title: RNA-seq_brain_biologicalRep1


title: stomach_normal_rep6

status: Public on Jun 10 2019

type: RNA

city: Xuzhou

first: Li

last: Li

state: Jiangsu

address: No. 99 West Huaihai Road, Xuzhou, Jiangsu 221002, P.R. China.

country: China

institute: the Affiliated Hospital of Xuzhou Medical University

description: Gene expression data from human normal stomach tissue

hyb_protocol: GeneChip Hybridization Wash and Stain Kit

scan_protocol: GeneChip Scanner 3000

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human normal stomach tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: gender

value: male


title: MeDIP-seq-M-input

type: SRA

city: Hangzhou

first: Yichen

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

department: College of Medicine

institute: Zhejiang University

library_source: genomic

data_processing:
After sequencing images generated, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Human genome (UCSC HG19) using HISAT2 software (V2.1.0).
Aligned reads were used for peak calling of the MeDIP regions using MACS V2, statistically significant MeDIP enriched regions (peaks) were identified for each sample at a q-value threshold of 10-5 using MACS v2. LncRNAs, mRNAs and Small ncRNAs associated MeDIP enriched regions (peaks) were annotated by the nearest gene using the newest UCSC RefSeq database.
Statistically significant differentially methylated regions (DMRs) between two groups promoters were identified by diffReps (Cut-off: log2FC=1.0, p-value=10-4).
Genome_build: hg19
Supplementary_files_format_and_content: The signal profiles in UCSC binary wig file format were generated from MeDIP-seq data, which can be visualized in UCSC Genome Broswer.

molecule: genomic DNA

source_name: liver

growth_protocol: HepG2 cells were seeded in 6-well plates

extract_protocol:
Genomic DNA was isolated from cancer cells by using the AllPrep® DNA/RNA Mini Kit (Qiagen, Germany).
Purified genomic DNA was sonicated to obtain fragments with a size range of 200-500 bp for MeDIP-seq. Following end repair of the DNA samples with the addition of deoxyadenosine and adaptor ligation based on the Illumina paired-end protocol, the DNA fragments were immunoprecipitated with anti-5-methylcytosine antibody. Then, the precipitated fragments were amplified by PCR, and 300-600 bp DNA fragments were selected by using AMPure XP beads. The completed libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on an Illumina flow cell, an amplified in situ.

treatment_protocol: HepG2 cells were cocultured with MenSC cells via transwell co-culture system.

tag: cell type

value: hepatocellular carcinoma cell

tag: tissue

value: liver

tag: cell line

tag: antibody

tag: genotype/variation

value: MenSC therapy


title: NET-CAGE_mouse_kidney_biologicalRep2_technicalRep3

city: Yokohama

first: Shruti

last: Bhagat

state: Kanagawa

address: W424, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Center for Integrative Medical Sciences

country: Japan

institute: RIKEN, Yokohama

library_source: transcriptomic

data_processing:
Library strategy: RNA-seq (CAGE)
For all our datasets we performed the following steps, (i) split reads by barcode, (ii) trimmed reads to remove barcode sequences and (iii) removed reads aligned to rRNA sequences (Human: GenBank U13369.1; Mouse: GenBank BK000964.3). These steps were performed using MOIRAI (Hasegawa et al., 2014) for human cell line data and using Trimmomatic v 0.36 (Bolger et al., 2014) and MOIRAI (Hasegawa et al., 2014) for mouse tissue data. For all CAGE based data and mouse RNA-seq data, sequences with base ‘N’ were also removed.
Non rRNA reads were mapped hg19 genome and human reference gene model Gencode v27lift37 comprehensive using  STAR v 2.5.0a with the following parameters for indexing: --runThreadN 12 --runMode genomeGenerate --genomeDir genome.fa --sjdbGTFfile Gencodeannotation.gtf and the following parameters for mapping: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --out FilterMultimapNmax 1 --readFilesCommand zcat.
Transcription start sites for CAGE based data were identified using bedtools v 2.2.25 (Quinlan and Hall, 2010) as described here: http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment
Genome_build: Human: hg19 and Mouse:mm9
Supplementary_files_format_and_content: Bed 6 file for trasncription start sites. Scores represent aggregated tags with same starting position.

organism: Mus musculus

source_name: Kidney

growth_protocol: MCF-7, HeLa-S3 and HepG2 cells were cultured at 37 ˚C under 5% CO2 in DMEM with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS. GM12878 and K562 cells were cultured at 37 ˚C under 5% CO2 in RPMI 1640 with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS.

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Frozen mouse tissue samples were used for total and nascent RNA extraction. Tissue was homogenized using PowerMasherII (FUJIFILM Wako Pure Chemical). The sample was transferred to BioMasherV (FUJIFILM Wako Pure Chemical) tube and added with pre-chilled 2 ml of Buffer C (Nuclei PURE Lysis Buffer (Sigma-Aldrich), 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution, 20 units of SUPERase IN RNase Inhibitor, 1 mM DTT, Triton X-100). 200 μL of the tissue lysate was sampled and mixed with 700 μL of QIAzol for total RNA extraction.
We added 2 ml of ice-cold Buffer D (10 ml of Sucrose Cushion solution (Sigma-Aldrich), 1.2 ml of Sucrose Cushion buffer (Sigma-Aldrich) and 11.2 μL of 1M DTT) to the bottom of a conical centrifuge tube on ice. Tissue lysate prepared above was gently mixed with 3.6 ml of Buffer D, and was carefully and slowly layered on top of the 2 ml of Buffer D in the conical centrifuge tube. Then, the tube was centrifuged at 13,000 G for 45 minutes at 4 ˚C to collect nuclei pellets. The pellets were washed once with 500 μL of Buffer C.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).

treatment_protocol: For the time course experiment, MCF-7 cells were serum-starved for 16 hours, and heregulin beta-1 was added to the medium at a final concentration of 10 nM. Cells were harvested at 0 (no treatment), 15, 30, 45, 60, 120, 180 and 360 minutes in triplicates.

value: kidney

tag: urea treatment

tag: strain

tag: age

value: 8 weeks

tag: molecule subtype

value: Nascent RNA


title: MeDIP-seq-C-input

value: control


title: MeDIP-seq-M5


title: MeDIP-seq-M3


title: NET-CAGE_mouse_kidney_biologicalRep2_technicalRep2


title: NET-CAGE_mouse_kidney_biologicalRep2_technicalRep1


title: MeDIP-seq-C5


title: NET-CAGE_mouse_kidney_biologicalRep1_technicalRep3

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Frozen mouse tissue samples were used for total and nascent RNA extraction. Tissue was homogenized using gentleMACS Dissociator (Miltenyi Biotec).  The sample was transferred to gentleMACS M tube (Miltenyi Biotec) and added with pre-chilled 2 ml of Buffer C (Nuclei PURE Lysis Buffer (Sigma-Aldrich), 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution, 20 units of SUPERase IN RNase Inhibitor, 1 mM DTT, Triton X-100). Lysate was then filtered through gentleMACS SmartStrainers (100 μm) (Miltenyi Biotec). 200 μL of the tissue lysate was sampled and mixed with 700 μL of QIAzol for total RNA extraction.
We added 2 ml of ice-cold Buffer D (10 ml of Sucrose Cushion solution (Sigma-Aldrich), 1.2 ml of Sucrose Cushion buffer (Sigma-Aldrich) and 11.2 μL of 1M DTT) to the bottom of a conical centrifuge tube on ice. Tissue lysate prepared above was gently mixed with 3.6 ml of Buffer D, and was carefully and slowly layered on top of the 2 ml of Buffer D in the conical centrifuge tube. Then, the tube was centrifuged at 13,000 G for 45 minutes at 4 ˚C to collect nuclei pellets. The pellets were washed once with 500 μL of Buffer C.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).


title: NET-CAGE_mouse_kidney_biologicalRep1_technicalRep2


title: septic shock patient 046 [granulocytes]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description:
S_A_046
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

source_name: peripheral granulocytes from septic shock patient on ICU admission

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

growth_protocol: Blood was collected in S-Monovette® K3E tubes (Sarstedt, Nümbrecht, Germany) by venipuncture with presurgical patients and from a central venous catheter with ICU patients.

extract_protocol: Total RNA was purified from isolated granulocytes stored in RNAlater® (Ambion) using the miRVana miRNA isolation kit (Applied Biosystems).

treatment_protocol: Granulocytes were prepared from 2 mL blood by positive selection (StraightFrom™ Whole Blood CD15 MicroBeads, Miltenyi Biotec).

tag: diagnosis

value: septic shock

value: peripheral granulocytes


title: presurgical patient 003 [granulocytes]

description:
S_B_003
Gene expression data from peripheral granulocytes of presurgical patient.

source_name: peripheral granulocytes from presurgical patient

value: presurgical


title: septic shock patient 034 [granulocytes]

description:
S_A_034
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: septic shock patient 035 [granulocytes]

description:
S_A_035
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: septic shock patient 045 [granulocytes]

description:
S_A_045
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: NET-CAGE_mouse_kidney_biologicalRep1_technicalRep1


title: stomach_normal_rep3


title: stomach_normal_rep5


title: septic shock patient 020 [granulocytes]

description:
S_A_020
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: septic shock patient 021 [granulocytes]

description:
S_A_021
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: stomach_normal_rep2


title: MeDIP-seq-C3


title: stomach_normal_rep1

value: female


title: septic shock patient 018 [granulocytes]

description:
S_A_018
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: gastric_tumor_rep14

description: Gene expression data from human gastric tumor

source_name: human gastric tumor


title: MeDIP-seq-M2


title: MeDIP-seq-C2


title: Poxn mutant rep3

city: New Haven

first: Zhe

last: He

state: CT

address: Carlson Lab / KBT 1142 Dept. of Molecular, Cellular, and Developmental Biology Yale University P.O. Box 208103

department: Molecular, Cellular and Developmental Biology

country: USA

institute: Yale University

data_processing:
Trim Galore! (0.4.0) was used to perform quality control and adapter trimming on the raw reads.
STAR (2.4.2a) was then used to align reads to the D. melanogaster genome (FlyBase release r6.09)
The differential analysis was performed using Htseq and DESeq2.
Genome_build: FlyBase release r6.09
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each sample; csv file from DESeq2 includes normalized abundance measurements.

organism: Drosophila melanogaster

source_name: Wing

extract_protocol:
The wings from w1118 Canton-S and poxn flies aged 3 days were hand-dissected and frozen immediately in liquid nitrogen. Three independent replicates were collected per genotype, each replicate containing 8000 wings, from 4000 flies. RNA extraction was performed using an RNeasy Mini Kit (QIAGEN 74104) with on-column DNase treatment (QIAGEN 79254).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wing

value: 3 days after eclosion

tag: genotype/strain

value: Poxn 70


title: Poxn mutant rep2


title: NET-CAGE_mouse_brain_biologicalRep1_technicalRep2

source_name: Brain

value: brain


title: NET-CAGE_mouse_brain_biologicalRep1_technicalRep1


title: septic shock patient 019 [granulocytes]

description:
S_A_019
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: stomach_normal_rep4


title: septic shock patient 011 [granulocytes]

description:
S_A_011
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: gastric_tumor_rep13


title: CAGE_mouse_kidney_biologicalRep2_technicalRep3

value: Total RNA


title: gastric_tumor_rep15

value: male


title: gastric_tumor_rep11


title: NET-CAGE_mouse_brain_biologicalRep1_technicalRep3


title: CAGE_mouse_kidney_biologicalRep2_technicalRep2


title: gastric_tumor_rep10


title: septic shock patient 010 [granulocytes]

description:
S_A_010
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: gastric_tumor_rep12


title: Poxn mutant rep1


title: w1118 rep3

value: w1118 Canton-S


title: w1118 rep2


title: CAGE_mouse_kidney_biologicalRep1_technicalRep3


title: CAGE_mouse_kidney_biologicalRep2_technicalRep1


title: septic shock patient 008 [granulocytes]

description:
S_A_008
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: septic shock patient 007 [granulocytes]

description:
S_A_007
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: septic shock patient 013 [granulocytes]

description:
S_A_013
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: gastric_tumor_rep9


title: gastric_tumor_rep8


title: w1118 rep1


title: 10X_HDLEC

city: Edinburgh

first: Ian

middle: R

last: McCracken

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

description: Custom paired end, all reads informatiive. Read lengths: Read 1 = 26bp, Read 2 = 98bp, i7 index = 8bp

data_processing:
Raw reads were processed using the 10X Cell Ranger pipeline v2.1.1 ( 10X Genomics) in order to perform read alignment, filtering, barcode and UMI (unique molecular identifier) counting, and subsequently generate gene-cell matrices.
Genome_build: GRCh38

source_name: human dermal lymphatic endothelial cell

growth_protocol: HDLECs (Heidelberg, Germany) maintained with Endothelial Cell Media MV2 (PromoCell, Heidelberg, Germany) supplemented with Penicillin-Streptomycin (P/S) (100 U/ml) (Gibco, Penicillin-Streptomycin (P/S) (100 U/ml) (Gibco, Paisley, UK). Cells harvested using 1X Trypsin-EDTA.

extract_protocol: Construction of single cell RNA-sequencing libraries was conducted using the Single Cell 3' Reagent Kit (10X Genomics, Pleasanton, USA) in accordance with the manufacturer’s protocol.

value: HDLEC

tag: passage number


title: septic shock patient 002 [granulocytes]

description:
S_A_002
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: CAGE_mouse_kidney_biologicalRep1_technicalRep1


title: 10X_five_factor_protocol_day4

source_name: hESC derived cells from day4 of five factor differentiation protocol

growth_protocol: hES cells differentiatied to human embryonic stem cell derived endothelial product (hESC-ECP) using five factor differentiation protocol from Zhang et al., PNAS, 2017. Cells detached at day 4 using TrypLE Express Enzyme (Thermo Fisher Scientific, Waltham, USA).


title: gastric_tumor_rep7


title: septic shock patient 001 [granulocytes]

description:
S_A_001
Gene expression data from peripheral granulocytes of septic shock patient on ICU admission.


title: 10X_five_factor_protocol_day6

source_name: hESC derived cells from day6 of five factor differentiation protocol

growth_protocol: hES cells differentiatied to human embryonic stem cell derived endothelial product (hESC-ECP) using five factor differentiation protocol from Zhang et al., PNAS, 2017. Cells detached at day 6 using TrypLE Express Enzyme (Thermo Fisher Scientific, Waltham, USA).


title: CAGE_mouse_brain_biologicalRep1_technicalRep3


title: 10X_five_factor_protocol_day2

source_name: hESC derived cells from day2 of five factor differentiation protocol

growth_protocol: hES cells differentiatied to human embryonic stem cell derived endothelial product (hESC-ECP) using five factor differentiation protocol from Zhang et al., PNAS, 2017. Cells detached at day 2 using TrypLE Express Enzyme (Thermo Fisher Scientific, Waltham, USA).


title: CAGE_mouse_brain_biologicalRep1_technicalRep2


title: gastric_tumor_rep5


title: 10X_day_8_RC11

source_name: hESC derived cells from day8 of hESC-ECP differentiation protocol

growth_protocol: hES cells differentiatied to human embryonic stem cell derived endothelial product (hESC-ECP) using differentiation protocol from MacAskill et al.,Molecular Therapy, 2018. Cells detached at day 8 using TrypLE Express Enzyme (Thermo Fisher Scientific, Waltham, USA).


title: gastric_tumor_rep6


title: CAGE_mouse_brain_biologicalRep1_technicalRep1


title: CAGE_mouse_kidney_biologicalRep1_technicalRep2


title: Pv3

city: Lisbon

first: Henrique

last: Silveira

address: Rua da Junqueira, 100

department: Global Health and Tropical Medicine

country: Portugal

institute: Instituto de Higiene e Medicina Tropical, IHMT, UNL

data_processing:
Illumina reads were checked for quality control using FastQC v0.11.5 and analysed using Trinity platform for de novo transcriptome assembly v2.4.0.
Trimmomatic was used to trim low-quality reads and high quality paired-end reads were assembled using Trinity Assembler and aligned using Bowtie2 v2.3.2.
Transcript quantification was performed using RSEM module v1.2.25.
Genome_build: Trinity_aquasalis.fasta (available on the series record)
Supplementary_files_format_and_content: tab-delimited matrix file include raw counts for each Sample

organism: Anopheles aquasalis

source_name: midguts

extract_protocol:
Mosquito midguts were collected from mosquitoes submerged in ice-cold PBS and transferred to RNAlater (Ambion). RNA was harvested using Trizol reagent and treated with RNase-Free DNase I (Qiagen). RNA integrity was confirmed using 2100 Bioanalyzer (Agilent) and total RNA was used for library preparation and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A. aquasalis mosquitoes  were: i) membrane-fed on P. vivax infected blood, ii) membrane-fed on blood with inactivated gametocytes or iii) fed on 10 % sugar solution.

value: 3-5 days old adult

tag: Sex

value: midguts

tag: treatment

value: P. vivax-blood fed mosquitoes

tag: time-point

value: 18-24h after meal


title: Pv2


title: 10X_day_6_RC11

source_name: hESC derived cells from day6 of hESC-ECP differentiation protocol

growth_protocol: hES cells differentiatied to human embryonic stem cell derived endothelial product (hESC-ECP) using differentiation protocol from MacAskill et al.,Molecular Therapy, 2018. Cells detached at day 6 using TrypLE Express Enzyme (Thermo Fisher Scientific, Waltham, USA).


title: LSF_ChIPseq [LSF+ Input_di-nucleosome]

city: Ipswich

first: HANG GYEONG

middle: GYEONG

last: CHIN

state: MA

address: 240 County Road, NEB

department: Research

institute: New England Biolabs, Inc

description: LSF+ Input_di-nucleosome

data_processing:
Basecalls performed using CASAVA version 1.4. BWA was used for mapping reads to the human reference genome (hg19). Before running MACS for peak calling, the mapping quality of the mapped reads was checked and reads of low mapping quality (MAPQ) were discarded to reduce potential noise in peak calling.
A data-driven cut-off of MAPQ was determined for discerning reads of hight and quality (The distribution of MAPQ was used to select a cut off); summary statistics of mapping were collected. We selected MAPQ of 20 as a cut off for reads of high quality, and discarded reads with score below 20.
After quality control (QC), the sequence depth ranged over (18M-24M). Each IP and its matched Input are also balanced in sequence depth. Peaks were called using MACS.
The maximum cross correlation between + and - reads was computed to estimate the correct DNA fragment size of each library. MACS was specifically run to identify peaks using the DNA fragment sizes of mono and di-nucleosome data sets.
A p-value cut-off of 10E-5 was used to select significant peaks.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TDF files were generated using the igvtools package.
Supplementary_files_format_and_content: BED file was generated that is a tab-delimited text file that defines a feature track.

growth_protocol: The HEK293T-derived, stable cell line was grown in DMEM media containing 10% FBS.

extract_protocol:
The cells harvested following the ChIP procedure using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology). Chromatin was immunoprecipitated with HA antibody (Abcam 9110) and was captured by Protein A magnetic beads. Cross-links were reversed, and DNA was purified, separating the mono- versus di-nucleosome sized DNA fragments.
50 ng of ChIP-ed DNA were used for the DNA library preparation using the NEBNext Ultra II DNA library Prep Kit for Illumina (NEB E76745S).

treatment_protocol: The cells were grown in DMEM media containing 5 uM RSL1 ligand for 24 hr at 37 degrees C.

value: HA-tagged LSF

tag: inducer

tag: chip antibody

value: Anti-HA tag, ChIP grade (Abcam ab9110)

tag: nucleosome structure

value: di-nucleosome


title: 10X_day_4_RC11

source_name: hESC derived cells from day4 of hESC-ECP differentiation protocol

growth_protocol: hES cells differentiatied to human embryonic stem cell derived endothelial product (hESC-ECP) using differentiation protocol from MacAskill et al.,Molecular Therapy, 2018. Cells detached at day 4 using TrypLE Express Enzyme (Thermo Fisher Scientific, Waltham, USA).


title: LSF_ChIPseq [LSF+ IP_di-nucleosome]

description: LSF+ IP_di-nucleosome


title: LSF_ChIPseq [LSF- Input_di-nucleosome]

description: LSF- Input_di-nucleosome

value: DMSO


title: Pv1

value: female

tag: tissue


title: 10X_day_12_H9

source_name: hESC derived cells from day12 of hESC-ECP differentiation protocol

growth_protocol: hES cells differentiatied to human embryonic stem cell derived endothelial product (hESC-ECP) using differentiation protocol from MacAskill et al.,Molecular Therapy, 2018. Cells detached at day 12 using TrypLE Express Enzyme (Thermo Fisher Scientific, Waltham, USA).

tag: cell line


title: Bl3

value: Non-infected blood-fed mosquitoes


title: gastric_tumor_rep4

tag: gender


title: 10X_day_8_H9_rep3


title: Ob_liver_chow_7w_3

city: Tsukuba

first: Tetsuya

last: Okuda

state: Ibaraki

address: Central6, 1-1-1, Higashi

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description:
Gene expression after 7 weeks regular chow feeding of mouse liver
CLV3

hyb_protocol: The Cy3-labelled cRNA (0.6 μg) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1× Agilent fragmentation buffer and 2 × Agilent blocking agent, added 25 μl of 2 × Agilent hybridization buffer, and hybridized to SurePrint G3 Mouse GE v2 8×60K Microarray (Agilent Technologies) for 17 hours at 65 °C in a rotating Agilent hybridization oven.

scan_protocol: After hybridization, the microarray slide was washed 1 minute at room temperature with Agilent GE Wash Buffer 1 and 1 minute with 37 °C Agilent GE Wash buffer 2, and scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8×60K array slides (Scan Area 61 × 21.6 mm, Scan resolution 3 μm, Dye channel is set to Green PMT 100 %).

data_processing:
The scanned images were analyzed with Agilent Feature Extraction Software 12.0.3.1 using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method.

source_name: liver, 7w, regular chow

label_protocol: Cy3-labeled cRNA was prepared from 0.1 μg total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated using NucleoSpin® RNA Midi (MACHEREY-NAGEL, Duren, Germany) from tissues.

value: liver

value: 12 weeks

value: regular chow


title: Ob_liver_LCKD_7w_3

description:
Gene expression after 7 weeks LCKD feeding of mouse liver
KLV3

source_name: liver, 7w, LCKD

value: LCKD


title: Ob_cortex_chow_7w_3

description:
Gene expression after 7 weeks regular chow feeding of mouse cerebral cortex
CBR_6

source_name: cerebral cortex, 7w, regular chow

value: cerebral cortex


title: gastric_tumor_rep1


title: Ob_liver_LCKD_7w_2

description:
Gene expression after 7 weeks LCKD feeding of mouse liver
KLV_2


title: gastric_tumor_rep2

value: male


title: LSF_ChIPseq [LSF- IP_di-nucleosome]

description: LSF- IP_di-nucleosome

tag: genotype/variation


title: Ob_cortex_LCKD_chow_7w_3

description:
Gene expression after 7 weeks LCKD feeding of mouse cerebral cortex
KBR_5

source_name: cerebral cortex, 7w, LCKD


title: gastric_tumor_rep3


title: Ob_liver_LCKD_7w_1

description:
Gene expression after 7 weeks LCKD feeding of mouse liver
KLV_1


title: 10X_day_8_H9_rep1


title: LSF_ChIPseq [LSF+ Input_mono]

description: LSF+ Input_mono

value: mono-nucleosome


title: Bl2

value: 3-5 days old adult


title: Bl1

value: midguts


title: LSF_ChIPseq [LSF+ IP_mono]

description: LSF+ IP_mono


title: Unf3

value: Sugar-fed mosquitoes


title: LSF_ChIPseq [LSF- Input_mono]

description: LSF- Input_mono


title: 10X_day_6_H9


title: 10X_day_4_H9


title: 10X_day_0_H9

source_name: human embryonic stem cell (hESC)

growth_protocol: hESC maintained on vitronectin matrix (Life Technologies, Paisley, UK) with StemPro hESC media (Life Technologies, Paisley, UK) detached using StemPro Accutase (Life Technologies, Paisley, UK) for scRNA-seq prior to commencing endothelial differentiation.


title: Unf2

description:
R1: intact raw data has been lost (missing 001.fastq.gz and 004.fastq.gz files due to invalid compression data)
R2: intact raw data has been lost (missing 003.fastq.gz and 006.fastq.gz files due to invalid compression data)

value: 18-24h after meal


title: LSF_ChIPseq [LSF- IP_mono]

description: LSF- IP_mono

value: HA-tagged LSF


title: TAIL-seq exp #2 fly embryo

status: Public on Jun 09 2019

city: Daejeon

first: Young-suk

last: Lee

address: 1113 CMS(E16), 291 Daehak-ro, Yuseong-gu,

department: Department of Bio and Brain Engineering

country: South Korea

institute: KAIST

description: TAIL-seq for activated egg(0-2hr), set #2

data_processing:
The base calls and signal intensities were processed by Illumina RTA 1.17.21.3 for HiSeq 2500, or RTA 1.17.28 for MiSeq. The read 1 sequences were reanalyzed for more sensitive basecalling using AYB 2. The read 1 sequences were aligned to the common contaminants set, which is composed of rDNA repeat units (GenBank accession U13369.1), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences, and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP 2013-03-31 with maximum 5% mismatches allowed. Clusters with any match to the contaminants were removed from the subsequent analyses. The sequences having completely identical nucleotides in the 21st to 35th cycle in read 1 (representative region of the insert) and the 1st to 15th cycle in read 2 (degenerate bases in 3' adapter) are deduplicated by leaving only a cluster with the maximum PHRED quality sum of read 1. The degenerate and fixed delimiter sequence in 3' adapter was clipped out from read 2 by searching perfect match of delimiter sequence ("GTCAG" as in the direction of read 2) between the 14th and 16th cycles in read 2. The clusters missing a delimiter sequence or having low diversity in degenerate region (at least two occurrences for all of A, C, G and T) were removed from further analyses.
The fluorescence signal intensities were processed into "Relative T signal" as described in our previous paper (Chang et al, 2014b). The signals from a spike-in sample were purified with an outlier filter based on robust Mahalanobis distance (mvoutlier package 1.9.9; quan=0.5, alpha=0.025). Random 500 clusters per each spike-in were chosen for parameter calculation of a Gaussian mixture hidden Markov model (GMHMM). We trained the model using Baum-Welch algorithm implemented in the GHMM library (http://ghmm.org) with topology and initial parameters shown in fig. S1A and table S7 and S8 (1,000 iterations). The procedure was iterated to maximize likelihood, not using any property (eg. designed length of poly(A) tail) of spike-ins. Relative T signals outside the range of [-5, 5] were clipped into the range for both training and later calculations.
The length of poly(A) tails were first measured with base call-based "Strategy II" described in fig. S1A. For clusters with the measured length is shorter than 8 nt, the length is called as the final poly(A) tail length. For the others, normalized T signals starting from the first position in T-stretch detected by Strategy II were analyzed with the GMHMM. The hidden states were decoded with the standard Viterbi algorithm implemented in the GHMM library. The number of cycles with state 1 and 2 was called as the length of poly(A) tail. For the estimation of performance, we applied the process to all spike-in samples except the clusters used for the parameter fitting of the model.
The remaining reads after contaminant filter and the first duplication filters were then aligned to the genome sequences (UCSC hg19, positions of splicing junctions were processed from the UCSC Genome Browser database for version of Jan 24, 2013) using GSNAP 2013-03-31. Three different versions of alignments to genome were used in this study. (1) R1 alignment: using only the full read 1 sequences which are 51 nt long. This was used for identification of a cluster. (2) R2 short alignment: using only 40 nt right next to the 3' adapter of read 2. This was used in searching for the poly(A)-free 3' hydroxyl ends. (3) paired alignment: using the full read 1 sequences and part of read 2 sequences trimmed of degenerate bases and delimiter. We filtered out poly(A) stretches encoded from genome using this alignment set. All the alignments were performed with maximum mismatches of 5%, minimum mapping quality of 3. All multi-mapped reads were removed. The remaining PCR artifacts with few mismatches were removed again using the R1 alignment with 15 degenerate bases inside the 3' adapter region. To detect that kind of artifacts, we clustered the R1 alignments with maximum distance between mapped positions of 10 bp, they were then clustered again within the first cluster using degenerate bases from read 2 of respective reads with CD-HIT-EST 4.5.4 (word size=6, sequence identity=0.85). For a set of detected duplicates, we chose a read with maximum sum of PHRED quality in read 1 to leave.
For classification and transcript-level analyses, we compiled reference annotations for human and mouse using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The R1 alignments were annotated with intersection with the compiled annotations using BEDTools {Quinlan, 2010 #66}. When multiple annotations were overlapped to an alignment, we chose a class for the statistics requiring exclusive assignment of a genomic source type by the following priority: miRNA, rRNA, tRNA, Mt-tRNA, snoRNA, scRNA, srpRNA, snRNA, lncRNA, RNA, ncRNA, misc_RNA, Cis-reg, ribozyme, RC, IRES, frameshift_element, LINE, SINE, Simple_repeat, Low_complexity, Satellite, DNA, LTR, CDS, 3' UTR, 5" UTR, intron, Other, Unknown (higher priority first). The transcript-level analyses were performed using our custom non-redundant RefSeq (nrRefSeq) transcript set, which is a reduced set retaining only the longest isoform or transcript when regions overlap with each other. The positions of read 1 in nrRefSeq transcripts were positioned with BEDTools intersection between alignments to genome sequences and nrRefSeq annotation set, and then translated to the transcript-level coordination with in-house software.
As poly(A) tails were initially detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3' end modification of poly(A) tails was limited to the last 30 nucleotides of insert. To exclude A stretches obviously encoded from genomic sequence (with or without 3' end modifications), we masked detected poly(A) tail ranges with read 2 alignments so that the 3'-most position of alignable (not clipped) is eliminated from poly(A) tail or its 3' end modifications. All statistics regarding transcript-level modification rates were calculated for transcripts having more than 200 tags with poly(A) tails longer than 8 nt.
Genome_build: hg19/hg38
Supplementary_files_format_and_content: The untemplated-nd file is an output file of tailseeker 1 with the untemplated tail informtion of the RNA fragment. The first two columns represent the tile and cluster id of the fragment; the forth column is the refseq id; and the last column is the untemplated tail sequence. The all.txt, mapped.txt and association.txt file are output files of tailseeker3 with the untemplated tail informtion of the RNA fragment. The first two columns represent the tile and cluster id of the RNA fragment. The third column of the association.txt file is the ensembl gene id. The sixth column of the all.txt and mapped.txt file is the estimated poly(A) tail length and the last column is the untemplated tail sequence. The mapped.txt file only contains RNA fragments from all.txt that are mapped to the genome.

source_name: Drosophila embryo

growth_protocol: HeLa cells were maintained in DMEM (Welgene) supplemented with  10% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted from HeLa cells by TRIzol reagent (Invitrogen, 15596-018) and purified by RNeasy MinElute column (Qiagen, 74204) according to manufacturer’s instruction.
TAIL-seq was carried out as described previously (Chang et al., 2014b). Briefly, 25-50  ug of total RNAs (>200 nt) were extracted by TRIzol (Invitrogen), purified by RNeasy  MinElute column (Qiagen), and rRNA-depleted by using Ribo-zero kit (Epicentre). The  RNAs were ligated to the biotinylated 3′ adaptor, and partially digested by RNase T1.  The fragmented RNAs were pull-downed with streptavidin beads, phosphorylated at the  5′ end, and gel purified (500-1000 nt). The purified RNAs were ligated to the 5′ adaptor, reverse-transcribed, and amplified by PCR.

treatment_protocol: HeLa cells were transfected twice with 40 nM of siRNAs using  Lipofectamine 3000 (Invitrogen). A mixture of 2-4 different siRNAs was used  to knockdown each gene. In combinatorial knockdown, we mixed siRNA pools to have a  final concentration of 40 nM.

tag: cell type

tag: development stage

value: 0-2hr after egg laying (AEL)


title: Long-term PD rep4

city: Guangzhou

first: Meijun

last: Si

state: Guangdong

address: 600 Tianhe Ave.

department: Nephrology

institute: The 3rd Affiliated Hospital of Sun Yat-sen University

data_processing:
Cell Ranger Single Cell Software Suite (v3.0) was used for quality controlling, sample demultiplexing, barcode processing and single cell 3’ gene counting. Original base calling files were demultiplexed into FASTQ data using the bcl2fastq Conversion Software.
After quality controlling by FastQC software, the data was aligned with the nucleotide sequence database using the Basic Local Alignment Search Tool (BLAST).Then reads were mapped to the GRCh38 human transcriptome using STAR with default parameters.
The gene barcode matrix was generated using only valid barcodes and reliable mapped non-PCR repeats of UMI.
To compare scRNA-seq data between different libraries, the gene-cell-barcode matrix of each sample was normalized by subsampling reads from higher-depth libraries until they have an equal number of confidently mapped reads per cell. The Cell Ranger aggr pipeline was used for equalizing the read depth between libraries before merging in order to avoid the batch effect introduced by sequencing depth when combining data from multiple samples.
The gene-cell-barcode matrix from each sample was normalized towards the grand median UMI counts per cell by a scaling factor (computed as median_reads_per_barcode/reads_per_barcode). The matrix is log-transformed then mean-centered and scaled per-gene.  For each cell, we quantified the number of expressed genes and the proportion of the transcript counts derived from mitochondrial genes.
Any cell with less than 200 genes or more than 30% of mitochondrial UMI counts was filtered out. Finally, the resulting expression matrix was filtered to remove genes detected in <3 cells. We focused on highly variable genes for principal component analysis (PCA). For each dataset, we used the Seurat R package to detect variable genes based on fitting a relationship between the mean and the dispersion of each gene as an input for PCA.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include the normalized gene-cell-barcode expression matrix  for each sample and combined analysis

source_name: Peritoneal dialysis fluid

extract_protocol:
About 10,000 cells were loaded to each channel and then partitioned into Gel Beads in emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, fragmentation and 5’ adaptor and sample index attachment.
1μl of sample was diluted 1:10 and ran on the Agilent Bioanalyzer High Sensitivity chip for qualitative analysis. Libraries were sequenced on an Illumina HiSeq4000 (Illumina) using a custom paired-end sequencing mode (26 bp for read 1 and 98 bp for read 2).
Single cells were processed through the Chromium Single Cell 3’ Solution platform using the Chromium Single Cell 3’ Gel Bead, Chip and Library Kits (10X Genomics) following the manufacturer’s protocol.

tag: sample type

value: Peritoneal cells from effluent of long-term PD patients


title: Long-term PD rep3


title: Long-term PD rep2


title: Ob_cortex_LCKD_chow_7w_2

description:
Gene expression after 7 weeks LCKD feeding of mouse cerebral cortex
KBR_2

tag: age

tag: strain


title: HC rep3

source_name: Peritoneal tissue

value: Cells dissociated from normal peritoneum


title: Ob_liver_chow_7w_2

description:
Gene expression after 7 weeks regular chow feeding of mouse liver
CLV_2

value: female


title: Ob_cortex_chow_7w_1

description:
Gene expression after 7 weeks regular chow feeding of mouse cerebral cortex
CBR_1


title: Short-term PD rep4

value: Peritoneal cells from effluent of short-term PD patients


title: Short-term PD rep5


title: Short-term PD rep6


title: Ob_cortex_LCKD_chow_7w_1

description:
Gene expression after 7 weeks LCKD feeding of mouse cerebral cortex
KBR_1


title: Short-term PD rep3


title: Ob_liver_chow_7w_1

description:
Gene expression after 7 weeks regular chow feeding of mouse liver
CLV_1

value: liver


title: Ob_cortex_chow_7w_2

description:
Gene expression after 7 weeks regular chow feeding of mouse cerebral cortex
CBR_2

value: 12 weeks


title: Short-term PD rep1


title: Unf1


title: Long-term PD rep1


title: HC rep1


title: HC rep2


title: Short-term PD rep2


title: DE52NGSUKBR102833: Donor 3

city: Bonn

first: Florian

last: Hoss

address: Sigmund-Freud-Str. 196

department: Institute of Innate Immunity

institute: University Clinics, University of Bonn

data_processing:
Reads were aligned to the human genome (build GRCh38/hg38) using STAR aligner (Dobin et al., 2013) with default settings and transcript annotations from Ensembl GRCh38.90
Transcript abundances for all samples were quantified using Kallisto (Bray et al., 2016) with default settings
Transcript abundances were summarized to gene level abundances using the tximport Bioconductor Package (Soneson et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including tpm values per gene for each sample, generated with tximport package.

source_name: Monocyte derived Macrophages

growth_protocol: PBMCs were isolated from blood from healthy donors, monocytes were CD14 selected and differentiated with GM-CSF into macrophages

extract_protocol:
RNeasy MiniKit (Quiagen)
SENSE mNRA-Seq Library Kit V2 (Lexogen)

treatment_protocol: LPS priming 3h 2 ng/ ml

value: human monocyte derived macrophages

tag: differentiation treatment

value: GM-CSF


title: DE79NGSUKBR102832: Donor 5


title: DE63NGSUKBR102829: Donor 4


title: DE36NGSUKBR102830: Donor 2


title: DE09NGSUKBR102831: Donor 1


title: TAIL-seq exp #8 siTUT3/5 (siTENT4A/B) siRNA2

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) knockdown HeLa cells, different siRNA, set #8

source_name: HeLa

value: human cervical cancer cell line

value: HeLa

tag: condition

value: TUT3 (TENT4B) and TUT5 (TENT4A)


title: TAIL-seq exp #7 siCont

description: TAIL-seq for control knockdown HeLa cells, set #7

value: control knockdown


title: undifferentiated PFX#9 hiPSC ReproFF2/n

city: Kobe

first: Takako

last: Yamamoto

address: Minatojima-minamimachi

institute: foundation for biomedical Research and Innovation at Kobe

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45oC, 60 rpm on Gene Chip Human Genome U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: PFX#9 hiPSC

label_protocol: biotin

growth_protocol: on-Feeder: Cells were cultured and maintained on mitomycin C-treated SNL76/7 cells (SIM strain embryonic fibroblast, ECACC; European Collection of Cell Culture) with hESC culture media containing 20% knockout serum replacement (KSR; Life Technologies, Carlsbad, CA, USA), 200 mM L-glutamine , 1% non-essential amino acids , 0.1 mM 2-mercaptoethanol  and 4 ng/mL basic fibroblast growth factor .   Feeder-free: Cells were  cultured with culture medium Essential 8 , Stem-Partner® SF or Ripro FF2  on rhVitronectin-N (VTN-N, Thermo Fisher Scientific)-coated dish.   EB: Cells cultured on VTN-N coated well with 4mL of Es8 were scraped off with a cell scraper , dissociated by pipetting, transferred into a low attachment 6-well plate  and cultured with Essential 6 (Es6) with 10uM rock inhibitor for one day and with Es6 alone for 13 days for EB formation.

extract_protocol: Total RNA was extracted with the RNeasy Mini kit, according to manufacturer’s instructions.

value: human induced pluripotent stem cells


title: TAIL-seq exp #6 siTUT3/5 (siTENT4A/B)

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) knockdown HFF cells, set #6

source_name: HFF

value: human foreskin fibroblast cell line

value: HFF


title: undifferentiated H9 hESC Es8/n

source_name: H9 hESC

value: human embryonic stem cells


title: undifferentiated PFX#9 hiPSC Es8/n


title: differentiated H9 hESC Es8/n


title: undifferentiated KhES-1 hESC SPM/n

source_name: KhES-1 hESC


title: TAIL-seq exp #6 siCont

description: TAIL-seq for control knockdown HFF cells, set #6


title: undifferentiated KhES-1 hESC Es8/n


title: TAIL-seq exp #8 siCont siRNA2

description: TAIL-seq for control knockdown HeLa cells, different siRNA, set #8


title: TAIL-seq exp #8 siTUT3/5 (siTENT4A/B)

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) knockdown HeLa cells, set #8


title: undifferentiated PFX#9 hESC SPM/n


title: undifferentiated KhES-1 hESC ReproFF2/n


title: TAIL-seq exp #8 siCont

description: TAIL-seq for control knockdown HeLa cells, set #8


title: differentiated KhES-1 hESC Es8/n


title: differentiated PFX#9 hiPSC Es8/n


title: undifferentiated H9 hESC on-Feeder


title: undifferentiated KhES-1 hESC on-Feeder


title: TAIL-seq exp #5 siTUT3/5 (siTENT4A/B)

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) knockdown HFF cells, set #5


title: undifferentiated PFX#9 hiPSC on-Feeder


title: TAIL-seq exp #5 siCont

description: TAIL-seq for control knockdown HFF cells, set #5


title: TAIL-seq exp #4 siTUT3/5 (siTENT4A/B)

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) knockdown HeLa cells, set #4


title: TAIL-seq exp #4 siMTR4

description: TAIL-seq for MTR4 knockdown HeLa cells, set #4

value: MTR4 knockdown


title: TAIL-seq exp #4 siCont

description: TAIL-seq for control knockdown HeLa cells, set #4


title: TAIL-seq exp #3 siCont

description: TAIL-seq for control knockdown HeLa cells, set #3


title: TAIL-seq exp #3 vector

description: TAIL-seq for vector overexpression HeLa cells, set #3

value: vector overexpression


title: TAIL-seq exp #3 siTUT3/5 (siTENT4A/B)

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) knockdown HeLa cells, set #3


title: TAIL-seq exp #3 siTUT3/5 (siTENT4A/B) siRNA2

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) knockdown HeLa cells, different siRNA, set #3


title: TAIL-seq exp #3 FLTUT5 (FLTENT4A)

description: TAIL-seq for TUT5 (TENT4A) overexpression HeLa cells, set #3

value: TUT5 (TENT4A) overexpression


title: TAIL-seq exp #3 siTUT1/6

description: TAIL-seq for TUT1 and TUT6 knockdown HeLa cells, set #3

value: TUT1 and TUT6 knockdown


title: TAIL-seq exp #3 FLTUT3/5 (FLTENT4A/B)

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) overexpression HeLa cells, set #3


title: TAIL-seq exp #1 siTUT3/5 (siTENT4A/B)

description: TAIL-seq for TUT3 (TENT4B) and TUT5 (TENT4A) knockdown HeLa cells, set #1


title: RNA-seq siTUT3/5 siRNA2

description: rRNA-depleted RNA-seq

data_processing:
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow.
Illumina reads were mapped to the hg38 genome using Bowtie 2 with default options
Transcript (i.e. gene) quantification was based on non-redundant RefSeq using RSEM with fragment mean length 200 and standard deviation length 100
Genome_build: hg38
Supplementary_files_format_and_content: a tab-delimited file including gene identifier, transcript identifiers, length, expected count, TPM, FPKM

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM (Welgene) containing 10% FBS (Welgene)

extract_protocol:
Total RNA was extracted by using TRIzol (Invitrogen) and the quality check was done by Agilent 2100 Bioanalyzer.
RNA- seq libraries were constructed using TruSeq stranded total RNA library prep kit (Illumina) and sequenced in Illumina Nextseq 500 v2 to yield single-end 76nt reads.

treatment_protocol: For plasmid transfection, HeLa cells were transfected with Lipofectamine 3000 reagent (Thermo) or Metafectene reagent (Biontex). For knockdown, HeLa cells were transfected twice with 40 nM siRNAs by Lipofectamine 3000 during 4 days. For combinatorial knockdown, equal amount of siRNAs against each gene was mixed to have a final concentration of 40 nM.

value: TUT3/5 siRNA treated


title: TAIL-seq exp #1 siTUT5 (siTENT4A)

description: TAIL-seq for TUT5 (TENT4A) knockdown HeLa cells, set #1

value: TUT5 (TENT4A) knockdown


title: RNA-seq siTUT3/5 siRNA1

description: rRNA-depleted RNA-seq


title: RNA-seq siCont siRNA1

description: rRNA-depleted RNA-seq

value: Negative control siRNA treated


title: RNA-seq siCont siRNA2

description: rRNA-depleted RNA-seq


title: TNP_25_524_8B_Embryo

status: Public on Jun 08 2019

city: RTP

first: Thomas

last: Knudsen

state: North Carolina

address: 109 T.W. Alexander Drive

institute: U.S. EPA

data_processing:
Preprocessing of the sequence reads including adapter read clipping was conducted using tools developed by Expression Analysis.
Process sequenced reads were aligned to the Rattus norvegicus genome rn5.
The RNA-Seq by Expectation Maximum (RSEM) pipeline (Version 1.1.13) was used to estimate the read abundance across all samples.
Differential gene expression was determined using EBSeq (Version 1.4.1). The RSEM gene counts were used as input with upper quartile normalization and a false discovery rate (FDR) threshold of 0.05. Genes were considered differentially expressed with a posterior probability (PPDE) greater than 0.95.
Genome_build: rn5
Supplementary_files_format_and_content: Processed data files are text files containing unfiltered read counts.

organism: Rattus norvegicus

source_name: rat whole embryo proper

extract_protocol:
Embryos or visceral yolk sacs were placed in 500 ul RNAlater (Ambion) for total RNA extraction using standard methods.
The RNA was prepared for sequencing using the Tru Seq™ Sample Preparation Kit (Illumina, Part #15026486) according to the manufacturer’s protocols. For each sample, 500 ng of total RNA was used to prepare the cDNA libraries. RNA Seq libraries were sequenced for 50‐bp pair-end reads on an Illumina HiSeq 2000 using the TruSeq SBS Kit (Illumina, Version #3) by IQVIA Institute for Human Data Science, formerly Expression Analysis, Inc. (RTP, NC, USA).

value: embryo

tag: chemical

tag: concentration (µm)

tag: timepoint


title: TNP_25_524_8A_Embryo


title: TNP_25_524_4_AB_YS

source_name: rat visceral yolk sac

value: visceral yolk sac


title: TNP_25_524_7_AB_YS


title: TNP_25_524_7A_Embryo


title: TNP_25_524_7B_Embryo


title: TNP_25_524_4A_Embryo


title: TNP_25_524_8_AB_YS


title: TNP_25_524_3A_Embryo


title: TNP_25_524_3_AB_YS


title: TNP_25_524_3B_Embryo


title: TAIL-seq exp #3 FLTUT3 (FLTENT4B)

description: TAIL-seq for TUT3 (TENT4B) overexpression HeLa cells, set #3

value: human cervical cancer cell line

value: TUT3 (TENT4B) overexpression


title: TNP_25_523_8B_Embryo


title: TNP_25_524_4B_Embryo


title: TNP_25_523_8A_Embryo


title: TNP_25_523_7B_Embryo


title: TAIL-seq exp #1 siTUT3 (siTENT4B)

description: TAIL-seq for TUT3 (TENT4B) knockdown HeLa cells, set #1

value: HeLa

value: TUT3 (TENT4B) knockdown


title: TNP_25_523_4B_Embryo


title: TNP_25_523_7_AB_YS


title: TAIL-seq exp #1 siCont

description: TAIL-seq for control knockdown HeLa cells, set #1

value: control knockdown


title: TNP_25_523_8_AB_YS


title: TNP_25_523_4A_Embryo


title: TNP_25_523_4_AB_YS


title: TNP_25_523_3B_Embryo


title: TNP_25_523_3A_Embryo


title: TNP_25_523_3_AB_YS


title: TNP_2_5_524_6B_Embryo


title: TNP_25_523_7A_Embryo


title: TNP_2_5_524_6A_Embryo


title: TNP_2_5_524_5B_Embryo


title: TNP_2_5_524_5A_Embryo


title: TNP_2_5_523_6A_Embryo


title: TNP_2_5_523_5A_Embryo


title: TNP_2_5_524_5_AB_YS


title: TNP_2_5_523_5B_Embryo


title: TNP_2_5_523_6_AB_YS


title: TNP_2_5_523_6B_Embryo


title: HPP_5_524_9A_Embryo


title: HPP_5_524_9B_Embryo


title: HPP_5_524_9_AB_YS


title: TNP_2_5_523_5_AB_YS


title: HPP_5_524_10B_Embryo


title: HPP_5_523_10A_Embryo


title: HPP_5_523_9B_Embryo


title: HPP_5_523_9A_Embryo


title: HPP_5_523_9_AB_YS


title: HPP_5_524_10_AB_YS


title: HPP_30_524_14A_Embryo


title: HPP_30_524_13B_Embryo


title: HPP_30_524_14_AB_YS


title: HPP_5_523_10_AB_YS


title: HPP_5_523_10B_Embryo


title: HPP_30_524_13_AB_YS


title: Dex_CDGHDM 6

city: Reno

first: William

middle: T

last: Gerthoffer

state: Nevada

address: 1440 N Virginia St

department: Pharmacology

institute: University of Nevada, Reno

description:
ribosome-depleted
Dexamethasone treated 6

data_processing:
Sequencing adapters were trimmed and bases identifified with Illumina Casava 1.9 base calling software
Fastq files were analyzed with Sailfish-cir (Li et al., Bioinformatics 2017 15:33(14):2131-2139)
Normalized abundance (TPM) was calculated for linear RNA transcripts and circularRNAs according to Li et al., 2017
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt file including TPM for each transcript in each sample

source_name: lung

extract_protocol:
Lung lobes stored in RNALater solution were weighed (~25-30 mgs) and minced into 2-3 mm pieces. Total RNA was extracted with QIAzol Lysis Reagent (Qiagen, 1023537) using Zirconia beads (Biospec,11079110ZX) and a Mini-Bead Beater16™.  Total RNA, including microRNA, was isolated using a Qiagen miRNEasy kit (#217004). Three methods were used to determine RNA concentration and RNA quality -  spectrophotometry of total RNA (NanoDrop 1000), gel filtration of RNA integrity (RNA 6000 Nano Kit, Agilent 2100 Bioanalyzer), and fluorescent dye binding (Quant-iT RiboGreen Kit, Invitrogen55).  RNA quality determined by A260/280 ranged from 1.8 to 2.2, A260/230 >2 and RIN values ranged from 6.9 to 8.6.
Initial RNA quantification was performed with a Qubit RNA assay kit, followed by RIN determination with an Agilent 2100 Bioanalyzer. cDNA libraries were prepared using 2 micrograms of total RNA for ribosomal reduction, directional RNA-seq, paried-end, 150 nucleotide. Final quantification was performed with a Kapa Library Quant kit. Stranded cDNA libraries were sequenced using an Illunina HiSeq 25000 instrument (HiSeq v4 reagents) at read depth of 100M reads/sample.
Ribosome reduction, stranded, 100 nt paired-end RNA-seq

treatment_protocol: Allergic sensitization of the lungs was elicited with house dust mite extract and the mucosal adjuvant cyclic di-GMP according to Raundahl et al. (J Clin Invest 2015 125(8): 3037-50). AntimiR-155-treated mice received 3 doses of 2 mg/kg, i.v. antisense miR-155 oligonucleotide complexed with TheraSilence lipid nanoparticles on days 11, 18 and 25. Dexamethasone-treated mice recieved 3 doses of 3 mg/kg, i.p. on days 11, 18 and 25 of the 35d protocol.

tag: treatment

value: Dexamethasone-treated; house dust mite extract and mucosal adjuvant cyclic di-GMP sensitized

value: BALB/c AnNHsd

value: lung, left lobe

value: 87 days


title: Dex_CDGHDM 5

description:
ribosome-depleted
Dexamethasone treated 5


title: HPP_30_523_14B_Embryo


title: HPP_5_524_10A_Embryo


title: HPP_30_523_14A_Embryo


title: HPP_30_523_13B_Embryo


title: Dex_CDGHDM 4

description:
ribosome-depleted
Dexamethasone treated 4


title: Dex_CDGHDM 3

description:
ribosome-depleted
Dexamethasone treated 3


title: AM155 11

description:
ribosome-depleted
AntimiR-155 treated 6


title: Dex_CDGHDM 1

description:
ribosome-depleted
Dexamethasone treated 1


title: Dex_CDGHDM 2

description:
ribosome-depleted
Dexamethasone treated 2


title: HPP_30_523_13A_Embryo


title: HPP_30_523_13_AB_YS


title: HPP_30_523_14_AB_YS


title: AM155 8

description:
ribosome-depleted
AntimiR-155 treated 5


title: HPP_15_524_12B_Embryo


title: HPP_30_524_13A_Embryo


title: AM155 5

description:
ribosome-depleted
AntimiR-155 treated 3


title: HPP_15_524_12_AB_YS


title: AM155 3

description:
ribosome-depleted
AntimiR-155 treated 2


title: HPP_15_524_11A_Embryo


title: HPP_15_524_12A_Embryo


title: HPP_30_524_14B_Embryo


title: AM155 6

description:
ribosome-depleted
AntimiR-155 treated 4


title: AM155 2

description:
ribosome-depleted
AntimiR-155 treated 1


title: HPP_15_524_11B_Embryo


title: CDG_HDM 13

description:
ribosome-depleted
CDG_HDM sensitized 10

value: house dust mite extract and mucosal adjuvant cyclic di-GMP sensitized


title: HPP_15_524_11_AB_YS


title: RNA-Seq CX3CL1-ct_6

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm10 using TopHat2.0. The TopHat program uses high-throughput short read aligner Bowtie to align the reads to the reference genome. Differential expression test was performed using CUFFDIFF module of CUFFLINKS pipeline with adjusted p-value <0.05 as significance cutoff. ENSEMBL gene annotation was used for gene quantification.
Genome_build: mm10
Supplementary_files_format_and_content: Text table format for FPKM values.

source_name: hippocampus

growth_protocol: Tg-CX3CL1-ct mice were generated in the Animal Resource Center of Case Western Reserve University and were backcrossed with C57BL/6J mice for 6 generations before crossing with CaMKIIα-tTA mice purchased from Jackson Lab. Mice were housed in designated animal rooms at 23°C on a 12 h light/dark cycle with food and water available ad libitum. Tg-CX3CL1-ct and CaMKIIα-tTA mice were set for breeding. At P4, the littermate pups of WT, CaMKIIα-tTA and Tg-CX3CL1-ct/tTA were sacrificed and the brain tissues were collected.

extract_protocol:
Once the mice were ready to be sacrificed for tissue extraction, the mice underwent a sacrifice and the head was cooled in liquid nitrogen. The brain was then dissected to isolate the hippocampus region and homogenize it in a Trizol lysis buffer. The homogenized hippocampus tissue was then kept on ice until all samples were ready to be processed for the next step. After homogenizing all hippocampi, the samples were processed by using Qiagen RNeasy Microarray Tissue Mini Kit to extract the total RNA according to the protocol in the handbook. Next, the total RNA integrity and quality were assessed using a BioAnalyzer (Agilent) at the Lerner Research Institute Core Facility.
The transcriptome sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA sample preparation kit (San Diego, CA) according to the manufacturer’s instructions.  Briefly, a minimum of 100 nanograms of high quality total RNA (with RIN >= 7.0) was used to begin the ribosomal RNA deplete (verified using BioAnalyzer RNA nanochip), followed by RNA fragmentation, first and second strand cDNA synthesis, fragment end-repair, adaptor ligation, and purification.  Each sequencing library was tagged with a 6 nucleotide long barcode that identifies from which sample a sequence was derived.  All sequencing libraries were quantified on a Qubit fluorometer before equal molar amounts of each library are pooled for sequencing.  Cluster generation of the purified sequencing libraries was done on the cBot using the TruSeq PE Cluster Kit v4.  The sequencing was performed with the TruSeq SBS Kit (2x100 cycles, paired end) on the Illumina HiSeq 2500 (Illumina, Inc., San Diego, CA, USA).

tag: sample group


title: RNA-Seq CX3CL1-ct_5


title: HPP_15_523_12B_Embryo


title: RNA-Seq CX3CL1-ct_4


title: CDG_HDM 7

description:
ribosome-depleted
CDG_HDM sensitized 9


title: CDG_HDM 10

description:
ribosome-depleted
CDG_HDM sensitized 8


title: RNA-Seq CX3CL1-ct_3


title: HPP_15_523_12_AB_YS


title: RNA-Seq CX3CL1-ct_2


title: CDG_HDM 4

description:
ribosome-depleted
CDG_HDM sensitized 7


title: HPP_15_523_12A_Embryo


title: CDG_HDM 14

description:
ribosome-depleted
CDG_HDM sensitized 6


title: RNA-Seq CAMK_2

value: CAMK


title: RNA-Seq CAMK_3


title: RNA-Seq WT_2

value: WT


title: RNA-Seq WT_3


title: RNA-Seq CX3CL1-ct_1


title: CDG_HDM 9

description:
ribosome-depleted
CDG_HDM sensitized 4


title: CDG_HDM 12

description:
ribosome-depleted
CDG_HDM sensitized 5


title: RNA-Seq CAMK_1


title: HPP_15_523_11A_Embryo


title: HPP_15_523_11B_Embryo


title: CDG_HDM 8

description:
ribosome-depleted
CDG_HDM sensitized 3


title: P091_Biopsy3

type: genomic

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

description:
DNA extracted from placenta tissue.
NewBiopsies_PsychArray-24v1.3.txt

hyb_protocol: According to the manual of Infinium II Assay (Illumina, USA).

scan_protocol: The scanning of the bead-chips was performed on an iScan, using the iScan Control software (Illumina, USA)

data_processing:
The genotypes, B allele frequencies and LogR values were processed by the Genotyping module of GenomeStudio software. We subsequently fed these data into siCHILD algorithm, which is equipted with haplarithmisis (Zamani Esteki et al. 2015, AJHG).
Image data was analyzed using Genomestudio with genotyping module (Illumina).

source_name: Placenta tissue

label_protocol: The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 labelling by extension, according to the manual of Infinium II Assay (Illumina, USA).

extract_protocol: A total of 9 mL of peripheral venous blood from parents and 4 mL of umbilical cord blood were collected into ethylenediaminetetraacetic acid-containing tubes (BD Vacutainer, Becton, Dickinson and Co) for DNA extraction. DNA was isolated from blood and the placental tissue using PureLinkÂ® Genomic DNA Kit (Invitrogen, Life Technologiesâ¢) according to manufacturerâs protocol. DNA samples were eluted with 200 ÂµL of PureLinkÂ® Genomic Elution Buffer (10 mM Tris-HCl, pH 9.0, 0.1 mM EDTA) and stored at -20 Â°C until analysis. NanoDrop 2000 (Thermo Fisher Scientific Inc.) was used to assess DNA concentration and purity.

tag: dna sample

value: Multi cell

tag: quartet

tag: conception

value: IVF

tag: birthweight at delivery

value: AGA


title: P091_Biopsy2


title: P153_Biopsy3


title: P153_Biopsy2


title: Control_524_2B_Embryo

tag: tissue

value: embryo

value: control


title: P070_Biopsy3

value: NAT

value: SGA


title: CDG_HDM 5

description:
ribosome-depleted
CDG_HDM sensitized 2


title: Control_524_2A_Embryo


title: RNA-Seq WT_1


title: Saline 10

description:
ribosome-depleted
Unsensitized 5

value: Saline


title: P162_Biopsy3


title: HPP_15_523_11_AB_YS

value: visceral yolk sac


title: KO

city: Beijing

first: Yong

last: Tang

address: Tsinghua University

department: Medical School

institute: Tsinghua Universtity

data_processing:
After removing adaptor and low quality reads by using cutadapt (1.9.1) with default option, the clean reads were aligned to the mouse Grcm38 with geocode GRCm38.87 by hisat2 (2.0.4)
After alignment, the BAM files for each individual alignment were used to analyze the differential expression of genes with Cufflinks (version 2.2.1).
Genome_build: Grcm38
Supplementary_files_format_and_content: The data in Gene expression.xls  is FPKM (Fragments Per Kilobase per Million ), please see value_1 (the FPKM of WT) and value_2 (the FPKM of KO).

source_name: skin

growth_protocol: isolate skin tissue from 3-old-days mice

extract_protocol:
Skin tissues were grinded and then TRIZOl were added to extract the total cell mRNA
Sequencing libraries were generated using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina

tag: cell type

value: skin cells

tag: genotype/variation


title: P162_Biopsy2


title: WT

value: wildtype


title: Control_524_1A_Embryo


title: Saline 5

description:
ribosome-depleted
Unsensitized 3

value: BALB/c AnNHsd


title: Saline 8

description:
ribosome-depleted
Unsensitized 4

value: lung, left lobe


title: Control_524_1B_Embryo


title: P142_Biopsy2


title: P142_Biopsy3


title: Control_524_2_AB_YS


title: Control_524_1_AB_YS


title: P080_Biopsy3


title: Control_523_2B_Embryo


title: P070_Biopsy2


title: Saline 4

description:
ribosome-depleted
Unsensitized 2

value: 87 days


title: P080_Biopsy2


title: C3, rep 2

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplex and convert reads to FASTQ format
Reads from each lane were combined into individual files using standard UNIX commands
Trimmomatic (v0.33)  was used to trim low quality bases and remove adapter sequences with a 4 bp sliding window, cutting when the read quality dropped below 15 or read length was less than 36 bp.
Bowtie (v1.1.2) was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession AE000516) with the -S option to produce SAM files as output.
HTSeq software suite (v0.6.0) was used to analyze aligned and determine counts per gene feature in the M. tuberculosis CDC1551 genome
edgeR (v3.2) was used to normalize data by estimating effective library sizes using trimmed mean M-values
R was used for statistical analysis and differential gene expression by fitting a negative binomial model to each set of conditions and testing for differences utilizing the GLM functionality edgeR package
Genome_build: Mycobacterium marinum M reference genome (GCA_000018345.1)
Supplementary_files_format_and_content: xlsx spreadsheets containing Counts per million (CPM) and fold-change data.

organism: Mycobacterium marinum

source_name: C3_Bacterial Cell

growth_protocol: M. marinum cultures were grown to saturation in 7H9 defined broth and diluted to an OD600 of 0.8 in 50 ml of Sauton's defined broth with 0.05% Tween 80 and antibiotics as required (C3 was grown with 50 μg/ml hygromycin). After 48 h of growth at 30°C, cells were harvested by centrifugation. Whole-cell lysates were generated by lysing the mycobacterial cells with a Mini-Bead Beater-24 (BioSpec).

extract_protocol:
Total RNA was extracted from 50 ml of M. marinum grown in Sauton's defined media using an RNeasy minikit (Qiagen) according to the manufacturer's recommendation with the following modifications. After bacterial cells were harvested, they were resuspended in 1 ml of RLT buffer containing 0.1% 2-mercaptoethanol and transferred to a 2-ml screw-cap tube containing glass beads. The mixture was homogenized in a mini-bead beater (BioSpec Products) with three 30-s pulses. RNA samples were treated with DNase I.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in two lanes of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, single-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

value: M strain (ATCC BAA-535)

value: MMAR_0039::Tn mutant complemented with MMAR_0039

tag: time point

value: After 48 h of growth at 30°C


title: Control_523_2A_Embryo


title: Saline 2

description:
ribosome-depleted
Unsensitized 1

tag: age


title: P106_Biopsy5

description:
DNA extracted from placenta tissue.
NewBiopsies_PsychArray-24v1.1.txt

value: Multi cell


title: CDG_HDM 3

description:
ribosome-depleted
CDG_HDM sensitized 1

value: house dust mite extract and mucosal adjuvant cyclic di-GMP sensitized

tag: strain


title: C3, rep 1


title: P073_Biopsy3

value: AGA


title: 120A3, rep 2

source_name: 120A3_Bacterial Cell

value: MMAR_0039::Tn mutant


title: wild type

city: Shanghai,China

first: long

last: li

address: 320 Yueyang Road

institute: State Key Laboratory of Cell Biology

hyb_protocol: Following Fragment and Label cRNA, 26.7µL of biotin-labeled cRNA sample were hybridized for 16 hr at 45℃ on GeneChip Primeview Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The file RMA data.txt (available on the series record) contains the RMA signal for all probe sets including ERCC. The sample table does not include data for ERCC.

source_name: gastric cancer HS746T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® 3' IVT PLUS Reagent Kit, 2017,Affymetrix)

growth_protocol: HS746T cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS. The cell culture media contained 100 U/mL penicillin and 100 mg/mL streptomycin. All cells were cultured at 37℃ in 5% CO2 atmosphere.

extract_protocol: Cells were harvested and flash frozen on dry ice, and RNA was harvested using Trizol reagent.

treatment_protocol: over-expression of GFI1 in HS746T cells by lenti-virus.

value: gastric cancer cell line

tag: cell line


title: GFI1 Over-expression

value: GFI1 over-expression


title: P106_Biopsy4

value: IVF


title: Control_523_2_AB_YS

value: control


title: P073_Biopsy2

value: NAT


title: Control_523_1B_Embryo

value: embryo


title: P017_Biopsy3


title: 120A3, rep 1


title: P172_Biopsy5

value: SGA


title: Control_523_1A_Embryo


title: WT, rep 2

source_name: WT_Bacterial Cell

value: Wild Type


title: WT, rep 1


title: P172_Biopsy4


title: P017_Biopsy2


title: Control_523_1_AB_YS

value: visceral yolk sac


title: vector_2

status: Public on Jun 07 2019

city: Boston

first: Osamu

last: Kikuchi

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

data_processing:
Data was processed using Illumina Bcl2fastq
Sequencing reads were aligned to hg19 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output
Genome_build: hg19
Supplementary_files_format_and_content: comma seperated value (CSV) files for all samples. STAR_Gene_Counts.csv reports raw counts.

source_name: LMSU

growth_protocol: LMSU cells were grown in Nutrient Mixture F-10 Ham medium.

extract_protocol:
RNeasy mini kit (Promega, Inc.) was used for RNA collection.
Libraries were prepared using Roche Kapa mRNA Hyper sample preparation kits from 100ng of purified total RNA according to the manufacturer's protocol

value: LMSU

value: yes

tag: doxycycline

value: human gastric cancer cell line with p53 mutation (R175H)


title: R248Q-2

growth_protocol: HGC27 cells were grown in alpha-MEM medium.

tag: p53 mutant overexpression

tag: replicate

value: human gastric cancer cell line without p53


title: R273H-2


title: R175H-2


title: vector_1


title: p53_shRNA-2_1

value: no


title: GFP-2


title: GFP-1


title: R248Q-1


title: scramble_shRNA_2


title: p53_shRNA-1_1


title: p53_shRNA-1_2


title: R175H-1


title: GFP_sg-1_1


title: scramble_shRNA_1


title: R273H-1


title: GFP_V2_2


title: TNP_2_5_524_6_AB_YS

tag: chemical

tag: concentration (µm)

tag: timepoint


title: EBVGC lymph node 1

city: Fukuoka

first: Hirofumi

last: Ohmura

address: 3-1-1 Maidashi

institute: Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software.

label: Cy5 and Cy3

source_name: EBVGC lymph node

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA from the sample was purified and assessed using Infinium HD FFPE QC assay protocol (Illumina, Inc., CA, USA). DNA samples were bisulfite-converted with the EZ DNA Methylation Kit (Zymo Research, CA, USA).

tag: diagnosis

value: Epstein-Barr virus-associated gastric cancer

value: Metastatic lymph node sample

tag: gender

value: Male


title: GFP_sg-1_2


title: p53_shRNA-2_2


title: GFP_V2_1


title: Salmonella_exposed_ind2

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, alignment to the genome (GRCh38), barcode assignment for each cell and gene counting by unique molecular identifier (UMI) counts.
Overall we sequenced 5986 cells with ~42,000 mean reads per cell, ~2,800 median UMI count per cell and ~900 median genes per cells.
Only genes with at least one UMI count detected in at least one cell were used
Data was normalized to a library size factor. Factors were calculated by dividing total UMI counts in each cell to the median of the total UMI counts across all cells
Data was transformed to log10 scale (log10(UMI count+1))
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmonella_exposed_cells.txt file includes UMI counts table for each gene in each cell in the sample
Supplementary_files_format_and_content: GSE132300_data_matrix.txt.gz file includes the normalized data.

source_name: PBMCs

growth_protocol: Venous blood was drawn from the cubital vein of volunteers and PBMCS were isolated as described in Li et al. Cell 2016. The cells were counted and frozen until used. A day before experiment, the cells where defrosted, suspended in medium (RPMI 1640 with L- Glutamine supplemented with 10% heat inactivated fetal bovine serum and 1mM sodium pyruvate) and plated on untreated plates. A day after, the cells were collected from the dish. To avoid cell lost, the dish was washed with medium and the remaining cells were added to the collected cells. The cells were then manually counted with trypan blue.

extract_protocol:
4 hours after infection, the cells were washed with PBS, resuspended in 120ul of 5mM EDTA and incubated 5min in RT to detach cells that might have attached the dish. The EDTA was then washed and the cells were counted with trypan blue, suspended with 0.04% BSA in PBS and directly used for single-cell sequencing by the Chromium Single Cell 3’ Reagent version 2 kit and Chromium Controller (10X Genomics, CA, USA) as previously described at Zheng, G. X. Y. et al Nature Communications 2017.
Libraries were prepared by the Chromium Single Cell 3’ Reagent version 2 kit and Chromium Controller (10X Genomics, CA, USA) as previously described at Zheng, G. X. Y. et al Nature communications 2017.

treatment_protocol: Salmonella strain used in this study was derived from the wild-type strain SL1344 containing GFP (pFPV25.1; Addgene). Cultures of Salmonella were grown in Luria-Bertani (LB) medium at 37°c for 16 hours and used for PBMCs infection at MOI 5 for the exposed cells. After 30 min of internalization, the cells were washed and suspended with media containing 50 ug/ml gentamicin to eliminate Salmonella that were not internalized. The cells were incubated for 4 hours at 37°c in 5% CO2 in non-treated cell culture plates.

tag: infection

value: Salmonella enterica serovar Typhimurium

tag: time (post-infection)

value: 4 hours post-infection

value: PBMCs


title: MH_design_profiling

city: Seattle

first: Jay

last: Shendure

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: Universtiy of Washington

data_processing:
Sequencing reads were first clusterd based on UMIs and paired-end reads were merged using PEAR 0.9.6 with default settings. Mereged reads were aligned to reference using EMBO’s needleall software with the following scoring matrix: match=5, mismatch=-4, gap-open=-20, gap-extension=-0.5.
Aligned reads were further processed with home build pipeline using python.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.txt,  files were generated using python

source_name: HEK 293T

extract_protocol:
DNeasy Blood & Tissue Kit QIAGEN
genomic DNA barcoded PCR

value: HEK 293T


title: NHEJ_profiling_rep2


title: NHEJ_profiling_rep3


title: Biosample_8606_4132_58666_HYL2CBGX2_K562_InSituHiC_NHS_2_ACAGTG

city: Ithaca

first: Charles

last: Danko

state: NY

address: 235 Hungerford Drive

department: Computational Biology

institute: Cornell University

data_processing:
Fastq files were processed using the Aiden Lab's Juicer pipeline. The reference genome used was hg19, and the restriction enzyme was MboI
The resulting contact matices (.hic files) were produced at resolutions of 20 Mb, 10 Mb, 5 Mb, 2.5 Mb, 1 Mb, 500 Kb, 250 Kb, 100 Kb, 50 Kb, 25 Kb, 10 Kb, 5 Kb, and 1 Kb, using only high quality reads (MAPQ score >= 30)
Genome_build: hg19
Supplementary_files_format_and_content: hic files - highly compressed binary files that store contact matrices at multiple resolutions

source_name: K562 immortalized cell line

growth_protocol: Human K562 chronic myelogenous leukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium containing 10% FBS, 100 U/ml penicillin & 100 μg/ml streptomycin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min, quenched and permeabilized. Nuclei were digested with MboI and ends were biotinylated with biotin-14-dATP followed by in-situ ligation. Crosslinks were reversed and DNA was purified, sonicated and pulled down by streptavidin beads.
DNA was end repaired with T4 DNA polymerase, DNA polymerase I large (Klenow) polymerase and T4 polynucleotide kinase. DNA ends were adenylated by dATP and Klenow (3'-5' exo-) polymerase. Illumina Truseq adapters were ligated to the DNA ends and PCR amplified for 10 cycles. Library was purified with Qiaquick PCR purfication kit and sequenced on Illumina Nextseq 500.

treatment_protocol: Growing K562 cells were concentrated in 10 ml of the same growth medium and placed in a 37°C water bath (NHS) or 42°C water bath (HS) for 30 min.


title: Biosample_8606_4132_58664_HYL2CBGX2_K562_InSituHiC_NHS_1_ATCACG


title: Biosample_8606_4132_58665_HYL2CBGX2_K562_InSituHiC_HS_1_CGATGT


title: NHEJ_profiling_rep1


title: WB_ind4_naive_rep1

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (GRCh38), and gene counting.
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log2 scale, and minimal expression threshold was set to 2.
The three replicates of each sample were averaged, except for 3 samples we excluded due to low coverage (<100K exonic reads), and therefore for 3 samples (TLR10#1 t=4h, TLR10#2 t=0 and WT#3 t=0), only 2 replicates were averaged.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads mapped to exons (log2 scale) for each sample

growth_protocol: Venous blood was drawn from the cubital vein of 4 volunteers and WB cells and PBMCS were isolated. The cells were counted, suspended in medium (RPMI 1640 with L- Glutamine supplemented with 10% heat inactivated fetal bovine serum and 1mM sodium pyruvate), divided to 3-4 replicates and plated on untreated plates.

extract_protocol:
At the indicated time points after infection the cells were washed with PBS, then suspended with RLT buffer (from RNeasy Mini Kit, Qiagen) + 1% β-mercaptoethanol and kept in -80°c until further extraction. RNA was then extracted with RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared according to Cel-seq libraries protocol (Hashimshony, T. et al Genome Biology 2016) with a minor modification: the starting material was purified bulk RNA.

treatment_protocol: Salmonella strain used in this study was derived from the wild-type strain SL1344 containing GFP (pFPV25.1; Addgene). Cultures of Salmonella were grown in Luria-Bertani (LB) medium at 37°c for 16 hours and used for WB cells and PBMCs infection at MOI 25 for the exposed cells, and PBS was added to the naive samples. After 30 min of internalization, the cells were washed and suspended with media containing 50 ug/ml gentamicin to eliminate Salmonella that were not internalized. The cells were incubated for the time indicated in each experiment at 37°c in 5% CO2 in non-treated cell culture plates.

tag: subject status

value: healthy individual

tag: individual id

tag: time post-infection (hours)

tag: tissue/cell type

value: WB cells


title: WB_ind3_naive_rep2


title: WB_ind4_naive_rep2


title: WB_ind4_exposed_rep4


title: WB_ind3_exposed_rep3


title: WB_ind2_exposed_rep4


title: WB_ind4_exposed_rep3


title: WB_ind3_exposed_rep2


title: WB_ind3_naive_rep1


title: WB_ind2_exposed_rep3


title: WB_ind4_naive_rep4


title: WB_ind4_exposed_rep1


title: WB_ind4_exposed_rep2


title: WB_ind4_naive_rep3


title: WB_ind3_exposed_rep1


title: WB_ind3_exposed_rep4


title: WB_ind2_naive_rep4


title: WB_ind2_exposed_rep1


title: Biosample_8606_4132_58667_HYL2CBGX2_K562_InSituHiC_HS_2_GCCAAT


title: WB_ind1_exposed_rep1


title: WB_ind1_exposed_rep2


title: WB_ind1_exposed_rep3


title: WB_ind2_naive_rep1


title: WB_ind1_exposed_rep4


title: WB_ind3_naive_rep3


title: WB_ind2_exposed_rep2


title: WB_ind2_naive_rep3


title: WB_ind2_naive_rep2


title: WB_ind1_naive_rep3


title: WB_ind1_naive_rep2


title: PBMCs_ind4_naive_rep2


title: PBMCs_ind4_naive_rep3


title: PBMCs_ind3_naive_rep3


title: PBMCs_ind3_naive_rep4


title: PBMCs_ind4_naive_rep1


title: PBMCs_ind3_exposed_rep4


title: PBMCs_ind4_exposed_rep2


title: PBMCs_ind3_naive_rep1


title: PBMCs_ind4_exposed_rep3


title: WB_ind1_naive_rep1


title: PBMCs_ind4_exposed_rep1


title: PBMCs_ind2_exposed_rep4


title: PBMCs_ind3_exposed_rep1


title: PBMCs_ind3_naive_rep2


title: PBMCs_ind3_exposed_rep2


title: PBMCs_ind3_exposed_rep3


title: PBMCs_ind2_exposed_rep3


title: PBMCs_ind2_naive_rep3


title: PBMCs_ind2_naive_rep4


title: PBMCs_ind2_exposed_rep2


title: WB_ind1_naive_rep4


title: PBMCs_ind2_exposed_rep1


title: PBMCs_ind2_naive_rep1


title: PBMCs_ind1_exposed_rep4


title: PBMCs_ind2_naive_rep2


title: PBMCs_ind1_exposed_rep3


title: PBMCs_ind4_exposed_rep4


title: PBMCs_ind1_exposed_rep2


title: PBMCs_ind1_exposed_rep1


title: PBMCs_ind1_naive_rep3


title: PBMCs_ind1_naive_rep2


title: Monocytes_exposed_rep3

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (GRCh38), and gene counting.
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log2 scale, and minimal expression threshold was set to 4.
The 2-4 replicates of each sample were averaged.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads mapped to exons (log2 scale) for each sample

growth_protocol: Venous blood was drawn from the cubital vein of one volunteer (for each cell type) and PBMCs were isolated as described in Li et al. 2016. The cells were counted, suspended in medium (RPMI 1640 with L- Glutamine supplemented with 10% heat inactivated fetal bovine serum and 1mM sodium pyruvate), divided to 2-4 replicates and plated on untreated plates.

treatment_protocol: Salmonella strain used in this study was derived from the wild-type strain SL1344 containing GFP (pFPV25.1; Addgene). Cultures of Salmonella were grown in Luria-Bertani (LB) medium at 37°c for 16 hours and used for PBMCs infection at MOI 25 for the exposed cells, and PBS was added to the naive samples. After 30 min of internalization, the cells were washed and suspended with media containing 50 ug/ml gentamicin to eliminate Salmonella that were not internalized. The cells were incubated for the time indicated in each experiment at 37°c in 5% CO2 in non-treated cell culture plates. The  PBMCs were then labeled with the following antibodies: CD3 and CD56, and sorted as follows: monocytes were sorted according to their location in FSC/SSC plot, NKT cells were sorted according to double positive gate for CD3+CD56+.

tag: sorted population

value: sorted monocytes from isolated PBMCs


title: PBMCs_ind1_naive_rep1


title: Monocytes_exposed_rep2


title: Monocytes_naive_rep2


title: NKT_naive_rep1

value: sorted NKT cells from isolated PBMCs


title: NKT_naive_rep3


title: Monocytes_exposed_rep1


title: NKT_exposed_rep3


title: NKT_exposed_rep4


title: NKT_naive_rep4


title: naïve

data_processing:
Reads:  R1 contains the cell barcode (16 nt) and UMI (10 nt). R2 contains the cDNA sequence. I1 contains the sample index.
The Cell Ranger 2.1.1 Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, alignment to the genome (GRCh38), barcode assignment for each cell and gene counting by unique molecular identifier (UMI) counts.
Overall we sequenced 7000 cells; 3515 cells from the naïve sample, with ~80,500 mean reads per cell, ~1800 median UMI count per cell and ~800 median genes per cells. For the exposed sample we sequenced 3485 cells with ~76,000 mean reads per cell, ~1800 median UMI count per cell and ~830 median genes per cells.
Only genes with at least one UMI count detected in at least one cell were used
Data was normalized to a library size factor. Factors were calculated by dividing total UMI counts in each cell to the median of the total UMI counts across all cells
Data was transformed to log10 scale (log10(UMI count+1))
Genome_build: GRCh38
Supplementary_files_format_and_content: [*cells.txt ] the UMI count of each gene in each cell
[data_matrix.txt] the normalized UMI counts of the genes in the cells from both samples (naive and exposed; 7000 cells).

extract_protocol:
4 hours after infection, the cells were washed with PBS, counted with trypan blue, suspended with 0.04% BSA in PBS and directly used for single-cell sequencing by the Chromium Single Cell 3’ Reagent version 2 kit and Chromium Controller (10X Genomics, CA, USA) as previously described at Zheng, G. X. Y. et al Nature Communications 2017.
Libraries were prepared by the Chromium Single Cell 3’ Reagent version 2 kit and Chromium Controller (10X Genomics, CA, USA) as previously described at Zheng, G. X. Y. et al Nature communications 2017.

treatment_protocol: Salmonella strain used in this study was derived from the wild-type strain SL1344 containing GFP (pFPV25.1; Addgene). Cultures of Salmonella were grown in Luria-Bertani (LB) medium at 37°c for 16 hours and used for PBMCs infection at MOI 25 for the exposed cells, and PBS was added to the naive samples. After 30 min of internalization, the cells were washed and suspended with media containing 50 ug/ml gentamicin to eliminate Salmonella that were not internalized. The cells were incubated for 4 hours at 37°c in 5% CO2 in non-treated cell culture plates.

value: control

value: 0 hr

tag: cell type


title: Monocytes_naive_rep1


title: Salmonella_exposed

value: 4 hr


title: NKT_naive_rep2


title: TLR10_4_t4_rep2

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (GRCh38), and gene counting.
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log2 scale, and minimal expression threshold was set to 2.
The three replicates of each sample were averaged, except for 3 samples we excluded due to low coverage (<100K exonic reads), and therefore for 3 samples (TLR10#1 t=4h, TLR10#2 t=0 and WT#3 t=0), only 2 replicates were averaged.
Genome_build: GRCh38
Supplementary_files_format_and_content: [*rep*txt]  the processed normalized gene count table of each replicate
[data_matrix.txt]  the average expression levels of each sample (from 3 replicates)

growth_protocol: Venous blood was drawn from the cubital vein of volunteers and PBMCS were isolated as described in Li et al. 2016. The cells were counted and frozen until used. A day before experiment, the cells where defrosted, suspended in medium (RPMI 1640 with L- Glutamine supplemented with 10% heat inactivated fetal bovine serum and 1mM sodium pyruvate) and plated on untreated plates. A day after, the cells were collected from the dish. To avoid cell lost, the dish was washed with medium and the remaining cells were added to the collected cells. The cells were then manually counted with trypan blue and normalized so the same amount of cells was used for each individual (1-5*10^5 cells per replicate, depends on the amount of live cells in the least concentrated sample).

treatment_protocol: Salmonella strain used in this study was derived from the wild-type strain SL1344 containing GFP (pFPV25.1; Addgene). Cultures of Salmonella were grown in Luria-Bertani (LB) medium at 37°c for 16 hours and used for PBMCs infection at MOI 25 for the exposed cells, and PBS was added to the naive samples. After 30 min of internalization, the cells were washed and suspended with media containing 50 ug/ml gentamicin to eliminate Salmonella that were not internalized. The cells were incubated for the time indicated in each experiment at 37°c in 5% CO2 in non-treated cell culture plates.

tag: genotype

tag: individual (ind name)


title: TLR10_4_t8_rep2

value: 8 hr


title: TLR10_4_t8_rep1


title: TLR10_4_t4_rep1


title: TLR10_4_t0_rep2


title: TLR10_4_t0_rep1


title: PBMCs_ind1_naive_rep4


title: TLR10_3_t8_rep3


title: TLR10_3_t8_rep2


title: TLR10_3_t8_rep1


title: NKT_exposed_rep1


title: TLR10_3_t4_rep3


title: NKT_exposed_rep2


title: TLR10_4_t8_rep3


title: TLR10_3_t4_rep2


title: TLR10_4_t4_rep3


title: TLR10_3_t0_rep3


title: TLR10_3_t4_rep1


title: TLR10_3_t0_rep2


title: TLR10_4_t0_rep3


title: TLR10_3_t0_rep1


title: TLR10_2_t8_rep3


title: TLR10_2_t0_rep2


title: TLR10_2_t0_rep1


title: TLR10_1_t4_rep3


title: TLR10_2_t4_rep3


title: TLR10_2_t4_rep2


title: TLR10_2_t8_rep1


title: TLR10_1_t8_rep1


title: TLR10_2_t8_rep2


title: TLR10_1_t8_rep2


title: TLR10_1_t8_rep3


title: TLR10_1_t4_rep2


title: TLR10_2_t0_rep3


title: TLR10_1_t0_rep2


title: TLR10_1_t0_rep1


title: TLR10_1_t4_rep1


title: TLR10_1_t0_rep3


title: WT_4_t8_rep2

value: WT


title: WT_4_t8_rep1


title: WT_4_t4_rep3


title: WT_4_t4_rep2


title: WT_4_t4_rep1


title: WT_4_t0_rep3


title: WT_4_t0_rep2


title: WT_4_t0_rep1


title: WT_3_t8_rep3


title: WT_3_t8_rep2


title: WT_3_t4_rep3


title: WT_2_t8_rep2


title: WT_3_t4_rep1


title: WT_4_t8_rep3


title: TLR10_2_t4_rep1


title: WT_3_t0_rep3


title: WT_3_t0_rep2


title: WT_2_t8_rep3


title: WT_1_t8_rep2


title: WT_1_t8_rep3


title: WT_3_t4_rep2


title: WT_2_t0_rep2


title: WT_2_t0_rep3


title: WT_1_t8_rep1


title: WT_1_t4_rep2


title: WT_1_t4_rep1


title: WT_2_t4_rep2


title: WT_3_t8_rep1


title: WT_2_t0_rep1


title: WT_1_t0_rep3


title: WT_2_t4_rep3


title: WT_1_t0_rep2


title: WT_2_t8_rep1


title: WT_1_t0_rep1


title: mDC in vitro, biological rep 2

city: Milano

first: Silvia

last: Gregori

state: Non-US/Canada

address: via olgettina , 58

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy (SR-TIGET),  IRCCS San Raffaele Scientific Institute.

description:
313_mDCinVitro
in vitro differentiated mDC

data_processing:
Raw RNA sequences were trimmed using Skewer and then aligned against the human reference genome GRChv38 using STAR v2.5.3a with '--quantMode GeneCounts' option.
DESeq2 was used for calling transcripts to determine the total counts per gene and to calculate differential gene expression between samples and clustering.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include absolute reads count per gene for each Sample

molecule: polyA RNA

source_name: cultured monocytes from peripheral blood of healthy donor

extract_protocol:
RNA was isolated using RNeasy Micro or RNA MiRNeasy Kit (QIAGEN, CA, USA) and 10 ng of total or poly-adenylated RNA was converted to cDNA by random primers amplification.
The library was constructed and amplified from cDNA using the Nextera DNA Library Prep Kit with unique dual adaptors (Illumina, NY USA).

treatment_protocol: Cells were washed with PBS and frozen as dried pellet

tag: selection

value: no selection (bulk population)

tag: culture conditions

value: monocytes cultured wih GM-CSF/IL-4 for 5 days and with LPS for 2 days


title: DC10 in vitro, biological rep 2

description:
313_DC10inVitro
in vitro differentiated DC-10

value: monocytes cultured with GM-CSF/IL-4/IL-10 for 7 days


title: DC10 in vitro, biological rep 1

description:
312_DC10inVitro
in vitro differentiated DC-10


title: DC10 ex vivo, biological rep 4

description:
031B_DC10exVivo
ex vivo isolated DC-10

source_name: peripheral blood CD14+CD16+CD141+CD163+ cells from healthy donor

value: FACS-isolation based on positivity for CD14 CD16 CD141 and CD163 markers

value: no in vitro culture


title: DC10 ex vivo, biological rep 3

description:
030B_DC10exVivo
ex vivo isolated DC-10


title: DC10 ex vivo, biological rep 2

description:
029B_DC10exVivo
ex vivo isolated DC-10


title: mDC in vitro, biological rep 1

description:
312_mDCinVitro
in vitro differentiated mDC