title: Cord Blood_TD109 [methylation]

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: E11EPI_scRNA-seq [D20]

status: Public on Feb 09 2021

type: SRA

city: Nottingham

first: Fei

last: Sang

address: QMC

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

library_source: transcriptomic

data_processing:
Basecalls by Illumine Software Suite
Raw PE reads were trimmed against adaptor sequences by scythe (v0.981), and quality-trimmed by sickle (v1.33) using default settings.
Trimmed reads from single cell sequencing then were directionally aligned to Sus scrofa v11.1 by hisat2 (v2.1.0) with --know-splicestie-infile. Uniquely and correctly mapped reads were extracted for the downstream analysis.
htseq-count was used to count the number of reads aligned to each gene (Sus scrofa v11.1 ensembl annotation build 91).  Gene expression level was calculated and normalised by Transcripts Per Kilobase Million (TPM).
Trimmed reads from bisulfite sequencing were aligned and analyzed by Bismark pipeline
Genome_build: sus scrofa v11.1
Supplementary_files_format_and_content: tab-delimited text files for raw read counts and tpms of each gene, as well as rpms; methylation levels

molecule: polyA RNA

organism: Sus scrofa

source_name: Pig embryo

growth_protocol:
embryos were obtained from artificially inseminated pigs
BS-seq: The Sda/GM2-positive (PGCs) and -negative (Somatic) cells collected by FACS were lysed with lysis buffer (0.1% SDS, 50 ng/ml carrier RNA (QIAGEN) and 1 mg/ml proteinase K (Zymo Research) in DNase-free water) for 60 min at 37°C

extract_protocol:
scRNA-seq: Single cells were collected manually into lysis buffer following the SMARTSEQ. 2 protocol published by Picelli et al., 2014 (Nat. Protocols 9, 171-181)
BS-seq: PBAT libraries were prepared as described by Tang et al. (2015)
scRNA-seq: Libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina), as used Picelli et al., 2014..
BS-seq: Libraries were subjected to paired-read 150bp sequencing on HiSeq 4000 sequencing system (Illumina)

tag: breed

value: Generic pig

tag: cell type


title: Bilateral nuclues of the solitary tract sections [WSc15]

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

country: USA

institute: University of New Mexico

description: Sections anatomically confirmed with DAPI and NeuN flourescent signal collected using Laser Capture microdissection

data_processing:
Target gene signals normalized to median expression of each sample across all genes followed by centering the delta CT values across all samples within a gene.
Matrix normalized worksheet reports normalized signal (against median gene expression).

label: EvaGreen

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat brain NTS

label_protocol: qPCR reactions were performed using a combination of 96.96 and 192.24 BioMark™ Dynamic IFC Arrays (Fluidigm®, South San Francisco, CA) enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions (Spurgeon et al. 2008). Each run consisted of 30 amplification cycles (15s at 95°C, 5s at 70°C, 60s at 60°C). Ct values were calculated by the Real-Time PCR Analysis Software (Fluidigm). Intron-spanning PCR primers for every assay were designed and tested for proper targeted amplification before use on a BioMark array.

extract_protocol: Laser capture microdissection was used to obtain precise regional samples from NTS.

treatment_protocol: The 25 uL injection consisted of a 1:1 ratio of anti-miR-376a and anti-miR-135a Locked Nucleic  303 Acid (LNA, Exiqon, 41,42 ) 10 uM solution in artificial cerebrospinal fluid, this condition was  304 considered AM-Combo. A negative control antisense oligonucleotide LNA (a sequence that  305 does not align to any known microRNA or mRNA transcript), called “Scrambled”. No surgery  306 and sham surgery conditions were also assayed. Sham surgeries included cannulas that were  307 inserted and an empty needle was placed for the duration of the corresponding injection time  308 were also performed.

tag: strain

value: Wistar Kyoto (WKY) Rat

tag: animal id

tag: treatment

value: Scrambled


title: Bilateral nuclues of the solitary tract sections [WSc13]


title: E11EPI_scRNA-seq [F29]


title: Cord Blood_TD102 [methylation]

type: genomic

city: Tokyo

first: Kohei

last: Kashima

address: 7-3-1 Hongo Bunkyo-ku

department: Pediatrics

country: Japan

institute: The University of Tokyo Hospital

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: background correction and dye-bias equalization (Noob) was performed using minfi package (v. 1.20.2), and furthermore, beta-mixture quantile normalization (BMIQ) was performed using ChAMP package(v. 2.6.0).

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: CBMC

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Qiagen AllPrep kit.

treatment_protocol: Mononuclear cells were separated by gradient centrifugation using Ficoll-Hypaque from cord blood and postnatal peripheral blood samples within 24 h of the sample collection.

tag: gender

value: male

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

value: Yes

tag: gestational age

tag: birthweight sdscore

value: parous

value: Cesarean

value: No

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Cord Blood_TD085 [methylation]

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: E11EPI_scRNA-seq [F20]

tag: breed

tag: cell type


title: Cord Blood_TD100 [methylation]

tag: gender

value: female

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

value: primipara

value: Vaginal


title: E11EPI_scRNA-seq [D15]


title: Cord Blood_TD093 [methylation]

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E11EPI_scRNA-seq [F12]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [WSc11]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [WSc10]


title: E11EPI_scRNA-seq [D11]


title: Bilateral nuclues of the solitary tract sections [WSh02]

value: Sham


title: Bilateral nuclues of the solitary tract sections [WSc12]


title: Bilateral nuclues of the solitary tract sections [WSc09]


title: Cord Blood_TD088 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: Cord Blood_TD104 [methylation]

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Cord Blood_TD077 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc


title: Cord Blood_TD098 [methylation]

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: E11EPI_scRNA-seq [F19]

tag: breed

tag: cell type


title: E11EPI_scRNA-seq [F28]


title: Cord Blood_TD078 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E11EPI_scRNA-seq [F11]


title: Bilateral nuclues of the solitary tract sections [WSc08]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD079 [methylation]

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WSc07]

tag: strain


title: Cord Blood_TD087 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E11EPI_scRNA-seq [D28]

tag: breed

tag: cell type


title: Cord Blood_TD069 [methylation]

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: gestational diabetes mellitus


title: Cord Blood_TD081 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: chorioamnionitis

tag: placenta previa


title: Cord Blood_TD073 [methylation]

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Cord Blood_TD075 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: gestational diabetes mellitus


title: Bilateral nuclues of the solitary tract sections [WSc05]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [WSc06]


title: Cord Blood_TD086 [methylation]

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: chorioamnionitis

tag: placenta previa


title: Cord Blood_TD071 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: idiopathic prom without inflammation

tag: preeclampsia


title: E11EPI_scRNA-seq [D17]

tag: breed

tag: cell type


title: Bilateral nuclues of the solitary tract sections [WSc03]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [WSc04]


title: E11EPI_scRNA-seq [D27]


title: E11EPI_scRNA-seq [F18]


title: E11EPI_scRNA-seq [D16]


title: Cord Blood_TD076 [methylation]

tag: gender

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WSc02]

tag: strain


title: Cord Blood_TD067 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Cord Blood_TD061 [methylation]

tag: gender

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology


title: Bilateral nuclues of the solitary tract sections [WC27]

tag: strain

tag: animal id

tag: treatment

value: Cocktail


title: Bilateral nuclues of the solitary tract sections [WSc14]


title: Cord Blood_TD072 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WC26]


title: E11EPI_scRNA-seq [D14]

tag: breed

tag: cell type


title: E11EPI_scRNA-seq [F17]


title: Bilateral nuclues of the solitary tract sections [WC25]

tag: strain


title: Bilateral nuclues of the solitary tract sections [WC24]

tag: animal id


title: E11EPI_scRNA-seq [F24]


title: E11EPI_scRNA-seq [D13]


title: E11EPI_scRNA-seq [C39]


title: E11EPI_scRNA-seq [E15]


title: Bilateral nuclues of the solitary tract sections [WC23]

tag: treatment


title: Cord Blood_TD059 [methylation]

tag: gender

tag: batch

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Cord Blood_TD080 [methylation]

tag: estimated bcell

tag: estimated cd4t

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: E11EPI_scRNA-seq [E9]

tag: breed

tag: cell type


title: E11EPI_scRNA-seq [C34]


title: Bilateral nuclues of the solitary tract sections [WC22]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [WC21]


title: Bilateral nuclues of the solitary tract sections [WC20]


title: E11EPI_scRNA-seq [C35]


title: Bilateral nuclues of the solitary tract sections [WC19]


title: E11EPI_scRNA-seq [C28]


title: Cord Blood_TD058 [methylation]

tag: gender

tag: batch

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [WC18]

tag: strain


title: Cord Blood_TD054 [methylation]

tag: estimated bcell

tag: estimated cd4t

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WC17]

tag: animal id

tag: treatment


title: tNet-PIPseq Proteinase K+Rnase V1 + RnaseOnetreated R749H slow pol II

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with proteinase K,  Rnase V1 + RNaseOne

data_processing:
Library strategy: tNet-PIPseq
Paired-end 150 base reads (after removing barcodes and trimming adaptor sequences) were uniquely mapped to the hg19 UCSC human genome hisat2
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: Data sets were processed into Bedgraph files.  tNet-MaP seq, tNetPIP seq and tNET-seq edits were processed using  pipelines available at https://github.com/rnabioco/rnastruct. Putative protein footprints were subtracted in files labelled no FP. Structure score files that include reads mapped to repetitive elements are labelled non-unique. DMS files were background subtracted (bgsub).

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H

extract_protocol: Following RNAase digestion, samples with treated with Proteinase K at 1mg/ml  for 15mins at 37º and then 65 º for 30mins to reverse crosslinks.  RNA was purifed with trizol extraction and RNA fragments were convereted into sequencing libraries with lexogen small RNA kit.

treatment_protocol: After induction of pol II mutant and treatment with  a-amanitin, cells were treated with 0.1% formaldehyde for 3 mins followed by 125mM glycine for 5mins.  After immunoprecipitation of pol II bound RNA, sample was treated with Proteinase K  then with 0.1U of RNaseV1 and 0.5U RNaseOne for 15mins at room temp

tag: cell line

tag: growth conditions

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: E11EPI_scRNA-seq [C25]

tag: breed

tag: cell type


title: E11EPI_scRNA-seq [C27]


title: Cord Blood_TD052 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [WC16]

tag: strain

tag: animal id

tag: treatment


title: Cord Blood_TD056 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WSc01]


title: Cord Blood_TD063 [methylation]

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: idiopathic prom without inflammation


title: PDT-LUAD#19

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava1.7 software was used for base calling.
Adapter and low-quality sequences were removed by cutadapt (v1.2.1).
After quality control, poly-A/T sequences were also removed by PRINSEQ (v0.19.2).
For fusion gene discovery, the reads were also aligned to the reference human genome hg19 and potential gene fusion transcripts were detected by deFuse (v0.6.2).
Genome_build: Human (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include deFuse-predicted fusion sequences, their statistiscs and genomic annotaions.

source_name: Lung cancer organoid (tumoroid)

growth_protocol: The lung tumoroid line was generated and cultured using a method reported by the Hans Clevers laboratory (Sachs et al. EMBO J 2019;38(4).embj.2018100300).

extract_protocol:
RNA was harvested using Trizol reagent. The mRNA in total RNA was converted into a library of template molecules suitable for subsequent cluster generation using the Illumina TruSeq Stranded mRNA Library Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: lung cancer organoid

tag: organoid derived from

value: lymph node metastasis originating from lung adenocarcinoma

tag: disease state

value: lung adenocarcarcinoma

tag: Stage


title: Cord Blood_TD055 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: preeclampsia

tag: placenta previa


title: tNet-PIPseq Rnase V1 + RnaseOnetreated R749H slow pol II Rep3

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with Rnase V1 + RNaseOne

molecule: nuclear RNA

growth_protocol: Rpb1 WT and mutant cells were grown in DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

extract_protocol:
[tNet_MaPseq]  IP's were prepared from DNAseI solublilized nuclear extracts (~1.5X 10E7 cells). Precipitated RNA was was purified by Trizol extraction and random primed.  DMS and DMSO treated RNA was reverse transcribed under MaP conditions.  All tNetSeq and tNetMaP-Seq libraries were constructed using the KAPA stranded RNAseq kit.
[tNet_PIPseq]  Following RNAase digestion, samples with treated with Proteinase K at 1mg/ml  for 15mins at 37º and then 65 º for 30mins to reverse crosslinks.  RNA was purifed with trizol extraction and RNA fragments were convereted into sequencing libraries with lexogen small RNA kit.

treatment_protocol:
After induction of pol II mutant and treatment with  α-amanitin, cells were treated with 0.1% formaldehyde for 3 mins followed by 125mM glycine for 5mins.  After immunoprecipitation of pol II bound RNA, sample was treated with 0.1U of RNaseV1 and 0.5U RNaseOne for 15mins at room temp
Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.

tag: growth conditions

tag: antibody

tag: genotype

value: R749H slow pol II

tag: treatment

value: Rnase V1 + RNaseOne

tag: cell line


title: E11EPI_scRNA-seq [C36]

tag: breed

value: Generic pig

tag: cell type


title: E11EPI_scRNA-seq [C40]


title: Bilateral nuclues of the solitary tract sections [WC14]

tag: strain

value: Wistar Kyoto (WKY) Rat

tag: animal id


title: Bilateral nuclues of the solitary tract sections [WC13]


title: Cord Blood_TD050 [methylation]

tag: gender

value: male

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

value: Yes

tag: idiopathic prom without inflammation


title: E11EPI_scRNA-seq [C33]

tag: breed

tag: cell type


title: Cord Blood_TD060 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

value: No

tag: parity

tag: delivery

value: Cesarean

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: preeclampsia

tag: placenta previa


title: E11EPI_scRNA-seq [C29]


title: E11EPI_scRNA-seq [C32]


title: Bilateral nuclues of the solitary tract sections [WC12]

tag: strain

tag: animal id

tag: treatment


title: tNet-PIPseq Rnase V1 + RnaseOnetreated R749H slow pol II Rep2

tag: growth conditions

tag: antibody

tag: genotype

tag: cell line


title: Cord Blood_TD062 [methylation]

tag: gender

value: female

tag: batch

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

value: parous

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: idiopathic prom without inflammation


title: tNet-PIPseq Rnase V1+ RNaseOne treated WT pol II Rep3

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

tag: growth conditions

tag: antibody

tag: genotype

value: WT pol II

tag: treatment

tag: cell line


title: Cord Blood_TD057 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: parity

value: primipara

tag: delivery

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: preeclampsia

tag: placenta previa


title: E11EPI_scRNA-seq [C31]

tag: breed

tag: cell type


title: tNet-PIPseq Rnase V1+ RNaseOne treated WT pol II Rep2

tag: growth conditions

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

tag: antibody

tag: genotype

tag: treatment

tag: cell line


title: Cord Blood_TD047 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

value: Vaginal

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: idiopathic prom without inflammation


title: Cord Blood_TD043 [methylation]

tag: estimated gran

tag: estimated mono

tag: parity

tag: delivery

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: preeclampsia

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WC11]

tag: strain

tag: animal id

tag: treatment

value: Cocktail


title: E11EPI_scRNA-seq [E11]

tag: breed

tag: cell type


title: Cord Blood_TD053 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi


title: Cord Blood_TD051 [methylation]

tag: estimated gran

tag: estimated mono

tag: parity

tag: delivery

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Cord Blood_TD049 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age


title: Cord Blood_TD044 [methylation]

tag: estimated gran

tag: estimated mono

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi


title: Cord Blood_TD046 [methylation]

tag: gender

tag: batch

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Cord Blood_TD023 [methylation]

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age


title: Bilateral nuclues of the solitary tract sections [WC10]

tag: strain

tag: animal id

tag: treatment


title: E11EPI_scRNA-seq [C38]

tag: breed

tag: cell type


title: Cord Blood_TD048 [methylation]

tag: gender

tag: batch

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: Cord Blood_TD022 [methylation]

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: preeclampsia

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WC09]

tag: strain

tag: animal id

tag: treatment


title: tNet-PIPseq Rnase V1+ RNaseOne treated WT pol II Rep1

tag: growth conditions

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

tag: genotype

tag: cell line


title: Cord Blood_TD030 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: tNet-PIPseq Rnase V1 treated R749H slow pol II Rep3

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with Rnase V1

treatment_protocol:
After induction of pol II mutant and treatment with  α-amanitin, cells were treated with 0.1% formaldehyde for 3 mins followed by 125mM glycine for 5mins.  After immunoprecipitation of pol II bound RNA, sample was treated with 0.1U of RNaseV1 for 15mins at room temp
Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.

tag: growth conditions

tag: antibody

tag: genotype

tag: treatment

value: Rnase V1

tag: cell line


title: Cord Blood_TD037 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: preeclampsia

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WC07]

tag: strain

tag: animal id


title: Bilateral nuclues of the solitary tract sections [WC08]

tag: treatment


title: E11EPI_scRNA-seq [C37]

tag: breed

tag: cell type


title: Cord Blood_TD045 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: tNet-PIPseq Rnase V1 treated R749H slow pol II Rep2

tag: growth conditions

tag: antibody

tag: genotype

value: R749H slow pol II

tag: treatment

tag: cell line


title: Bilateral nuclues of the solitary tract sections [WC06]

tag: strain

tag: animal id


title: J-Lat 10.6 TNFα rep1

city: Guangzhou

first: Xiancai

last: Ma

state: Guangdong

address: North Campus, Zhongshan Road II, No.74

department: Institute of Human Virology

country: China

institute: Sun Yat-sen University

description: Immortalized line of human T lymphocyte Jurkat cells

data_processing:
The RNA-Seq libraries were sequenced with HiSeq X Ten (Illumina) under PE150 protocol.
RNA-Seq reads were trimmed, filtered and quality-controlled by FastQC (Babraham Institute).
The reads were aligned to the human reference genome NCBI build 38 (GRCh38) by Hisat2, followed by calculating the reads per kilobase per million mapped reads (RPKM) (Kim et al, 2015).
Differentially expressed genes were filtered by DEGseq (Bioconductor) with log2FC of 1 and PvalueFDR cutoff of 0.05.
Filtered genes were plotted as volcanoplots by gplots (R Foundation).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for all gene within each sample.

growth_protocol: J-Lat 10.6-related cell lines were cultured in RPMI 1640 supplemented with 1% penicillin-streptomycin and 10% FBS. All cells were cultured in sterile incubator at 37℃ and 5% CO2. All cells have been tested for mycoplasma utilizing PCR assay and confirmed to be mycoplasma-free.

extract_protocol:
Cells within each group were removed supernatant and washed once with PBS. Total RNAs were extracted with TRIzol reagent. The qualities of these RNAs were evaluated by Nanodrop (ThermoFisher) and BioAnalyzer 2100 (Aglient).
The RNA-Seq libraries were performed with TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced with HiSeq X Ten (Illumina) under PE150 protocol.

treatment_protocol: Cells within wildtype and CHAF1A-KO groups were treated with DMSO for 24 hours. Cells within TNFα group were treated with 20 ng/ml TNFα for 24 hours.

tag: cell type

value: Jurkat-derived pseudotyped HIV-1-infected monoclonal cells

value: TNFα

value: wildtype


title: tNet-PIPseq Rnase V1 treated R749H slow pol II Rep1


title: J-Lat 10.6 TNFα rep2


title: tNet-PIPseq Rnase V1 treated WT pol II Rep3


title: E11EPI_scRNA-seq [E10]

tag: breed

value: Generic pig


title: tNet-PIPseq Proteinase K+Rnase V1+ RNaseOne treated WT pol II

value: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT


title: Cord Blood_TD040 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

value: No

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

value: Yes

tag: preeclampsia

tag: placenta previa


title: Bilateral nuclues of the solitary tract sections [WC05]

tag: strain

value: Wistar Kyoto (WKY) Rat

tag: animal id

tag: treatment


title: Cord Blood_TD035 [methylation]

tag: gender

value: female

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

value: Cesarean

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation


title: Cord Blood_TD034 [methylation]

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

value: parous

tag: delivery

tag: maternal age

tag: maternal bmi

tag: preeclampsia


title: Bilateral nuclues of the solitary tract sections [WC04]

tag: strain

tag: animal id

tag: treatment


title: Bilateral nuclues of the solitary tract sections [WC15]


title: J-Lat 10.6 CHAF1A-KO rep1

tag: cell type

value: DMSO

tag: genotype


title: tNet-PIPseq Rnase V1 treated WT pol II Rep1

tag: growth conditions

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

tag: antibody

value: WT pol II

tag: cell line


title: Bilateral nuclues of the solitary tract sections [WC03]

value: Cocktail


title: J-Lat 10.6 WT rep2


title: tNet-PIPseq RNaseOne treated R749H slow pol II Rep2

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with RNaseOne

treatment_protocol:
After induction of pol II mutant and treatment with  α-amanitin, cells were treated with 0.1% formaldehyde for 3 mins followed by 125mM glycine for 5mins.  After immunoprecipitation of pol II bound RNA, sample was treated with 0.5U of RNaseOne for 15mins at room temp
Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

value: RNaseOne


title: Bilateral nuclues of the solitary tract sections [WC01]


title: Bilateral nuclues of the solitary tract sections [WC02]


title: tNet-PIPseq RNaseOne treated R749H slow pol II Rep3

value: R749H slow pol II


title: J-Lat 10.6 WT rep1

value: Jurkat-derived pseudotyped HIV-1-infected monoclonal cells


title: tNet-PIPseq Rnase V1 treated WT pol II Rep2

value: Rnase V1


title: J-Lat 10.6 CHAF1A-KO rep2


title: UC-MSC  #2

first: Yan

last: Xu

address: No. 600 Tianhe Road

department: Biotherapy Center

institute: The Third Affiliated Hospital of Sun Yat-Sen University

description: UC-MSC  rep2

data_processing:
For sample 1-sample 10, the sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set， then expression level of gene was calculated by RSEM (v1.2.12).
For sample 11-sample 16,data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:   Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%. Using String Tie for readcount and FPKM calculation. Differential expression analyses were performed using the limma package.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.

source_name: Umbilical cord-derived MSCs

growth_protocol: MSCs were cultured in L-DMEM (Gibco) supplemented with 10% FBS, 1% glutamine, 1% penicillin/streptomycin, 2 ng/mL bFGF. For co-culture, MSCs (1×105 cells) were plated into 24-well plate (Corning) and cultured 24 h before co-culture with lymphocytes. The next day, human peripheral blood mononuclear cells were collected from healthy donors and red blood cells were removed by ammonium chloride lysis buffer for 5 min at room temperature, and then centrifuged at 300 g for 5 min. After washed twice with PBS (containing 3% FCS), cells were incubated with an anti-mouse CD3 antibody (Catalog # 100204, Biolegend ) at 4 ℃ for 30 min. CD3+ T cells were sorted by CD3 MicroBeads (Catalog # 130-050-101, Miltenyi Biotec, Germany) and suspended in RPMI1640 at 2.5×106 cells/mL and add 1mL to the 24-well plates in the presence or absence of MSCs.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
For sample 1-sapmle 10, Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China.    For sample 11-sample 16, a total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

treatment_protocol: T cell activation was induced by phytohaemagglutinin (PHA, Sigma-Aldrich) at the final concentration of 5 μg/mL. After co-culture for 48 hours, CD3+ T cells were collected and sequenced.

value: Umbilical cord-derived MSCs

value: Normal


title: Cord Blood_TD024 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

value: No

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: placenta previa


title: tNet-PIPseq RNaseOne treated R749H slow pol II Rep1

tag: growth conditions

tag: antibody

tag: genotype

tag: treatment

tag: cell line


title: tNet-PIPseq RNaseOne treated WT pol II Rep3

treatment_protocol:
After induction of pol II mutation and treatment with α-amanitin, cells were treated with 0.1% formaldehyde for 3 mins followed by 125mM glycine for 5mins.  After immunoprecipitation of pol II bound RNA, sample was treated with 0.5U of RNaseOne for 15mins at room temp
Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.


title: UC-MSC  #1

description: UC-MSC  rep1

tag: cell type


title: BM-MSC  #2

description: BM-MSC  rep2

source_name: Bone marrow-derived MSCs

value: Bone marrow-derived MSCs


title: tNet-PIPseq RNaseOne treated WT pol II Rep2


title: BM-MSC  #1

description: BM-MSC  rep1


title: tNet-PIPseq RNaseOne treated WT pol II Rep1


title: OM-MSC  #2

description: OM-MSC  rep2

source_name: Olfactory mucosa-derived MSCs

value: Olfactory mucosa-derived MSCs


title: tNet-MaPseq R749H slow pol II Rep3

description:
nascent nuclear RNA
Anti-pol II nascent RNA treated with DMS

data_processing:
Library strategy: tNet-MaPseq
Paired-end 150 base reads (after removing barcodes and trimming adaptor sequences) were uniquely mapped to the hg19 UCSC human genome hisat2
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: Data sets were processed into Bedgraph files.  tNet-MaP seq, tNetPIP seq and tNET-seq edits were processed using  pipelines available at https://github.com/rnabioco/rnastruct. Putative protein footprints were subtracted in files labelled no FP. Structure score files that include reads mapped to repetitive elements are labelled non-unique. DMS files were background subtracted (bgsub).

treatment_protocol:
After induction of pol II mutant and treatment with  α-amanitin, cells were treated with 2% DMS for 5mins at 37C followed by 30% final mercaptoethanol.
Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.

value: DMS


title: Cord Blood_TD033 [methylation]

tag: gender

value: female

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

value: primipara

tag: delivery

value: Cesarean

tag: maternal age

tag: maternal bmi

value: Yes

tag: preeclampsia


title: EA1909_12_a TET3 knockdown, TNFα(+)

city: Kitakyushu

first: Akio

last: Kawabe

address: 1-1, Iseigaoka Yahata-nishi

institute: University of Occupational and Environmental Health, Japan

description: TET3 knockdown, TNFα(+)

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hrs at 45˚C on Clariom S Array, Human. Arrays was washed and stained in the GeneChip™ Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom™ S array (Thermo Fisher Scientific) was scanned using GeneChip™ Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: The data were analyzed with Expression Console™ Software 1.4 (Thermo Fisher Scientific) offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: biotin

source_name: Fibroblast-like synoviocytes were transfected with siRNA targeting TET3, and then stimulated with TNFα

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific) following the manufacturer's instructions.

extract_protocol: Total RNA was isolated using RNeasy® mini Kit (Qiagen).

tag: transfection

value: siRNA targeting TET3

tag: treatment

value: stimulated with TNF[alpha]


title: EA1909_11_a TET3 knockdown, TNFα(–)

description: TET3 knockdown, TNFα(–)

source_name: Fibroblast-like synoviocytes were transfected with siRNA targeting TET3, and then unstimulated with TNFα

value: unstimulated with TNF[alpha]


title: tNet-MaPseq R749H slow pol II Rep2

tag: growth conditions

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

tag: genotype

tag: cell line


title: Cord Blood_TD028 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated nk

tag: estimated nrbc

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: placenta previa


title: Cord Blood_TD027 [methylation]

value: male

tag: estimated gran

tag: estimated mono

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

tag: maternal age

tag: maternal bmi

tag: preeclampsia


title: Cord Blood_TD018 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated nk

tag: estimated nrbc

tag: paternal age

tag: paternal bmi


title: EA1909_09_a control siRNA, TNFα(–)

description: control siRNA, TNFα(–)

source_name: Fibroblast-like synoviocytes were transfected with non-targeting control siRNA, and then unstimulated with TNFα

tag: transfection

value: non-targeting control siRNA

tag: treatment


title: OM-MSC  #1

description: OM-MSC  rep1

tag: cell type


title: tNet-PIPseq Rnase V1 + RnaseOnetreated R749H slow pol II Rep1

tag: growth conditions

tag: antibody

tag: genotype

value: R749H slow pol II

value: Rnase V1 + RNaseOne

tag: cell line


title: EA1909_08_a TET3 knockdown, TNFα(+)

description: TET3 knockdown, TNFα(+)


title: tNetSeq R749H slow pol II Rep3

description:
nascent nuclear RNA
Anti-pol II nascent RNA

data_processing:
Library strategy: tNET-Seq
Paired-end 150 base reads (after removing barcodes and trimming adaptor sequences) were uniquely mapped to the hg19 UCSC human genome hisat2
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: Data sets were processed into Bedgraph files.  tNet-MaP seq, tNetPIP seq and tNET-seq edits were processed using  pipelines available at https://github.com/rnabioco/rnastruct. Putative protein footprints were subtracted in files labelled no FP. Structure score files that include reads mapped to repetitive elements are labelled non-unique. DMS files were background subtracted (bgsub).

treatment_protocol: Amr Rpb1 was induced with doxycycline (2.0 ug/ml)  for 12-16 hr then treated with α-amanitin (2.5 mg/ml) for a further 42 hr before harvesting.

value: untreated


title: EA1909_07_a TET3 knockdown, TNFα(–)

description: TET3 knockdown, TNFα(–)


title: EA1909_10_a control siRNA, TNFα(+)

description: control siRNA, TNFα(+)

source_name: Fibroblast-like synoviocytes were transfected with non-targeting control siRNA, and then stimulated with TNFα


title: EA1909_06_a control siRNA, TNFα(+)

description: control siRNA, TNFα(+)


title: tNetSeq R749H slow pol II Rep2


title: EA1909_05_a control siRNA, TNFα(–)

description: control siRNA, TNFα(–)


title: Cord Blood_TD019 [methylation]

tag: estimated gran

tag: estimated mono

tag: have valid rna expression data?

value: No

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

value: Vaginal

tag: maternal age

tag: maternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: tNetSeq R749H slow pol II Rep1

tag: growth conditions

tag: antibody

tag: genotype

tag: treatment

tag: cell line


title: Cord Blood_TD017 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: paternal age

tag: paternal bmi


title: Effector_CD8+T cell_rep2

city: Nagoya

first: masaya

last: onishi

address: Kawasumi, Mizuho

department: Virology & Liver unit

institute: Nagoya City University Graduate School of Medical Sciences

hyb_protocol: Labeled complementary RNA (cRNA) was prepared from 100ng total RNA using Low Input Quick-Amp Labeling Kit, one color Cy3 protocol (Agilent Technologies), and hybridized to the Agilent SurePrint G3 Mouse GE Microarray 8 x 60K Ver2.0 Chips (Agilent Technologies).

scan_protocol: Detection was performed using Agilent SureScan G4900DA software (Agilent Technologies). Raw data were extracted using the software provided by Agilent Feature Extraction Software (v11.5.1.1).

data_processing: Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by the quantile method.

organism: Mus musculus

source_name: Effector_COR93-specific_CD8+T cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100  ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HBV-transgenic (HBV-Tg) mouse (lineage 1.3.32, inbred B6, H-2b)  expresses all of the HBV antigens and replicates HBV in the liver and kidney at high levels without any evidence of cytopathology. C57BL/6 (B6) mice (H-2b) were obtained from the breeding colonies of Japan SLC. In all experiments, the HBV-Tg and B6 mice were matched for age (8-10 weeks), sex (male), and serum HBeAg levels in their serum before experimental manipulations for HBV-Tg mice. The splenic CD8+ T cells ofCOR93 T cell receptor transgenic (TCR-Tg) mice (lineage BC10.3, inbred CD45.1, H-2b) recognize a Kb-restricted epitope located between residues 93 and 100 in the HBV core antigen (HBcAg; MGLKFRQL). These T cells exhibit a naïve T cell phenotype.

extract_protocol: Intrahepatic lymphocytes (IHLs) and spleen cells were prepared as shown here. Livers were perfused with 10 ml of PBS via the portal vein to remove circulating lymphocytes and the liver tissue was pressed through a 70 μm cell strainer (Corning) with the plunger of a 1 ml syringe and digested with 10 ml of RPMI 1640 medium (Sigma-Aldrich), containing 0.02% (w/v) collagenase IV (Sigma-Aldrich) and 0.002% (w/v) DNase I (Sigma-Aldrich), for 40 minutes at 37 °C. Cell suspension was collected after removing hepatocytes and connecting tissues by slow speed centrifugation (3 minutes, 20 x g). The cells were washed with RPMI 1640 and then overlaid on Percoll/Histopaque solution consisting of 12% Percoll (GE Healthcare) and 88% Histopaque-1083 (Sigma-Aldrich). After centrifugation for 20 minutes at 750 × g, the IHLs were isolated at the interface. The lymph mononuclear cells were washed twice with RPMI 1640 medium and used for further analysis. Spleen cells were isolated by pressing through a 70 μm cell strainer and washed three times with RPMI 1640 medium containing 5% fetal bovine serum (FBS) and used for further analysis. Lymphmononuclear cells isolated from the liver of HBV-Tg mice and spleen of immunized B6 mice were purified for CD8+CD45.1+ cells, i.e., COR93-specific CD8+ T cells, using MACS (Miltenyi Biotec). Total RNA was isolated from naïve and these COR93-specific CD8+ T cells using RNeasy Mini Kit (QIAGEN).

treatment_protocol: Spleen cells were isolated from BC10.3 mice and CD8+ cells were purified from those spleen cells by negative selection using MACS (Miltenyi Biotec) according to the manufacturer’s instructions. 3 × 10^6 CD8+ T cells  per mouse were adoptively transferred into MHC-class I matched HBV-Tg or nontransgenic recipients. Effector HBV-specific CD8+ T cells were generated by adoptively transferring COR93-specific TCR-Tg T cells into B6 mice that were then immunized with a COR93 peptide (purchased from Scrum) and a monoclonal anti-CD40 antibody (clone FGK4.5; BioXCell).

tag: strain background

tag: age

value: 8-10 week

tag: genotype

value: wild type genotype vaccinated with HBV core peptide

tag: tissue/cell type

value: IHL_CD8+ T cells

value: transplanted with HBV-specific CD8+ T cells from Cor93 TCR (BC10.3) transgenic mice immunized with a COR93 peptide (purchased from Scrum) and a monoclonal anti-CD40 antibody


title: Cord Blood_TD016 [methylation]

tag: gender

tag: batch

tag: parity

value: primipara

tag: delivery

value: Cesarean

tag: maternal age

tag: maternal bmi

tag: assisted reproductive technology

value: Yes

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: tNetSeq WT pol II Rep2

tag: growth conditions

tag: antibody

value: WT pol II

tag: treatment

tag: cell line


title: Effector_CD8+T cell_rep1

tag: strain background

tag: gender

tag: age

tag: genotype

tag: tissue/cell type


title: EA1909_04_a TET3 knockdown, TNFα(+)

description: TET3 knockdown, TNFα(+)

tag: transfection

value: siRNA targeting TET3

value: stimulated with TNF[alpha]


title: EA1909_03_a TET3 knockdown, TNFα(–)

description: TET3 knockdown, TNFα(–)

value: unstimulated with TNF[alpha]


title: Cord Blood_TD012 [methylation]

value: female

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

value: parous

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology


title: Cord Blood_TD036 [methylation]

tag: gender

value: male

tag: batch

tag: estimated bcell

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Tolelant_CD8+T cell_rep1

source_name: Tolelant_COR93-specific_CD8+T cell

tag: strain background

tag: age

tag: genotype

value: HBV-Tg mice (lineage 1.3.32, inbred B6, H-2b)

tag: tissue/cell type

tag: treatment

value: transplanted with HBV-specific CD8+ T cells from Cor93 TCR (BC10.3) transgenic mice


title: Tolelant_CD8+T cell_rep2


title: C. diphtheriae delta-rnj2 Rep 3

status: Public on Feb 08 2021

city: Bielefeld

first: Manuel

last: Wittchen

address: Universitaetsstr. 27

department: Center for Biotechnology

country: Germany

institute: Bielefeld University

data_processing:
Base calling with Illumina CASAVA
quality trimming with trimmomatic v0.36 from both ends with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:39
reverse complementing of R1 reads
mapping with bowtie2 2.2.7, --ff read orientation, default parameters
converting SAM to BAM with samtools 1.2
visualization and read counting with readXplorer 2.2.3
Analysis of differentially transcribed genes with DESeq2 in default parameters
Genome_build: RefSeq NC_002935.1
Supplementary_files_format_and_content: List_of_differentially_transcribed_genes.xlsx contains raw counts, normalized read counts and log2foldchanges and adjusted p-values for each gene.

organism: Corynebacterium diphtheriae

source_name: bacterial culture

growth_protocol: Overnight cultures of C. diphtheriae NCTC 13129 and its delta-rnj2 mutant were used to inoculate fresh cultures in HIB at 30 C.

extract_protocol:
C. diphtheriae RNA was prepared using RNeasy Mini Kits and RNase-free DNase Sets according to the manufacture’s protocol (Qiagen). Briefly, cell pellets harvested from 3 ml log-phase cultures, cultivated in triplicates per condition, were suspended into 200 μl of chilled 10 mM RNA-free Tris-HCl, pH 8.0.  The suspension was added to a fast-protein tube (Q BIOgene) containing 700 μl RLT buffer (RNeasy Mini Kit, Qiagen), and cells were lysed using a Ribolyser (Hybaid). After centrifugation at 13,000 x g, RNA was purified from the supernatants accordingly. Purified RNA was treated by DNase (Qiagen) and subsequently cleaned by an RNeasy clean up kit (Qiagen). RNA quality was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies) with an Agilent RNA Pico 6000 kit. RNA samples with the RNA integrity number (RIN) values of > 8.0 were stored at -800C for prior to RNA-seq analysis.
2 µg total RNA from C. diphtheriae NCTC 13129 and the delta-rnj2 mutant were used. Stable RNAs were depleted with the RiboZero Kit according to manufacturer's instructions (Epicentre). Afterwards the remaining mRNA was purified using RNA MinElute columns (Qiagen) and checked for quality with the Bioanalyzer (Agilent). Fragmentation of mRNA, reverse transcription to cDNA, adenylation of 3' ends, adapter ligation and PCR amplification were performed according to TrueSeq Stranded mRNA library instructions (Illumina). Prior to paired-end sequencing of the whole transcriptome cDNA libraries on an Illumina MiSeq, the quality and concentration of the libraries were checked using the Bioanalyzer (Agilent).

tag: strain

value: Gene rnj2 (DIP1463) deleted

tag: growth phase

value: exponential growth


title: C. diphtheriae delta-rnj2 Rep 2


title: EA1909_02_a control siRNA, TNFα(+)

description: control siRNA, TNFα(+)

tag: transfection

value: non-targeting control siRNA


title: tNetSeq WT pol II Rep1

tag: growth conditions

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

value: untreated

tag: cell line


title: C. diphtheriae delta-rnj2 Rep 1


title: Cord Blood_TD008 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

value: No

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: delivery

value: Cesarean

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy


title: Cord Blood_TD014 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

value: primipara

value: Yes

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Naïve_CD8+T cell_rep1

source_name: Naïve_COR93-specific_CD8+T cell

tag: strain background

tag: age

value: 8-10 week

tag: genotype

value: COR93 T cell receptor transgenic mice (lineage BC10.3, inbred CD45.1, H-2b)

tag: tissue/cell type

value: Spleen_CD8+ T cells

tag: treatment


title: Naïve_CD8+T cell_rep2


title: C. diphtheriae Wildtype Rep 3

tag: strain

tag: growth phase


title: C. diphtheriae Wildtype Rep 2


title: EA1909_01_a control siRNA, TNFα(–)

description: control siRNA, TNFα(–)

tag: transfection

value: unstimulated with TNF[alpha]


title: Cord Blood_TD013 [methylation]

tag: gender

value: female

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

value: parous

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy


title: Cord Blood_TD021 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Cord Blood_TD010 [methylation]

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity


title: P_9_150

city: Montpellier

first: Timothy

middle: John

last: TRANBARGER

address: 911 avenue agropolis BP 64501

department: Ecology, Biodiversity and Functioning of Continental Ecosystems (ECOBIO)

country: France

institute: Institut de Recherche pour le Développement

data_processing:
The 454 pyrosequence analysis, de novo assembly performed following the methods described previously using an automated pipeline previously described and with support of the SouthGreen Bioinformatics Platform (http://southgreen.cirad.fr/), and the high performance cluster of the Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (Argout et al., 2008; Tranbarger et al., 2011).
For the Illumina samples, low quality reads were removed using Cutadapt. Trimmed reads were mapped using the BWA-MEM package with default parameters (Li 2012). Samtools was used to count mapped reads and the number of reads per kilobase and million reads (RPKM) were then calculated (Li et al., 2009]). The oil palm predicted transcripts used for mapping was downloaded from the NCBI website (http://www.ncbi.nlm.nih.gov/, GCF_000442705.1_EG5_rna.fna; January 2015).
Supplementary_files_format_and_content: xlsx; RPKM read counts

organism: Elaeis guineensis

source_name: Pedicel of fruit (150 Days after pollination, DAP) without abscission zone (AZ), and treated with ethylene for 9 hours

growth_protocol: Oil palm (Elaeis guineensis Jacq.) cultivated at Krabi Golden Tenera plantation, from a tenera clone (clone C) produced in Thailand.

extract_protocol:
For RNA extractions, the fruit bunches were collected and the base of fruits containing the AZ were sampled as follows: the spikelets were removed from the bunches, rinsed in water, then individual fruit containing the base of the fruit containing the AZ were removed with scalpel, then the base of the fruit containing the AZ were dissected (approximately 50 AZ pieces were collected per sample), weighed at approximately 3 grams then froze immediately in liquid nitrogen. Backcross material were cleaned and processed with the same procedure. Total AZ weights were approximately 3-6 grams. Total RNA from mesocarp, pedicel and the base of the fruit enriched in AZs, treated or not with ethylene was extracted as previously described [Morcillo F et al.,Tree Physiol. 2006;26(5):585-594].
Total RNA (1 μg) was used to synthesize cDNA using the first-strand cDNA synthesis kit (ImProm-IITM Reverse Transcription System, Promega). The titanium kit was used (according to Roche GS FLX Titanium manual) and cDNAs derived from the different tissues and different ethylene treatment time points were tagged independently and then mixed together in one sample for 454 pyrosequencing carried out by the National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand. Sequencing of the three natural abscission samples (AZ30, AZ120 and AZ160) collected in Thailand was complete by the company GATC Biotech (www.gatc-biotech.com).

treatment_protocol: For each sample group, independent bunches were collected from distinct individuals of the same genotype. Spikelets were then collected in the centre of each bunch and sets of 6 spikelets were randomly sampled from them and put in individual hermetically sealed 50 l volume boxes. In absence of ethylene treatment, ethylene absorber (ETHYL-GONE, http://www.biosafer.com/ethyl-gone.php) was added in the box. All the boxes were kept at ambient temperature (approximately 30°C), and after 24 h of treatment the number of fruit separating from the spikelets were counted. Using the concentration of ethylene (10 μl l-1) that induced and synchronized the highest amount of fruit shedding (Roongsattham et al., 2012), fruit from 30 and 150 DAP were treated with ethylene. Spikelets were treated with or without ethylene, and every 3 h, treated or untreated spikelets were collected and shedding was quantified for each stage of development. For each time point, the pedicel and the base of the fruit containing the primary and adjacent AZs were isolated and frozen immediately in liquid nitrogen. Samples from two independent experiments were collected immediately after bunches were harvested.

tag: tissue

value: Pedicel from fruit

tag: developmental stage

value: 150 DAP (150 Days after pollination)

tag: treatment

value: Treated with ethylene for 9 hours


title: P_3_150

source_name: Pedicel of fruit (150 Days after pollination, DAP) without abscission zone (AZ), and treated with ethylene for 3 hours

value: Treated with ethylene for 3 hours


title: AZ_9_150

source_name: Base of oil palm fruit (150 Days after pollination, DAP) containing abscission zone (AZ), and treated with ethylene for 9 hours

value: Abscission zone (AZ) from fruit


title: P_0_150

source_name: Pedicel of fruit (150 Days after pollination, DAP) without abscission zone (AZ) , and before ethylene treatment (control)

value: Before ethylene treatment (control)


title: P_6_150

source_name: Pedicel of fruit (150 Days after pollination, DAP) without abscission zone (AZ), and treated with ethylene for 6 hours

value: Treated with ethylene for 6 hours


title: AZ_3_150

source_name: Base of oil palm fruit (150 Days after pollination, DAP) containing abscission zone (AZ), and treated with ethylene for 3 hours


title: AZ_9_30

source_name: Base of oil palm fruit (30 Days after pollination, DAP) containing abscission zone (AZ), and treated with ethylene for 9 hours

value: 30 DAP (30 Days after pollination)


title: C. diphtheriae Wildtype Rep 1

tag: strain

value: untreated

tag: growth phase

value: exponential growth


title: AZ_6_30

source_name: Base of oil palm fruit (30 Days after pollination, DAP) containing abscission zone (AZ), and treated with ethylene for 6 hours


title: AZ_0_30

source_name: Base of oil palm fruit (30 Days after pollination, DAP) containing abscission zone (AZ), and before ethylene treatment (control)


title: AZ_3_30

source_name: Base of oil palm fruit (30 Days after pollination, DAP) containing abscission zone (AZ), and treated with ethylene for 3 hours


title: tNetSeq WT pol II Rep3

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

tag: growth conditions

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep.

tag: antibody

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)

tag: genotype

value: WT pol II

tag: cell line


title: Patient10 with LM primary CRC cancer tissue (circRNA)

city: Soochow

first: Qiaoming

last: Zhi

address: No.188 Shizi Road

institute: Soochow university

description:
S10_3
circular RNA expression

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: The slides were scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 10 out of 20 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: Tissue specimen

label_protocol: The Arraystar Super RNA Labeling Kit (Arraystar Inc.) was used according to the manufacturer’s guideline for CircRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including CircRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: disease state

value: colorectal cancer (CRC) with liver metastasis

tag: gender

tag: age

value: colorectal cancer tissue


title: Cord Blood_TD011 [methylation]

source_name: CBMC

value: male

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

value: No

value: primipara

tag: delivery

value: Cesarean

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa

value: Yes


title: Cord Blood_TD003 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

value: parous


title: Patient9 with LM primary CRC cancer tissue (circRNA)

description:
S9_3
circular RNA expression

tag: disease state

value: female

tag: age

tag: tissue


title: Patient8 with LM primary CRC cancer tissue (circRNA)

description:
S8_3
circular RNA expression


title: Patient7 with LM primary CRC cancer tissue (circRNA)

description:
S7_3
circular RNA expression


title: Patient6 with LM primary CRC cancer tissue (circRNA)

description:
S6_3
circular RNA expression


title: Patient5 with LM primary CRC cancer tissue (circRNA)

description:
S5_3
circular RNA expression


title: Cord Blood_TD009 [methylation]

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: Patient3 with LM primary CRC cancer tissue (circRNA)

description:
S3_3
circular RNA expression

tag: gender


title: Patient9 without LM primary CRC cancer tissue (circRNA)

description:
S9_2
circular RNA expression

value: colorectal cancer (CRC) without liver metastasis


title: Cord Blood_TD004 [methylation]

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia

tag: placenta previa


title: Patient4 with LM primary CRC cancer tissue (circRNA)

description:
S4_3
circular RNA expression

tag: disease state

tag: age

tag: tissue


title: Patient2 with LM primary CRC cancer tissue (circRNA)

description:
S2_3
circular RNA expression


title: Patient1 with LM primary CRC cancer tissue (circRNA)

description:
S1_3
circular RNA expression


title: Patient10 without LM primary CRC cancer tissue (circRNA)

description:
S10_2
circular RNA expression


title: Patient7 without LM primary CRC cancer tissue (circRNA)

description:
S7_2
circular RNA expression


title: Patient8 without LM primary CRC cancer tissue (circRNA)

description:
S8_2
circular RNA expression


title: Patient6 without LM primary CRC cancer tissue (circRNA)

description:
S6_2
circular RNA expression


title: Patient3 without LM primary CRC cancer tissue (circRNA)

description:
S3_2
circular RNA expression


title: Patient4 without LM primary CRC cancer tissue (circRNA)

description:
S4_2
circular RNA expression


title: Patient1 without LM primary CRC cancer tissue (circRNA)

description:
S1_2
circular RNA expression


title: Patient5 without LM primary CRC cancer tissue (circRNA)

description:
S5_2
circular RNA expression


title: Patient2 without LM primary CRC cancer tissue (circRNA)

description:
S2_2
circular RNA expression


title: Cord Blood_TD002 [methylation]

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: Cord Blood_TD007 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: have valid rna expression data?

tag: gestational age

tag: birthweight sdscore

tag: parity

tag: chorioamnionitis

tag: idiopathic prom without inflammation

tag: preeclampsia


title: Cord Blood_TD005 [methylation]

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: delivery

tag: maternal age

tag: maternal bmi

tag: paternal age

tag: placenta previa


title: Cord Blood_TD001 [methylation]

tag: gender

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: paternal bmi

tag: assisted reproductive technology

tag: smoking before pregnancy

tag: gestational diabetes mellitus


title: Patient10 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S10_3
lncRNA/mRNAs expression

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the lncRNA/mRNAs that at least 10 out of 20 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.#5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s  instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany)

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: disease state

value: Colorectal cancer (CRC) with liver metatasis

tag: age

tag: tissue

value: colorectal cancer (CRC) tissue


title: AZ_6_150

source_name: Base of oil palm fruit (150 Days after pollination, DAP) containing abscission zone (AZ), and treated with ethylene for 6 hours

value: Abscission zone (AZ) from fruit

tag: developmental stage

value: 150 DAP (150 Days after pollination)

tag: treatment

value: Treated with ethylene for 6 hours


title: Patient9 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S9_3
lncRNA/mRNAs expression


title: Patient7 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S7_3
lncRNA/mRNAs expression


title: Patient5 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S5_3
lncRNA/mRNAs expression


title: PBMCs, Osteoarthritis rep2

city: Shanghai

first: liying

last: Jiang

address: Pudong

institute: collaboration research centre

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., 2016).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample ...

source_name: Blood

growth_protocol: Cells were collected directly for subsequent experiments.

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).
Next-generation libraries were prepared using VAHTS TM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).

treatment_protocol: PBMCs were subjected to RNA seqencing directly.

tag: cell type

value: Peripheral blood mononuclear cell

value: Osteoarthritis patients


title: PBMCs, Healthy rep3

value: Healthy Control


title: PBMCs, Osteoarthritis rep3


title: PBMCs, Osteoarthritis rep1


title: SKN3_WGBS

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Sequences were all aligned to the GRCh38 analysis set.
Reads from ChIP-seq and targeted sequencing for knock-out validation were mapped using BWA v0.7.17 with default settings of the BWA-MEM algorithm.
WGBS/RNA-seq reads were adapter and quality (Q10) trimmed using BBDuk from BBTools v38.73 (https://sourceforge.net/projects/bbmap/) (t=10 ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=10 minlen=2)
Trimmed WGBS reads were aligned as well as deduplicated using BISCUIT  v0.3.12 (https://github.com/zhou-lab/biscuit) with default options
Per-base methylation calling was performed with MethylDackel  v0.4.0 (https://github.com/dpryan79/MethylDackel) after excluding biased ends
Trimmed RNA-seq reads were aligned using STAR v2.7.3a based on GENCODE Release 33 annotations with the ENCODE standard options
ENCODE blacklisted regions were excluded from all analyses.
Variants were identified with GATK v4.1.5.0 using HaplotypeCaller.
Genome_build: hg38
Supplementary_files_format_and_content: Salmon quantification files were obtained using Salmon v1.1.0 with default settings of the gentrome-based option
Supplementary_files_format_and_content: ChIP-seq bigWig files were obtained through first binning raw tag counts into 10 kb windows using bedtools76 v2.29.0 with intersectBed (-c) in combination with the makewindows command. Next, library size normalization consisted of dividing binned tag counts by the total number of mapped reads after filtering, while input normalization involved taking the log2 ratio of ChIP signals by those of the input (i.e., without immunoprecipitation) with the addition of pseudocount (1) to avoid division by 0. Additionally, quantitative normalization entailed the multiplication of original signal (either in CPM or as log2 ratio over input) by the genome-wide modification percentage information obtained from mass spectrometry.
Supplementary_files_format_and_content: narrowPeak of H3K27ac peaks were called using MACS v2.2.6 (-g hs -q 0.01)
Supplementary_files_format_and_content: WGBS bigWig files in 1 kb bins were calculated by taking per-base methylation calls and dividing the number of methylated base-calls divided by the total number of calls per window.
Supplementary_files_format_and_content: RNA-seq bigWig files were created through deepTools v3.3.1 with bamCoverage --normalizeUsing CPM
Supplementary_files_format_and_content: RData file containing the H3K27ac consensus peakset count matrix (dba.rda) was produced with DiffBind v2.14.0.
Supplementary_files_format_and_content: RData file containing a subsetted beta value matrix (mCG.450k.rda) was generated by filtering the genome-wide CpG matrix to include only CpG sites also covered by the Illumina 450k array.

source_name: SKN-3 cells

extract_protocol:
DNA was extracted from flash frozen cell pelets of about 5 million cells using DNeasy Blood & Tissue Kit from QIAGEN Cat. #69508.
Libraries were generated from 1000 ng of genomic DNA spiked with 0.1% (w/w) unmethylated λ DNA (Roche Diagnostics) and fragmented to 300–400 bp peak sizes using the Covaris focused-ultrasonicator E210. Fragment size was controlled on a Bioanalyzer High Sensitivity DNA Chip (Agilent) and NxSeq AmpFREE Low DNA Library Kit (Lucigen) was applied. End repair of the generated dsDNA with 3' or 5' overhangs, adenylation of 3' ends, adaptor ligation, and clean-up steps were carried out as per Lucigen’s recommendations. The cleaned-up ligation product was then analyzed on a Bioanalyzer High Sensitivity DNA Chip (Agilent). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research) according to the manufacturer’s protocol. DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems) according to the manufacturer’s protocol. The amplified libraries were purified using Ampure XP Beads (Beckman Coulter), validated on Bioanalyzer High Sensitivity DNA Chips, and quantified by PicoGreen.

tag: cell line

value: Patient-derived head and neck squamous cell carcinoma cell line

tag: genotype

value: NSD1 mutant


title: Patient4 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S4_3
lncRNA/mRNAs expression

tag: gender


title: PBMCs, Healthy rep1


title: PBMCs, Healthy rep2


title: Patient2 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S2_3
lncRNA/mRNAs expression

value: male


title: Patient10 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S10_2
lncRNA/mRNAs expression

value: Colorectal cancer (CRC) without liver metatasis


title: Patient8 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S8_2
lncRNA/mRNAs expression


title: SCC4_WGBS

source_name: SCC-4 cells


title: Patient1 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S1_3
lncRNA/mRNAs expression


title: Patient9 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S9_2
lncRNA/mRNAs expression


title: Patient7 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S7_2
lncRNA/mRNAs expression


title: BICR78_WGBS

source_name: BICR-78 cells


title: Patient6 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S6_3
lncRNA/mRNAs expression


title: Det562_KO4_WGBS

source_name: Detroit-562 cells

value: NSD1 knock-out


title: Det562_KO2_WGBS


title: Patient3 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S3_3
lncRNA/mRNAs expression


title: AZ_0_150

source_name: Base of oil palm fruit (150 Days after pollination, DAP) containing abscission zone (AZ), and before ethylene treatment (control)

value: Before ethylene treatment (control)


title: Det562_KO1_WGBS


title: Patient6 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S6_2
lncRNA/mRNAs expression


title: Cal27_KO17_WGBS

source_name: Cal-27 cells


title: Patient4 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S4_2
lncRNA/mRNAs expression


title: Det562_WGBS

value: NSD1 wild-type


title: FaDu_KO1_WGBS

source_name: FaDu cells

value: FaDu


title: Cal27_KO1_WGBS


title: TAT-E1_RNA-seq

city: shanghai

first: qiongqiong

last: hou

address: huanke road 199

institute: shanghaitech university

data_processing:
based on HiSeq Xten (illunima) sequencing platform and Paired-End was used
Raw data were filtered by FASTX-Toolkit to generate clean reads and were mapped to human GRCh38 using Hisat
Stringtie software was used to count Fragments PerKilobase Million (FPKM)
edgeR software was used to statistical quantification
Gene expression was presented with GO&KEGG annotation
Genome_build: human GRCh38

source_name: cerebral organoid

extract_protocol:
Samples were washed in 1×Hank’s balanced salt solution (HBSS) and Total RNA samples were extracted with Trizol
Basaed on HiSeq Xten (illunima) platform and Base Calling was transformed to Sequenced Reads. Paired-end (PE150) was used.

value: neuroepithellum

tag: brain region

value: derived from cortex

value: cerebral organoid


title: Cal27_WGBS


title: Patient5 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S5_2
lncRNA/mRNAs expression

value: colorectal cancer (CRC) tissue


title: TAT-S2_RNA-seq

value: TAT-Scr


title: Patient2 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S2_2
lncRNA/mRNAs expression


title: FaDu_WGBS


title: Patient3 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S3_2
lncRNA/mRNAs expression

value: female


title: Patient1 without LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S1_2
lncRNA/mRNAs expression


title: TAT-S1_RNA-seq


title: TAT-465-481_ChIP-seq_input

description:
E2_peaks.txt
E2_input_clean

data_processing:
based on HiSeq Xten (illumina) sequencing platform and Paired-End (PE150) was used
ChIP-seq reads were aligned to the human GRCh38 genome and Burrows Wheeler Aligner (BWA) was used
Sequenced reads were trimmed for adaptor sequence using Skewer
Fragment sizes were predicted with MACS and normalized strand coefficient (NSC) was counted
peaks were called using MACS2 and MEME and Dreme software were used in demonstrating motif sequence
Genome_build: human GRCh38
Supplementary_files_format_and_content: txt; peak counts

extract_protocol:
Samples were sheared in 1×Hank’s balanced salt solution (HBSS) and fixed in 1% formaldehyde to link proteins to DNA. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Specific antibody of H3K9me2 was used in immunoprecipitation and genomic DNA was purified.
All procedures followed the guidelines provided by Illumina Paired-End DNA Sample Prep Kit. Briefly, after purified from ChIP samples, DNA was end repaired and then added with A and adapter for amplification.


title: TAT-Scr_ChIP-seq

description:
S2_peaks.txt
S2_clean

value: TAT-scrambled


title: TAT-Scr_ChIP-seq_input

description:
S2_peaks.txt
S2_input_clean


title: TAT-465-481_ChIP-seq

description:
E2_peaks.txt
E2_clean


title: Z1141

city: Dallas

first: Sara

middle: K

last: Hildebrand

state: TX

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

description: N4bp1 KO + LPS

data_processing:
Base calling and demultiplexing was performed using CASAVA 1.8.2
fastq.gz files were aligned to the mm10 reference genome/transcriptome using tophat-2.0.10
Transcripts were assembled and differential expression performed using cufflinks-2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: text file containing gene FPKM values for each sample
Supplementary_files_format_and_content: Excel files include FPKM values for each sample group

source_name: peritoneal macrophages

growth_protocol: The peritoneal macrophages were cultured at 37 °C in 95% air and 5% CO2 in DMEM cell culture medium (DMEM containing 10% FBS (BioFluid), 1% penicillin and streptomycin (Life Technologies))

extract_protocol:
Total RNAs from the cells were extracted using the RNeasy Plus kit with genomic DNA elimination (Qiagen), according to the manufacturer’s instructions.
Libraries were prepared with KAPA Stranded mRNA-Seq Kit (KK8420, KAPA Biosystems), according to the manufacturer’s instructions.

treatment_protocol: The peritoneal macrophages were untreated or treated with R848 (20 ng/ml) or LPS (10 ng/ml) for 2 hrs.

tag: strain

value: peritoneal macrophages

value: N4bp1 KO

value: LPS treated


title: Z1144

description: N4bp1 KO + LPS


title: Z1142

description: N4bp1 WT + R848

value: wild-type

value: R848 treated


title: Z1143

description: N4bp1 KO + R848


title: Z1140

description: N4bp1 WT + LPS


title: Fibroblast-WT-rep1

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5) on Affymetrix Mouse Genome 430 2.0 Array

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

data_processing: Data processing was preformed using R/Bioconductor packages, performing a rma normalisation and limma based differential expression analysis with an adjustment of the p-values for multiple testing via the Benjamini and Hochberg algorithm.

source_name: Mouse fibroblast

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

growth_protocol: Live fibroblast were sorted by flow cytometry from age- and gender-matched wild-type, InvEE and InvEE tumour-associated back skin of PDGFRα-H2B-eGFP reporter mice.

extract_protocol: RNA was isolated from sorted cells using the Qiagen RNeasy kit and amplified once using NuGEN Pico Kit

treatment_protocol: Dissected skin was scraped free of muscle and dermal fat and incubated overnight at 4°C in 0,25% trypsin solution. The interfollicular epidermis was scraped away and dermis was minced and enzymatically dissociated for 45 minutes at 37°C using a mixture of 1,25 mg/ml collagenase type I (Invitrogen), 0,5 mg/ml collagenase type II (Worthington), 0,5 mg/ml collagenase type IV (Sigma), 0,1 mg/ml hyaluronidase IVS (Sigma) and 50 U/ml DNase I (Roche). Normal, inflammatory and papilloma-associated fibroblasts were isolated by flow cytometric sorting on a BD FACSAria cell sorting system of GFP-positive cells from 7-weeks-old wild-type, InvEE and InvEE tumour-associated back skin of male mice containing a PDGFRα-H2B-eGFP allele

value: skin

value: fibroblast

value: normal


title: Fibroblast-WT-rep2


title: Z1138

description: N4bp1 WT + R848


title: S60641

description: N4bp1 KO

value: no treatment


title: S61206

description: N4bp1 KO


title: S61208

description: N4bp1 WT


title: Z1139

description: N4bp1 KO + R848


title: S60634

description: N4bp1 WT


title: Astrocyte_Zeb2_KD2

city: Houston

first: Haichao

last: Wei

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

data_processing:
The quality of all sequenced samples was analyzed using FastQC.
Reads were mapped to the Mm10. Mapping and transcript assembly were performed with TopHat v2.1.0 and Cufflinks v2.2.1 respectively using default parameters.
The gene read counts of samples were normalized and compared to control samples using DESeq2
Genome_build: Mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: Primary astrocytes from P4-P7 postnatal brain

extract_protocol:
Total RNA isolation using TRIzol according to detailed manufacturer’s instructions.
Libraries were constructed with the NEBNext Ultra Directional RNA library Prep Kit for Illumina (E7420, New England Biolabs) by following the manufacturer’s instructions.

treatment_protocol: Cells were transduced with Zeb2 knockdown lentivirus and selected using puromycin (1ug/ml) after 48hr for 3 days.

value: Primary astrocytes


title: Fibroblast-WT-rep3


title: Astrocyte_Zeb2_KD1


title: MCR:SATB2-SATB2

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
ChIP-Seq aligned to zebrafish Zv9 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: danRer7
Supplementary_files_format_and_content: called peaked in bed file

organism: Danio rerio

source_name: zebrafish primary melanoma tumor

growth_protocol: Zebrafish Tg(mitfa:BRAFV600E); p53-/-; mitfa-/- one cell stage embryos were injected with a MiniCoopR (MCR) expression vector to induce melanocyte-specific overexpression of either EGFP (control) or human SATB2, raised to adulthood and monitored for melanoma formation.

extract_protocol:
Zebrafish melanomas were excised, finely minced using a scalpel blade and cross linked using 1.1% formaldehyde. The tumor suspension was mechanically homogenized on ice, and passed through a 100 μm filter. Whole cell extracts were sonicated to solubilize the chromatin, and target bound fragments (average size of 300 bp) were isolated with antibodies as indicated.
Purified immunoprecipitated DNA was prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end-repaired and libraries were prepared using the NEBNext Multiplex Oligos Kit (18-cycle PCR enrichment step). Amplified fragments between 150 and 350bp were isolated by agarose gel electrophoresis, and run on an Illumina Hi-Seq2000.

value: primary melanoma tumor

tag: antibody

value: SATB2 (Santa Cruz:sc-81376)

value: Tg(mitfa:BRAFV600E); p53-/-; mitfa-/-


title: MCR:SATB2-Input


title: Fibroblast-Pap-rep3

value: Tumor-associated


title: Fibroblast-InvEE-rep3

value: inflammation


title: Z1145

description: N4bp1 WT + LPS


title: Fibroblast-Pap-rep1


title: Fibroblast-InvEE-rep2


title: Fibroblast-WT-rep4


title: Fibroblast-Pap-rep2


title: Fibroblast-Pap-rep4


title: Fibroblast-InvEE-rep4


title: Fibroblast-InvEE-rep1


title: Astrocyte_Zeb2_ctr2

treatment_protocol: Cells were transduced with control lentivirus and selected using puromycin (1ug/ml) after 48hr for 3 days.

value: WT


title: Astrocyte_Zeb2_ctr1


title: US-1630685

city: London

first: Christopher

last: Chiu

address: Hammersmith Campus, Du Cane Road

department: Infectious Disease

institute: Imperial College London

data_processing:
Adaptors were removal by SeqPrep.
RNAseq reads were mapped to human B38 genome with Omicsoft OSA aligner.
Read counts mapped to the human ensemble genes (Release 75) were calculated with RSEM.
RNAseq that did not pass QC were exclude from downstream analysis. The gene count data were normalized and differential gene expression was calculated by DESeq2 (R package, version 1.18.1)
Genome_build: human B38
Supplementary_files_format_and_content: file contains gene counts for all genes in the samples submitted

source_name: Nasal Scrape

extract_protocol:
RNAseq cDNA library was prepared with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat Sample Prep Kit (Illumina, #RS-122-2203). Starting with 100 ng of total RNA, cytoplasmic ribosomal RNA was removed by hybridization to a biotinylated probe selective for ribosomal RNA species, followed by streptavidin bead binding and sample purification.  The resulting cytoplasmic rRNA-depleted sample was chemically fragmented and converted into single-stranded cDNA using reverse transcriptase and random hexamer primers, with the addition of Actinomycin D to suppress DNA-dependent synthesis of the second strand.  Double-stranded cDNA was created by removing the RNA template and synthesizing the second strand in the presence of dUTP in place of dTTP.  A single A base was added to the 3’ end to facilitate ligation of sequencing adapters, which contain a single T base overhang.  Adapter-ligated cDNA was amplified by polymerase chain reaction to increase the amount of sequence-ready library.  During this amplification the polymerase stalls when it encounters a U base, rendering the second strand a poor template.  Accordingly, amplified material used the first strand as a template, thereby preserving the strand information.  Final cDNA libraries were analyzed for size distribution using the Agilent Tapestation 2200 (D1000 kit, Agilent # 5067-5582 and 5067-5583), quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824), then normalized to 2 nM in preparation for sequencing. Prepared libraries were sequenced with 2 × 50 bp paired-end reads on the Illumina HiSeq 2500 sequencer with a minimum of 3 GB of raw RNA sequencing data (Illumina, San Diego, USA).
TruSeq Stranded Total RNA Ribo-Zero library preparation

tag: donor id

tag: batch

value: new

tag: timepoint

tag: outcome

value: Uninfected

tag: symptom

value: Nasal Scrape


title: Patient8 with LM primary CRC cancer tissue (lncRNA/mRNA)

description:
S8_3
lncRNA/mRNAs expression

source_name: Tissue specimen

tag: disease state

value: Colorectal cancer (CRC) with liver metatasis

value: female

value: colorectal cancer (CRC) tissue


title: longRNAseq_WT rep3

city: Barcelona

first: Eva Maria

last: Novoa

address: Dr. Aiguader 88

country: Spain

institute: Center for Genomic Regulation

data_processing:
trimming: cutadapt v.1.9.1
mapping: STAR v2.7.0f
mismatch analysis: mpileup2stats
Genome_build: vM21 annotation
Supplementary_files_format_and_content: tab delimited file with frequency of mismatches, insertions and deletions obtained with mpileup2stats

source_name: brain

growth_protocol: Total RNA was extracted from total mouse brain

extract_protocol:
total RNA was extracted and size-selected (>200 bp), and this material was used as starting point for the libraries.
TruSeq Total RNA Illumina sequencing

treatment_protocol: TRMT1L KO was compared to WT

value: brain

tag: genotype/variation


title: US-1596621

value: pilot

tag: tissue


title: US-1635402

value: Infected

value: cold


title: US-1630691


title: longRNAseq_KO rep2

value: TRMT1L KO


title: US-1596603


title: longRNAseq_WT rep2


title: longRNAseq_KO rep3


title: US-1630616


title: longRNAseq_WT rep1


title: US-1596617


title: US-1630659


title: US-1596605