title: 11192

city: Salt Lake City

first: Sheri

last: Holmen

state: UT

address: 2000 Circle of Hope Dr.

department: Surgery

institute: University of Utah

description:
Eliminated due to QC issue
14154X29

data_processing:
Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583)
The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824)
Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis
DNA sequences were determined using the HiSeq 50 Cycle Single-Read Sequencing version 4
Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot
Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001)
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002)
Generated reads mapped to reference genome
Eight samples eliminated due to quality control measures
Differential expression analysis performed using DESeq2 variance stabilizing transformation
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample before differential expression analysis

source_name: melanoma

extract_protocol:
Frozen primary tumor samples embedded in OCT were macrodissected. For RNA extraction and DNase treatment, the Roche High Pure miRNA Isolation Kit was used in accordance with the manufacturer's protocol (5080576001).
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold. Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples. Stranded RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold per the manufacturer’s instructions (RS-122-2301 and RS-122-2302).

value: melanoma

tag: age

value: sacrified day 56


title: 11355

status: Public on Nov 21 2018

type: SRA

country: USA

description:
star_counts22.txt
14154X28

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

value: sacrified day 46

tag: genotype


title: 11361

description:
star_counts22.txt
14154X27

value: sacrified day 53


title: 11358

description:
star_counts22.txt
14154X25


title: 11360

description:
star_counts22.txt
14154X26


title: 10819

description:
star_counts22.txt
14154X23


title: RB_K4_1

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

library_source: genomic

data_processing:
Reads were mapped to the human reference genome (GRCh37/hg19) with Bowtie2 (2.2.9) using default parameters.
PCR duplicates were removed with Picard Tools MarkDuplicates (1.97)
BAM files were filtered to include reads with MAPQ>10 and blacklist regions were excluded. The merged consensus blacklist was obtained from the Kundaje lab at Stanford University (Stanford, CA, USA).
Reads were extended to 200bp and RPKM normalized, counted in bins of length 50 and converted to bigWig format using DeepTools (2.4.1).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: normalized bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: HAP1 cells

growth_protocol: HAP1 cells were cultured in IMDM media supplemented with 10% FBS and 1% L-Glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
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.

tag: cell line

value: RING1B KO

tag: chip antibody

value: H3K4me3 (Cell Signaling Technology; C42D8, 9751)


title: E2_K4_2

value: EZH2 KO


title: E2_Ub_1

value: H2AK119ub (Cell Signaling Technology; D27C4; 8240S)


title: 10996

description:
star_counts22.txt
14154X24

value: sacrified day 58


title: A2_K4_1

value: ASXL2 KO


title: E2_Ub_2


title: Input

value: WT


title: RB_K27_1

value: H3K27me3 (Cell Signaling Technology; C36B11, 9733S)


title: RB_K27_2


title: RB_Ub_2


title: RB_Ub_1


title: E2_K4_1


title: A2_K27_2


title: A2_Ub_1


title: A2_Ub_2


title: E2_K27_1


title: A1_Ub_2

value: ASXL1 KO


title: A2_K27_1


title: 11197

description:
Eliminated due to QC issue
14154X30

value: sacrified day 49


title: 10932

description:
star_counts22.txt
14154X19


title: 10930

description:
Eliminated due to QC issue
14154X20

value: sacrified day 75


title: E2_K27_2


title: 11017

description:
Eliminated due to QC issue
14154X21

value: sacrified day 44


title: A1_Ub_1


title: 8195

description:
star_counts22.txt
14154X17

value: sacrified day 37


title: A1_K4_1


title: A1_K4_2


title: A1_K27_1


title: 9868

description:
Eliminated due to QC issue
14154X18

value: melanoma

value: sacrified day 48


title: 7873

description:
star_counts22.txt
14154X14


title: 7788

description:
star_counts22.txt
14154X15

value: sacrified day 42


title: A1_K27_2


title: 9819

description:
star_counts22.txt
14154X16

value: sacrified day 34


title: 9389

description:
Eliminated due to QC issue
14154X13


title: WT_Ub_2


title: B1_K27_1

value: BAP1 KO


title: B1_K4_2

value: H3K4me3 (Cell Signaling Technology; C42D8, 9751)


title: B1_K4_1


title: B1_Ub_1


title: B1_Ub_2


title: B1_K27_2


title: 3125

description:
star_counts22.txt
14154X11

value: sacrified day 41


title: 3971

description:
star_counts22.txt
14154X10

value: sacrified day 36


title: 3126

description:
Eliminated due to QC issue
14154X9

value: sacrified day 59


title: WT_K4_2


title: WT_Ub_1

value: H2AK119ub (Cell Signaling Technology; D27C4; 8240S)


title: WT_K27_2

value: WT


title: 4083

description:
star_counts22.txt
14154X12

value: sacrified day 40


title: 10995

description:
star_counts22.txt
14154X22

value: sacrified day 88


title: 5548

description:
star_counts22.txt
14154X5


title: 5477

description:
Eliminated due to QC issue
14154X6

value: sacrified day 65


title: 3143

description:
star_counts22.txt
14154X8

value: sacrified day 53


title: Control Input DNA Dox Plus, 12hr

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Input DNA

data_processing:
ChIP-Seq: Sequenced 51bp reads were aligned to the reference genome (mouse hg9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Custom scripts were first used to generate wiggle files (RPM normalized) from bow-tie aligned BED files, and then the wiggle files were convered to BW files using the wigToBigWig tool.
genome build: hg19
Supplementary_files_format_and_content: BW files containing reads mapped to hg19 assembly; TEXT file containing the list of binding sites as defined by SISSRs [PMID: 18684996]

growth_protocol: To induce NPC differentiation, G3-hESCs were plated in Matrigel-coated dishes and grown for 24 h in mTeSR1 medium before medium was switched to DMEM/B27 medium supplemented with activin/TGFß/BMP pathway inhibitors.

extract_protocol:
For ChIP-Seq, Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with A/G-conjugated magnetic beads with a HA-antibody.
ChIPed DNA was amplified using a TruSeq ChIP Library prep kit.

treatment_protocol: G3-hESC to NPC differentiation in the presence or absence of DOX.

tag: treatment

value: Doxycycline Plus

value: H9 hESCs with Dox inducible Glis3 expression

tag: time

value: 12 hr

value: none (input)


title: WT_K4_1


title: 4326

description:
star_counts22.txt
14154X7

value: melanoma

value: sacrified day 46


title: HA-GLIS3 ChIP-Seq Dox Minus, 12hr

description: ChIP DNA

value: Doxycycline Minus

value: HA antibody (Cell Signaling, Catalog # C29F4)


title: WT_K27_1

value: H3K27me3 (Cell Signaling Technology; C36B11, 9733S)


title: 5613

description:
star_counts22.txt
14154X2

value: sacrified day 37


title: 7472

description:
star_counts22.txt
14154X4

value: sacrified day 71


title: HA-GLIS3 ChIP-Seq Dox Plus, 12hr

description: ChIP DNA


title: 5611

description:
star_counts22.txt
14154X3


title: Control Input DNA Dox Minus, 12hr

description: Input DNA


title: CPNDL_3

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description: CPNDL.txt

data_processing:
Aligned to UCSC mm10 avec TopHat v. 2.0.11
Number of reads per feature counted with Htseq v.0.6.1
Genes were filtered with the following specification: at least 20 reads per Million in at least one sample
Bulk1 (SSN and CPNSL_d/e) and Bulk2 (CPNDL and CPNSL_1-4) expression values were normalized using CPNSL mean expression value for each experiment
Normalized expression values are presented as log10(expression + 10)
Genome_build: mm10
Supplementary_files_format_and_content: .txt file containing normalized log10(expression values+10)

source_name: retrogradely labeled callosal projection neurons from deep layers of the neocortex

extract_protocol:
Qiagen Rneasy Plus Micro; Smarter
Nextera

value: Cortical Neurons

value: C57Bl/6 wild-type mice

tag: labeling

value: retrograde labeling from contralateral primary somatosensory cortex


title: 5474

description:
star_counts22.txt
14154X1

value: sacrified day 51


title: CPNDL_1

description: CPNDL.txt


title: CPNSL_d

description: CPNSL.txt

source_name: retrogradely labeled callosal projection neurons from superficial layers of the neocortex


title: CPNSL_4

description: CPNSL.txt


title: CPNDL_4

description: CPNDL.txt


title: CPNSL_3

description: CPNSL.txt


title: SSN_c

description: SSN.txt

source_name: layer 4 Tomato+ spiny stellate neurons

value: Scnn1a-Cre X CAG-tgTomato reporter (L4 Tom mice)


title: CPNSL_1

description: CPNSL.txt


title: donor 44 JQ1 activated

city: Heidelberg

first: Marina

last: Lusic

address: Im Neuenheimer Feld 400

country: Germany

institute: Heidelberg University Hospital

description: ribo-zero

data_processing:
Reads were processed using BBMap with parameters maxindel=200000 xstag=unstranded ambiguous=random xmtag=t scoretag=t pairedonly=t minavgquality=20 maqb=51 minid=0.91.
We counted abundances for all genes. They are available in SupplementaryCountsTableRNAseq.txt
Genome_build: hg19
Supplementary_files_format_and_content: counted abundances for all genes

source_name: CD4+ T cells

extract_protocol:
5x106 DMSO and 500 nM JQ1 treated CD4+ T cells from three independent donors were used for RNA extraction with InviTrap Spin Kit (Stratec Biomedical) according to the manufacturer’s instructions
Libraries for sequencing were prepared by using rRNA depletion kit NEBNext® and NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Sequencing was performed with 2 × 75 bp read length on the NextSeq platform.

tag: activation

value: activated

tag: donor


title: donor 44 CTRL activated

description: ribo-zero

value: control


title: CPNDL_2

description: CPNDL.txt


title: CPNSL_e

description: CPNSL.txt


title: donor 42 JQ1 activated

description: ribo-zero


title: SSN_b

description: SSN.txt


title: donor 42 CTRL activated

description: ribo-zero


title: donor 41 CTRL activated

description: ribo-zero


title: donor 44 JQ1 resting

description: ribo-zero

value: resting


title: SSN_a

description: SSN.txt


title: donor 44 CTRL resting

description: ribo-zero


title: donor 41 JQ1 resting

description: ribo-zero


title: donor 41 CTRL resting

description: ribo-zero


title: donor 41 JQ1 activated

description: ribo-zero


title: donor 42 JQ1 resting

description: ribo-zero


title: donor 42 CTRL resting

description: ribo-zero


title: CPNSL_2

description: CPNSL.txt


title: 0.8uM_CHIR

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

data_processing:
Paired-end sequencing reads were mapped to hg38 mouse genome using STAR tool(v2.5.2b).
After mapping, fragments per kilobase million (FPKM) was calculated by Cufflinks (v2.2.1) tool using the following strand-specific Cuffnorm option: --library-type=fr-firststrand.
Functional annotation of differentially expressed genes (DEGs) and enrichment analyses were performed using DAVID (v6.8) and Gene Set Enrichment Analysis (GSEA, v2.2.4), respectively, and genes were considered differentially expressed at the fold change > 3 and FPKM > 5. R (v3.3.2) package was used for statistical analyses and scatter plot generation, and RNA-Seq results were visualized using Integrative Genomics Viewer (IGV).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Brain organoids

growth_protocol: hESCs was maintained in TeSR-E8 medium. Day 7 embryoid bodies were cultured in midbrain specification medium supplemented with specific cytokines and small molecules. Brain organoids were cultured in brain organoid maturation medium containing supplements supporting neuronal functionality.

extract_protocol:
Total RNA was extracted from all samples using RNeasy Plus Mini Kit (74134, Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Day 7 embryoid bodies were treated distinct combination of SMAD inhibitors for comparison. Day 30 brain organoids were generated by distinct concentration of CHIR99021 to apply the in vitro WNT gradient.

value: Cultured brain organoid

value: 30 days after differentiation

value: Wild type


title: 8WM

value: 8 weeks after maturation


title: 3uM_CHIR_3WM


title: NS

source_name: Embryoid body

value: Cultured embryoid body

value: 7 days after differentiation


title: hESCs

source_name: Embryonic stem cells

value: Cultured cells

value: Passage 30


title: 2uM_CHIR


title: DA


title: 20WM

value: 20 weeks after maturation


title: LS


title: 0uM_CHIR


title: wo_SMADi


title: GAAKO2_G9

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

data_processing:
reads were aligned both to human mature miRNAs (miRBase v.20), using the CASAVA software (Illumina).
Genome_build: miRBAse v.20
Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: gastrocnemius

extract_protocol:
For plasma samples EDTA was used as anticoagulant. Heart and gasatrcnemii were dissected and flash-freezen using liquid nitrogen. miRNA enriched-total RNA was extracted using miRNeasy kit (QIAGEN) for tissues or using miRNeasy serum/plasma kit (qiagen) for plasma.
Small RNA libraries were constructed using a Truseq small RNA sample preparation kit (Illumina) following the manufacturer′s protocol. Using multiplexing, we combined up to 12 samples into a single lane in order to obtain sufficient coverage

value: gastrocnemius

value: 9 months

value: gaa -/-


title: GAAKO3_G9


title: WT3_G9

value: wild-type


title: WT1_G9


title: WT2_G9


title: Z138 SMARCA4 KD AI rep3

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
bcl2fastq v2.17.1.14 was used to generate fastq files.
Reads were aligned with HiSAT2 to G1k V37
Reads were assigned to genes using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: Text file of the counts matrix of all samples generated by htseq-count

source_name: Mantle Cell Lymphoma

growth_protocol: Cell lines were grown in IMDM supplemented with 10% fetal calf serum, penicillin (100units/mL) and streptomycin (100um/mL)

extract_protocol:
RNA was isolated using Qiagen RNeasy kit
Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit

treatment_protocol: Cells lines were cultured the presense of doxycycline and either DMSO or 3uM ibrutinib + 3uM venetoclax

value: Mantle Cell Lymphoma

value: Ibrutinib plus venetoclax

value: SMARCA4 shRNA knockdown


title: Z138 SMARCA4 KD AI rep2


title: Z138 SMARCA4 KD AI rep1


title: Z138 SCR KD

data_processing:
bcl2fastq v2.17.1.14 was used to generate fastq files.
Reads were aligned to human genome (G1k V37) using bwa
Peak-calling was performed using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bed files from MACS2 for each sample

extract_protocol:
Cell were washed in ice cold PBS then lysed in lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40)
Nextera DNA library prep kit

treatment_protocol: Cells lines were cultured the presense of doxycycline

value: control shRNA


title: Z138 SMARCA4 KD


title: Z138 SCR KD AI rep3


title: GAAKO3_G3

value: 3 months


title: Z138 SCR KD AI rep1


title: Z138 SMARCA4 KD DMSO rep3

value: DMSO


title: Z138 SMARCA4 KD DMSO rep2


title: GAAKO1_G3


title: GAAKO1_H9

source_name: heart

value: heart


title: Z138 SCR KD DMSO rep1


title: WT1_G3


title: GAAKO1_G9


title: Z138 SMARCA4 KD DMSO rep1


title: WT3_G3


title: GAAKO3_H9


title: Z138 SCR KD DMSO rep2


title: Z138 SCR KD AI rep2


title: WT1_H9


title: RNA-Seq Dox Plus, 48hr

data_processing:
RNA-Seq: Paired end reads were mapped to the human genome (hg19) using STAR aligner and htseq-count was used to count reads per gene which were utilized in edgeR for differential expression analysis.
STAR aligned BAM files were processed with bamtools and bedtools to generate bedgraph files, followed by RPM normalization. The resulting bedgraph files were then converted to BW files using bedGraphToBigWig tool.
genome build: hg19
Supplementary_files_format_and_content: BW files containing reads mapped to hg19 assembly

extract_protocol:
For RNA-Seq, total RNAs from cells with/without DOX were extracted using a PureLink RNA mini Kit (ThermoFisher Scientific)
For RNA-Seq, extracted RNA was amplified using a RiboZero Gold RNA Library preparation kit

value: Doxycycline Plus

value: H9 hESCs with Dox inducible Glis3 expression

value: 48 hr


title: GAAKO2_H3


title: RNA-Seq Dox Minus, 7d

value: Doxycycline Minus

value: 7 d


title: GAAKO2_G3


title: WT3_H9


title: WT2_H3


title: RNA-Seq Dox Plus, 72hr

value: 72 hr


title: RNA-Seq Dox Minus, 48hr


title: GAAKO2_H9


title: WT2_H9


title: GAAKO1_H3


title: GAAKO3_H3


title: RNA-Seq Dox Minus, 72hr


title: WT1_H3


title: RNA-Seq Dox Plus, 12hr

value: 12 hr


title: WT2_G3

value: gastrocnemius


title: RNA-Seq Dox Minus, 12hr


title: RNA-Seq Dox Plus, 7d


title: RNA-Seq Dox Plus, 24hr

value: 24 hr


title: T47D R1810A Mutant RNAP2 CDK9 ChIP-seq

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

country: Spain

institute: CRG-Centre for Genomic Regulation

description:
T47D cell expressing HA tagged R1810a Mutant form RNAP2
For CDK9, 150 μg   chromatin was incubated with 15μg of antibody  anI-CDK9 (SC-8338) followed by 42μl of Protein A-Agarose Beads (Diagnose) .

data_processing:
Trimmomatic was used to trim sequencing adapters and low-quality ends
BWA was used to align reads to the genome reference sequence
MACS2 was used to identify binding sites
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files with the normalised read counts profiles

source_name: T47D cells

growth_protocol: T47D carrying a single copy of luciferase reporter gene driven by MMTV promoter (T47D-MTVL), were grown in RPMI-1640 medium without phenol red supplemented with 10% dextran coated charcoal treated FBS (DCC/FBS), 2mM L-glutamine, 100U/ml penicillin-streptomycin at 37C with 5% CO2.

extract_protocol:
T47D-MTVL cells, without treatment or transfected with alpha-amanitin resistant HA-tagged wild type (WTr) versus R1810Ar mutant RNAP2 were cross-linked for 10 minutes with 1% formaldehyde. Lysate were sonicated to a DNA fragment size range of 200-300bp using a Biorupter sonicator (Diagenode). CDK9 Immunoprecipitated from , 150 μg   chromatin with 15μg of anti-CDK9  (H-169.SC-8338)) antibody followed by 42μl of Protein A-Agarose Beads (Diagenode).
Libraries were prepared using standadr Illumina instruction of  NEBNext® ChIP-Seq Library Prep Reagent.

treatment_protocol: Using standard protocol of Lipofectamine 3000 transfection,T47D–MMTVL cells were transfected with alpha-amanitin resistant HA-tagged either wild type (WTr) or R1810Ar mutant RNAP2 for 24 hours followed by alpha-amanitin treatment (6µg/ml) for 12hours before chromatin prepration.

tag: r5020 treatment

value: Untreated

tag: chip antibody (catlogue number )

tag: chip antibody (vendor)

value: Santa Cruz

tag: chip antibody lot/batch #

value: lot no # C0415


title: PD PZ6

source_name: plasma

value: plasma

tag: disease

value: Pompe disease

value: 59 years


title: RNA-Seq Dox Minus, 24hr


title: PD PZ5

value: 68 years


title: Z138 SCR KD DMSO rep3

value: Mantle Cell Lymphoma

value: DMSO

value: control shRNA


title: PD PZ4

value: 58 years


title: T47D WT RNAP2  CDK9 ChIP-seq

description:
T47D cell expressing HA tagged Wild type RNAP2
For CDK9, 150 μg   chromatin was incubated with 15μg of antibody  anI-CDK9 (SC-8338) followed by 42μl of Protein A-Agarose Beads (Diagnose) .


title: PD PZ2

value: 9 months


title: CTR5

value: healthy

value: 39 years


title: PD PZ1

value: 2 years and 6months


title: CTR6

value: 57 years


title: CTR3

value: 27 years


title: Melatonin_oocyte_replicate3

city: Yangling

first: Jianmin

last: Su

state: Shaanxi

address: Taicheng 3

country: China

institute: Northwest A&F University

description: replicate3 of melatonin treated group: 10−9 M melatonin treated oocytes

data_processing:
Before mapping, we filtered the sequencing reads, because they have polyA, low quality, and adapters.
The filtered reads were then mapped to the Ensembl Bos taurus genome UMD3.1 (http://asia.ensembl.org/Bos_taurus/Info/Index) by using SOAPaligner/SOAP2 (Li, et al. 2009). More than three mismatches were not allowed in the alignment.
Data normalization was conducted by converting the uniquely mapped transcript reads to reads per kb per million (RPKM), which quantifies the expression levels of genes
EBSeq software was used to detect the differentially expressed genes among different groups with the cutoff of fold change >2 and P < 0.05.
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: Tab-delimited xls files include RPKM values for each transcript in different samples.

organism: Bos taurus

extract_protocol:
Pools of 7 oocytes were washed three times in RNase-free PBS solution and transferred into the lysis buffer immediately on ice. Samples were then centrifuged at 10000 rpm for 30 s at 4°C, and stored at -80°C.
7 oocyt for each sample were directly lysed and used for cDNA synthesis using SuperScript III (Thermo Fisher Scientific). To construct the cDNA library, cDNAs were amplified and fragmented with the NEBNext Ultra DNA Library Prep Kit (E7370, New England Biolabs). Paired-end 150 bp sequencing was performed on the HiSeq2000 (Illumina) platform.

treatment_protocol: ooyctes were cultured in oocyte maturation media with 0 and 10-9 mol/L melatonin to assess whether melatonin positively affects nuclear maturation of bovine oocytes and subsequent development of cloned embryos in vitro.

tag: breed

value: Holstein

value: oocyte

tag: developmental stage

value: metaphase II (MII)

value: 10−9 M melatonin


title: CTR4

value: plasma

tag: age


title: CTR1

tag: tissue

value: 14 years


title: Melatonin_oocyte_replicate2

description: replicate2 of melatonin treated group: 10−9 M melatonin treated oocytes


title: RNA-Seq Dox Minus, 0hr

value: Doxycycline Minus

value: H9 hESCs with Dox inducible Glis3 expression

value: 0 hr


title: Melatonin_oocyte_replicate1

description: replicate1 of melatonin treated group: 10−9 M melatonin treated oocytes


title: Control_oocyte_replicate3

description: replicate3 of control group: 0 M melatonin treated oocytes

value: none (control)


title: Control_oocyte_replicate2

description: replicate2 of control group: 0 M melatonin treated oocytes


title: 204542 (control)

type: genomic

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

description: Copy number variation in fetal alcohol spectrum disorder

hyb_protocol: Standard Illumina protocol for Illumina HumanOmni 2.5M chip

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina platform we used iPattern, PennCNV, and QuantiSNP. We defined a stringent set of variants when each variant was called by at least by two algorithms.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

label: Standard Illumina protocol

source_name: genomic DNA from Saliva Samples

extract_protocol: DNA was obtained from saliva collection kits, and extracted using manufactures protocols.

tag: gender

value: Female

tag: status

value: control

value: saliva


title: 204541 (case)

scan_protocol: Standard Illumina protocol for Illumina HumanOmni 2.5M chip

value: Male

value: fetal alcohol spectrum disorder


title: 204540 (case)

label_protocol: Standard Illumina protocol for Illumina HumanOmni 2.5M chip


title: 204537 (case)


title: 204539 (case)


title: 204538 (case)


title: 204535 (control)


title: PD PZ3

value: Pompe disease

value: 15 years

tag: genotype


title: 204536 (control)


title: 204534 (control)


title: 204532 (control)


title: 204533 (case)


title: 204530 (case)


title: 204531 (case)


title: 204529 (control)


title: CTR2

value: healthy

value: 5 years


title: 204528 (case)


title: 204525 (control)


title: 204526 (control)


title: 204527 (case)


title: 203901 (case)


title: 203898 (case)


title: 203897 (case)


title: 203900 (case)


title: 204524 (control)


title: 203899 (case)


title: Control_oocyte_replicate1

description: replicate1 of control group: 0 M melatonin treated oocytes

value: Holstein

value: oocyte

value: metaphase II (MII)

tag: treatment


title: 203896 (case)


title: 203894 (case)


title: 203895 (control)


title: 203891 (case)


title: 198128 (case)


title: 203892 (control)


title: 203889 (case)


title: 203888 (case)


title: 198127 (control)


title: 198126 (case)


title: 198122 (control)


title: 198121 (case)


title: 198119 (case)


title: 198120 (case)


title: 198117 (case)


title: CRC-402

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

country: Japan

institute: Kinki university School of Medicine

hyb_protocol: according to manufacturer's protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis)

scan_protocol: Arrays were scanned using the Agilent G2565CA microarray scanner using Feature Extraction software version 10.7.3.1

data_processing: Data precessing was performed using Agilent genomic workbench software version 6.5.0.18

source_name: FFPE colorectal cancer tumor tissue

label_protocol: according to manufacturer's protocol (Agilent Genomic DNA Enymatic Labeling Kit)

extract_protocol: genomic DNA isolated using QIAamp DNA Micro kit (Qiagen)

treatment_protocol: patients were treated with bevacizumab in combination with oxaliplatin or irinotecan

value: female

tag: tumor location

value: right

value: colon cancer

tag: specimen type

value: post-operative

source_name: gender matched reference (Promega)

tag: tissue origin

value: blood


title: CRC-394


title: CRC-399

value: left

value: rectal cancer


title: 190687 (control)

value: Female

value: control

value: saliva


title: CRC-395

value: male


title: CRC-388


title: CRC-401


title: CRC-392


title: CRC-385


title: 198118 (case)

value: fetal alcohol spectrum disorder


title: CRC-381


title: 198125 (case)


title: 190686 (control)

value: Male


title: 190685 (control)


title: CRC-377


title: CRC-384


title: CRC-378

value: biopsy


title: CRC-382


title: CRC-380


title: 190683 (control)


title: CRC-375


title: 198116 (case)


title: 190680 (control)


title: 190681 (control)


title: CRC-372


title: 190682 (control)


title: 190684 (control)


title: 187271 (control)


title: 187273 (control)


title: CRC-368


title: 187270 (control)


title: CRC-379


title: CRC-371


title: CRC-356


title: 187267 (control)


title: 187269 (control)


title: CRC-367


title: 187268 (control)


title: 187265 (control)


title: 187266 (control)


title: 187264 (control)


title: CRC-352

value: multiple cancer


title: CRC-341


title: CRC-345


title: CRC-346


title: CRC-326

value: multiple


title: 187262 (control)


title: 187263 (control)


title: 187261 (control)


title: CRC-350


title: CRC-312


title: CRC-333


title: CRC-334


title: CRC-330


title: CRC-339


title: CRC-325


title: 187260 (control)


title: CRC-309


title: 187258 (control)


title: 187259 (control)


title: CRC-308


title: CRC-296


title: 187255 (control)


title: CRC-318


title: 187257 (control)


title: 187253 (control)


title: CRC-306


title: CRC-302


title: 187248 (control)


title: 187252 (control)


title: CRC-293


title: 187250 (control)


title: CRC-283


title: CRC-288


title: 187240 (case)


title: 187243 (case)


title: miRNA-sperm-FS3-breeder rooster

first: Shengru

last: Wu

address: 22 St.XiNong

department: College of Animal Science and Technology

description:
miRNA-Sample 16
Sperm sample from breeder roosters which fed with diet with extra 2.50mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_sperm.xlsx
processed data file: differentially_expressed_miRNAs_in_sperm.xlsx

data_processing:
lncRNA samples: Reads mapping and transcriptome assembling: The 125 bp paired-end raw reads were firstly processed through FastQC to obtain the clean data, by removing the reads that contain sequencing adapter contaminations or poly-N and the low quality reads whose Q value were less than 20. At the same time, Q20, Q30 and GC content of the clean data were calculated. Index of the reference genome was built using Bowtie v2.0.6 and the clean reads from six cDNA libraries were merged and mapped to the Gallus gallus 4 (Ensembl 85; http://www.ensembl.org/Gallus_gallus/Info/Index) using TopHat. The mapped reads were assembled into transcripts using Cufflinks [29]. Briefly, ribosomal RNA in sequencing data was removed. We aligned all reads to ribosomal RNA of chicken download from ensemble by bowtie2. Then those aligned reads were removed from fastq files.
lncRNA samples: Coding potential and identification of lncRNAs: By using the Cuffcompare program, the assembled transcripts were annotated . The known protein-coding transcripts and the transcripts whose length were smaller than 200 bp were firstly removed, and the remaining unknown transcripts were used to screen for putative lncRNAs. Then, the coding potential for the remaining transcripts was calculated by CNCI and CPC. A transcript was deemed to be lncRNA if the coding potentials were scored to be less than −1 by CPC software and the coding potentials were scored to be less than 0 by CNCI software, which suggest that this transcript has no capacity of coding for proteins. Briefly, those candidate transcripts whose length were longer than 200nt and the intersection between both coding prediction tools CPC and CNCI were deemed to be lncRNA.
lncRNA samples: Analysis of differential expression patterns: Expression levels of all transcripts, including putative lncRNAs and mRNAs, were quantified as FPKM using the Cuffdiff program from the Cufflinks package. Differential gene expression was determined using DESeq with a P value < 0.05 and log2foldchange >1 or < -1.
miRNA samples: Raw sequencing reads were filtered to obtain mappable sequences using ACGT101-4.2 (LC Sciences, Hangzhou, China). Subsequently, unique sequences with lengths from 18 to 26 nt were mapped to specific species precursors in miRBase21.0 (ftp://mirbase.org/pub/mirbase/CURRENT/) and the genomes of Gallus gallus 4 or other selected species (with the exclusion of specific species) by using Bowtie v2.0.6 to identify known miRNAs and novel 3p- and 5p- derived miRNAs according to the details of the previous study. Modified reads per million reads was used to quantify the normalized reads.
miRNA samples: The differential expression of miRNAs based on normalized counts was analyzed using Student’s t test and the significance threshold was set as P < 0.05 or P < 0.05 and log2foldchange >1 or < -1.
Genome_build: galGal4 (Gallus_gallus-4.0)
Supplementary_files_format_and_content: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
Supplementary_files_format_and_content: Genes_and_predicted_lncRNAs_fpkm_expression_in_sperm.xlsx
Supplementary_files_format_and_content: differentially_expressed_mRNAs_and_lncRNAs_in_breeder_roosters.xls
Supplementary_files_format_and_content: differentially_expressed_mRNAs_and_lncRNAs_in_offspring_broilers.xls
Supplementary_files_format_and_content: differentially_expressed_mRNAs_and_lncRNAs_in_sperm.xls
Supplementary_files_format_and_content: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
Supplementary_files_format_and_content: miRNA_expression_in_sperm.xlsx
Supplementary_files_format_and_content: differentially_expressed_miRNAs_in_breeder_roosters.xls
Supplementary_files_format_and_content: differentially_expressed_miRNAs_in_offspring_broilers.xls
Supplementary_files_format_and_content: differentially_expressed_miRNAs_in_sperm.xls

organism: Gallus gallus

source_name: sperm

extract_protocol:
For sperm samples, total RNA from 25 sperm samples of breeder roosters were extracted using Phenol Water (Solarbio, Beijing, China). Equal quantities of the 5 RNA samples extracted from the 5 sperm samples from the same treatments were pooled into one, and five pooled RNAs samples were used for further RNA sequencing. Meanwhile, all 25 RNA samples of sperm were used for stem-loop qRT-PCR validation. For liver samples, only breeder roosters and offspring broilers from CON and FS2 groups were used for sequencing and further qRT-PCR validation. Total RNA from 10 breeder roosters’ and 40 1-day-old broiler’ liver were extracted using Trizol reagent (Invitrogen, CA, USA). 4 RNA samples of 1-day-old broilers’ livers from same replication were mixed equally together as a pooled RNA sample according to the purity and quantity of total RNA. In total, 6 RNA samples from 6 breeder roosters and 6 pooled RNA samples from 24 one-day-old broilers were used for further library construction. Meanwhile, all 10 RNA samples from breeder roosters’ livers and all 40 RNA samples from 40 one-day-old broilers’ livers were used for qRT-PCR validation.
Library construction protocol for lncRNA: Approximately 3 μg of total RNA was used to prepare an LncRNA library. According to protocol of Epicentre Ribo-zero™ Gold Kit (Illumine, San Diego, USA), ribosomal RNA was removed and the rRNA-depleted RNA (Poly A+ and Poly A－ RNA) were collected [24, 25, 43]. Subsequently, high strand-specificity libraries were generated using the rRNA-depleted RNA and a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following the manufacturer’s recommendations. Briefly, the rRNA-depleted RNA was fragmented using divalent cations under elevated temperature in NEBNext. First-strand cDNA was synthesized using random hexamer primers and M-MuLV reverse transcriptase (RNase H−). Subsequently, second-strand cDNA synthesis was performed using second-strand synthesis reaction buffer, DNA polymerase I, and RNase H. Remaining overhangs were converted into blunt ends by exonuclease/polymerase activity. After adenylation of the 3’ ends of the DNA fragments, NEBNext adaptors with hairpin loop structures were ligated to the fragments to prepare them for hybridization. To select cDNA fragments that are 150–200 bp in length, the fragments in each of the library were purified with an AMPure XP system (Beckman Coulter, Brea, CA, USA). Then 3 μl USER Enzyme (NEB, Ipswich, MA, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. The qPCRs were performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. The PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, the paired-end sequencing (2*125bp) were performed on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China).
Library construction protocol for miRNA: Approximately 1 μg of total RNA from each prepared RNA samples were used to prepare small RNA libraries respectively by using TruSeq Small RNA Sample Prep™ Kits (Illumina, San Diego, USA). Then the single-end sequencing (1*50bp) were performed on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China)

treatment_protocol: Based on a single factor experiment design, 200 1-day-old Arbor Acres breeder roosters (Beijing Arbor Acres Poultry Breeding Co. Ltd. China. P. R) were randomly assigned to five treatments with five replicates per treatment and 8 birds per replicate. The breeder roosters from each treatment were fed with a standard diet mainly consisting of corn and soybean meal (Supplementary Table S2), the only difference between treatments was the concentration of folate in the feeds (0, 0.25, 1.25, 2.50, 5.00 mg folate /kg feed, respectively named as CON, FS1, FS2, FS3, and FS4 groups). The photoperiod and the supply of feed were available according to the recommendations established by Aviagen Broiler Breeders Company, U.S.A. The water was available ad libitum. Meanwhile, 600 1-day-old Arbor Acres breeding hens (Beijing Arbor Acres Poultry Breeding Co. Ltd. China. P. R) were kept in the same environment with breeder roosters and fed with corn-soybean meals contains extra folate. At 32 weeks of age, 1 breeder rooster from each replicate was selected and mated with 16 breeding hens by artificial insemination technology. The artificial insemination sustained for 3 weeks, and at 35 weeks of age, fertile eggs of 5 consecutive days from each replication of each treatment were collected and hatched. Then, the new-born broilers were grouped according to their paternal diets (five treatment with five replicates per treatment and 8 birds per replicate were randomly selected) and were then raised to 21 days by feeding with corn-soybean meals (Supplementary Table S3) without extra folate supplement. The water, diet, and photoperiod were all available ad libitum.

value: sperm

value: 35-week-old breeder roosters

value: 2.50mg/kg folate group


title: 187244 (control)


title: 187251 (case)


title: 187241 (control)


title: CRC-284


title: 187249 (control)


title: 187254 (control)


title: CRC-290


title: CRC-268

value: female

value: colon cancer


title: CRC-255

value: right

value: post-operative

value: blood


title: CRC-252

value: left

value: rectal cancer


title: CRC-289


title: CRC-274


title: 187239 (case)

value: saliva


title: CRC-241


title: CRC-273

value: male


title: 187242 (case)

value: Female

value: fetal alcohol spectrum disorder


title: CRC-254


title: CRC-267


title: miRNA-sperm-FS4-breeder rooster

description:
miRNA-Sample 17
Sperm sample from breeder roosters which fed with diet with extra 5.00mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_sperm.xlsx
processed data file: differentially_expressed_miRNAs_in_sperm.xlsx

value: 5.00mg/kg folate group


title: CRC-258


title: CRC-248


title: CRC-269


title: miRNA-liver-FS2-offspring broiler1-ln

description:
miRNA-Sample 10
Liver sample from offspring broilers whose father fed with diet with extra 1.25mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_offspring_broilers.xlsx

source_name: liver

value: liver

value: 1-day-old offspring broilers

value: 1.25 mg/kg folate group


title: miRNA-liver-CON-offspring broiler2

description:
miRNA-Sample 8
Liver sample from offspring broilers whose father fed with basic diet without extra folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_offspring_broilers.xlsx

value: Control group


title: 187238 (case)


title: miRNA-sperm-FS1-breeder rooster

description:
miRNA-Sample 14
Sperm sample from breeder roosters which fed with diet with extra 0.25mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_sperm.xlsx
processed data file: differentially_expressed_miRNAs_in_sperm.xlsx

value: sperm

value: 35-week-old breeder roosters

value: 0.25mg/kg folate group


title: CRC-280

value: colon cancer


title: miRNA-liver-CON-offspring broiler1

description:
miRNA-Sample 7
Liver sample from offspring broilers whose father fed with basic diet without extra folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_offspring_broilers.xlsx


title: miRNA-liver-FS2-offspring broiler3

description:
miRNA-Sample 12
Liver sample from offspring broilers whose father fed with diet with extra 1.25mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_offspring_broilers.xlsx


title: 187235 (control)

value: control


title: miRNA-sperm-CON-breeder rooster

description:
miRNA-Sample 13
Sperm sample from breeder roosters which fed with basic diet without extra folate.
Small RNA
processed data file: miRNA_expression_in_sperm.xlsx
processed data file: differentially_expressed_miRNAs_in_sperm.xlsx


title: miRNA-liver-CON-offspring broiler3

description:
miRNA-Sample 9
Liver sample from offspring broilers whose father fed with basic diet without extra folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_offspring_broilers.xlsx


title: 187236 (control)

value: Male


title: 187232 (case)


title: miRNA-liver-FS2-offspring broiler2

description:
miRNA-Sample 11
Liver sample from offspring broilers whose father fed with diet with extra 1.25mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_offspring_broilers.xlsx


title: miRNA-liver-FS2-breeder rooster2

description:
miRNA-Sample 5
Liver sample from breeder roosters which fed with diet with extra 1.25mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_breeder_roosters.xlsx


title: 187233 (case)


title: miRNA-liver-FS2-breeder rooster1

description:
miRNA-Sample 4
Liver sample from breeder roosters which fed with diet with extra 1.25mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_breeder_roosters.xlsx


title: miRNA-liver-FS2-breeder rooster3

description:
miRNA-Sample 6
Liver sample from breeder roosters which fed with diet with extra 1.25mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_breeder_roosters.xlsx


title: 184372 (control)


title: 184371 (control)


title: 184370 (control)


title: miRNA-liver-CON-breeder rooster2

description:
miRNA-Sample 2
Liver sample from breeder roosters which fed with basic diet without extra folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_breeder_roosters.xlsx


title: miRNA-liver-CON-breeder rooster1

description:
miRNA-Sample 1
Liver sample from breeder roosters which fed with basic diet without extra folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_breeder_roosters.xlsx


title: lncRNA-sperm-FS4-breeder rooster

description:
lncRNA-Sample 17
Sperm sample from breeder roosters which fed with diet with extra 5.00mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_sperm.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_sperm.xlsx


title: lncRNA-sperm-FS1-breeder rooster

description:
lncRNA-Sample 14
Sperm sample from breeder roosters which fed with diet with extra 0.25mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_sperm.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_sperm.xlsx


title: lncRNA-sperm-FS3-breeder rooster

description:
lncRNA-Sample 16
Sperm sample from breeder roosters which fed with diet with extra 2.50mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_sperm.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_sperm.xlsx

value: 2.50mg/kg folate group


title: miRNA-liver-CON-breeder rooster3

description:
miRNA-Sample 3
Liver sample from breeder roosters which fed with basic diet without extra folate.
Small RNA
processed data file: miRNA_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_miRNAs_in_breeder_roosters.xlsx


title: 184369 (control)

description: Copy number variation in fetal alcohol spectrum disorder


title: lncRNA-sperm-CON-breeder rooster

description:
lncRNA-Sample 13
Sperm sample from breeder roosters which fed with basic diet without extra folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_sperm.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_sperm.xlsx


title: 187237 (control)


title: 184368 (control)


title: lncRNA-liver-FS2-offspring broiler3

description:
lncRNA-Sample 12
Liver sample from offspring broilers whose father fed with diet with extra 1.25mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_offspring_broilers.xlsx


title: lncRNA-sperm-FS2-breeder rooster

description:
lncRNA-Sample 15
Sperm sample from breeder roosters which fed with diet with extra 1.25mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_sperm.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_sperm.xlsx

value: 1.25mg/kg folate group


title: lncRNA-liver-FS2-offspring broiler1

description:
lncRNA-Sample 10
Liver sample from offspring broilers whose father fed with diet with extra 1.25mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_offspring_broilers.xlsx


title: lncRNA-liver-FS2-offspring broiler2

description:
lncRNA-Sample 11
Liver sample from offspring broilers whose father fed with diet with extra 1.25mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_offspring_broilers.xlsx


title: lncRNA-liver-CON-offspring broiler3

description:
lncRNA-Sample 9
Liver sample from offspring broilers whose father fed with basic diet without extra folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_offspring_broilers.xlsx


title: lncRNA-liver-CON-offspring broiler2

description:
lncRNA-Sample 8
Liver sample from offspring broilers whose father fed with basic diet without extra folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_offspring_broilers.xlsx


title: CRC-231

value: left

value: rectal cancer

value: biopsy

value: blood


title: CRC-227

value: female

value: post-operative


title: lncRNA-liver-FS2-breeder rooster3

description:
lncRNA-Sample 6
Liver sample from breeder roosters which fed with diet with extra 1.25mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_breeder_roosters.xlsx

value: liver


title: CRC-228

value: male


title: CRC-240

value: right


title: 184367 (control)

value: saliva


title: lncRNA-liver-CON-offspring broiler1

description:
lncRNA-Sample 7
Liver sample from offspring broilers whose father fed with basic diet without extra folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_offspring_broilers.xlsx

value: 1-day-old offspring broilers

value: Control group


title: CRC-223

value: colon cancer


title: 184366 (control)

value: control


title: CRC-224


title: CRC-219


title: CRC-232


title: 184365 (control)

value: Male


title: lncRNA-liver-FS2-breeder rooster2

description:
lncRNA-Sample 5
Liver sample from breeder roosters which fed with diet with extra 1.25mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_breeder_roosters.xlsx

value: 35-week-old breeder roosters

value: 1.25 mg/kg folate group


title: CRC-221

value: left


title: CRC-218

value: rectal cancer


title: 184364 (control)


title: CRC-210

value: biopsy


title: lncRNA-liver-CON-breeder rooster3

description:
lncRNA-Sample 3
Liver sample from breeder roosters which fed with basic diet without extra folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_breeder_roosters.xlsx


title: 184362 (control)


title: miRNA-sperm-FS2-breeder rooster

description:
miRNA-Sample 15
Sperm sample from breeder roosters which fed with diet with extra 1.25mg/kg folate.
Small RNA
processed data file: miRNA_expression_in_sperm.xlsx
processed data file: differentially_expressed_miRNAs_in_sperm.xlsx

value: sperm

value: 1.25mg/kg folate group


title: lncRNA-liver-FS2-breeder rooster1

description:
lncRNA-Sample 4
Liver sample from breeder roosters which fed with diet with extra 1.25mg/kg folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_breeder_roosters.xlsx


title: 184359 (control)

value: Female


title: 184360 (control)


title: lncRNA-liver-CON-breeder rooster1

description:
lncRNA-Sample 1
Liver sample from breeder roosters which fed with basic diet without extra folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_breeder_roosters.xlsx

value: liver


title: untreated_24h

city: Hong Kong

first: Kwai

middle: Fung

last: Hui

state: Hong Kong

address: L7-01, Laboratory Block, FMB, 21 Sassoon Road, Pokfulam

department: Paediatrics and Adolescent Medicine

country: Hong Kong

institute: HKU

data_processing:
Reads from sequencing were assigned to samples using CASAVA, and adapter sequences, reads with more than 5 % unknown bases and reads with more than 50 % bases of quality score lower than or equal 10 were filtered.
Sequence alignment, expression quantification and differential expression analysis were performed with the CLC Genomics Workbench Version 7.0.4 (CLC bio).
Reads after filtering were aligned to the human genome (hg19) first with default parameters except for similarity fraction (set to 0.9), length fraction (set to 0.8) and strand specific (set to reverse).
The unmapped read were then aligned to the EBV genome (NC_007605).
Expression quantification was performed separately for human and EBV genes and differential expression analysis was performed with Kal’s test with Bonferroni correction.
Genome_build: hg19 and NC_007605.1
Supplementary_files_format_and_content: CLC files of differential expression analysis were generated using CLC Genomics Workbench Version 7.0.4 (CLC bio).

source_name: AGS-BX1 cells

extract_protocol:
RNeasy® Plus Mini Kit (Qiagen)
Indexed sequencing library construction was carried out using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). The libraries were denatured and diluted to optimal concentration before applying to cluster generation in the flow cell. Cluster generation was carried out using the HiSeq PE Cluster Kit v3 cBot (Illumina). Pair-end sequencing of 101 bp was carried out in the Illumina HiSeq 1500 in CGS, HKU with the Illumina HiSeq SBS Kit v3.

treatment_protocol: C7 10mM

tag: cell type

value: EBV-positive gastric carcinoma cells


title: C7_24h


title: C7_8h


title: untreated_8h


title: 184358 (control)


title: 184357 (case)

value: fetal alcohol spectrum disorder


title: 184356 (case)

value: saliva


title: P03_pp65mLCL_all_beta

city: Munich

first: Andreas

last: Moosmann

address: Marchioninistr. 25

department: AGV

institute: Helmholtz Center Munich

data_processing:
Demultiplex with Je-Demultiplex-Illu (Galaxy Version 1.2.1.), with 0 or 1 barcode tolerance for single and dual indexed samples, respectively.
Quality filter with custom fastqFilter software (Built under Galaxy Version 1.0 by LAFUGA), minimum read length after trimming 100 nt, quality threshold 20
TCR clonotype alignment and assembly with MiXCR (Version 1.8.1.) run on Java (Version 1.8.0_60). Command lines:    mixcr align --loci TRB --species hsa --report ALIGN_REPORT_samplename.txt -OminSumScore=258 -OvParameters.geneFeatureToAlign={FR3End\(-26\):FR3End\(+3\)} -OcParameters.geneFeatureToAlign={CBegin:CBegin\(+20\)} -OjParameters.geneFeatureToAlign={FR4Begin\(-3\):FR4End} -OjParameters.parameters.floatingRightBound=false -OvParameters.parameters.minAlignmentLength=25 -OjParameters.parameters.minAlignmentLength=25 -OvParameters.parameters.absoluteMinScore=115 -OjParameters.parameters.absoluteMinScore=125 -OvParameters.parameters.relativeMinScore=0.8 -OjParameters.parameters.relativeMinScore=0.8 -OcParameters.parameters.relativeMinScore=0.8 -OvParameters.parameters.maxHits=5 -OjParameters.parameters.maxHits=5 -OvParameters.parameters.scoring.gapPenalty=-28 -OjParameters.parameters.scoring.gapPenalty=-28 File_with_Galaxy_forward_reads.fastqsanger.fastq File_with_Galaxy_reverse_reads.fastqsanger.fastq align_samplename.vdjca  mixcr exportAlignmentsPretty --skip 10000 --limit 50 align_samplename.vdjca pretty_alignment_samplename.txt  mixcr assemble --report ASSEBMBLE_REPORT_samplename.txt -OassemblingFeatures=[CDR3] -OminimalClonalSequenceLength=6 -OqualityAggregationType=Average -ObadQualityThreshold=20 -OmaxBadPointsPercent=0 -OaddReadsCountOnClustering=true -OcloneClusteringParameters.searchDepth=2 -OcloneClusteringParameters.searchParameters=oneMismatch -OcloneClusteringParameters.clusteringFilter.specificMutationProbability=1E-4 align_samplename.vdjca clones_samplename.clns  mixcr exportClones --filter-out-of-frames --filter-stops -count -fraction -sequence -aaFeature CDR3 -vHit -vHitsWithScore -jHit -jHitsWithScore -dHit -cHit -lengthOf CDR3 -quality -minFeatureQuality CDR3 clones_samplename.clns clones_samplename.txt    Replace "samplename" with the name of the sample and "input" with the forward and reverse read file names downloaded from Galaxy
Reformatting MiXCR output in R (Version 3.4.2.) with a custom Script written in R Studio (Version 1.1.383): Remove irrelevant columns, add sample metadata, replace V gene names by V gene group names in cases where distinction of closely related V genes is not possible
Supplementary_files_format_and_content: tab-delimited .txt file containing TCR clonotype data and sample metadata.
Supplementary_files_format_and_content: Columns: V.gene | CDR3.sequence (translated CDR3 amino acid sequence) | J.gene | Read.count (Reads per clonotype) | Clone.fraction (Proportion of reads on all sample reads) | CDR3.nt.seq | CDR3.nt.length | Donor | Treatment | Cell.type | Serostatus | HLA.class.I (Donor HLA type)

source_name: peripheral blood mononuclear cells

growth_protocol:
Four different CMV-derived peptides, namely CRV (HLA-C*07:02), FRC (HLA-C*07:02), RPH (HLA-B*07:02), and TPR (HLA-B*07:02), were separately used to stimulate and selectively expand virus- specific T cells from CMV-positive donors P01-P08 in the presence of IL-2.
At 6±1 days, the cells of each well were resuspended, distributed to two wells, and 1 ml of fresh culture medium supplemented with IL-2 was added to each well. Cells were harvested at day 10 of culture.
Validation experiment: PBMCs from 3 healthy donors P01-P03 were co-cultured with irradiated autologous B cells transformed with a minimal EBV virus which additionally carries one CMV antigen (pp65 or IE1), or no CMV antigen (control, CTRL).
After 9 days and then every 7 days, the stimulator cells were replaced with fresh irradiated transformed B cells. At each time point, samples were taken. The co-culture was terminated after 30 days.

extract_protocol:
RNA extraction was performed on bulk cells (either unsorted or CD8-enriched using MACS) with the Qiagen RNeasy kit.
1 μg RNA per sample was reversely transcribed to cDNA with the QuantiTect Reverse Transcription Kit (Qiagen) using a primer designed to target both the Cβ1 and Cβ2 regions of the TCR RNA. cDNA was amplified in two subsequent PCRs using Pfu DNA polymerase (Thermo Scientific).
The first PCR was a multiplex PCR comprising 42 distinct forward primers that bind to the Vβ region and cover all possible human TCR Vβ segments, and a reverse primer that anneals to the Cβ1 and Cβ2 regions. Forward and reverse primers carried sequences complementary to Illumina Read 2 and Read 1 primer sequences.
In the second PCR, index primers (NEBNext Multiplex Oligos for Illumina; New England BioLabs) were used to attach barcodes and the i5 and i7 adapters for binding to the Illumina flow cell (Supplementary Fig. 2).
After each PCR step, the PCR product was purified using Agencourt AMPure XP magnetic beads (Beckman Coulter). The correct length and amount of the PCR products for sequencing was confirmed using the Agilent DNA 1000 Kit and the Bioanalyzer 2100 (Agilent).
To enhance the nucleotide diversity of TCR reads facilitating cluster recognition and avoiding artifacts in q-score calibration and base calling, three different forms of the reverse primer, with 0, 1 or 2 arbitrary nucleotides between the Cβ-binding sequence and the Illumina Read 1 sequence were used.
All primers were used in equimolar amounts (a total of 10μM; for primer sequences see Supplementary Table 1). The first PCR consisted of only 10 amplification cycles to minimize PCR amplification bias.

treatment_protocol: Libraries were prepared from ex vivo peripheral blood mononuclear cells (labelled "unstim") or after 10-day stimulation with one out of four immunogenic, HLA-matched CMV peptides. Libraries from whole antigen stimulation (mini-LCL libraries) were prepared after 23 or 30-day stimulation.

tag: cmv status

value: positive

tag: cmv peptide

value: pp65 mini-LCL

tag: cell subpopulation

value: unsorted

tag: culture time (days)

tag: productive reads

tag: clonotype count


title: P03_CTRLmLCL_all_beta

value: control mini-LCL


title: P03_IE1mLCL_all_beta

value: IE1 mini-LCL


title: P02_CTRLmLCL_all_beta


title: CRC-237

value: female

value: colon cancer

value: post-operative

value: blood


title: CRC-204

value: right

value: biopsy


title: CRC-202

value: left

value: rectal cancer


title: CRC-207

value: male


title: CRC-200


title: CRC-199


title: P01_IE1mLCL_all_beta


title: P01_pp65mLCL_all_beta


title: P02_IE1mLCL_all_beta


title: P01_CTRLmLCL_all_beta


title: CRC-197


title: CRC-194


title: 184354 (case)

value: Male


title: N05_CRVstim_CD8_beta

growth_protocol:
Four different CMV-derived peptides, namely CRV (HLA-C*07:02), FRC (HLA-C*07:02), RPH (HLA-B*07:02), and TPR (HLA-B*07:02), were separately used to stimulate and selectively expand virus- specific T cells from CMV-positive donors P01-P08 in the presence of IL-2.
At 6±1 days, the cells of each well were resuspended, distributed to two wells, and 1 ml of fresh culture medium supplemented with IL-2 was added to each well. Cells were harvested at day 10 of culture.

value: CRVLCCYVL


title: N05_FRCstim_CD8_beta

value: FRCPRRFCF


title: 184351 (case)

value: fetal alcohol spectrum disorder

value: saliva


title: 184353 (case)

value: Female


title: N05_RPHstim_CD8_beta

value: positive

value: RPHERNGFTVL


title: 184350 (case)


title: N05_TPRstim_CD8_beta

data_processing:
Demultiplex with Je-Demultiplex-Illu (Galaxy Version 1.2.1.), with 0 or 1 barcode tolerance for single and dual indexed samples, respectively.
Quality filter with custom fastqFilter software (Built under Galaxy Version 1.0 by LAFUGA), minimum read length after trimming 100 nt, quality threshold 20
TCR clonotype alignment and assembly with MiXCR (Version 1.8.1.) run on Java (Version 1.8.0_60). Command lines:    mixcr align --loci TRB --species hsa --report ALIGN_REPORT_samplename.txt -OminSumScore=258 -OvParameters.geneFeatureToAlign={FR3End\(-26\):FR3End\(+3\)} -OcParameters.geneFeatureToAlign={CBegin:CBegin\(+20\)} -OjParameters.geneFeatureToAlign={FR4Begin\(-3\):FR4End} -OjParameters.parameters.floatingRightBound=false -OvParameters.parameters.minAlignmentLength=25 -OjParameters.parameters.minAlignmentLength=25 -OvParameters.parameters.absoluteMinScore=115 -OjParameters.parameters.absoluteMinScore=125 -OvParameters.parameters.relativeMinScore=0.8 -OjParameters.parameters.relativeMinScore=0.8 -OcParameters.parameters.relativeMinScore=0.8 -OvParameters.parameters.maxHits=5 -OjParameters.parameters.maxHits=5 -OvParameters.parameters.scoring.gapPenalty=-28 -OjParameters.parameters.scoring.gapPenalty=-28 File_with_Galaxy_forward_reads.fastqsanger File_with_Galaxy_reverse_reads.fastqsanger align_samplename.vdjca  mixcr exportAlignmentsPretty --skip 10000 --limit 50 align_samplename.vdjca pretty_alignment_samplename.txt  mixcr assemble --report ASSEBMBLE_REPORT_samplename.txt -OassemblingFeatures=[CDR3] -OminimalClonalSequenceLength=6 -OqualityAggregationType=Average -ObadQualityThreshold=20 -OmaxBadPointsPercent=0 -OaddReadsCountOnClustering=true -OcloneClusteringParameters.searchDepth=2 -OcloneClusteringParameters.searchParameters=oneMismatch -OcloneClusteringParameters.clusteringFilter.specificMutationProbability=1E-4 align_samplename.vdjca clones_samplename.clns  mixcr exportClones --filter-out-of-frames --filter-stops -count -fraction -sequence -aaFeature CDR3 -vHit -vHitsWithScore -jHit -jHitsWithScore -dHit -cHit -lengthOf CDR3 -quality -minFeatureQuality CDR3 clones_samplename.clns clones_samplename.txt    Replace "samplename" with the name of the sample and "input" with the forward and reverse read file names downloaded from Galaxy
Reformatting MiXCR output in R (Version 3.4.2.) with a custom Script written in R Studio (Version 1.1.383): Remove irrelevant columns, add sample metadata, replace V gene names by V gene group names in cases where distinction of closely related V genes is not possible
Supplementary_files_format_and_content: tab-delimited .txt file containing TCR clonotype data and sample metadata.
Supplementary_files_format_and_content: Columns: V.gene | CDR3.sequence (translated CDR3 amino acid sequence) | J.gene | Read.count (Reads per clonotype) | Clone.fraction (Proportion of reads on all sample reads) | CDR3.nt.seq | CDR3.nt.length | Donor | Treatment | Cell.type | Serostatus | HLA.class.I (Donor HLA type)

treatment_protocol: Libraries were prepared from ex vivo peripheral blood mononuclear cells (labelled "unstim") or after 10-day stimulation with one out of four immunogenic, HLA-matched CMV peptides

value: negative

value: TPRVTGGGAM


title: N05_unstim_CD8_beta

value: 0 (ex vivo)


title: N09_unstim_all_beta

value: unsorted


title: N08_unstim_all_beta


title: CRC-184

value: post-operative

value: blood


title: CRC-188

value: left


title: CRC-182

value: right

value: colon cancer


title: CRC-189

value: male


title: N07_unstim_all_beta


title: 184349 (case)

value: Male


title: 184346 (case)


title: 184347 (case)


title: N06_unstim_all_beta


title: N05_unstim_all_beta


title: N03_unstim_all_beta


title: CRC-179

value: female


title: N04_unstim_all_beta


title: P16_unstim_all_beta


title: N02_unstim_all_beta


title: N01_unstim_all_beta


title: 184344 (case)

value: fetal alcohol spectrum disorder


title: 184343 (case)

value: saliva


title: P15_unstim_all_beta


title: P13_unstim_all_beta


title: 184345 (case)


title: 184342 (case)

value: Female


title: P12_unstim_all_beta

value: positive


title: CRC-177

value: biopsy


title: P11_unstim_all_beta


title: CRC-172


title: CRC-176


title: CRC-173


title: CRC-171

value: rectal cancer


title: CRC-192


title: 184340 (case)


title: CRC-166


title: 184341 (case)


title: P14_unstim_all_beta


title: P04_unstim_all_beta


title: P06_unstim_all_beta


title: P05_unstim_all_beta


title: P08_unstim_all_beta


title: P10_unstim_all_beta


title: P09_unstim_all_beta


title: P07_unstim_all_beta


title: 184339 (case)


title: CRC-165


title: CRC-161


title: 184337 (case)


title: CRC-158


title: P08_RPHstim_CD8_beta

value: RPHERNGFTVL


title: CRC-157


title: P08_FRCstim_CD8_beta

value: FRCPRRFCF


title: P08_TPRstim_CD8_beta

value: TPRVTGGGAM


title: 184336 (case)


title: 184338 (case)


title: P08_CRVstim_CD8_beta

value: CRVLCCYVL


title: P08_unstim_CD8_beta

value: 0 (ex vivo)


title: 184334 (case)


title: P07_RPHstim_CD8_beta


title: P07_FRCstim_CD8_beta


title: 184332 (case)


title: P07_CRVstim_CD8_beta


title: P06_RPHstim_CD8_beta


title: P06_TPRstim_CD8_beta


title: P06_FRCstim_CD8_beta


title: P07_unstim_CD8_beta


title: 184335 (case)


title: 184329 (case)


title: P06_CRVstim_CD8_beta


title: 184328 (control)

value: control


title: P06_unstim_CD8_beta


title: lncRNA-liver-CON-breeder rooster2

description:
lncRNA-Sample 2
Liver sample from breeder roosters which fed with basic diet without extra folate.
processed data file: Genes_and_predicted_lncRNAs_fpkm_expression_in_livers_of_breeder_roosters_and_offspring_broilers.xlsx
processed data file: differentially_expressed_mRNAs_and_lncRNAs_in_breeder_roosters.xlsx

value: liver

tag: developmental stage

value: 35-week-old breeder roosters

value: Control group


title: P05_TPRstim_CD8_beta


title: CRC-150

tag: age

value: left

value: post-operative

value: blood


title: CRC-142

value: male

tag: tissue

value: colon cancer


title: CRC-149

tag: gender


title: P05_FRCstim_CD8_beta

value: positive


title: CRC-144


title: 184327 (case)

value: Female

tag: status

value: fetal alcohol spectrum disorder

value: saliva


title: CRC-139

value: female

value: rectal cancer

value: biopsy


title: P05_CRVstim_CD8_beta

value: CRVLCCYVL


title: 184325 (case)

value: Male


title: CRC-147


title: 184324 (control)

value: control


title: CRC-146


title: 184322 (control)


title: P05_unstim_CD8_beta

value: 0 (ex vivo)


title: 184321 (control)


title: P04_RPHstim_CD8_beta

value: RPHERNGFTVL


title: P04_FRCstim_CD8_beta

value: FRCPRRFCF


title: P04_TPRstim_CD8_beta

value: TPRVTGGGAM


title: P07_TPRstim_CD8_beta


title: CRC-134

value: left

value: post-operative

value: blood


title: CRC-138

value: male

value: colon cancer


title: 184320 (case)

value: Female

value: fetal alcohol spectrum disorder


title: P04_CRVstim_CD8_beta

value: positive


title: CRC-128

value: female

value: rectal cancer


title: 184317 (case)

value: saliva


title: Spleen of sham rat 2 (S2)

type: RNA

city: Kumamoto

first: Junji

last: Saruwatari

state: Select One...

address: 5-1 Oe-honmachi, Chuo-ku

department: Department of Pharmacology and Therapeutics

institute: Kumamoto University

description:
microRNA
microRNA expression data from whole spleen tissue of sham rat.

hyb_protocol: Following fragmentation, 21.5 μL of biotin-labeled cRNA were hybridized for 16-18 hr at 48°C on Affymetrix GeneChip® miRNA 4.0 Array in conjugate with the FlashTag® Biotin HSR RNA Labeling Kit.  GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned using the the GeneChip® Scanner 3000 (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0 using Affymetrix default analysis settings and the Robust Multiarray Average (RMA) algorithm was used for normalization of the data to generate single expression value for each probe set.

label: biotin

organism: Rattus norvegicus

source_name: Whole spleen tissue of sham rat S2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 130-1000 ng total RNA.

growth_protocol: Approximately 50 mg of whole spleens were collected from three PPVL rats as well as sham rats.

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

treatment_protocol: After midline abdominal incision under anesthesia, the portal vein was separated from the surrounding tissue in three rats.  A ligature (silk gut 3–0) was placed around a 20-gauge blunt tipped needle lying along the portal vein.  Subsequent removal of the needle yielded a calibrated stenosis of the portal vein.  Spleen tissues were collected ten days after ligation.  In sham-operated rats (n = 3), the same operation was performed, but no ligature was placed.

value: spleen

tag: strain

value: Sprague-Dawley

value: sham


title: 184316 (control)

description: Copy number variation in fetal alcohol spectrum disorder

value: control


title: P04_unstim_CD8_beta

value: 0 (ex vivo)


title: CRC-120


title: CRC-115

value: right


title: P03_TPRstim_all_beta

value: TPRVTGGGAM

value: unsorted


title: 184315 (control)

value: Male


title: Spleen of sham rat 3 (S3)

source_name: Whole spleen tissue of sham rat S3

tag: treatment


title: P03_RPHstim_all_beta

value: RPHERNGFTVL


title: 184308 (case)


title: Spleen of sham rat 1 (S1)

source_name: Whole spleen tissue of sham rat S1


title: CRC-114

tag: tumor location

value: left

value: post-operative

value: blood


title: 184307 (case)

value: fetal alcohol spectrum disorder


title: Spleen of PPVL rat 3 (P5)

description:
microRNA
microRNA expression data from whole spleen tissue of partial portal vein ligation rat.

source_name: Whole spleen tissue of PPVL rat P5

value: partial portal vein ligation


title: Spleen of PPVL rat 2 (P3)

source_name: Whole spleen tissue of PPVL rat P3


title: P03_FRCstim_all_beta

value: positive

value: FRCPRRFCF


title: Spleen of PPVL rat 1 (P1)

source_name: Whole spleen tissue of PPVL rat P1

value: spleen


title: 184306 (control)

value: saliva


title: CRC-107

value: male

value: rectal cancer

tag: specimen type


title: P03_CRVstim_all_beta

value: CRVLCCYVL


title: P03_unstim_all_beta

value: 0 (ex vivo)


title: 184304 (case)


title: 184303 (control)

value: control


title: 184302 (case)

value: Female


title: CRC-111

tag: tissue origin


title: 184301 (case)


title: 184300 (control)


title: P02_FRCstim_all_beta

value: unsorted


title: P02_CRVstim_all_beta


title: CRC-97

value: right

value: colon cancer


title: P02_unstim_all_beta


title: P01_TPRstim_CD8_beta

value: TPRVTGGGAM


title: CRC-109

value: female

value: left

value: post-operative

value: blood


title: CRC-101


title: CRC-102

value: biopsy


title: CRC-105


title: P02_TPRstim_all_beta

value: positive


title: CRC-95


title: 184298 (case)

value: Male

value: fetal alcohol spectrum disorder

value: saliva


title: CRC-94

value: male

value: rectal cancer


title: P05_RPHstim_CD8_beta

value: RPHERNGFTVL


title: P01_RPHstim_CD8_beta


title: CRC-100


title: P01_CRVstim_CD8_beta

value: CRVLCCYVL


title: 184294 (control)

value: control


title: 184297 (control)

value: Female


title: P01_FRCstim_all_beta

value: FRCPRRFCF

value: unsorted


title: 184296 (control)


title: 184293 (control)


title: P01_unstim_CD8_beta

value: 0 (ex vivo)


title: 184291 (control)


title: 184292 (control)


title: 184288 (control)


title: CRC-87

value: left


title: 184286 (control)


title: CRC-96

value: post-operative


title: CRC-85

value: right

value: colon cancer

value: blood


title: Spleen of sham rat 2 (S2)

description: Gene expression data from whole spleen tissue of sham rat.

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip® Rat Gene 2.0 ST Array.  GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Thermo Fisher Scientific).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50-500 ng total RNA.

value: spleen

value: Sprague-Dawley

value: sham


title: CRC-82

value: female


title: 184285 (control)

value: Male

value: saliva


title: Spleen of sham rat 3 (S3)


title: CRC-81

value: male


title: CRC-78

value: rectal cancer


title: 184282 (control)

value: Female

value: control


title: CRC-75


title: CRC-69


title: CRC-68


title: 184283 (control)


title: Spleen of sham rat 1 (S1)


title: CRC-91


title: Spleen of PPVL rat 2 (P3)

description: Gene expression data from whole spleen tissue of partial portal vein ligation rat.

value: partial portal vein ligation


title: LIF+PD rep1

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

institute: University of Padua

data_processing:
Tophat2 (with defaults parameters) was use to align reads to reference genome (mm10)
Cufflinks was used to assemble transcriptome and CuffDiff  to quantify the levels of gene expression (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing aboundance of genes in FPKM, (genes.fpkm_tracking)

source_name: Embryonic Stem cells

growth_protocol: Murine ES cells were cultured on Gelatin-coated plates in N2B27 medium in the presence of different combinations of the cytokine LIF and the inhibitors CH (GSK3 inhibitor, CHIR99021, 3µM) and PD (Mek inhibitor, PD0325901, 1µM), as indicated in the title of each sample

extract_protocol:
Cells were lysed and total RNA was extracted with the RNAeasy kit from Qiagen according to manufactorer's instructions
Library were constructed from 1µg of polyA RNA using Illumina protocols

treatment_protocol: Rex1GFPd2 cells were derived and expanded for 6 passages in 2i, then cells were expanded in the indicated conditions for 5 additional passages. Cells were splitted every 3 days at a density of 15,000 cells/cm^2 and fresh medium was provided daily.

tag: cell line

tag: passage number

tag: condition

value: LIF+PD


title: Spleen of PPVL rat 1 (P1)


title: 184281 (control)


title: CRC-62

value: left


title: CRC-57

value: post-operative


title: CRC-53

value: right


title: CH+LIF rep1

value: CH+LIF


title: CH+LIF rep2


title: 2i rep1


title: CRC-52

value: colon cancer

value: blood


title: CRC-51


title: 184279 (case)

value: fetal alcohol spectrum disorder


title: CRC-58


title: 2i+LIF rep2


title: 184276 (control)


title: 184275 (case)


title: 184273 (case)


title: 2i rep2


title: 184274 (control)


title: 2i+LIF rep1


title: 184270 (case)


title: 184271 (case)


title: 184277 (case)


title: 184269 (case)


title: 184266 (case)


title: Spleen of PPVL rat 3 (P5)

value: spleen

value: Sprague-Dawley


title: 184265 (case)

value: Male


title: 184267 (case)

value: saliva


title: CRC-49

value: male


title: 184263 (case)


title: CRC-46

value: rectal cancer


title: CRC-42

value: female


title: CRC-37


title: CRC-39


title: CRC-40


title: CRC-45


title: CRC-47


title: 184261 (case)


title: 184260 (case)


title: CRC-32


title: 184258 (case)

value: Female


title: CRC-30


title: CRC-25


title: 184262 (case)


title: CRC-26


title: 184257 (case)


title: CRC-24


title: 184256 (case)


title: 184255 (case)


title: CRC-23


title: CRC-38


title: 184252 (case)


title: 184254 (case)


title: CRC-21

value: biopsy


title: 184251 (case)


title: 184250 (case)


title: 184248 (case)


title: 184247 (control)

value: control


title: CRC-20


title: CRC-17


title: CRC-16

value: left


title: P01_unstim_all_beta

tag: cmv status

value: positive

tag: cmv peptide

tag: cell subpopulation

value: unsorted

value: 0 (ex vivo)


title: CRC-13

value: post-operative


title: CRC-12

value: colon cancer

value: blood


title: 184246 (case)

value: fetal alcohol spectrum disorder


title: 184245 (case)


title: CRC-10


title: Sedentary_Subject10

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: Arrays were hybridized with 10 ug cRNA, except for sample S13 which was hybridized with 6.90 ug cRNA. After injection, HG U133 Plus 2.0 arrays were hybridized for 16 hours at 45C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with user-prepared reagents.

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000 system from Affymetrix.

data_processing: Data were analyzed using Robust Multi-Array Average (RMA).

source_name: Sedentary

label_protocol: Simultaneous cRNA synthesis and biotin labeling via 3' IVT protocol

extract_protocol: Standard Affymetrix Protocol

tag: Sex

tag: pre pmax (w)

tag: post pmax (w)

tag: perc increase in pmax

tag: pre vo2max

tag: post vo2max

tag: perc increase in vo2max


title: Sedentary_Subject9


title: 184284 (control)

tag: gender

tag: status

tag: tissue


title: Sedentary_Subject8


title: CRC-8

tag: age

tag: tumor location

value: right

tag: specimen type

tag: tissue origin


title: LIF+PD rep2

tag: cell line

tag: strain

tag: passage number

tag: condition

value: LIF+PD


title: Sedentary_Subject7

tag: Sex

value: Male

tag: pre pmax (w)


title: Sedentary_Subject6

tag: post pmax (w)

tag: perc increase in pmax


title: DB_Rep (assay v2.1)

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString.com) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer's instructions.  For each assay, a high-density scan (600 fields of view) was performed

data_processing: The analysis of raw data was performed with nSlover Analysis Software provided by NanoString Technologies. The raw data were normalized using quantile algorithm and log2

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Trizol according to manufacture's instructions

value: DB


title: DOHH2_Rep (assay v2.1)


title: TS (assay v2.1)

source_name: TS

value: TS


title: REC1_8H_OTX

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.). The data were normalised using quantile method.

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA extraction was performed using a commercially available reagent (TRIzol, Thermo Fisher Scientific, Waltham, MA) according to the manufactures’ recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

tag: cell type

value: mantle cell lymphoma cell line

tag: treated with

value: BET Bromodomain inhibitor OTX015 (MK-8628)

tag: time point


title: MM1S (assay v2.1)


title: RPMI_8226 (assay v2.1)


title: Sedentary_Subject5

tag: pre vo2max

tag: post vo2max

tag: perc increase in vo2max


title: Sedentary_Subject4


title: Sedentary_Subject3


title: U_266 (assay v2.1)


title: REC1_8H_DMSO

value: DMSO (vehicle control)


title: REC1_4H_OTX


title: REC1_4H_DMSO


title: Sedentary_Subject2


title: REC1_2H_OTX


title: REC1_2H_DMSO


title: SU_DHL1 (assay v2.1)


title: SUPM2 (assay v2.1)


title: REC1_24H_OTX


title: Exercise_Subject9

source_name: Exercise


title: Exercise_Subject10


title: Exercise_Subject7


title: REC1_24H_DMSO


title: Exercise_Subject8


title: MAC_1 (assay v2.1)


title: KI_JK (assay v2.1)

value: KI-JK


title: L82 (assay v2.1)


title: Karpas_299 (assay v2.1)


title: JB6 (assay v2.1)


title: FE_PD (assay v2.1)

value: FE-PD


title: SSK41 (assay v2.1)


title: Exercise_Subject6


title: Sedentary_Subject1


title: TMD8 (assay v2.1)


title: WSU_DLCL2 (assay v2.1)


title: MAVER1_2H_DMSO


title: VL51 (assay v2.1)


title: Exercise_Subject3


title: REC1_12H_OTX


title: REC1_12H_DMSO


title: MAVER1_8H_OTX


title: Exercise_Subject2


title: MAVER1_4H_DMSO


title: MAVER1_4H_OTX


title: MAVER1_2H_OTX


title: Exercise_Subject4


title: Exercise_Subject1


title: MAVER1_8H_DMSO


title: MAVER1_24H_DMSO


title: VAL (assay v2.1)

source_name: VAL

value: VAL


title: MAVER1_24H_OTX


title: Exercise_Subject5


title: U_2932 (assay v2.1)


title: SU_DHL_8 (assay v2.1)


title: SU_DHL_7 (assay v2.1)


title: SU_DHL_6 (assay v2.1)


title: C2_AQ1_2uM_4

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

data_processing:
Illumina Sequencing by HiSeq4000
Sequenced reads were trimmed for adaptor sequence, then mapped to either GRCh38 or CanFam3.1 reference genome using HISAT2 v.2.0.5
Uniquely-mapped reads aligned to exons were counted with HTSeq v.0.6.1, then tested for the presence of DEGs by the DESeq2 R package v.1.14.1
Genome_build: GRCh38 or CanFam3.1
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each Sample

organism: Canis lupus familiaris

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1% penicillin/streptomycin (Gibco, Thermo Scientific, Waltham, USA). The C2 culture medium was supplemented with 1 mM sodium pyruvate.

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit (Qiagen Italia, Milano, Italy).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded in 6-well plates (9x105 cells/well) and treated with two doses of AQ1 (1 µM and 2 µM) for 12 hours. For each experiment, we included also untreated and DMSO-treated cells. Five different experiments were conducted for each cell line.

value: Adult

value: Dog-derived mast cell tumor

tag: passages

tag: treatment

value: 2uM G-quadruplex-biding ligand AQ1


title: SU_DHL_4 (assay v2.1)


title: SU_DHL_5 (assay v2.1)


title: normal_post surgery_patient3_3

city: odense

first: mads

last: thomassen

address: soender boulevard 29

country: Denmark

institute: odense university hospital

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: Robust multi-array average expression measure (rma) [7] was applied to perform background correction, quantile normalization, and expression index calculation of all microarrays. Only perfect match probes were used for data analysis

source_name: normal_post surgery_3

label_protocol: MessageAmpTM III RNA amplification kit

extract_protocol: RNeasy Micro kit (Qiagen)

treatment_protocol: liquid nitrogen

tag: gender

value: female

tag: tissue

value: breast

tag: patient number

tag: disease status

value: normal


title: normal_post surgery_patient3_2

source_name: normal_post surgery_2


title: SU_DHL_2 (assay v2.1)

tag: cell line


title: C2_AQ1_2uM_3


title: tumor_pre surgery_patient3

source_name: tumor_pre surgery

value: tumor


title: normal_pre surgery_patient3

source_name: normal_pre surgery


title: MAVER1_12H_OTX


title: tumor_post surgery_patient3

source_name: tumor_post surgery


title: C2_AQ1_2uM_2


title: JEKO1_4H_OTX


title: JEKO1_4H_DMSO


title: normal_post surgery_patient2_3


title: SU_DHL_10 (assay v2.1)


title: C2_AQ1_2uM_1


title: RIVA (assay v2.1)

source_name: RIVA

value: RIVA


title: Rec_1 (assay v2.1)


title: RCK8 (assay v2.1)


title: tumor_post surgery_patient2


title: C2_AQ1_1uM_3

value: 1uM G-quadruplex-biding ligand AQ1


title: C2_AQ1_1uM_4


title: JEKO1_2H_DMSO


title: C2_AQ1_1uM_2


title: C2_AQ1_1uM_1


title: JEKO1_8H_OTX


title: OCI_Ly7 (assay v2.1)


title: JEKO1_8H_DMSO


title: normal_post surgery_patient2_1

source_name: normal_post surgery_1


title: normal_pre surgery_patient1


title: JEKO1_12H_OTX


title: JEKO1_24H_DMSO


title: JEKO1_24H_OTX


title: normal_post surgery_patient2_2


title: tumor_post surgery_patient1


title: tumor_pre surgery_patient2


title: GRANTA519_8H_DMSO


title: normal_post surgery_patient1_2


title: normal_pre surgery_patient2


title: JEKO1_2H_OTX


title: OCI_Ly3 (assay v2.1)


title: normal_post surgery_patient1_3


title: JEKO1_12H_DMSO


title: GRANTA519_4H_OTX


title: tumor_pre surgery_patient1


title: C2_DMSO_2

value: DMSO


title: OCI_Ly2 (assay v2.1)


title: OCI_Ly19 (assay v2.1)


title: C2_DMSO_3


title: OCI_Ly18 (assay v2.1)


title: C2_CTRL_4


title: OCI_LY1_DMSO_4hrs, Sample_15 (assay V3A)

tag: time


title: OCI_LY1_OTX015_4hrs, Sample_16 (assay V3A)


title: C2_DMSO_1


title: normal_post surgery_patient1_1


title: OCI_LY1_OTX015_24hrs, Sample_14 (assay V3A)


title: GRANTA519_2H_OTX


title: GRANTA519_2H_DMSO


title: GRANTA519_4H_DMSO


title: OCI_LY1_DMSO_24hrs, Sample_13 (assay V3A)


title: C2_CTRL_3


title: Karpas_1718 (assay v2.1)


title: Karpas_422 (assay v2.1)


title: C2_CTRL_2


title: C2_CTRL_1


title: HBL1_OTX015_4hrs, Sample_12 (assay V3A)


title: HBL1_OTX015_24hrs, Sample_11 (assay V3A)


title: JVM-2 (assay v2.1)


title: HBL1_DMSO_4hrs, Sample_10 (assay V3A)


title: Granta_519 (assay v2.1)

value: Granta 519


title: MAVER_1 (assay v2.1)


title: GRANTA519_12H_OTX

value: mantle cell lymphoma cell line


title: Jeko_1 (assay v2.1)


title: OCI_LY1_OTX015_24hrs, Sample_7 (assay V3A)


title: HBL_1 (assay v2.1)


title: OCI_LY1_OTX015_4hrs, Sample_8 (assay V3A)


title: OCI_LY1_DMSO_4hrs, Sample_6 (assay V3A)


title: GRANTA519_24H_DMSO


title: GRANTA519_12H_DMSO


title: DOHH2 (assay v2.1)


title: OCI_Ly10 (assay v2.1)


title: OCI_LY1_DMSO_24hrs, Sample_5 (assay V3A)


title: GRANTA519_24H_OTX

value: BET Bromodomain inhibitor OTX015 (MK-8628)


title: HBL1_OTX015_24hrs, Sample_3 (assay V3A)


title: HBL1_DMSO_24hrs, Sample_9 (assay V3A)


title: MEC_1 (assay v2.1)

value: MEC 1


title: OCI_Ly1 (assay v2.1)


title: HBL1_DMSO_4hrs, Sample_2 (assay V3A)


title: HBL1_DMSO_24hrs, Sample_1 (assay V3A)


title: MAVER1_12H_DMSO

value: DMSO (vehicle control)


title: DB (assay v2.1)

source_name: DB

value: DB


title: HBL1_OTX015_4hrs, Sample_4 (assay V3A)


title: normal_post surgery_patient3_1


title: CH34(delta rpoQ,R) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 2

status: Public on Nov 20 2018

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

hyb_protocol: Hybridisation was done by the service provider IMGM Laboratories GmbH (Martinsried)

scan_protocol: Agilent DNA microarray Scanner were used by the service provider IMGM Laboratories GmbH (Martinsried)

data_processing: The mean intensity of the pixels of the surrounding area was subtracted from the mean density of the pixels of the spots to give the signal strength

organism: Cupriavidus metallidurans

source_name: cells

label_protocol: Labeling was done by the service provider IMGM Laboratories GmbH (Martinsried)

growth_protocol: C. metallidurans strains were grown in Mineral salts medium + 0.2 % Na-gluconate to a cell turbidity of 100 Klett, 30 µM metal mix was added and after 10 min  cells were harvest by centrifugation for 1' at RT in 2.0 ml tubes.

extract_protocol: RNeasy Plus Kit (Qiagen) was used according to the manufacturers manual including on-column DNase digestion. PCR were done to check for DNA contaminations, only RNA was used that did not generate products in the PCR reaction. RNA quality was checked on formamide gels and measured as RIN on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: 30 µM metal mix was added at a cell turbitity of 100 Klett for 10 min

tag: genotype/variation

value: CH34(delta rpoQ,R)


title: CH34(delta rpoQ,R) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 3


title: CH34(delta rpoP,E,cnrH) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 2

value: CH34(delta rpoP,E,cnrH)


title: CH34(delta rpoP,E,cnrH) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 1


title: CH34(delta rpoP,E,cnrH) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 3


title: CH34 with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 2


title: CH34 without


title: CH34(delta rpoQ,R) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 1


title: CH34 with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 3


title: CH34(delta rpoL,M,O) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 3

value: CH34(delta rpoL,M,O)


title: CH34(delta rpoI,J,K) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 3

value: CH34(delta rpoI,J,K)


title: CH34(delta rpoI,J,K) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 1


title: CH34(delta rpoL,M,O) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 1


title: CH34(delta rpoI,J,K) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 2


title: CH34 with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 1


title: CH34(delta rpoL,M,O) with 30 µM metal mix (Co,Ni,Zn,Cd,Cu), replicate 2


title: OCI_Ly8 (assay v2.1)


title: PAA085 CD16n

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

hyb_protocol: High quality RNA was reverse transcribed and hybridized on Affymetrix HuGene 2.0 ST microarrays

scan_protocol: Standard Affymetrix scanning protocol

data_processing: RMA normalization using R/Bioconductor oligo package

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol performed by the Génome Québec Innovation Centre (Montreal, Qc, Canada).

growth_protocol: Monocyte subsets were differentiated into immature dendritic cells (DC) (MDDC, monocyte-derived DC) by culture in the presence of GM-CSF and IL-4 (20 ng/ml (R&D Systems) in RPMI media with 2% FBS for six days. Media containing cytokines was refreshed every two days

extract_protocol: Total RNA was isolated using RNeasy columns kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were collected by leukapheresis and cryopreserved until use.

tag: stimulation

value: HIV

tag: donor


title: PAA080 CD16p

value: Media


title: PAA082 CD16p


title: PAA106 CD16p


title: PAA084 CD16n

value: LPS


title: PAA105 CD16p


title: PAA103 CD16n


title: PAA101 CD16n


title: PAA099 CD16p


title: PAA083 CD16n


title: PAA081 CD16p


title: PAA104 CD16p


title: PAA102 CD16n


title: PAA079 CD16n


title: PAA094 CD16p


title: PAA093 CD16p


title: PAA088 CD16p


title: PAA087 CD16p


title: PAA098 CD16p


title: PAA097 CD16n


title: PAA078 CD16n


title: PAA089 CD16n


title: PAA091 CD16n


title: PAA096 CD16n


title: GRANTA519_8H_OTX

tag: cell type


title: PAA100 CD16p


title: PAA090 CD16n


title: PAA092 CD16p


title: PAA095 CD16n


title: PAA077 CD16n


title: PAA086 CD16p


title: C2_DMSO_4

value: Adult

value: Dog-derived mast cell tumor


title: IL17HC36RH

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Gene expression data from PBMC samples obtained from Healthy controls

hyb_protocol: hybridized to Affymetrix HG U133+ PM GeneChips following standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw microarray gene expression data was normalized using RMA in R and subjected to several quality control procedures. Differentially expressed genes were identified using a linear modelling approach in the limma package in R and only genes with FDR corrected p-values < 0.05 for multiple testing (using the Benjamini-Hochberg method) were considered significant.

label_protocol: standard Affymetrix protocol; RNA was isolated and reverse transcribed into cDNA using a High Capacity cDNA Reverse Transcription Kit with random hexamers. RT-qPCR was performed for each gene target in duplicate using Taqman Universal PCR Master Mix, No AmpErase UNG on 7900HT Fast Real-Time PCR System. GAPDH was used as a normalizer to obtain fold changes and t-tests were performed to determine significance. Thermal cycling conditions were 95˚C for 10 minutes followed by 40 cycles of 95˚C for 15 seconds and 60˚C for 1 minute.

growth_protocol: sample collection: Lung samples were obtained by hypertonic-saline sputum induction, bronchoscopy, bronchoalveolar lavage and endobronchial epithelial brushing as previously described (Hinks et al., 2015).

extract_protocol: RNA was isolated from the samples using the Absolutely RNA Nanoprep Kit. RNA quality was assessed using a Bioanalyzer 2100 and samples were hybridized to Affymetrix HG U133+ PM GeneChips

tag: disease state

value: Healthy controls

value: PBMC

value: Male

tag: age


title: IL17SA18LL

description: Gene expression data from PBMC samples obtained from Severe asthma

value: Severe asthma

value: Female


title: IL17SA13ER


title: IL17SA20HC


title: IL17HC02HW


title: IL17HC20MD


title: IL17HC42SA


title: IL17HC16BB


title: IL17SA12RH


title: IL17HC24HT


title: IL17HC15TW


title: IL17SA19KG


title: IL17SA07SW


title: IL17HC12TJ


title: IL17HC08IB


title: IL17SA06WS


title: IL17HC09SM


title: IL17HC17TH


title: IL17SA16TH


title: IL17SA04AS


title: IL17HC14KA


title: HT1912011248_MCF712h_COL20

city: Macau

first: Edwin

last: Cheung

address: Avenida da Universidade,Taipa

department: faculty of health sciences

institute: University of Macau

data_processing:
For processing the HT samples, demultiplexing was performed using Fluidigm’s HT Demultiplexer Perl script (available on series record).
cell barcode is included in the R1 reads.
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: MCF7_HT_fpkm.txt: tab-delimited text files include FPKM values for each single cell
Supplementary_files_format_and_content: HT_barcodes.txt: tab-delimited text files include cell barcodes
Supplementary_files_format_and_content: demultiplex_perl_script.tar: tar archive contains perl script files include Fluidigm’s HT Demultiplexer Perl script

molecule: polyA RNA

growth_protocol: MCF-7 ERα-positive human breast cancer cell lines were obtained from ATCC and maintained in DMEM and RPMI 1640 media (Gibco), respectively. Both media were supplemented with 5 % fetal bovine serum (FBS) (Gibco) and grown in a 37°C incubator with 5% CO2.

extract_protocol: Nextera XT Index Kit v2 (96 Indices, 384 Samples) is used for C1-HT.

treatment_protocol: Three days prior to E2 stimulation, MCF-7 cells were transferred into phenol-red free DMEM/F12 and RPMI media (Gibco), respectively. Both media were supplemented with 5 % charcoal/dextran-stripped FBS (Hyclone). Cells were then stained with CellTracker Green CMFDA or Orange CMTMR (Molecular Probes) 24 h before drug treatment. Stained cells were treated with either ethanol (vehicle) or E2 at 2 time points (0 and 12 h), before being dissociated and triturated into single-cell suspensions for single-cell analyses.

value: breast


title: HT1912011248_MCF712h_COL19