

extract_protocol:
RNA were harvested using Trizol and RNA were extracted using Qiagen RNeasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Dextran Sulfate Sodium (DSS) (MP Biomedicals; relative molecular mass 36,000–50,000, Cat #160110) was added to drinking water at 2 % (w/v) either for 5 days and then allowed to recover by drinking water for additional 3 days.

value: Intestinal Ephithelial Cell

tag: passages


title: Input DNA rep-1

description: DNA plasmid


title: RORaΔIECDSS-rep.2


title: RORaΔIECDSS-rep.1


title: RORaΔIECcontrol-rep.2


title: Input DNA rep-2

description: DNA plasmid


title: RORaf/fcontrol-rep.1


title: RORaf/fcontrol-rep.2


title: AGS_mock

description: Gene expression after stable transfection of empty vector

source_name: AGS stably transfected with empty vector

value: gastric cancer

value: AGS

value: control


title: RORaΔIECcontrol-rep.1


title: Lineage low cKit+ Sca1+ cells, CSF_1380

value: bone marrow


title: Input DNA rep-5

description: DNA plasmid


title: HCT116 half of 300 cells input, bait 1, 2, 3, 4, 5, 6, 7, 8, 9 and 10

data_processing:
Sequence reads were mapped using bwa 0.7.12-r1039 to a reference genome composed of PhiX, BDGP5 (Drosophila), K12 (E. coli) and human (HG19). Alignments with mapping quality greater than 10 of the read 2 were used to determine the probe position. An extension region (region from the probe’s end to the first restriction site) was used to discriminate valid from mis-annealing events. The total number of alignments in the read 1 with the proper probe extension in the second read was reported by restriction fragment. Next the number of distinct transposon integration sites was also reported to remove PCR duplicates.
Genome_build: hg19/BDGP5/PhiX/K12
Supplementary_files_format_and_content: tab-delimited text files

growth_protocol: Human colon cancer cells (HCT116) were maintained in McCoy’s 5A modified medium (Life Technologies, 16600-082) supplemented with 10 % Fetal Bovine Serum (FBS), penicillin (Life Technologies) and streptomycin (Life technologies). Normal colon cells (HCEC, ScienCell, 2950) were maintained in Colonic Epithelial Cell Medium (ScienCell, 2951). Both cells were cultured under 5 % CO2 circumstance at 37 C.

extract_protocol:
Chromosome Conformation Capture (3C) was performed as described before with slight modification. Briefly, 1 million of the cells were fixed with 1 % monomeric formaldehyde for 10 min at RT and excess amount of the formaldehyde was captured by 0.125 M Glycine. Then cells were collected and suspended in 10 ml of nuclear isolation buffer (0.2 % NP-40, 10 mM Tris-cl, pH 7.5, 10 mM NaCl, x1 Proteinase inhibitor (Roche, 04693116001)) and incubated for 10 min on ice. Isolated nuclei were precipitated and washed with 1 ml of Buffer 2 (New England Biolabs, B7002S). Next, nuclei were re-suspended in 500 ul of x1.2 buffer 2. Un-crosslinked fraction was removed by adding 5 ul of 10 % SDS and incubated for 1 hr at 37 °C. Then excess amount of SDS was captured by TritonX-100. The chromatin DNA was fragmented by the incubation at 37 °C for overnight with HindIII (1 U/ul, New England Biolabs, R0104T). As a spiking control, same amount of chromatin was isolated from Drosophila S2 cell with same method and mixed with chromatin for analysis. After the inactivation of the enzyme, the solution was transferred to 50 ml tube containing 7 ml of ligation buffer (50 mM Tris-cl, pH 7.5, 10 mM MgCl2, 1 % Triton X-100) and incubate for 1 hr at 37 °C. Then 70 ul of 100 mM ATP, 70 ul of 1 M DTT and 2000 U of T4 DNA ligase were added. Then the solution was incubated at 16 °C for overnight followed by for 1 hr at RT. Crosslink was reversed with conventional methods. Finally, DNA was collected by ethanol precipitation followed by the purification with MSB Spin PCRapace (Stratec, 1020220200) and Zymo Clean & Concentrator-5 (Zymo Research, D4013). The digestion efficiency was estimated by qPCR. The quality of 3C DNA was visualized on 1 % agarose gel.
3C DNA was tagmented and adapter DNA which equipped with T7 RNA polymerase promoter was incorporated by limited cycle PCR using either Nextera or Nextera XT DNA sample prep kit (Illumnia, FC-121-1031, FC-131-1024). The resulting product was amplified by in vitro transcription (Maxiscript T7 kit, Life technology, AM1312M). The template DNA was fragmented by Turbo DNase I (Life technology, AM2239) prior to the RNA purification by RNeasy (Qiagen, 74104). For primer annealing, 1 ug of template RNA with 0.2uM of bait specific primer was denatured at 75 °C for 3 min and then mixed with x2 buffer of Platinum Quantitative RT-PCR ThermoScript One-Step System (Life technology, 11731-015) and 0.5U/ul of SUPERase In RNase inhibitor (Life technology, AM2694). The solution was incubated at 4 °C for 44-48 hrs. Then following the incubation at 65 °C for 5 min, the primer was extended by adding Thermoscript Plus/Platinum Taq mix at 60 °C for 30 min. After the inactivation of reverse transcriptase, bait-interactor chimeric DNA is enriched by PCR with Illumina P5 and bait specific primer. At last Illumina P7 sequence was incorporated with Nextera DNA sample prep kit by following manufacture’s instruction.

value: human colorectal carcinoma cell line

tag: probes


title: HCT116, 35 pg input, bait 5 repeat, replicate 6


title: HCT116 35 pg input, bait 6, 9 and 10, replicate 6


title: HCT116 35 pg input bait 3 and 4, replicate 6

value: RPB048_myc400_r1, RPB015_myc_enh_up_r


title: HCT116 35 pg input, bait 7, replicate 6


title: HCT116 35 pg input, bait 2, replicate 6


title: HCT116 35 pg input, bait 8, replicate 6


title: RORaf/fDSS-rep.2


title: HCT116 35 pg input, bait 7, replicate 8


title: HCT116 35pg input, bait 1, replicate 6


title: HCT116 35 pg input, bait 8, replicate 8


title: E18.5 sample 3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from fetal pulmonary lymphatic endothelial cells at day E18.5.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: All sorted cell populations were collected directly into QIAzol for RNA extraction using the miRNeasy kit (Qiagen).

tag: developmental stage

value: fetal lung

value: pulmonary lymphatic endothelial cells


title: E18.5 sample 1

source_name: fetal pulmonary lymphatic endothelial cells


title: E17.5 sample 3

description: Gene expression data from fetal pulmonary lymphatic endothelial cells at day E17.5.


title: E16.5 sample 2

description: Gene expression data from fetal pulmonary lymphatic endothelial cells at day E16.5.


title: E16.5 sample 3


title: HCT116, 35 pg input, bait 5, replicate A9

tag: cell line


title: HCT116, 35 pg input, bait 5, replicate 4


title: HCT116 35 pg input, bait 6, 9 and 10, replicate 8


title: HCT116 35 pg input, bait 5, replicate 8


title: HCT116 35 pg input, bait 2, replicate 8


title: HCT116 35 pg input, bait 3 and 4, replicate 8


title: E17.5 sample 2


title: E17.5 sample 1


title: E18.5 sample 2


title: E16.5 sample 1


title: HCT116, 35 pg input, bait 5, replicate 2


title: HCT116 35 pg input, bait 1, replicate 8


title: HCT116, 35 pg input, bait 5, replicate A6


title: HCT116, 35 pg input, bait 5, replicate 8


title: HCT116, 35 pg input, bait 5, replicate A3


title: HCT116, 35 pg input, bait 5, replicate 6


title: HCT116, 35 pg input, bait 5, replicate 10


title: HCT116, 35 pg input, bait 5, replicate A24


title: HCT116, 35 pg input, bait 5, replicate 14


title: HCT116, 35 pg input, bait 5, replicate 12


title: HCT116, 35 pg input, bait 5, replicate A2


title: HCT116, 35 pg input, bait 5, replicate 11


title: HCT116, 35 pg input, bait 5, replicate 3


title: HCT116, 35 pg input, bait 5, replicate A20


title: HCT116, 35 pg input, bait 5, replicate 5


title: HCT116, 35 pg input, bait 5, replicate 7


title: HCT116, 35 pg input, bait 5, replicate 13


title: HCT116, 35 pg input, bait 5, replicate A16


title: HCT116, 35 pg input, bait 5, replicate 9


title: HCT116 half of 300 cells input, bait 5, replicate 5


title: HCT116 half of 300 cells input, bait 5, replicate 10


title: HCT116 half of 300 cells input, bait 5, replicate 3


title: HCT116 half of 300 cells input, bait 5, replicate 2


title: HCT116 half of 300 cells input, bait 5, replicate 9


title: HCT116, 35 pg input, bait 5, replicate 15


title: HCT116, 35 pg input, bait 5, replicate 1


title: HCT116 bait 5 FP6h

description: Sample name: NW052.NW28HFP6hRPB009_151128

source_name: HCT116, bait 5, FP 6h

tag: spiking control

value: Drosophila S2 cell chromatin

value: Flavopiridol


title: HCEC bait 4

description: Sample name: NW046.HCECH015entidx150320_MID2

source_name: HCEC, bait 4

value: HCEC

value: human colonic epithelial cell line


title: HCT116 half of 300 cells input, bait 5, replicate 8


title: HCT116 bait 4

description: Sample name: NW046.28H015entidx150320_MID1

source_name: HCT116, bait 4


title: HCT116 bait 1 to 10 low cell input, rep1

description: Sample name: NW051.NW28H160cellMix150924

source_name: HCT116, bait 1 to 10, low cell input


title: HCEC bait 5 low cell input, rep10

description: Sample name: NW045.NWHCECH009ent10_MID10

source_name: HCEC, bait 5, low cell input