title: 0.3MG_rGAL4_w1118_1

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

state: New York

address: 4400 Vestal Parkway East

institute: Binghamton University

description:
0.3MG-1
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.3 M glucose food until fat body harvest

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Expression was normalized by applying upper-quartile normalization as defined in "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", Bullard et al. BMC Bioinformatics. 2010; 11: 94
Genome_build: dm3; MB8
Supplementary_files_format_and_content: normalized RPKM for each raw dataset, indexed by Flybase gene Accession (Fbgn number)

source_name: 0.3MG_rGAL4_w1118_fat body

growth_protocol: Males (Vienna Drosophila Resource Center #60000 w1118 stocks) were crossed to UAS-Dcr2; r4-GAL4 driver line virgin females to produce offspring that chronically express dsRNA to elicit RNA interference against the InR gene in the larval fat body.

extract_protocol:
Fat bodies were homogenized in Trizol and total RNA isolated after DNAse digestion.
RiboZero subtraction was used to remove rRNA and then reverse transcription, size exclusion, amplification, and bar coding produced the final library.
Reads using bar-coded cDNA were generated by Illumina Hi-Seq analyzer.

treatment_protocol: Larvae were reared until reaching wandering third instar stage, then fat bodies were isolated by shearing and separation by centrifugation before freezing in Trizol.

tag: Sex

value: female

tag: developmental stage

value: wandering third instar larva

tag: diet

tag: tissue

value: fat body


title: 1.7MG_rGAL4_w1118_3

status: Public on Apr 26 2019

type: SRA

department: Biological Sciences

country: USA

description:
1.7MG-3
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 1.7 M glucose food until fat body harvest

library_source: transcriptomic

molecule: total RNA

organism: Drosophila melanogaster

source_name: 1.7MG_rGAL4_w1118_fat body

tag: strain


title: 0.3MG_rGAL4_w1118_2

description:
0.3MG-2
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.3 M glucose food until fat body harvest


title: 1.7MG_rGAL4_w1118_2

description:
1.7MG-2
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 1.7 M glucose food until fat body harvest


title: 0.3MG_rGAL4_w1118_3

description:
0.3MG-3
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.3 M glucose food until fat body harvest


title: Batch 1-DMSO_Day 20

city: Beijing

first: Yifang

last: Liu

address: Haidian District

country: China

institute: Peking University

data_processing:
To compare gene expression proﬁle between paired-end and single-end libraries, we take only the read1 from our generated sequencing paired-end reads.
The read1 and the downloaded single-end read were trimmed to the same 40bp length by using Cutadapt.
The expression values for each sample were quantified by Salmon.
Genome_build: hg19 for human
Supplementary_files_format_and_content: expression values for each sample

organism: Homo sapiens

source_name: primary human hepatocyte

extract_protocol:
Total RNA from each sample was isolated using RNeasy Micro Kit (50) (Qiagen).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: human hepatocytes were cultured in different conditions for a few weeks and then collected for RNA extraction.

tag: tissue/cell type

value: primary human hepatocyte

tag: treatment

value: Cultured under DMSO condition for 20 days

tag: batch number

value: Batch 1


title: 1.7MF_rGAL4_w1118_2

description:
1.7F-2
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 1.7 M fructose food until fat body harvest

source_name: 1.7MF_rGAL4_w1118_fat body


title: 1.7MF_rGAL4_w1118_3

description:
1.7F-3
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 1.7 M fructose food until fat body harvest


title: 0.3MF_rGAL4_w1118_3

description:
0.3MF-3
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.3 M fructose food until fat body harvest

source_name: 0.3MF_rGAL4_w1118_fat body


title: 1.7MG_rGAL4_w1118_1

description:
1.7MG-1
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 1.7 M glucose food until fat body harvest


title: 1.7MF_rGAL4_w1118_1

description:
1.7F-1
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 1.7 M fructose food until fat body harvest


title: 0.3MF_rGAL4_w1118_2

description:
0.3MF-2
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.3 M fructose food until fat body harvest


title: 0.3MF_rGAL4_w1118_1

description:
0.3MF-1
VDRC's  w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.3 M fructose food until fat body harvest


title: mouse_173 P12 hyperoxia

type: RNA

city: Krakow

first: Anna

last: Madetko-Talowska

state: Krakow

address: Wielicka 265

department: Medical Genetics Chair of Pediatriics

country: Poland

institute: jagiellonian university medical College

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis — Low Input Quick Amp Labeling ver.6.5

scan_protocol: SureScan Microarray Scanner (Agilent, Santa Clara, USA)

data_processing: Feature Extraction Software (Agilent, Santa Clara, USA).

organism: Mus musculus

source_name: Murine blood MNC

extract_protocol: RNeasy Micro Kit (Qiagen, Hilden, Germany)

treatment_protocol: mice were stabled and bred at 24°C on a 12:12 light/dark cycle; on postnatal day 7 (P7) pups were assigned .within the litters (P12, P17, P28);  each litter was then randomized either to hyperoxia (75% oxygen) or normoxia (21% oxygen)

tag: age

value: day 12

tag: oxygen status

value: hyperoxia

source_name: Universal Mouse Reference RNA (Agilent)

tag: sample type

value: reference


title: mouse_177 P12 hyperoxia

label_protocol: Two-Color Microarray-Based Gene Expression Analysis — Low Input Quick Amp Labeling ver.6.5


title: mouse_183 P12 hyperoxia


title: mouse_188 P12 hyperoxia


title: mouse_179 P12 hyperoxia


title: CJP_NAc_21

city: Princeton

first: Catherine

middle: Jensen

last: Pena

state: NJ

address: Washington Road

department: Neuroscience

institute: Princeton University

description: normalized_expression_study1_cate_modified.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to mouse genome mm10 using HISAT. Uniquely aligned short reads were counted using HTSeq-counts.
Low and non-expressed genes with less than 5 reads in at least 80% of samples in a condition were omitted from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Counts in tab delimited text file generated using HTSeq-count

molecule: polyA RNA

source_name: NAc

extract_protocol:
All tissue was taken from adult male mice during the light cycle, 24 hours after behavioral testing. RNA was purified first by TriZol extraction followed by column purification sing Rneasy micro kits (Qiagen) according to manufacturer's protocol. All samples were found to have a high RIN value (>9; BioAnalyzer, Agilent). Chromatin was briefly crosslinked in 1% formaldehyde and sonicated to 200-600bp fragments. Samples were pooled by group to immunoprecipitate 1 microgram of chromatin with ChIP-grade H3K4me1 antibody (AbCam Ab8895) overnight at 4C. DNA from ChIP or Input (5%) was de-crosslinked overnight, RNA and protein degraded enzymatically, and purified by PCR purification kit (Qiagen).
RNA-seq libraries were prepared using Illumina TruSeq unstranded kit A and B for poly-A selected transcripts, according to protocol. ChIP-seq/Input libraries were prepared by NEBNext Ultra DNA kit with Illumina adaptors according to protocol.

value: male

tag: early life condition

value: ELS P2-12

tag: adult condition

value: Defeat


title: CJP_NAc_13

value: Standard


title: CJP_NAc_12


title: CJP_NAc_29


title: CJP_NAc_28


title: CJP_NAc_14


title: CJP_NAc_5


title: CJP_NAc_2


title: CJP_NAc_4


title: CJP_NAc_19


title: CJP_NAc_27


title: CJP_NAc_23


title: CJP_NAc_9


title: CJP_NAc_18


title: CJP_NAc_17


title: mouse_153 P12 hyperoxia


title: CJP_NAc_20


title: CJP_NAc_15


title: mouse_167 P12 hyperoxia


title: CJP_NAc_26

value: Control


title: CJP_NAc_3


title: CJP_NAc_22


title: CJP_NAc_1


title: CJP_NAc_8


title: CJP_NAc_10


title: CJP_NAc_11


title: CJP_NAc_24


title: FVEC5

description: normalized_expression_study2_cate_modified.txt

source_name: VTA


title: CJP_NAc_16


title: FVSC6


title: MHSD6

source_name: HIP


title: FVES3

value: Sub-threshold Variable Stress


title: MPED5

source_name: PFC


title: MPSC5


title: MPSD5


title: MPEC5


title: CJP_NAc_6


title: FVES5


title: MHED6


title: FVSS5


title: FVSC2


title: MHSC6


title: MHEC6


title: FVES6


title: FVSC5


title: CJP_NAc_25


title: FVSS2


title: CJP_NAc_7


title: FVSC4


title: FVEC4


title: FVES4


title: MPED6


title: MPSD6


title: FVSC1


title: FVES1


title: FVSS1


title: FVEC1


title: FNES5


title: FVEC3


title: FNEC5


title: FNSS5


title: FNSC5


title: FVSS4


title: FVEC2


title: FVES2


title: MHSD4


title: MHEC4


title: FNEC3


title: FVSC3


title: MHSC5


title: MHED4


title: MHEC5


title: FVSS3


title: MHED5


title: FNSS4


title: MPSD4


title: MHSD5


title: MHSC4


title: MPSC6


title: MPEC6


title: MPED4


title: MHEC3


title: MPSD3


title: MPED3


title: MPEC3


title: FNES3


title: MPSC3


title: MPSC4


title: FNES4


title: FNSC4


title: MPEC2


title: MHED1


title: FNES2


title: FNEC2


title: FNSC6


title: MHSD1


title: MHEC2


title: MHSD2


title: MHSD3


title: MHED3


title: MHSC2


title: FNSC2


title: FNSS2


title: MPED2


title: MHED2


title: FPEC3


title: MPEC4


title: FNSS1


title: MPSD2


title: FNES6


title: FNSC1


title: FPSS4


title: MHSC3


title: FNEC4


title: FNSS3


title: MPSC2


title: FPES5


title: FPEC5


title: FNSC3


title: FPSC5


title: MHEC1


title: MPEC1


title: FPSS5


title: MPSD1


title: FNEC1


title: MPSC1


title: FPES2


title: FNES1


title: FPEC2


title: FPEC4


title: FPES4


title: FPSC4


title: FPEC1


title: FPSC6


title: FPSS1


title: MHSC1


title: MPED1


title: FPSC3


title: FPES6


title: FPSS3


title: FPES3


title: Th17 WT rep D

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: Manuscript in preparation (Hamline M.Y., Wamstad J.A., Corcoran C.M., Miletiche, I., Fenge, J. Sharpe, P.T., Gearhart, M.D., Bardwell V.B., “OFCD Syndrome and Extraembryonic Defects are Revealed by Conditional Loss of the Polycomb-group Repressive Complex 1 (PRC1) Component BCOR.”)

data_processing:
Demultiplexed reads were trimmed with Trimmomatic (v0.32, parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25). Trimmed reads were mapped to the GRCm38 version of the mouse genome with STAR (v2.4.2a_modified), indexed and sorted with samtools (v1.0). PCR Duplicates were removed using Picard MarkDuplicates (2.17.10-SNAPSHOT).  Reads that overlap features in the Gencode M16 annotation were enumerated with Rsubread (1.22.3). Differential expression analysis was performed with R (v3.5.1) and DESeq2 (v1.20.0) using custom scripts available at https://github.com/micahgearhart/th17.
Genome_build: GRCm38
Supplementary_files_format_and_content: Coverage files (bigWig), raw counts and normalized FPKM values (csv) and ChIP peak locations (broadPeak).

source_name: Primary antigen-specific CD4+ T cells

growth_protocol: Mice were housed in specific pathogen-free conditions and transferred to the BSL-2 facility for infections.

extract_protocol: Total RNA was isolated from the Trizol samples and treated with DNase using an RNA isolation kit (Qiagen). Sequencing libraries were made from PolyA+ mRNA using the KAPA mRNA Hyper Prep kit per manufacturer’s instructions (KAPA Biosystems).

treatment_protocol: Mice 6-12 weeks of age were infected intranasally with 10 ul of 2 x 108 CFU per mouse of live Streptococcus pyogenes expressing 2W peptide (Sp-2W) in phosphate buffered saline

tag: cell type

tag: genotype

value: Bcorfl/fl;Lck-cre-;RorcGFP

tag: cre allele

tag: reporter allele

value: B6.129P2(Cg)-Rorctm2Litt/J; The Jackson Laboratory stock #007572

tag: antibody


title: FPSS2

tag: Sex

value: female


title: Th17-Tfh WT rep D


title: Plate_3_Q7

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

data_processing:
Adaptor sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were removed from Read 2 using Trimmomatic 0.36
Trimmed reads (from Read 2) were mapped using STAR 2.5.3a to the Ensembl mouse genome GRCm38.p5, release 90. Unaligned reads were subsequently aligned to standard ERCC (spike-in) reference sequences.
Cell barcodes (first 8 nucleotides) and Unique Molecular Identifiers (subsequent 10 nucleotides) were extracted from Read 1, and appended as additional fields to the aligned Read 2 bam file using Dropseqtools
Distinct exonic UMIs were counted for each gene in each cell, allowing for 1 mismatch, using standard Dropseqtools parameters. The final cell-by-gene counts were tallied into a full counts table
Genome_build: GRCm38.p5, release 90
Supplementary_files_format_and_content: STAR 2.5.3a quantification output, expressed as counts of Unique Molecular Identifiers for every gene in every cell

source_name: Labelled SCTNs from cervical and thoracic spinal cord

growth_protocol: C57BL mice (P6-7), with injections of CTB-Alexa 555 at P4 in cerebellum

extract_protocol:
For each sample, individual labelled cells were isolated by manual cell picking on a fluorescence dissecting scope, after incubating slices in ACSF with neuronal activity blockers (TTX, APV, DNQX) and pronase for 50 minutes. Each isolated cell was transferred to a 0.2mL PCR 8-tube strip containing 3 microliters of lysis buffer (0.2% Triton X-100) in Nuclease-free water with RNase inhibitor. Each 8-tube strip was flash frozen on dry ice and kept at -80C until library prep and sequencing.
Each single cell underwent the RT process, and cDNA was then pooled before amplification, using the SMART-SCRB technique (using SMARTer-based amplification with cell barcodess). Amplified cDNA was fragmented to ~250bp, ligated to Illumina sequencing adaptors with Encore Rapid kit, and sequenced on an Illumina HiSeq 2500 with 4-fold multiplexing (paired end, 25bp for Read 1 and 125bp for Read 2)

value: spinal cord

value: mouse spinocerebellar tract neurons (SCTNs)

tag: fluorescent reporter

tag: injection site

value: Cerebellum


title: Plate_2_Q6

tag: tissue


title: Tfh WT rep D

tag: strain


title: Plate_4_Q8


title: Plate_1_Q5


title: FPSC1


title: Th17 KO rep D

value: Bcorfl/fl;Lck-cre+;RorcGFP

value: B6.Cg-Tg(Lck-icre)3779Nik/J; The Jackson Laboratory stock #012837


title: Th17-Tfh KO rep D


title: RORgt-CXCR5- KO rep D


title: Th17-Tfh KO rep B


title: Tfh KO rep B


title: Tfh WT rep B


title: Th17-Tfh WT rep B


title: RORgt-CXCR5- WT rep B


title: RORgt-CXCR5- KO rep B


title: Tfh KO rep D


title: Th17 WT rep 6


title: RORgt-CXCR5- KO rep 1


title: RORgt-CXCR5- KO rep 3


title: RORgt-CXCR5- WT rep 1


title: FPSC2


title: Th17 WT rep 3


title: RORgt-CXCR5- KO rep 2


title: RORgt-CXCR5- WT rep D


title: RORgt-CXCR5- WT rep 2


title: FPES1


title: Th17 KO rep 3


title: Th17 KO rep 2


title: Th17 KO rep 1


title: Th17-Tfh WT rep 1


title: Tfh WT rep 3


title: Th17-Tfh WT rep 3


title: Th17-Tfh KO rep 1


title: Th17-Tfh KO rep 3


title: RORgt-CXCR5- WT rep 3


title: Th17-Tfh KO rep 2


title: Tfh KO rep 3


title: Tfh WT rep 1


title: ChIP Input

library_source: genomic

data_processing:
Reads were trimmed (Trimmomatic 0.32), mapped to the GRCm38 reference genome (BWA mem 0.7.12-r1039), sorted and indexed (Samtools 1.0).  Peaks were identified using MACS version 2.1.1.20160309 using the --broad --broad-cutoff 0.1 options.  BCOR peak locations were analyzed in relationship to the Gencode M16 reference annotation and the UCSC defined CpG islands using custom R scripts which are available at https://github.com/micahgearhart/th17.
Genome_build: GRCm38
Supplementary_files_format_and_content: Coverage files (bigWig), raw counts and normalized FPKM values (csv) and ChIP peak locations (broadPeak).

molecule: genomic DNA

source_name: in vitro differentiated Th17 cells

growth_protocol: CD4+ T cells were isolated from B6 mice using a CD4 T cell positive isolation kit (Stemcell) and stimulated for 3 days with Th17 polarizing conditions: plate-coated anti-CD3 (4 mg/ml; 2C11; BioXcell) and anti-CD28 (4 mg/ml; 37.51; BioXcell), IL-6 (60 ng/ml, Tonbo biosciences), TGF-β1 (0.8 ng/ml, Tonbo biosciences), IL-23 (20 ng/ml, Miltenyi), IL-1β (20 ng/ml; Tonbo biosciences), anti-IFN-γ (10 mg/ml; XMG1.2; ), anti-IL-12 (10 mg/ml; C17.8; Tonbo biosciences), and anti-IL-4 (10 mg/ml; 11B11; Tonbo biosciences). Cells were grown in IMDM media (Sigma) supplemented with 10% Fetal Bovine Serum (Omega), Pen/Strep (Life Technologies), Glutamax (Life Technologies), β-mercaptoethanol (Sigma), Hepes (Life Technologies), Sodium Pyruvate (Life Technologies), and MEM Non-Essential Amino Acids (Life Technologies).

extract_protocol: DNA was purified using a PCR purification kit (Qiagen) and cDNA sequencing libraries were made using the KAPA Hyper Prep kit per manufacturer’s instructions (KAPA Biosystems).

value: WT


title: Tfh KO rep 1


title: Tfh KO rep 2


title: BCOR ChIP


title: Tfh WT rep 2


title: Veh_END_rep1

city: Madrid

first: Silvana

last: Mouron

state: Madrid

address: Calle Melchor Fdez Almagro

department: Clinical Research

country: Spain

institute: CNIO

description: Gene expression after vehicle treatment in MMTV-PyMT mouse

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Microarray background subtraction was performed using the normexp method. To normalize the data set, we determined losses within array normalization and quantiles between array normalization.

source_name: mammary tumors

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Tumors were dissected. Total RNA was extracted and purified using RNeasy Mini-Kit (Qiagen, Valencia, CA, USA) following the manufacturer’s instructions.

treatment_protocol: Treatment with the different drugs was started at 7 weeks of age. B20-4.1.1 (Genentech, San Francisco, CA, USA) was prepared in 1× PBS and administered at 5 mg/kg intraperitoneally twice per week. Nintedanib  (Boehringer-Ingelheim, Ingelheim, Germany) was administered at 85 mg/kg/d by oral gavage.

value: mammary tumor

tag: treatment

value: vehicle

tag: gender


title: T0_rep1

description: Gene expression before any treatment

value: before any treatment


title: Veh_END_rep3


title: Nint_END_rep3

description: Gene expression after Nintedanib treatment in MMTV-PyMT mouse

value: nintedanib


title: Validation115

city: Toronto

first: Jeff

last: Wrana

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

data_processing:
The fastq files were obtained using Illumina CASAVA v1.8
The quality of fastq reads was examined by FASTQC and low quality 5' nucleotides were removed before mapping
The fastq read were mapped on human geneome (hg19) using Tophat 1.4.1
The read counts were calculated using customed R scripts to calculate transcript union reads per million reads (truRPMs)
Genome_build: hg19
Supplementary_files_format_and_content: Excel spread sheet was provided for coding gene expression of all the samples in this study

source_name: FFPE bladder tumor block

extract_protocol:
Total RNA with Trizol
The sequencing libraries were constructed using RiboZero and Illumina TruSeq RNA preparation kit following the kit instructions.

tag: cancer type

value: Non-muscle invasive bladder cancer

tag: grade

value: High grade

tag: Stage


title: Validation114


title: T0_rep3

description: Gene expression before any treatment


title: Validation120


title: Validation113


title: Validation110


title: Validation109


title: Validation117


title: Validation108


title: Validation107


title: Validation116


title: Validation119


title: Validation112


title: Validation111


title: B20_END_rep3

description: Gene expression after B20 treatment in MMTV-PyMT mouse


title: Nint_END_rep4


title: Nint_END_rep2


title: T0_rep2

description: Gene expression before any treatment


title: B20_END_rep4


title: B20_END_rep1


title: Nint_END_rep1


title: T0_rep4

description: Gene expression before any treatment


title: Veh_END_rep2


title: B20_END_rep2


title: Validation106


title: Validation118


title: Validation104


title: Validation105


title: Validation102


title: Validation101


title: Validation100


title: Validation99


title: Validation94

value: Low grade

value: pTa


title: Validation86


title: Validation93


title: Validation89


title: Validation95


title: Validation96


title: Validation83


title: Validation88


title: Validation90


title: Validation87


title: Validation97


title: Validation84


title: Validation80


title: Validation79


title: Validation76


title: Validation77


title: Validation85


title: Validation82


title: Validation98


title: Validation91


title: Validation81


title: Validation103


title: Validation70


title: Validation71


title: Validation92


title: Validation75


title: Validation65


title: Validation72


title: Validation67


title: Validation74


title: Validation63


title: Validation62


title: Validation61


title: Validation58


title: Validation68


title: Validation69


title: Validation54


title: Validation56


title: Validation57


title: Validation60


title: Validation59


title: Validation78


title: Validation51


title: Validation55


title: Validation53


title: Validation48


title: Validation64


title: Validation45


title: Validation46


title: Validation44


title: Validation52


title: Validation49


title: Validation50


title: Validation73


title: Validation66


title: Validation47


title: Validation43


title: Validation39


title: Validation38


title: Validation32


title: Validation36


title: Validation28


title: Validation26


title: Validation40


title: Validation41


title: Validation37


title: Validation35


title: Validation42


title: Validation31


title: Validation33


title: Validation34


title: Validation22


title: Validation21


title: Validation27


title: Validation30


title: Validation10


title: Validation11


title: Validation18


title: Validation24


title: Validation25


title: Validation20


title: Validation17


title: Validation19


title: Validation16


title: Validation23


title: Validation8


title: Validation7


title: Validation3


title: Validation5


title: Validation4


title: Validation15


title: Validation14


title: Validation13


title: Validation1


title: Gata2++05

city: Bethesda

first: Pu

middle: Paul

state: MD

address: 49 Convent Dr.

department: TFGB

institute: NHGRI/NIH

data_processing:
The raw data was processed using RTA (version 1.18.64) and CASAVA (version 1.8.2) for base calling.
Raw reads were aligned to the mouse genome reference (GRCm38) and transcript reference (GRCm38.78) using STAR (version 2.5.4a).
RSEM (version 1.3.0) was used to obtain RNA-seq transcript count matrix and to estimate relative transcript abundance at the gene level from the aligned reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file and includes transcript per million read counts for each sample for each gene (Ensembl gene ID was used)

source_name: leukemia

extract_protocol:
Frozen bone marrow cells are thawed and c-kit+ bone marrow cells are sorted. Then RNA was harvested using Trizol reagent. Total RNA was extracted with Direct-zol RNA miniprep Plus Kits (ZYMO RESEARCH). Poly-A selected stranded mRNA libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kits.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: c-kit+ bone marrow

value: end point (leukemia)

tag: genotype/variation


title: Gata2++06


title: Gata2++03


title: Gata2+f11


title: Validation29


title: Gata2+f07


title: Validation9


title: Gata2+f09


title: Validation2


title: Validation12


title: WT.fq

city: Cambridge

first: Moyra

last: Lawrence

address: Tennis Court Road

department: Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
adaptor-trimmed with TrimGalore
mapped to the mouse reference genome (GRCm38/mm10) with TopHat2
Strand-specific read counts were obtained with featureCounts
Transcript counts were normalized, and the statistical significance of differential expression between samples was assessed using the R Bioconductor DESeq2 package
Transcript counts normalized by DESeq2 size factors were subsequently normalized by their length.
Genome_build: mm10

source_name: E14tg2a embryonic stem cells

growth_protocol: Cells were seeded at the same density on gelatin-coated plates in medium containing Serum with LIF, the day before harvesting. Cells were dissociated with trypsin and centrifuged 3min 1400rcf. They were resuspended in PBS and centrifuged 3min 1400rcf. Pellets were snap frozen on dry ice and stored at -80 degrees.

extract_protocol:
Qiagen RNeasy mini kit
NextFlex Rapid Directional RNA-seq Kit (Bioo Scientific)
HiSeq4000 platform (Illumina), using V4 chemistry

treatment_protocol: DNAse

tag: line

value: Wild type E14tg2a

tag: medium

value: Serum with LIF


title: d0 - dropseq

city: Chicago

first: Nir

last: Drayman

state: IL

institute: University of Chicago

description: d0 - dropseq

data_processing:
Base calling was done using Illumina software
Alignment was done using STAR aligner
For bulk RNA-seq featureCounts was used to count gene expression
For scRNA-seq we used the Macosko et al. 2015 pipeline with minor modifications
Genome_build: Human: GRCh38 HSV-1: JN555585
Supplementary_files_format_and_content: dge files are single cell gene expresison matrices. Each row is a gene and is column is a single cell. Values are the counts (number of transcripts) for each gene in each cell. Data is not normalized
Supplementary_files_format_and_content: TPM.csv is a gene expression matrix for bulk RNAseq. First column is the gene id, each other column is a single sample. Samples are in biological duplicates. Values are TPM - transcripts per million

source_name: HDFn HSV-1 dICP0 infected

growth_protocol: Cells were grown in complete growth medium

extract_protocol:
For bulk RNA Qiagen miniprep RNA extractio colum were used. For drop-seq we followed the drop-seq protocol in Macosko et al 2015
Standard Illuimina protocol for bulk RNA-seq, according to Macosko et al. 2015 for drop-seq

treatment_protocol: Cells were infected with HSV-1 for 1 hr at room temperature in miminal volume, washed and incubated for 5 hours. For sorting, cells were detached and sorted on a FACSAria Fusion

tag: agent

value: dICP0 HSV-1


title: d0 - sorted icp4 positive rep2

description: d0 - sorted icp4 positive rep2

source_name: HDFn dICP0 infected (sorted)


title: d0 - sorted icp4 negative rep1

description: d0 - sorted icp4 negative rep1


title: mock - dropseq

description: mock - dropseq

source_name: HDFn mock-infected

value: mock


title: d0 - sorted icp4 positive rep1

description: d0 - sorted icp4 positive rep1


title: wt - dropseq

description: wt - dropseq

source_name: HDFn HSV-1 wt infected

value: wt HSV-1


title: Validation6


title: d0 - sorted icp4 negative rep2

description: d0 - sorted icp4 negative rep2


title: wt - sorted icp4 positive rep1

description: wt - sorted icp4 positive rep1

source_name: HDFn HSv-1 wt infected (sorted)


title: Zfp198_KO.fq

value: E14tg2a overexpressing Zmym2 from a stably integrated PiggyBac transgene


title: wt - sorted icp4 negative rep1

description: wt - sorted icp4 negative rep1


title: A549 METTL1 KD m7G-RIP Rep 3

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

country: Italy

institute: Istituto Italiano di Tecnologia - I

description:
Total RNA, including miRNAs, was extracted from indu.cible METTL1 knock-down A549 cells 5 days after doxycycline administration (200 ng ml−1 ). Heat-denatured RNA was immunoprecipitated with a specific antibody against m7G (MBL RN017M, Lot.001).
TK_LP_A549_METTL1KD_RIP_RAW_miRNA_counts.txt

data_processing:
Raw sequencing .bcl files were demultiplexed in FASTQ format using Illumina Basespace
Library adaptors were trimmed with Trimmomatic
Reads were mapped to the human genome with Bowtie2
Reads were summarized using featureCounts according to miRbase21 annotation
Genome_build: NCBI GRCh38/hg38
Supplementary_files_format_and_content: Raw miRNA counts in tab-separated value file

source_name: A549 human lung adenocarcinoma cell line

growth_protocol: Caco-2 cells were cultured in  Eagle's Minimum Essential Medium (Invitrogen), supplemented with 20% FBS and 1% penicillin/streptomycin/glutamine.

extract_protocol:
Cells were lysed in Qiazol (Qiagen) and total RNA was purified using the miRNAeasy mini kit (Qiagen)
Libraries were prepared using the NEBNext SmallRNA kit (NEB) according to the manufacturer’s recommendations

tag: cell line

tag: profiling strategy

value: m7G-RNA Immunoprecipitation in METTL1 Knock-down A549 Cells

tag: sample type

value: Immunoprecipitated RNA


title: A549 METTL1 KD m7G-RIP Rep 2


title: Caco2 M7G-RIP IP Rep 3

description:
Heat-denatured RNA was immunoprecipitated with a specific antibody against m7G (MBL RN017M, Lot.001).
TK_LP_Caco-2_RIP-Seq_RAW_miRNA_counts.txt

source_name: Caco-2 colorectal adenocarcinoma cell line

value: m7G-RNA Immunoprecipitation


title: wt - sorted icp4 positive rep2

description: wt - sorted icp4 positive rep2


title: mock - sorted rep2

description: mock - sorted rep2

source_name: HDFn mock infected (sorted)


title: wt - sorted icp4 negative rep2

description: wt - sorted icp4 negative rep2


title: Zfp198_OE.fq

value: E14tg2a with both alleles of Zmym2 knocked out using a Cas9-generated frameshift mutation


title: mock - sorted rep1

description: mock - sorted rep1


title: A549 METTL1 KD m7G-RIP Rep 1


title: Caco2 M7G-RIP IP Rep 2


title: Caco2 M7G-RIP IP Rep 1


title: Caco2 M7G-RIP Input Rep 1

value: INPUT RNA


title: Caco2 M7G-RIP Input Rep 2


title: A-2_SubAB

city: Shinjuku-ku

first: Tsuyoshi

last: Sekizuka

state: Tokyo

address: 1-23-1 Toyama

department: Pathogen Genomics Center

country: Japan

institute: National Institute of Infectious Diseases

description:
GeCKO v2 library A, biological replicate 2, SubAB treatment, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibA-normalized-compare.txt
SubAB_GeCKOv2_LibA_mageck.sgrna_summary.txt
SubAB_GeCKOv2_LibA_mageck.gene_summary.txt

data_processing:
Illumina RTA1.18.54 software used for basecalling
5' and 3' adapter and low quality trimming using skewer program (version 0.1.126)
Quality filtering (at Phred >= Q20) with split_libraries_fastq.py (version 1.9.1) of QIIME program
Read count of sgRNA using "sort" and "uniq" of unix command program
Reads align to sgRNA of Human GeCKO v2 library A/B
Normalization with following formula; normalized reads per sgRNA = reads per sgRNA / total reads for all sgRNAs in sample x 10^7
Statistic analysis using MAGeCK program (version 0.5.7)
Genome_build: Human GeCKO v2 library A/B
Supplementary_files_format_and_content: tab-delimited text files include raw read count, normalized read count and result of analysis with MAGeCK program.

source_name: HeLa CAS9#W7

growth_protocol: HeLa CAS9#W7 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) with 7.5μg/ml blasticidin . HeLa CAS9#W7 cells were infected with the pooled lentiviruses to express sgRNAs.

extract_protocol:
Genomic DNA from the frozen cells was purified by the conventional phenol-chloroform method.
First PCR amplification was carried out with 20 cycles using PrimeStar GXL DNA polymerase (Takara, Otsu, Japan) and the following primers (9 forward primers and 1 reverse primer): (Fw) 1stY1R1s0-8: CTACACGACGCTCTTCCGATCT[-/N/NN/NNN/NNNN/NNNNN/NNNNNN/NNNNNNN/NNNNNNNN]TCTTGTGGAAAGGACGAAACACCG (included 0-8 bp random sequence for increasing library complexity); and (Rv) 1stY2as: GCCACTTTTTCAAGTTGATAACGGACTAG. Second PCR amplification was carried out with 10 cycles using the following primers: (Fw) 2nd P5R1s:  AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; and (Rv) 2nd P7Y2as: CAAGCAGAAGACGGCATACGAGAT[CC/TT/AA/GG]GCCACTTTTTCAAGTTGATAACGGACTAG (included barcodes for multiplexing of different samples).
Amplicon sequencing of sgRNA in GeCKO v2.0 library plasmid

treatment_protocol: The sgRNA-expressing cells were treated with 10 ng/ml SubAB twice in two weeks.

value: HeLa

tag: genotype

value: SubAB treatment


title: A-1_SubAB

description:
GeCKO v2 library A, biological replicate 1, SubAB treatment, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibA-normalized-compare.txt
SubAB_GeCKOv2_LibA_mageck.sgrna_summary.txt
SubAB_GeCKOv2_LibA_mageck.gene_summary.txt


title: B-1_control for SubAB

description:
GeCKO v2 library B, biological replicate 1, control, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibB-normalized-compare.txt
SubAB_GeCKOv2_LibB_mageck.sgrna_summary.txt
SubAB_GeCKOv2_LibB_mageck.gene_summary.txt

value: control


title: A-2_control for SubAB

description:
GeCKO v2 library A, biological replicate 2, control, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibA-normalized-compare.txt
SubAB_GeCKOv2_LibA_mageck.sgrna_summary.txt
SubAB_GeCKOv2_LibA_mageck.gene_summary.txt


title: B-1_SubAB

description:
GeCKO v2 library B, biological replicate 1, SubAB treatment, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibB-normalized-compare.txt
SubAB_GeCKOv2_LibB_mageck.sgrna_summary.txt
SubAB_GeCKOv2_LibB_mageck.gene_summary.txt


title: Caco2 M7G-RIP Input Rep 3


title: A-1_control for SubAB

description:
GeCKO v2 library A, biological replicate 1, control, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibA-normalized-compare.txt
SubAB_GeCKOv2_LibA_mageck.sgrna_summary.txt
SubAB_GeCKOv2_LibA_mageck.gene_summary.txt


title: B-2_control for SubAB

description:
GeCKO v2 library B, biological replicate 2, control, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibB-normalized-compare.txt
SubAB_GeCKOv2_LibB_mageck.sgrna_summary.txt
SubAB_GeCKOv2_LibB_mageck.gene_summary.txt


title: B-2_SubAB

description:
GeCKO v2 library B, biological replicate 2, SubAB treatment, amplicon sequencing of sgRNA region in GeCKO v2.0 library plasmid
LibB-normalized-compare.txt
SubAB_GeCKOv2_LibB_mageck.sgrna_summary.txt
SubAB_GeCKOv2_LibB_mageck.gene_summary.txt


title: A549 BoRed-Seq Red Rep 2

description:
profiling strategy:
BoRed-Seq
TK_LP_A549_BoRed-Seq_RAW_miRNA_counts.txt

data_processing:
Library strategy: BoRed-Seq
Raw sequencing .bcl files were demultiplexed in FASTQ format using Illumina Basespace
Library adaptors were trimmed with Trimmomatic
Reads were mapped to the human genome with Bowtie2
Reads were summarized using featureCounts according to miRbase21 annotation
Genome_build: NCBI GRCh38/hg38
Supplementary_files_format_and_content: Raw miRNA counts in tab-separated value file

growth_protocol: A549 cells were cultured in DMEM (Invitrogen), supplemented with 10% FBS and 1% penicillin/streptomycin/glutamine.

treatment_protocol: Total RNA, including miRNAs, was extracted from mammalian cells. m7G residues were specifically reduced by treatment with NaBH4 in the presence of high concentrations of free m7GTP. Control samples were treated with acid-quenched NaBH4. The reduced m7G residues were subjected to nucleoside hydrolysis at low pH. A biotin-coupled aldehyde reactive probe (ARP) was covalently bound to the abasic RNA sites resulting from m7G reduction and hydrolysis, allowing pull-down with streptavidin-conjugated beads.

value: NaBH4-reduced RNA


title: A549 ShMETTL1 Rep 2

hyb_protocol: Labeled cRNA was hybridized overnight onto an Agilent SurePrint G3 Human Gene Expression Array v3 (8x60K).

scan_protocol: An Agilent DNA microarray scanner (model G2505C) was used for slide acquisition and spot analysis was performed with Feature Extraction software

data_processing: Data were background-corrected and normalized between arrays by means of Bioconductor package limma (Smyth, 2005).

label_protocol: 50 ng of RNA were labeled with Low Input QuickAmp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Cells were lysed in Qiazol (Qiagen) and total RNA was purified using the miRNAeasy mini kit (Qiagen)

treatment_protocol: A549 were infected with pLKO-TETon-Puro lentiviral vectors expressing shRNAs against the coding sequence of human METTL1 or a scrambled control. Cells (5 × 10^5) were  mixed in 2 ml culture medium supplemented with 8 μg ml−1 polybrene, followed by spinfection (60 min, 900g, 25°C) and further incubated overnight at 37 °C overnight. The cells were replated in fresh medium containing 1 μg ml−1 of puromicin and kept in selection medium for 7 days. shRNA was induced by treatment with 200 ng ml−1 doxycycline for 5 days.

tag: shRNA

value: METTL1 Sh1


title: A549 ShCTRL Rep 3

value: Scramble Ctrl


title: A549 BoRed-Seq Ctrl Rep 1

value: Control (non-reduced) RNA


title: A549 BoRed-Seq Red Rep 1


title: A549 BoRed-Seq Ctrl Rep 2


title: A549 ShCTRL Rep 4


title: T01-CK

city: zhenjiang

first: meiyan

last: wang

address: xiangshanjiedao

institute: jiangsu university

data_processing:
Raw reads were pre-processed to obtain the clean reads by removing reads containing ploy-N, reads containing adapter and low-quality reads from raw data were filtered with FASTQ-Quality-Filter tool.
HISAT2 generate a database of splice junctions based on the gene model annotation ﬁle, which was used to align the paired-end clean reads to the reference genome of grape
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then, the number of fragments per kilobase of transcript per Million fragments mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GCA_000003745.2 12X scaffolds: 2,061 contigs: 14,634 N50: 102,851 L50: 1,362（https://www.ncbi.nlm.nih.gov/genome/401?genome_assembly_id=214125）
Supplementary_files_format_and_content: ctab files and xls files

organism: Vitis vinifera

source_name: the tissues in wound

growth_protocol: Incubator 20℃

extract_protocol:
The sample was ground in liquid nitrogen.Extraction of total RNA from grapes by Spin Column Plant Total RNA Purification Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The wound was treated with 10 μL of Y. lipolytica suspension (T-02 Y), or equal volume of sterile water as the control(T-01 CK).

value: Y. lipolytica

tag: age

value: after treatment of 3 days


title: A549 ShCTRL Rep 2


title: A549 ShMETTL1 Rep 1


title: T02-Y


title: Cells grown to mid exponential phase on minimal media with 5 mg/ml glucose 1

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

description:
Cells grown to mid exponential phase on minimal media with 5 mg/ml glucose as sole carbon source
MMGlucose_1

data_processing:
Base calling accuracy was measured by Phred quality score, and assessed with FastQC version 11.2
Reads were aligned against the Ensembl FASTA file for Bacteriodes thetaiotaomicron VPI-5482
Alignment to the genome was carried out using Bowtie2 version 2.2.4
Counts of reads aligning to genomic features were obtained using the featureCounts function from the R package Rsubread
Feature annotation was based on the Ensembl GFF file for Bacteroides thetaiotaomicron VPI-5482
Genome_build: Bacteroides thetaiotaomicron VPI-5482, ASM1106v1
Supplementary_files_format_and_content: One tab-delimited text file with raw read counts per gene and per sample. Gene IDs are as stated in the Ensembl GFF file for Bacteroides thetaiotaomicron VPI-5482

organism: Bacteroides thetaiotaomicron VPI-5482

source_name: Bacterial cells

growth_protocol: All cultures were grown under anaerobic conditions in a Don Whitley A35 workstation using Nitrogen and Anaerobic gas mix (10% CO2, 10%H2, 80% N2). Cells from a glycerol stock were inoculated into rich media (TYG) and grown overnight. This overnight culture was used to inoculate triplicate tubes of 5 ml of minimal media plus either glucose (5mg/l) or AAGP (10mg/ml) as sole carbon source. Cells at mid exponential phase (OD600 ~0.8) were harvested by centrifugation (400xg for 10 min at 4oC).

extract_protocol:
Sample processing, library prep and sequencing took place at Oxford Genomics Centre (University of Oxford, Oxford, UK). Material was quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and the size profile and integrity analysed on the 2200 or 4200 TapeStation (Agilent, RNA ScreenTape). RIN estimates for all samples were between 5.9 and 7.1. Input material was normalised to 1 ug prior to library preparation. The RNA was depleted of ribosomal RNA using  Ribo-Zero rRNA Removal Kit (Epicentre/Illumina, universal bacteria) following manufacturer’s instructions. Strand specific library preparation was completed using TruSeq Stranded mRNA kit (Illumina) following manufacturer’s instructions. Libraries were amplified (15 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using a HiSeq4000 75bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit), generating a raw read count of >29 million reads per sample.
Sample processing, library prep and sequencing took place at Oxford Genomics Centre (University of Oxford, Oxford, UK). The sequencing was done using the High-performance Illumina HiSeq4000 75bp system, 1 PE lane (240 million reads per lane). Briefly, the rRNA depleted RNA fraction was selected from the total RNA provided before conversion to cDNA. Second strand  cDNA synthesis incorporated dUTP. The cDNA was then end-repaired, A-tailed and adapter-ligated. Prior to amplification,  samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired  end sequencing over one lane of a flow cell. Data was aligned to the reference and quality checked.

treatment_protocol: After harvesting, the cells were stored in RNA Protect Bacterial Reagent (Qiagen) at -80C° until extraction.

tag: carbon source

value: 5 mg/ml glucose as sole carbon source


title: Cells grown to mid exponential phase on minimal media with 10 mg/ml bovine alpha 1 acid glycoprotein (AAGP) 3

description:
Cells grown to mid exponential phase on minimal media with 10 mg/ml bovine alpha 1 acid glycoprotein (AAGP) as sole carbon source
MMAAGP_3


title: Cells grown to mid exponential phase on minimal media with 5 mg/ml glucose 3

description:
Cells grown to mid exponential phase on minimal media with 5 mg/ml glucose as sole carbon source
MMGlucose_3


title: A549 METTL1 KD Rep 2

description:
profiling strategy:
miRNA-seq in METTL1 Knock-down
TK_LP_A549_METTL1KD_RAW_miRNA_counts.txt

treatment_protocol: Total RNA, including miRNAs, was extracted from inducible METTL1 knock-down A549 cells 5 days after doxycycline administration (200 ng ml−1 )

value: RNA


title: A549 ShCTRL Rep 1


title: Cells grown to mid exponential phase on minimal media with 5 mg/ml glucose 2

description:
Cells grown to mid exponential phase on minimal media with 5 mg/ml glucose as sole carbon source
MMGlucose_2


title: Cells grown to mid exponential phase on minimal media with 10 mg/ml bovine alpha 1 acid glycoprotein (AAGP) 1

description:
Cells grown to mid exponential phase on minimal media with 10 mg/ml bovine alpha 1 acid glycoprotein (AAGP) as sole carbon source
MMAAGP_1


title: Cells grown to mid exponential phase on minimal media with 10 mg/ml bovine alpha 1 acid glycoprotein (AAGP) 2

description:
Cells grown to mid exponential phase on minimal media with 10 mg/ml bovine alpha 1 acid glycoprotein (AAGP) as sole carbon source
MMAAGP_2


title: A549 METTL1 KD Rep 3


title: A549 m7G-RIP IP Rep 4

description:
profiling strategy:
m7G-RNA Immunoprecipitation
TK_LP_A549_RIP-Seq_RAW_miRNA_counts.txt

treatment_protocol: Heat-denatured RNA was immunoprecipitated with a specific antibody against m7G (MBL RN017M, Lot.001).


title: A549 m7G-RIP IP Rep 2


title: A549 ShMETTL1 Rep 3


title: A549 ShMETTL1 Rep 4


title: A549 m7G-RIP Input Rep 4


title: A549 m7G-RIP IP Rep 1


title: A549 m7G-RIP IP Rep 3


title: A549 m7G-RIP Input Rep 3


title: SEF1-VP16_YPGly_repeat 2

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression after 5.5 h of subculture

hyb_protocol: The Agilent Gene Expression Hybridization Kit (5188-5242, Agilent Technologies) was used for hybridization according to the manufacturer's instruction. Briefly, 16 ml of Alexa dye labeled cDNA in water was denatured at 98°C for 3 min in a reaction volume of 40 ml containing 4 ml Agilent 10x blocking Agent and 20 ml of Agilent 2x GEx Hybridization Buffer HI-RPM. Denatured dye-labeled cDNAs were subsequently hybridized to a custom L. kluyveri 8x15K microarray (Design ID: 563206, Agilent Technologies) at 65°C and rotated at 10 rpm on an Agilent hybridizer for 17 h. After hybridization, the microarrays were washed using the Agilent Gene Expression Wash Kit (5188-5327, Agilent Technologies). Briefly, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 and 1 min with 37°C GE Wash buffer 2, and then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned at 535 nm (for Alexa Flour® 555 dye) on the Agilent DNA Microarray Scanner (US9230696) using one color scan setting for 8x15k array slides (scan area: 61 x 21.6 mm; scan resolution: 5 mm; dye channel: green; green PMT: 100%; tiff: 16 bit; XDR: 0.10).

data_processing: Scanned images were analyzed with the Feature Extraction 10.5.1.1 Software (Agilent Technologies) using default parameters (protocol: GE1_105_Dec08 and grid: 023206_D_F_20131222; provided by the IMB Genomics Core Lab, Academia Sinica, Taiwan) to obtain the background subtracted and spatially detrended Processed Signal intensities. Features flagged in the Feature Extraction Software as the feature non-uniform outlierswere excluded.

label: Alexa Flour 555

organism: Lachancea kluyveri

source_name: SEF1-VP16 gain-of-function mutant cells, YPGly, biological repeat 2

label_protocol: For Alexa dye-labeled cDNA synthesis, the kit SuperScriptTM Plus Indirect cDNA Labeling System (L101402, Invitrogen by Thermo Fisher Scientific) was used according to the manufacturer's instruction. Briefly, 10 mg of DNase-treated RNA were reverse-transcribed using the anchored oligo[(dT)20-VN] primers and the cDNA was labeled with aminoallyl-dUTP followed by a column purification (28106, QIAquick DNA Purification Kit, Qiagen).  The aa-cDNA was then labeled with Alexa Flour® 555 dye (A-32756, Invitrogen by Thermo Fisher Scientific) and purified with the Qiagen column (28106, QIAquick DNA Purification Kit, Qiagen).

growth_protocol: Cells were grown in the YPD medium at 28°C overnight.

extract_protocol: Total RNA were extracted by phenol-chloroform followed by ethanol precipitation. gDNA contaminations wete removed by the TURBO DNA-free kit (AM1907, Ambion). The final RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was checked with the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells from overnight cutures were subsequently diluted into YPD and YPGly in a cell density of 0.2 OD600/ml, incubated for 5.5 h at 30°C, and harvested.

tag: strain


title: A549 m7G-RIP Input Rep 1


title: A549 METTL1 KD Rep 1


title: A549 m7G-RIP Input Rep 5


title: SEF1-VP16_YPGly_repeat 1

source_name: SEF1-VP16 gain-of-function mutant cells, YPGly, biological repeat 1


title: A549 m7G-RIP Input Rep 2


title: A549 m7G-RIP IP Rep 5


title: SEF1-VP16_YPGly_repeat 4

source_name: SEF1-VP16 gain-of-function mutant cells, YPGly, biological repeat 4


title: Wild type_YPGly_repeat 3

source_name: Wild type cells, YPGly, biological repreat 3


title: SEF1-VP16_YPGly_repeat 3

source_name: SEF1-VP16 gain-of-function mutant cells, YPGly, biological repeat 3


title: Wild type_YPGly_repeat 4

source_name: Wild type cells, YPGly, biological repreat 4


title: Wild type_YPGly_repeat 2

source_name: Wild type cells, YPGly, biological repreat 2


title: SEF1-VP16_YPD_repeat 1

source_name: SEF1-VP16 gain-of-function mutant cells, YPD, biological repeat 1


title: SEF1-VP16_YPD_repeat 3

source_name: SEF1-VP16 gain-of-function mutant cells, YPD, biological repeat 3


title: SEF1-VP16_YPD_repeat 4

source_name: SEF1-VP16 gain-of-function mutant cells, YPD, biological repeat 4


title: Wild type_YPD_repeat 4

source_name: Wild type cells, YPD, biological repreat 4


title: Wild type_YPGly_repeat 1

source_name: Wild type cells, YPGly, biological repreat 1


title: 4953_3_Hep1_control_CCGTCCC

city: Amsterdam

first: Cun

last: Wang

address: Plesmanlaan 121,

department: Division of Molecular Carcinogenesis

country: Netherlands

institute: The Netherlands Cancer Institute

data_processing:
The reads were sequenced using a stranded RNA protocol
The reads that are of low complexity or repetitive sequences are filtered
The reads are mapped to the transcriptome.  Reads that do not map to the transcriptome are used for a whole genome mapping in the last step.
Samples are aligned with HiSat2. settings: --min-intronlen 20 --max-intronlen 500000 --rna-strandness F  -k 5 --minins 0 --maxins 500 --fr --new-summary
Steps performed: link, count, QCstrandness, eset
Read counts are determined.Count parameters    Count library type stranded: true  Icount (based on HTSeq-count) GTF version: Homo_sapiens.GRCh38.87.gtf    mode -> union: If a read is mapped to a region with overlapping genes, this read will be dismissed. However, when stranded RNA sequencing has been performed, the read can be used there is an overlap of 2 genes which are in opposite direction.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: control

growth_protocol: Cells were cultured in DMEM with 10% FBS, glutamine and penicillin/streptomycin (Gibco®) at 37 °C / 5% CO2.

extract_protocol:
Cells were treated with 10 μM XL413 for 4 days. The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina).
polyA+ stranded RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: liver cancer cell line

tag: treatment

value: none (control)


title: 4172_10_BJ-XL413_GTCCGCA

source_name: XL413 treatment

treatment_protocol: Cells were treated with 10 μM XL413 for 4 days.

value: BJ

value: Human non-transformed cell line

value: 10 μM XL413 for 4 days


title: LOX-Q67L TMV small RNA seq 2

city: Notre Dame

first: Ye

last: Zhang

state: IN

address: Galvin Life Sciences Center

department: Biological sciences

institute: University of Notre Dame

data_processing:
Basecalls performed using CASAVA
Quality controled using FastQC
Adaptor trimmed with Cutadapt
Alignment performed using Bowtie2 against miBase human mature miRNA reference
Supplementary_files_format_and_content: The raw counts were concatenated into a single txt

source_name: LOX-Q67L TMVs

growth_protocol: LOX melanoma cells (a gift from Prof. Oystein Fodstad, Oslo University) were cultured in RPMI (RPMI-1640 Life Technologies) supplemented with 10% (v/v) EquaFetal Serum (Atlas Biologicals), 2 mM L-glutamine and 100 U/mL penicillin-streptomycin (Life Technologies). LOXARF6-GTP cells were maintained similarly with the addition of 200 μg/mL Gentamycin and Hygromycin-B selection reagents.

extract_protocol:
TMVs were isolated with serial centrifugation. Both cells and TMVs small RNAs were extracted using the miRvana miRNA isolation kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Human LOX melanoma cells

tag: passages


title: 4953_4_Hep1_XL413_GTCCGCA


title: LOX-Q67L TMV small RNA seq 3


title: Wild type_YPD_repeat 2

source_name: Wild type cells, YPD, biological repreat 2


title: 4172_9_BJ-control_CCGTCCC


title: SEF1-VP16_YPD_repeat 2

source_name: SEF1-VP16 gain-of-function mutant cells, YPD, biological repeat 2


title: LOX TMV small RNA seq 3

source_name: LOX TMVs


title: LOX TMV small RNA seq 2


title: LOX TMV small RNA seq 1


title: sef1_YPGly_repeat 2

source_name: sef1 deletion mutant cells, YPGly, biological repreat 2


title: LOX-Q67L TMV small RNA seq 1


title: Wild type_YPD_repeat 3

source_name: Wild type cells, YPD, biological repreat 3


title: sef1_YPGly_repeat 3

source_name: sef1 deletion mutant cells, YPGly, biological repreat 3


title: sef1_YPGly_repeat 4

source_name: sef1 deletion mutant cells, YPGly, biological repreat 4


title: Wild type_YPD_repeat 1

source_name: Wild type cells, YPD, biological repreat 1


title: Sandwich_D8_B2

city: beijing

first: meng

middle: gao

last: fan

state: Haidian District/Beijing

address: yiheyuan road no.5

institute: peking university

description:
processed data file:
update.xlsx

data_processing:
To compare gene expression proﬁle between paired-end and single-end libraries, we take only the read1 from our generated sequencing paired-end reads.
The read1 and the downloaded single-end read were trimmed to the same 40bp length by using Cutadapt.
The expression values for each sample were quantified by Salmon.
Genome_build: hg19 for human
Supplementary_files_format_and_content: Excel files include the expression values for each sample

source_name: primary human hepatocyte

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The isolated hepatocytes were seeded on collagen type I-coated plate with a density of 2.5*10e5/cm2. Serum-free medium routinely used for hepatocytes culture (WME): William’s medium E containing B27, Glutmax and Pen Strep. 2C condition: WME supplemented with two molecule compouds. 5C condition: WME supplemented with with five molecule compouds.

tag: batch number

value: Batch 1

value: Cultured under sandwich condition for 8 days

value: primary human hepatocyte

tag: time

value: 8 days


title: sef1_YPGly_repeat 1

source_name: sef1 deletion mutant cells, YPGly, biological repreat 1


title: Sandwich_D27_B2

description:
processed data file:
update.xlsx

value: Cultured under sandwich condition for 27 days

value: 27 days


title: sef1_YPD_repeat 4

source_name: sef1 deletion mutant cells, YPD, biological repreat 4


title: Sandwich_D5_B2

description:
processed data file:
update.xlsx

value: Cultured under sandwich condition for 5 days

value: 5 days


title: WT_YPGly_repeat 4

source_name: Wild type cells, YPGly, biological repreat 4


title: sef1_YPD_repeat 2

source_name: sef1 deletion mutant cells, YPD, biological repreat 2


title: sef1_YPD_repeat 3

source_name: sef1 deletion mutant cells, YPD, biological repreat 3


title: NULL_D8_B2

description:
processed data file:
update.xlsx

data_processing:
The transcriptome reads were mapped using the TopHat2 program.
The gene expression level was calculated by using FPKM  for human samples.
Genome_build: hg19 for human
Supplementary_files_format_and_content: Excel files include the expression values (FPKM)  for each sample

treatment_protocol: The isolated hepatocytes were seeded on collagen type I-coated plate with a density of 2.5*105/cm2. Serum-free medium routinely used for hepatocytes culture (WME): William’s medium E containing B27, Glutmax and Pen Strep. 2C condition: WME supplemented with two molecule compounds. 5C condition: WME supplemented with with five molecule compounds.

value: WME

value: Batch 2


title: WT_YPGly_repeat 2

source_name: Wild type cells, YPGly, biological repreat 2


title: acx4-4_H3K23Ac_rep1-input

city: Beijing

first: Yusheng

last: Zhao

address: Yuanmingyuan Road #2, Haidian District

institute: China agricultural university

data_processing:
The reads were aligned to the TAIR10 Arabidopsis reference genome using Bowtie program with default parameters. Reads that perfectly and uniquely mapped to the genome were retained for further analysis.Wiggle (WIG) format were generated using MACS program and visualized using IGV.Acetylation enriched peaks were identified by SICER program with a window size setting =200 bp, gap size = 200 bp , false discovery rate (FDR) ≤ 0.05 and fold change≥1.5.
Genome_build: tair10
Supplementary_files_format_and_content: bw

organism: Arabidopsis thaliana

source_name: young seedlings

growth_protocol: Seeds were grown on MS medium plates supplemented with 20 g/L sucrose and 0.8% agar at 22°C under long-day (23 h) illumination

extract_protocol:
Chromatin Immunoprecipitation
For ChIP-seq library, a 10-ng quantity of ChIP or input DNA was used to prepare a high-throughput sequencing library. The blunt-ended DNA were treated with Klenow fragment (New England BioLabs, Ipswich, MA) and  dATP to 3’-dA-tailed and ligated to the adapters. Then amplification were carried out using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (E6240, NEB) according to the manufacturer’s protocol.

tag: developmental stage

value: 10-day-old whole seedlings

tag: ecotype

value: acx4-4 mutant


title: NULL_D0.5_B2

description:
processed data file:
update.xlsx

value: Cultured under Null condition for 0.5 days

value: 0.5 days


title: WT_YPGly_repeat 3

source_name: Wild type cells, YPGly, biological repreat 3


title: acx4-4_H3K14Ac_rep2-input


title: WT_YPD_repeat 2

source_name: Wild type cells, YPD, biological repreat 2


title: WT_YPD_repeat 4

source_name: Wild type cells, YPD, biological repreat 4


title: DMSO_D0.5_B2

description:
processed data file:
update.xlsx

value: Cultured under DMSO condition for 0.5 days


title: sef1aft1_Low-iron_repeat 3

source_name: sef1aft1 double deletion mutant cells, YPD+200mM BPS, biological repreat 3

treatment_protocol: Cells from overnight cutures were subsequently diluted into YPD+400mM ferrous iron and YPD+200mM BPS in a cell density of 0.5 OD600/ml, incubated for 5.5 h at 30°C, and harvested.


title: WT_YPGly_repeat 1

source_name: Wild type cells, YPGly, biological repreat 1


title: NULL_D5_B2

description:
processed data file:
update.xlsx


title: WT_YPD_repeat 1


title: Sandwich_D15_B2

description:
processed data file:
update.xlsx

value: Cultured under sandwich condition for 15 days

value: 15 days


title: sef1_YPD_repeat 1

source_name: sef1 deletion mutant cells, YPD, biological repreat 1


title: WT_YPD_repeat 3

source_name: Wild type cells, YPD, biological repreat 3


title: NULL_D3_B2

description:
processed data file:
update.xlsx

value: 3 days


title: acx4-4_H3K14Ac_H3K18Ac rep1-input and H3K23Ac_rep2-input

description:
acx4-4_H3K14Ac_rep1-input
acx4-4_H3K18Ac_rep1-input
acx4-4_H3K23Ac_rep2-input


title: sef1aft1_Low-iron_repeat 4

source_name: sef1aft1 double deletion mutant cells, YPD+200mM BPS, biological repreat 4


title: NULL_D27_B2

description:
processed data file:
update.xlsx


title: NULL_D15_B2

description:
processed data file:
update.xlsx


title: acx4-4_H3K23Ac_rep2

tag: chip-antibodies

value: anti-H3K23ac (07-355; Millipore)


title: 5C_D0.5_B2

description:
processed data file:
update.xlsx

value: Batch 1

value: Cultured under 5C condition for 0.5 days

value: primary human hepatocyte


title: acx4-4_H3K9Ac-input


title: acx4-4_H3K18Ac_rep2-input


title: sef1aft1_Low-iron_repeat 2

source_name: sef1aft1 double deletion mutant cells, YPD+200mM BPS, biological repreat 2


title: sef1aft1_Low-iron_repeat 1

source_name: sef1aft1 double deletion mutant cells, YPD+200mM BPS, biological repreat 1


title: acx4-4_H3K14Ac_rep2

value: anti-H3K14ac (Millipore; 07-353)


title: NULL_D1.5_B2

description:
processed data file:
update.xlsx

source_name: primary human hepatocyte

value: 1.5 days


title: acx4-4_H3K23Ac_rep1


title: F-PHHs_B2

description:
processed data file:
update.xlsx

value: fresh isolated

value: 0 hours


title: DMSO_D5_B2

description:
processed data file:
update.xlsx

value: WME+DMSO

value: 5 days

value: Batch 2


title: sef1aft1_High-iron_repeat 2

source_name: sef1aft1 double deletion mutant cells, YPD+400mM ferrous iron, biological repreat 2


title: F-PHHs_B1

description:
processed data file:
update.xlsx


title: sef1aft1_High-iron_repeat 3

source_name: sef1aft1 double deletion mutant cells, YPD+400mM ferrous iron, biological repreat 3


title: sh332

city: Fukuoka

first: Teppei

last: Sakoda

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

description: shHAVCR2 KASUMI-3 006

hyb_protocol: 600ng of cRNA from each sample was fragmented and hybridized to the array using a Gene Expression Hybridization kit (Agilent).

scan_protocol: The array was scanned with Surescan Microarray Scanner (Agilent), and raw microarray data were loaded into Gene Spring GX software (Version 14.5; Agilent).

data_processing: According to the guided workflow for Agilent single color experiment, normalization algorithm of 75-percentile shift was used, and the preprocessing baseline was adjusted to median of all samples. Statistical analysis for GSEA was performed as described.

source_name: KASUMI-3, TIM-3 KD by shRNA (shHAVCR2 2), replicate

label_protocol: Cyanine 3-labeled complementary RNA (cRNA) was synthesized with Low Input Quick Amp Labeling kit, one-color.

extract_protocol: Total RNA was extracted by using Isogen2 (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a Qubit 2.0 (Invitrogen).

treatment_protocol: Cells were incubated with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum  at 37 ºC in a humidified incubator with 5% CO2, in the presence of 3 μg/mL of puromycin.

value: acute myeloid leukemia (AML) cell line

tag: genotype/variation

value: shRNA-mediated HAVCR2 knock-down (KD)


title: sef1aft1_High-iron_repeat 4

source_name: sef1aft1 double deletion mutant cells, YPD+400mM ferrous iron, biological repreat 4


title: acx4-4_H3K18Ac_rep1

value: 10-day-old whole seedlings

value: acx4-4 mutant

value: anti-H3K18ac (ab1191; Abcam)


title: Scramble1

description: shHAVCR2 KASUMI-3 001

source_name: KASUMI-3, scrambled control

tag: cell line

value: scrambled control


title: aft1_Low-iron_repeat 3

source_name: aft1 deletion mutant cells, YPD+200mM BPS, biological repreat 3


title: DMSO_D8_B2

description:
processed data file:
update.xlsx

value: 8 days


title: sh131

description: shHAVCR2 KASUMI-3 003

source_name: KASUMI-3, TIM-3 KD by shRNA (shHAVCR2 1)


title: sh331

description: shHAVCR2 KASUMI-3 005

source_name: KASUMI-3, TIM-3 KD by shRNA (shHAVCR2 2)


title: acx4-4_H3K18Ac_rep2

source_name: young seedlings


title: acx4-4_H3K14Ac_rep1


title: WT_H3K18Ac_rep2-input

value: wild type


title: acx4-4_H3K9Ac

value: anti-H3K9ac (Millipore; 07-352)


title: WT_H3K23Ac_rep1-input


title: DMSO_D15_B2

description:
processed data file:
update.xlsx

value: primary human hepatocyte

value: 15 days


title: WT_H3K14Ac_rep2-input


title: DMSO_D3_B2

description:
processed data file:
update.xlsx

value: 3 days


title: DMSO_D27_B2

description:
processed data file:
update.xlsx

value: 27 days


title: WT_H3K14Ac_H3K18Ac_rep1-input and H3K23Ac_rep2-input

description:
WT_H3K14Ac_rep1-input
WT_H3K18Ac_rep1-input
WT_H3K23Ac_rep2-input


title: WT_H3K9Ac-input


title: 5C_D5_B2

description:
processed data file:
update.xlsx


title: DMSO_D1.5_B2

description:
processed data file:
update.xlsx

value: 1.5 days


title: WT_H3K23Ac_rep2

value: anti-H3K23ac (07-355; Millipore)


title: aft1_Low-iron_repeat 1

source_name: aft1 deletion mutant cells, YPD+200mM BPS, biological repreat 1


title: 5C_D8_B2

description:
processed data file:
update.xlsx


title: aft1_Low-iron_repeat 2

source_name: aft1 deletion mutant cells, YPD+200mM BPS, biological repreat 2


title: aft1_Low-iron_repeat 4

source_name: aft1 deletion mutant cells, YPD+200mM BPS, biological repreat 4


title: Scramble2

description: shHAVCR2 KASUMI-3 002

source_name: KASUMI-3, scrambled control, replicate


title: aft1_High-iron_repeat 3

source_name: aft1 deletion mutant cells, YPD+400mM ferrous iron, biological repreat 3


title: aft1_High-iron_repeat 4

source_name: aft1 deletion mutant cells, YPD+400mM ferrous iron, biological repreat 4


title: sef1aft1_High-iron_repeat 1

source_name: sef1aft1 double deletion mutant cells, YPD+400mM ferrous iron, biological repreat 1


title: 5C_D3_B2

description:
processed data file:
update.xlsx

source_name: primary human hepatocyte


title: sh132

description: shHAVCR2 KASUMI-3 004

source_name: KASUMI-3, TIM-3 KD by shRNA (shHAVCR2 1), replicate


title: aft1_High-iron_repeat 1

source_name: aft1 deletion mutant cells, YPD+400mM ferrous iron, biological repreat 1


title: 5C_D1.5_B2

description:
processed data file:
update.xlsx


title: sef1_Low-iron_repeat 4

source_name: sef1 deletion mutant cells, YPD+200mM BPS, biological repreat 4


title: aft1_High-iron_repeat 2

source_name: aft1 deletion mutant cells, YPD+400mM ferrous iron, biological repreat 2


title: Leg skin_rep3

city: Yangzhou

first: gaige

last: ji

address: no.58, Cang jie Road

institute: Jiangsu Institute of Poultry Science

description: Gene expression

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to The Agilent Chicken（V2）Gene Expression Microarray (4*44K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Gallus gallus

source_name: Leg skin, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Skin samples used in the present study were collected from a chicken breeding line in Jiangsu Li-hua Animal Husbandry Company (Jiangsu, China). All chickens lived under the same conditions and were raised using a standardized feeding method with free access to water.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

treatment_protocol: The dorsal skin was divided into two halves according to dorsal line axis. The right dorsal and leg skin  were sampled, immediately frozen in liquid nitrogen, and stored at –80˚C.

tag: tissue

value: Leg skin

value: 9 weeks


title: Leg skin_rep4

description: Gene expression

source_name: Leg skin, replicate 4


title: WT_H3K18Ac_rep1


title: Leg skin_rep2

description: Gene expression

source_name: Leg skin, replicate 2


title: sef1_Low-iron_repeat 2

source_name: sef1 deletion mutant cells, YPD+200mM BPS, biological repreat 2


title: Dorsal skin_rep2

description: Gene expression

source_name: Dorsal skin, replicate 2

value: Dorsal skin


title: Dorsal skin_rep4

description: Gene expression

source_name: Dorsal skin, replicate 4


title: Leg skin_rep1

description: Gene expression

source_name: Leg skin, replicate 1


title: sef1_Low-iron_repeat 1

source_name: sef1 deletion mutant cells, YPD+200mM BPS, biological repreat 1


title: 5C_D27_B2

description:
processed data file:
update.xlsx

value: Batch 2


title: Dorsal skin_rep3

description: Gene expression

source_name: Dorsal skin, replicate 3


title: WT_H3K14Ac_rep2

source_name: young seedlings

value: 10-day-old whole seedlings

value: anti-H3K14ac (Millipore; 07-353)


title: WT_H3K18Ac_rep2

value: anti-H3K18ac (ab1191; Abcam)


title: F-PHHs

description:
processed data file:
genes.fpkm_tracking_24h-Cutured hepatocytes.xlsx

value: fresh isolated

value: 0 hours

value: Batch 3


title: 5C_D15_B2

description:
processed data file:
update.xlsx


title: ZNS02

city: kyoto

first: yoshifumi

last: miyawaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Application, Kyoto University

description: 14 1001 ZNS02_(RaGene-1_0-st-v1).CEL(normalized)

hyb_protocol: Samples were hybridized to GeneChip Rat Gene 1.0 ST arrays  according to the manufacturer’s protocol

scan_protocol: Arrays were scanned using the Microarray Scanner System

data_processing:
The data were analyzed using GeneSpring GX13.1.1 software. The expression signals of the probe sets were calculated using RMA16.
probe group file: RaGene-1_0-st-v1
meta-probeset file: RaGene-1_0-st-v1_na32_rn4_2011-06-23

label: biotin

organism: Rattus norvegicus

source_name: rat striatum_ZNS

label_protocol: RNA was processed by Ambion WT Expression Kit and Affymetrix GeneChip Whole-Transcript Expression Arrays

extract_protocol: Total RNA was extracted using an RNeasy Plus Mini kit (Qiagen, Valencia, CA, USA)

tag: Sex

value: female

tag: treated with

value: ZNS 60mg/kg/day for 7 days

value: striatum


title: ZNS04

description: 14 1001 ZNS04_(RaGene-1_0-st-v1).CEL(normalized)


title: WT_H3K14Ac_rep1

tag: genotype

value: wild type


title: Dorsal skin_rep1

description: Gene expression

source_name: Dorsal skin, replicate 1


title: ZNS03

description: 14 1001 ZNS03_(RaGene-1_0-st-v1).CEL(normalized)


title: sef1_High-iron_repeat 1

source_name: sef1 deletion mutant cells, YPD+400mM ferrous iron, biological repreat 1


title: 2A LGI+Apoplast

city: Seropédica

first: Leonardo

middle: Araujo

last: Terra

state: RJ

address: Rodovia BR-465

country: Brazil

institute: Embrapa Agrobiologia

data_processing:
CLC Genomics Workbench version 7.5.1 program
reads containing ≤ 20 bp, and those mapping to rRNA 5S, 16S and 23S genes, were all discarded. Gene expression levels were given as reads per kilo base per million mapped reads (RPKM). The CLC Genomics Workbenche was used for mapping.
Differentially expressed transcripts were determined when the ratios of treatment to control RPKM values were less than 0.5 (down-regulated, fold-change ≤ -2) or higher than 2.0 (up-regulated, fold-change ≥ 2), and p-value < 0.05. The CLC Genomics Workbench version 7.5.1 (which performs the Student t test), the Deseq2 package (Anders and Huber 2010, Love et al., 2014) and the EdgeR package (Robinson et al. the binomial distribution, were used.
For estimating these values, three types of software were used: the CLC Genomics Workbench version 7.5.1 (which performs the Student's t-test), the Deseq2 package (Anders and Huber 2010; Love et al. 2014) and the EdgeR package (Robinson et al. 2010), the last two based on the binomial distribution.
Genome_build: genome of Nitrospirillum amazonense CBAmC (NCBI accession numbers CP022110.1, CP022111.1, CP022112.1 and CP022113.1)
Supplementary_files_format_and_content: Tab delimited text files include the reads of each biological sample, RPKM values for each Sample and statistical analysis.

organism: Nitrospirillum amazonense

source_name: Cultured cells

growth_protocol: The CBAmC strain of N. amazonense was routinely grown at 30 °C, 180 rpm, for 16 h, in liquid LGI mediumsupplemented with 5 g L-1 sucrose as a carbon source and 10 mM sodium glutamate as the sole source of nitrogen.

extract_protocol:
Total RNA was extracted from fresh cells using Trizol reagent (Invitrogen / Life Technologies) at 65 °C, followed by the use of the RNeasy Mini Kit (Qiagen). Then the RNA samples were treated with RNase-Free DNase I (Epicenter) to eliminate any residual genomic DNA. Ribosomal RNA (rRNA) was depleted from the samples using the MICROBExpress™ kit (Ambion), starting with 7 µg of total RNA, for mRNA enrichment.
The resulting samples were used to construct the cDNA libraries following the standard protocol of the Ion Total RNA-Seq v2. The libraries were sequenced using the Ion PI Sequencing 200 Kit v2 and an Ion ProtonTM sequencer (Thermo Fisher Scientific).

treatment_protocol: The flasks were kept in an incubator at 30 ºC, 180 rpm. Halfway through the exponential phase (O.D.600 = 1.4), each of the three cell suspensions was divided in two equal parts and put into new 125-mL flasks, totaling six new flasks, to which half volume of LGI medium (control) or apoplast fluid (treatment) was added in order to make biological triplicates of both control and treatment. After two hours of incubation under the same conditions above, 5 mL was collected from each bacterial suspension for subsequent RNA extraction and placed into RNase- Falcon tubes.

value: CBAmC

value: Nitrospirillum amazonense strain CBAmC cultured cells


title: 2C LGI+Apoplast


title: WT_H3K9Ac

value: anti-H3K9ac (Millipore; 07-352)


title: ZNS01

description: 14 1001 ZNS 01_(RaGene-1_0-st-v1).CEL(normalized)


title: TN1

city: ShenYang

first: Li

last: Hailong

state: Liaoning

address: NO. 3-11, Wenhua Road, Heping District

institute: Northeastern University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2
Software used for RPKM calculation: HTSeq 0.6.1p2
Software used for creation of the wig files: MACS
Genome_build: Cryptococcus neoformans var. grubii H99 .
Supplementary_files_format_and_content: tab-delimited text files include reads values for each Sample (RNA-seq), wig files for ChIP-seq

organism: Cryptococcus neoformans H99

source_name: H99 treated with TSA and NAM RNA-seq sample, replicate 1

extract_protocol: Transcriptome analysis: For the analysis of deacetylase inhibitors, C. neoformans cells were either not treated or treated with 3 μM TSA and 20 mM NAM in 50 ml of YPD medium at 30°C for 6 hrs. For the analysis of dac2Δ and dac4Δ, overnight cell cultures of the wild-type H99, dac2Δ and dac4Δ strains were subcultured in fresh YPD medium, and the cultures were incubated at 30°C until the cell density reached the exponential phase (approximately 6 to 7 hrs). Cells were then washed twice with ice-cold PBS supplemented with 3 μM TSA and 20 mM NAM, followed by RNA isolation using TRIzol reagent (Thermo Fisher Scientific, USA). Three micrograms of total RNA was processed using the TruSeq RNA sample preparation Kit (Illumina, USA).

value: wildtype

tag: growth phase

value: logarithmic phase, OD600=1.0


title: sef1_High-iron_repeat 2

source_name: sef1 deletion mutant cells, YPD+400mM ferrous iron, biological repreat 2


title: 993

source_name: H99 strain RNA-seq sample, replicate 3


title: WT_H3K23Ac_rep1

value: anti-H3K23ac (07-355; Millipore)


title: 24h-Cultured hepatocytes

source_name: primary human hepatocyte

value: primary human hepatocyte

value: WME

value: 24 hours


title: WT_Low-iron_repeat 1

source_name: Wild type cells, YPD+200mM BPS, biological repreat 1


title: sef1_Low-iron_repeat 3

source_name: sef1 deletion mutant cells, YPD+200mM BPS, biological repreat 3


title: 2B LGI+Apoplast


title: TN3

source_name: H99 treated with TSA and NAM RNA-seq sample, replicate 3


title: WT_Low-iron_repeat 4

source_name: Wild type cells, YPD+200mM BPS, biological repreat 4


title: TN2

source_name: H99 treated with TSA and NAM RNA-seq sample, replicate 2


title: 1B LGI+LGI


title: 1A LGI+LGI


title: saline01

description: 14 1001 saline01_(RaGene-1_0-st-v1).CEL(normalized)

source_name: rat striatum_saline

value: I.P. Saline for 7 days


title: WT_High-iron_repeat 4

source_name: Wild type cells, YPD+400mM ferrous iron, biological repreat 4


title: 22

source_name: dac2Δ strain RNA-seq sample, replicate 2


title: 41

source_name: dac4Δ strain RNA-seq sample, replicate 1


title: WT_High-iron_repeat 3

source_name: Wild type cells, YPD+400mM ferrous iron, biological repreat 3


title: WT_Low-iron_repeat 3

source_name: Wild type cells, YPD+200mM BPS, biological repreat 3


title: WT_High-iron_repeat 2

source_name: Wild type cells, YPD+400mM ferrous iron, biological repreat 2


title: 992

source_name: H99 strain RNA-seq sample, replicate 2


title: saline02

description: 14 1001 saline02_(RaGene-1_0-st-v1).CEL(normalized)


title: ChIP-Input.rep3

source_name: DAC4-FLAG ChIP-seq input sample, replicate 3

extract_protocol: ChIP assay: The ChIP assay was performed using the ChIP-IT High Sensitivity Kit (Active Motif, Carlsbad). The DAC4-FLAG strain cells were diluted in fresh YPD medium. Cells were fixed with 1% formaldehyde (Sigma, USA) for 15 mins and quenched by 125 mM glycine. Cells were washed three times with ice-cold PBS buffer supplemented with 125 mM glycine. Cells were then lysed with the lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.5% IGEPAL). Cell pellets were suspended in sonication buffer (20 mM Tris-HCL (PH 8.0), 2 mM EDTA, 1% Triton-X100, 150 mM NaCl, 1% SDS, 100 µM PMSF and 1x proteinase inhibitor). The samples were sheared with a Diagenode Pico device using 30 s on and off for 30 cycles. After centrifugation, the supernatant was collected and diluted in IP dilution buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl, 100 μM PMSF and 1x proteinase inhibitor). The immunoprecipitation was performed with 5 μg of anti-Flag ChIP grade antibody and Protein G Beads at 4°C overnight. The beads were then washed 4 times in IP dilution buffer. The sample was then eluted with elution buffer and treated with Proteinase K overnight at 65°C. DNA samples were purified with DNA purification columns. The ChIP-seq library was constructed with the MicroPlex Library Preparation Kit v2 (Diagenode, Liège, Belgium) according to the manufacturer’s instructions.

tag: antibody

value: none (input)


title: ChIP-Input.rep1

source_name: DAC4-FLAG ChIP-seq input sample, replicate 1


title: ChIP.rep3

description: ChIP-DNA

source_name: DAC4-FLAG strain ChIP-seq sample, replicate 3

value: Anti-Flag ChIP grade (AB1162, Abcam, USA)


title: 43

source_name: dac4Δ strain RNA-seq sample, replicate 3


title: ChIP.rep2

description: ChIP-DNA

source_name: DAC4-FLAG strain ChIP-seq sample, replicate 2


title: 1C LGI+LGI

source_name: Cultured cells

tag: strain


title: 42

source_name: dac4Δ strain RNA-seq sample, replicate 2


title: ChIP-Input.rep2

source_name: DAC4-FLAG ChIP-seq input sample, replicate 2


title: WT_High-iron_repeat 1

source_name: Wild type cells, YPD+400mM ferrous iron, biological repreat 1


title: WT_2

city: Sendai

first: Cristina

last: Sanchez

address: 2-1-1 Katahira, Aoba-ku

department: Graduate School of Life Sciences

institute: Tohoku University

data_processing:
Original files generated by the sequencing instrument were imported to the CLC Genomic Workbench software 9.5.3., with a library size of 200-500 bp.
Trimming of reads was performed with default values (except for with a minimum number of nucleotides on reads of 70) using the CLC Genomic Workbench software 9.5.3.
Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.5.3.
Genome_build: GenBank accession number NC_004463
Supplementary_files_format_and_content: A tab-delimited text file including the mapping reports (for WT_1, nasT_1, WT_2, and nasT_2)
Supplementary_files_format_and_content: Four tab-delimited text files including read counts and RPKM values for each sample
Supplementary_files_format_and_content: A tab-delimited text file including the differential expression analysis WT vs. ΔnasT

organism: Bradyrhizobium diazoefficiens

source_name: B. diazoeficiens USDA 110

growth_protocol: Cells of B. diazoefficiens were inoculated into 20 mL (optical density ~0.01 at 660 nm) of HMM medium wth 10 mM KNO3 in 100-mL bottles and reciprocally shaken (100 rpm, 30°C) for 24 h under anaerobic conditions.

extract_protocol:
Total RNA was isolated using hot phenol extraction. Digestion with DNase I (RQ1; Promega), purification with the RNeasy Mini Kit (Qiagen), and First-strand cDNA synthesis (SuperScript II reverse transcriptase; Invitrogen) were performed according to the manufacturer’s instructions.
Two biological replications were processed for each strain (wild-type USDA 110 and ΔnasT mutant). For each cDNA sample (four in total), 5 μg were used for RNA-seq analysis. Ribosomal RNAs was removed with the Ribo-Zero Magnetic Kit for Gram-negative Bacteria (Epicentre) and cDNA library was prepared with the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). These steps were performed by Hokkaido System Science Co., Ltd. (http://www.hssnet.co.jp/).

value: USDA 110


title: 21

source_name: dac2Δ strain RNA-seq sample, replicate 1


title: WT_1

source_name: Bradyrhizobium diazoefficiens USDA 110


title: 23

source_name: dac2Δ strain RNA-seq sample, replicate 3


title: Gene expression after 3 months air exposure

city: Tokyo shinjukuku

first: Akihiro

last: Tsutsumi

institute: Keio University

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: Scanned output files were analyzed using the Transcriptome Analysis Console (Affymetrix/Thermo Fisher Scientific).

label: bitoin

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual ,  Affymetrix).Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-2000c spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell type

value: lung cells


title: nasT_1

source_name: B. diazoeficiens ΔnasT mutant

value: delta nasT


title: 991

source_name: H99 strain RNA-seq sample, replicate 1


title: sef1_High-iron_repeat 3

source_name: sef1 deletion mutant cells, YPD+400mM ferrous iron, biological repreat 3


title: ChIP.rep1

description: ChIP-DNA

source_name: DAC4-FLAG strain ChIP-seq sample, replicate 1


title: tonsil CD4 T cells (CXCR5+PD-1high)

status: Public on Apr 25 2019

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

country: France

institute: Institut Curie

description: single-cell RNA-seq

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v2.0.1)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v2.0.1)
barcode processing, Cell Ranger Single Cell Software Suite (v2.0.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v2.0.1)
alignment, Cell Ranger Single Cell Software Suite (v2.0.1)
Genome_build: GRCh38

source_name: tonsil CD4 T cells (CXCR5+PD-1high)

extract_protocol:
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol
Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3’ v2 Reagent Kit, following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select; (3) adaptor ligation; (4) post ligation cleanup with SPRI select; (5) sample index PCR and cleanup with SPRI select beads.

tag: individual

value: donor 1


title: tonsil CD14+ cells

description: single-cell RNA-seq

source_name: tonsil CD14+ cells


title: Organoid8M_R9_C70

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
FASTQ sequences were mapped to human genome hg19 (GRCh37) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflelink
Read count profile were analyzed for the differential expression analysis using DESeq2 (version 1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample ...

growth_protocol: Retinal cell differentiation from H1 hESCs was performed. Briefly, cysts and adherent cultures were generated as described previously, with the starting day of cell differentiation designated as day 0. On day 15, adherent cultures were partially lifted at edges via one-minute dispase treatment (1 mg/ml in DMEM/F12), rinsed with DMEM/F12 medium, and then grown in a B27 medium (DMEM/F12 (3:1), 2% B27, NEAA). In a few hours, the adherent cultures were spontaneously detached as floating aggregates. In about one week, retinal organoids with a bright ring under an inverted microscope spontaneously formed, and were grown in a serum medium (DMEM/F12 (3:1), 8% fetal calf serum (Gibco), 2% B27, NEAA, 100 mM Taurine (Sigma), and 2mM GlutaMAX) on an orbital shaker. The medium was changed every three days unless stated otherwise.Retinal organoids and adherent cultures were fixed in 4% PFA for 15-30 minutes at room temperature and then processed for cryosectioning at 8 month.

extract_protocol:
Using ICELL8 multisample nanodispenser (Wafergen Biosystems), 50nl (3E4/ml) of the live cell or nuclear suspension was precisely dispensed into an ICELL8 nanowell microchip containing 5184 wells (150nl capacity) as described previously (Goldstein et al., 2017). Assuming a Poisson distribution frequency for the number of cells per well, about 30% of the nanowells were expected to contain a single nucleus under optimal conditions. Automated scanning fluorescent microscopy (using Olympus BX43 fluorescent microscope with a robotic stage) of the microchip was used to select ~1400 wells containing a single live cell or a single nucleus (CellSelect software, Wafergen Biosystems).  The candidate wells were manually evaluated for debris or clumps as an additional QC.
The chip was subjected to freeze-thaw in order to lyse the cells and 50 nl of reverse transcription and amplification solution (following ICELL8 protocol) was dispensed using the multisample nanodispenser to candidate wells. SCRB-seq was then performed on the candidate wells using pre-printed primer that adds a well-specific barcode to the (A)n mRNA tail of the cellular transcript. The cDNA libraries were pooled, concentrated (Zymo Clean and Concentrator kit, Zymogen) and purified (using 0.6x AMPure XP beads). 3’ transcriptome enriched library was made by Nextera XT Kit and 3’-specific P5 primer, and sequenced on Illumina Hiseq2500.

value: retinal organoid

tag: culture time

value: 8 month


title: Organoid8M_R9_C56


title: Organoid8M_R9_C57


title: BM HYPOXIC rep1

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

hyb_protocol: standard Agilent protocol

scan_protocol: Agilent Microarray Scanner

data_processing: Agilent Feature Extraction Software

source_name: Human Bone Marrow Stem Cells from healthy (BM) donor in hypoxic  condition

label_protocol: Cyanine-3 (Cy3) labeling with miRNA Complete Labeling and Hyb Kit  according to the manufacturer's instructions

growth_protocol: Mononuclear cells were washed with PBS (3X) and plated in DMEM medium (Corning, 10-013-CM, NY, USA), 1% antibiotics-antimycotics (Invitrogen, 15240-062, Carlsbad, CA, USA) and 10% Fetal bovine serum (FBS), into 100mm culture dish and incubated at 37°C in a humidified atmosphere at 5% carbon dioxide (CO2).Non-adherent cells were removed after 24h, the adherent cells carefully washed in Phosphate-buffer saline (PBS) and further expanded in fresh culture medium.

extract_protocol: RNA extraction by protocol reported in PMID: 24349422

treatment_protocol: The cells were cultured in normal and hypoxic conditions. Hypoxic culture conditions were obtained by BD GasPak EZ Anaerobe Gas Generating Pouch System (BD Biosciences, San Diego). As certified by the manufacturer, the Anaerobe Gas Generating Pouch System produces an atmosphere containing 10% carbon dioxide and 1% oxygen. Confluent healthy and CLI hMSC monolayers were subjected to normoxic and hypoxic culture for 24 hours. Cells were serum-starved in EBM plus 0.5% fetal bovine serum (FBS) at least 8h before hypoxic culture to minimize the effects of growth factors in the expansion media.

tag: treatment

value: hypoxia


title: PZ HYPOXIC rep1

source_name: Human Bone Marrow Stem Cells from end-stage  critical limb ischemia (CLI) patients (PZ) in hypoxic condition


title: PZ HYPOXIC rep2


title: PZ NORMO rep1

source_name: Human Bone Marrow Stem Cells from end-stage  critical limb ischemia (CLI) patients (PZ) in normal condition

value: normoxia


title: BM HYPOXIC rep2


title: Organoid8M_R9_C52


title: PZ NORMO rep2


title: Organoid8M_R9_C48


title: Organoid8M_R9_C68


title: Organoid8M_R9_C9


title: Gene expression after 3 months smoke exposure


title: BM NORMO rep2

source_name: Human Bone Marrow Stem Cells from healthy (BM) donor in normal  condition


title: tonsil CD4 T cells (CXCR5+PD-1low)

description: single-cell RNA-seq

source_name: tonsil CD4 T cells (CXCR5+PD-1low)


title: nasT_2


title: tonsil CD4 T cells (CXCR5+PD-1int)

description: single-cell RNA-seq

source_name: tonsil CD4 T cells (CXCR5+PD-1int)


title: Organoid8M_R9_C46


title: BM NORMO rep1


title: Organoid8M_R9_C44


title: WT_Low-iron_repeat 2

source_name: Wild type cells, YPD+200mM BPS, biological repreat 2


title: Organoid8M_R9_C35


title: Organoid8M_R9_C45


title: Organoid8M_R9_C3


title: Organoid8M_R9_C19


title: Organoid8M_R9_C38


title: Organoid8M_R9_C11


title: Organoid8M_R8_C71


title: Organoid8M_R9_C10


title: Organoid8M_R8_C55


title: Organoid8M_R8_C39


title: Organoid8M_R9_C34


title: Organoid8M_R8_C50


title: Organoid8M_R9_C18


title: Organoid8M_R9_C27


title: Organoid8M_R9_C24


title: Organoid8M_R8_C22


title: Organoid8M_R8_C17


title: Organoid8M_R8_C62


title: Organoid8M_R8_C8


title: Organoid8M_R8_C9


title: Organoid8M_R8_C19


title: Organoid8M_R8_C32


title: Organoid8M_R8_C24


title: Organoid8M_R8_C64


title: Organoid8M_R8_C10


title: Organoid8M_R8_C36


title: Organoid8M_R8_C20


title: Organoid8M_R8_C27


title: Organoid8M_R9_C53


title: Organoid8M_R8_C12


title: Organoid8M_R7_C63


title: Organoid8M_R7_C64


title: Organoid8M_R8_C15


title: Organoid8M_R8_C57


title: Organoid8M_R8_C0


title: Organoid8M_R7_C61


title: Organoid8M_R7_C46


title: Organoid8M_R7_C69


title: Organoid8M_R7_C39


title: Organoid8M_R7_C62


title: Organoid8M_R7_C59


title: Organoid8M_R7_C4


title: Organoid8M_R7_C60


title: Organoid8M_R7_C51


title: Organoid8M_R7_C43


title: Organoid8M_R7_C57


title: Organoid8M_R7_C35


title: Organoid8M_R7_C54


title: Organoid8M_R7_C15


title: Organoid8M_R8_C69


title: Organoid8M_R7_C21


title: Organoid8M_R7_C19


title: Organoid8M_R7_C56


title: Organoid8M_R7_C30


title: Organoid8M_R71_C62


title: Organoid8M_R71_C59


title: Organoid8M_R7_C26


title: Organoid8M_R7_C11


title: Organoid8M_R71_C49


title: Organoid8M_R71_C39


title: Organoid8M_R71_C56


title: Organoid8M_R71_C52


title: Organoid8M_R71_C47


title: Organoid8M_R71_C33


title: Organoid8M_R71_C50


title: Organoid8M_R71_C28


title: Organoid8M_R71_C41


title: Organoid8M_R7_C34


title: Organoid8M_R71_C45


title: Organoid8M_R71_C1


title: Organoid8M_R71_C14


title: Organoid8M_R71_C10


title: Organoid8M_R71_C27