title: NEUR_D10_rep2

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Developing Neuron Day 10 replicate 2

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Post CASAVA deplexing, .fastq files generated per library were import into the CLCbio Genomics Workbench (www.clcbio.com) and QC inspected, adaptor clipped, low quality trimmed, filtered, then mapped. Per quality trimming, 15bp from the 5' end of each read was globally removed along with 1bp from the 3' end. Bases with a call accuracy < 95% were trim-removed thereafter. Per filtering, reads having more than two ambiguities were discarded along with those having read length <15bp post post quality trimming. Per mapping, the "RNA-Seq" tool supported in the Workbench was used to locally align reads by library against the human genome (GRCh38/hg38) without masking; keeping only those mapped reads with >= 80% reference identity for >=80% read length. Post mapping, the number of reads falling in a RepeatMasker annotated "HERV" region (Library 20120124) were enumerated and the counts converted into "Reads Per Kilo base of transcript per Million mapped reads" ("RPKM") expression values. RPKM expression values were next organized by HERV region across libraries and imported into R (https://cran.r-project.org/). In R, RPKM expression values were pedestalled by 2, Log2 transformed, filtered to remove regions not having at least one transformed value >1, then quantile normalized.  Normalized values for remaining regions were then used to assess for and remove library-level outliers via tukey box plot, covariance-based PCA scatter plot, and pearson correlation heat map. For libraries not removed as outliers, normalization of RPKM expression values was repeated and the new normalized expression noise modeled using LOWESS (CV~mean). Based on the LOWESS fit, regions not having at least one normalized value >=2.00 were considered noise-biased and subsequently discarded as such.  For regions not discarded, differential expression across libraries was tested for using the one-factor ANOVA test under BH FDR MCC condition using sample type as the factor. Regions having a corrected P < 0.05 by this test were subset and deemed to be those having differential expression across the sample types tested. For those regions subset only, the TukeyHSD post-hoc test was further applied to identify which regions between sample types have an uncorrected P <0.05 and an absolute difference of means >=2. These regions were subsequently deemed to be differentially expressed between the two sample types compared.
Genome_build: hg38
Supplementary_files_format_and_content: RPKM enumerated expression for each RepeatMasker annotated HERV region in hg38.  Also provided are .txt files that describe the cross sample RPKM expression before normalization, after normalization (pre-noise filtering), and after noise filtering.

source_name: Developing Neuron

growth_protocol: For the three human iPSC lines, one was derived from fibroblasts and two from peripheral blood mononuclear cells.  All three of these lines were then reprogrammed via episomal plasmids and grown in Essential 8 medium of a 6-well plate with daily medium changes (Chen et al, 2012).  The Neural stem cells (NSCs) were derived from three episomally reprogrammed iPSC lines and one human ES cell line.  They were expanded in a neurobasal medium containing B27 and FGF2 (Efthymiou et al., 2014).  Where after, neuronal differentiation was initiated by medium exchange.  The Mature Neuron sample was obtained by growing NSCs for 21 days in neuronal differentiation medium (Shaltouki et al., 2013).

extract_protocol:
RNA extractions of iPSCs and NSCs were performed when cells were 70% confluent and at the indicated time point for the differentiated Neurons and Astrocytes.  All RNA was extracted with the RNAesy Mini Kit (Qiagen).
Libraries for each RNA extracted were prepared using 10ug in conjunction with the Illumina single-end Total RNA-Seq ribosome depletion kit.  Post preparation, libraries were single-end seqeunced (50bp) for >30M reads each.

tag: sample group

tag: differentiation days


title: NEUR_D10_rep1

status: Public on Aug 05 2020

type: SRA

country: USA

description: Developing Neuron Day 10 replicate 1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: NEUR_D7_rep2

description: Developing Neuron Day 7 replicate 2


title: miRNA_Subject_2101111

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

data_processing:
Standardized samples using log-transformed counts per million standardization
miRNA sequencing data processed in R
The count data was filtered to exclude universally lowly expressed transcripts, and data were normalized by quantiles using algorithms enabled through the DESeq2 processing pipeline.
Normalizing the data by median signal intensity using the DESeq2 package in R
Genome_build: mirBase v20
Supplementary_files_format_and_content: raw counts

source_name: Placenta of infants born at low gestational age

extract_protocol:
Recruited patients from the ELGAN cohort that were scheduled to give birth at participating institutions between 2002 to 2004. Patients involved in the study comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation.  Maternal, demographic, and clinical assessments were taken before and after delivery. Each infant's anthropometric measures, including birthweight, were recorded throughout hospitalization and at follow-up. Placenta samples were collected immediately after surgery and stored at -80 degrees C untile further analysis. RNA molecules with 18 nucleotides or greater were extraced with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) and quantified with the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, Ma) and tested for quality based on RNA integrity scores produced by the QIiAxcel system (Qiagen).
Isolated RNA samples were prepared using the HTG EdgeSeq miRNA Whole Transcriptome Assay, we measured the expression of 2,083 miRNA transcripts in the placenta using next-generation sequencing

tag: tissue

value: placenta

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)

tag: infarct (infarcted placenta) (0=absent, 1=present)

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)

tag: bmi (body mass index)

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: miRNA_Subject_2101101


title: Mature_Neuron

description: Mature Neuron

source_name: Mature Neuron


title: miRNA_Subject_2101171


title: miRNA_Subject_2101081


title: HEP_24h_VC-2

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: E1002 Biomedical Science Tower,  200 Lothrop Street

department: Department of Immunology

institute: University of Pittsburgh

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-VC-2

data_processing:
NextSeq500 75bp PE v2 High Output run, with 27 multiplexed samples per run
The fastq files were generated and trimmed through Basespace with application “FASTQ Generation v1.0.0”.
Differential expression analysis was performed with edgeR and DE genes were selected with a False Discovery Rate (FDR) < 0.05.
Genome_build: hg38, UCSC for Hep G2, and hg19, UCSC  for MDA-MB-231
Supplementary_files_format_and_content: .csv files delimited matrix showing raw counts of refGenes

growth_protocol: Both Hep G2 and MDA-MB-231 cell lines were purchased from ATCC (MA, USA). Cells were cultured in DMEM medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) at 37 °C with 5% CO2

extract_protocol:
The treated cells were harvested, and the cell pellets were snap frozen with liquid nitrogen and stored at−80°C.Total RNA was isolated with PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. After quantified using a NanoDrop Spectrophotometer ND-1000 (Thermo Fisher Scientific), the quality of the total RNA was verified on a Bioanalyzer by Cancer Genome Facility (SA, Australia) ensuring all samples had RINs >7.0. For both cell lines, the sequencing was performed in Ramaciotti Centrefor Genomics (NSW, Australia). The sample preparation for each cell line was TruSeq Stranded mRNA-seq with dual indexed, on the NextSeq500 v2 platform. The parameter was 75bp paired-end High Output.
Total RNA was isolated with PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol (Rev: 21 May 2012).  Sample preparation were employing TruSeq Stranded mRNA Library Prep Kit (Illumina) with 1μg input total RNA.

treatment_protocol: Drug treatments were designed as follows: pure complete medium,  vehicle control (VC; 0.25% Tween 80 with 10 mM in PBS), 2 mg/ml CKI, or 5FU (150 μg/ml for Hep G2 and 20 μg/ml for MDA-MB-231). Cells were treated with medium only, vehicle control, CKI, and 5Fu are labelled as “untreated”, “CKI”, and “5FU”.

tag: cell line

value: Hep G2

tag: tumor type

value: liver cancer

tag: treatment

value: VC

tag: time


title: miRNA_Subject_2101021


title: NEUR_D7_rep1

description: Developing Neuron Day 7 replicate 1

tag: sample group

tag: differentiation days


title: NEUR_D5_rep3

description: Developing Neuron Day 5 replicate 3


title: miRNA_Subject_2100961

tag: tissue

tag: asthma (0=absent, 1=present, 2=data not obtained)


title: NEUR_D5_rep2

description: Developing Neuron Day 5 replicate 2


title: NEUR_D3_rep3

description: Developing Neuron Day 3 replicate 3


title: miRNA_Subject_2100951

tag: birthweight (grams)

tag: sex (0=female, 1=male)


title: miRNA_Subject_2100941

tag: chorioamnionitis (0=absent, 1=present)

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)


title: NEUR_D3_rep2

description: Developing Neuron Day 3 replicate 2


title: miRNA_Subject_2100901

tag: infarct (infarcted placenta) (0=absent, 1=present)

tag: placwt (placenta weight) (grams)


title: miRNA_Subject_2100911

tag: mage (age of mother) (years)

tag: bmi (body mass index)


title: NEUR_D3_rep1

description: Developing Neuron Day 3 replicate 1


title: NSC_rep2

description: Neural Stem Cell replicate 2

source_name: NSC

value: NSC


title: NEUR_D10_rep3

description: Developing Neuron Day 10 replicate 3


title: miRNA_Subject_2100891

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: miRNA_Subject_2100881


title: miRNA_Subject_2100871


title: NSC_rep3

description: Neural Stem Cell replicate 3


title: miRNA_Subject_2100851


title: miRNA_Subject_2100783


title: iPSC_rep2

description: iPSC replicate 2

source_name: iPSC

value: iPSC


title: miRNA_Subject_2100781


title: iPSC_rep1

description: iPSC replicate 1


title: NEUR_D5_rep1

description: Developing Neuron Day 5 replicate 1


title: iPSC_rep3

description: iPSC replicate 3


title: miRNA_Subject_2100841


title: miRNA_Subject_2100711


title: miRNA_Subject_2100691


title: miRNA_Subject_2100712


title: miRNA_Subject_2100631


title: miRNA_Subject_2100621


title: miRNA_Subject_2100601


title: NSC_rep1

description: Neural Stem Cell replicate 1


title: miRNA_Subject_2100591


title: miRNA_Subject_2100571


title: miRNA_Subject_2100472


title: miRNA_Subject_2100391


title: miRNA_Subject_2100381


title: miRNA_Subject_2100371


title: miRNA_Subject_2100301


title: EGA5

type: RNA

city: Lausanne

first: Claudiane

last: Guay

state: Vaud

address: Du Bugnon 9

department: DNF

country: Switzerland

institute: University of Lausanne

description: Gene expression 28 days after EGA surgery

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Mouse Genome Oligo Microarray (4 x 44K, Agilent Technologies) based on the manufacturer’s standard protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

organism: Mus musculus

source_name: ob/ob EGA islets, biological replicate 5

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent Cyanine-3 (cy3) cRNA using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: RNA was extracted using the miRNeasy kit (Qiagen), according to manufacturer guidelines.

treatment_protocol: Pancreatic islets were isolated from lean (WT) mice or from ob/ob mice, 28 days after sham or EGA surgery.

value: pancreatic islets

tag: strain

tag: gender

value: male


title: EGA1

source_name: ob/ob EGA islets, biological replicate 1


title: EGA4

source_name: ob/ob EGA islets, biological replicate 4


title: Sham2

description: Gene expression 28 days after sham surgery

source_name: ob/ob sham islets, biological replicate 2


title: miRNA_Subject_1700731


title: miRNA_Subject_1700671


title: WT2

description: Gene expression in control mice

source_name: C57Bl/6J islets, biological replicate 2


title: SW162C-3 (unrelated control 1 clone 1_iPSC)

city: Manchester

first: Huw

middle: Batten

last: Thomas

state: Greater Manchester

address: Dover Street

department: Biological Sciences

country: United Kingdom

institute: University of Manchester

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW15_S79

data_processing:
Low quality bases and adpeter sequences were trimmed using Trimmomatic
Reads aligned to GRCh38 genome or transcriptome (Gencode v28 human gene annotation) using single pass mode of STAR aligner (v2.5.3a)
Differential expressio analysis was conducted using Bioconductor DESeq2 v1.20.0 using default parameters
rMATS v.4.0.2 was used to identify mis-splicing events filtering for events with a p-value <0.05 and FDR < 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file of read counts in all samples and rMATS txt output files

source_name: unrelated control 1 clone 1_iPSC

growth_protocol: iPSCells were cultured in feeder-free conditions at 37°C with 5% CO2 on VTN-coated 6-well tissue plates in TeSR-E8 with daily feeding.

extract_protocol:
Total RNA was extracted using TRI-Reagent(r) and purified using Rneasy column purification kit (Qiagen), including a Dnase digestion step.
Libraries were constructed using standard illumina TruSeq Stranded mRNA assay protocols

tag: subject status

value: unrelated control

tag: clone id

value: unrelated control 1 clone 1

tag: cell type

value: Human induced pluripotent stem cell (iPSC)


title: miRNA_Subject_1700601

tag: tissue


title: Sham3

source_name: ob/ob sham islets, biological replicate 3


title: SW171A-2 (unrelated control 2 clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW17_S81

source_name: unrelated control 2 clone 1_iPSC

value: unrelated control 2 clone 1


title: SW171A-1 (unrelated control 2 clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW16_S80


title: SW162C-2 (unrelated control 1 clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW14_S78


title: miRNA_Subject_1700561

tag: asthma (0=absent, 1=present, 2=data not obtained)


title: WT3

description: Gene expression in control mice

source_name: C57Bl/6J islets, biological replicate 3


title: miRNA_Subject_1700551

tag: birthweight (grams)


title: WT4

description: Gene expression in control mice

source_name: C57Bl/6J islets, biological replicate 4


title: SW162C-1 (unrelated control 1 clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW13_S77


title: EGA3

source_name: ob/ob EGA islets, biological replicate 3


title: EGA2

source_name: ob/ob EGA islets, biological replicate 2


title: miRNA_Subject_1700501

tag: sex (0=female, 1=male)


title: KW191B-3 (unaffected parent clone 2_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW12_S76

source_name: unaffected parent clone 2_iPSC

value: unaffected parent

value: unaffected parent clone 2


title: Sham1

source_name: ob/ob sham islets, biological replicate 1


title: KW191B-2 (unaffected parent clone 2_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW11_S75


title: SW171A-3 (unrelated control 2 clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW18_S82


title: miRNA_Subject_1700443

source_name: Placenta of infants born at low gestational age

tag: chorioamnionitis (0=absent, 1=present)


title: WT1

description: Gene expression in control mice

source_name: C57Bl/6J islets, biological replicate 1


title: KW191B-1 (unaffected parent clone 2_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW10_S74


title: miRNA_Subject_1700442

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)


title: KW191A-3 (unaffected parent clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW9_S73

source_name: unaffected parent clone 1_iPSC

value: unaffected parent clone 1


title: miRNA_Subject_1700431

tag: infarct (infarcted placenta) (0=absent, 1=present)


title: KW181B-3 (patient clone 2_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW6_S70

source_name: patient clone 2_iPSC

value: craniofacial developmental disorder Burn-McKeown Syndrome (BMKS) patient

value: patient clone 2


title: miRNA_Subject_1700441

value: placenta

tag: placwt (placenta weight) (grams)


title: KW191A-2 (unaffected parent clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW8_S72


title: miRNA_Subject_1700411

tag: mage (age of mother) (years)


title: KW181B-1 (patient clone 2_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW4_S68


title: miRNA_Subject_1700412

tag: bmi (body mass index)


title: KW181B-2 (patient clone 2_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW5_S69


title: miRNA_Subject_1700342

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)


title: KW181A-2 (patient clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW2_S66

source_name: patient clone 1_iPSC

value: patient clone 1


title: KW181A-1 (patient clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW1_S65


title: miRNA_Subject_1700341

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: KW191A-1 (unaffected parent clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW7_S71


title: miRNA_Subject_1700331


title: miRNA_Subject_1700282


title: SW171A-1 (unrelated control 2 clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW16_S58

source_name: unrelated control 2 clone 1_iNCC

treatment_protocol: iPSC colonies were resuspended neural crest induction (NCI) medium 50:50 DMEM:F12 (Sigma) supplemented with 1x Glutamax, 0.5% BSA and 30μM CHIR 99021 and 10μM Y-27632 and incubated for 48h with daily replenishment of medium. Cells were then incubated in NCI-only for a further 72h

value: Human induced neural crest cell (iNCC)


title: SW171A-2 (unrelated control 2 clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW17_S59


title: miRNA_Subject_1700242


title: miRNA_Subject_1700241


title: miRNA_Subject_1700221


title: miRNA_Subject_1700211


title: miRNA_Subject_1700343


title: KW181A-3 (patient clone 1_iPSC)

description:
processed data file: GEO_RNAseqSep2019.xlsx
KW3_S67


title: SW162C-1 (unrelated control 1 clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW13_S55

source_name: unrelated control 1 clone 1_iNCC


title: miRNA_Subject_1700181


title: KW191B-3 (unaffected parent clone 2_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW12_S54

source_name: unaffected parent clone 2_iNCC


title: SW171A-3 (unrelated control 2 clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW18_S60


title: miRNA_Subject_1700161


title: SW162C-3 (unrelated control 1 clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW15_S57


title: miRNA_Subject_1700112


title: KW191B-1 (unaffected parent clone 2_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW10_S52


title: miRNA_Subject_1700141


title: miRNA_Subject_1700281


title: KW191A-1 (unaffected parent clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW7_S49

source_name: unaffected parent clone 1_iNCC


title: miRNA_Subject_1700081


title: KW181B-3 (patient clone 2_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW6_S48

source_name: patient clone 2_iNCC


title: miRNA_Subject_1700091


title: KW191A-2 (unaffected parent clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW8_S50


title: KW181A-3 (patient clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW3_S45

source_name: patient clone 1_iNCC


title: miRNA_Subject_1700011


title: KW181B-1 (patient clone 2_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW4_S46


title: miRNA_Subject_1600901


title: miRNA_Subject_1600903


title: miRNA_Subject_1700102


title: miRNA_Subject_1600902


title: miRNA_Subject_1600891


title: KW181A-2 (patient clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW2_S44


title: SW162C-2 (unrelated control 1 clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW14_S56


title: miRNA_Subject_1600752


title: BruChase-seq_siPUM_rep3

city: Ann Arbor

first: Peter

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

description:
Sample_42735_293siPUM6h3
42735_GTTTCG

data_processing:
library strategy: BruChase-seq
Data processing for Bru-seq and BruChase-seq is described in Paulsen et al. (doi: 10.1016/j.ymeth.2013.08.015)
Data processing for SEQRS was performed using custom python scripts to split reads by barcode. 20mers were identified by location in the read using custom python scripts. Lower kmers can be easily calculated from 20mer reads
Genome_build: hg19 for Bru-seq and BruChase-seq
Supplementary_files_format_and_content: read count files contain count of reads over genes or exons where each read is split into fracitonal coverage over the length of the read. 20mer files contain the 20mer variable region extracted from the raw reads

extract_protocol:
Bru-seq and BruChase-seq were conducted as described in Paulsen et al. (doi: 10.1016/j.ymeth.2013.08.015) in HEK293 cells grown in the presence of siPUM1/2 or siNTC.
SEQRS was conducted on PUM1 PUM-HD and PUM2 PUM-HD as described in Campbell et al. (doi: 10.1038/nsmb.2847) with minor modifications including the use of Magnetic Halolink beads.

treatment_protocol: RNAi conditions and siRNA sequences were previously described by Bohn et al. (doi: 10.1093/nar/gkx1120) and include treatment with siRNAs for 48hrs to allow for PUM depletion prior for BrU labeling.

tag: cell line

value: human embyronic kidney cells

tag: genotype/variation

value: siPUM1 and siPUM2

tag: time point

tag: molecule subtype

value: BrU-labeled RNA


title: miRNA_Subject_1600861


title: BruChase-seq_siPUM_rep4

description:
Sample_42739_293siPUM6h4
42739_ATTCCT

tag: cell type


title: KW181A-1 (patient clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW1_S43

tag: subject status

tag: clone id


title: miRNA_Subject_1600751

tag: tissue

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)


title: KW191B-2 (unaffected parent clone 2_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW11_S53


title: BruChase-seq_siPUM_rep2

description:
Sample_42731_293siPUM6h2
42731_GATCAG


title: miRNA_Subject_1600742

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)


title: KW191A-3 (unaffected parent clone 1_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW9_S51


title: BruChase-seq_siPUM_rep1

description:
Sample_37269_293siPUM6h1
37269_GTCCGC


title: KW181B-2 (patient clone 2_iNCC)

description:
processed data file: GEO_RNAseqNov2019.xlsx
KW5_S47


title: miRNA_Subject_1600732

tag: infarct (infarcted placenta) (0=absent, 1=present)

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)


title: miRNA_Subject_1600722

tag: bmi (body mass index)

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: miRNA_Subject_1600702


title: Bru-seq_siPUM_rep3

description:
Sample_42734_293siPUM0h3
42734_GTGGCC

data_processing:
library strategy: Bru-seq
Data processing for Bru-seq and BruChase-seq is described in Paulsen et al. (doi: 10.1016/j.ymeth.2013.08.015)
Data processing for SEQRS was performed using custom python scripts to split reads by barcode. 20mers were identified by location in the read using custom python scripts. Lower kmers can be easily calculated from 20mer reads
Genome_build: hg19 for Bru-seq and BruChase-seq
Supplementary_files_format_and_content: read count files contain count of reads over genes or exons where each read is split into fracitonal coverage over the length of the read. 20mer files contain the 20mer variable region extracted from the raw reads

tag: cell line

tag: genotype/variation

tag: time point


title: miRNA_Subject_1600721


title: miRNA_Subject_1600701


title: miRNA_Subject_1600692


title: Bru-seq_siPUM_rep1

description:
Sample_37268_293siPUM0h1
37268_ATGTCA

tag: cell type

tag: molecule subtype


title: miRNA_Subject_1600661

tag: tissue


title: Bru-seq_siPUM_rep2

description:
Sample_42730_293siPUM0h2
42730_ACTTGA


title: BruChase-seq_control_rep1

description:
Sample_37267_293siNTC6h1
37267_AGTTCC

value: non-targeting control


title: Bru-seq_control_rep4

description:
Sample_42736_293siNTC0h4
42736_CGTACG


title: BruChase-seq_control_rep3

description:
Sample_42733_293siNTC6h3
42733_GGCTAC


title: miRNA_Subject_1600651

tag: asthma (0=absent, 1=present, 2=data not obtained)


title: miRNA_Subject_1600652

tag: birthweight (grams)


title: miRNA_Subject_1600631

tag: sex (0=female, 1=male)


title: miRNA_Subject_1600641

tag: chorioamnionitis (0=absent, 1=present)


title: Bru-seq_control_rep1

description:
Sample_37266_293siNTC0h1
37266_AGTCAA


title: miRNA_Subject_1600612

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)


title: Bru-seq_siPUM_rep4

description:
Sample_42738_293siPUM0h4
42738_ACTGAT


title: miRNA_Subject_1600561

tag: infarct (infarcted placenta) (0=absent, 1=present)


title: BruChase-seq_control_rep4

description:
Sample_42737_293siNTC6h4
42737_GAGTGG


title: BruChase-seq_control_rep2

description:
Sample_42729_293siNTC6h2
42729_TTAGGC


title: miRNA_Subject_1600511

tag: placwt (placenta weight) (grams)


title: D17-7512

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the human genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: human blood monocytes

growth_protocol: Fresh isolated human blood monocytes were  cultured with 50ng/mL M-CSF for 7 days to generate M0 status macrohages.

extract_protocol:
Qiagen RNeasy Micro Kit
KAPA mRNA HyperPrep Kit

treatment_protocol: Macrophages were treated with different signaling ligands for 24 hrs.

tag: treatment


title: D17-7513

value: Dopamine


title: D17-7510

value: Egf


title: D17-7509

value: Vegfa


title: D17-7508


title: miRNA_Subject_1600521

tag: mage (age of mother) (years)

tag: bmi (body mass index)


title: miRNA_Subject_1600611

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: D17-7511

value: Leptin


title: miRNA_Subject_1600491


title: Bru-seq_control_rep2

description:
Sample_42728_293siNTC0h2
42728_ATCACG

tag: cell line

tag: genotype/variation


title: D19-144096

growth_protocol: Fresh isolated human blood monocytes were  cultured with 50ng/mL M-CSF for 7 days to generate M0 status macrohages. Macrophages were differentiated into M1 macrophages (M1 Mac) by 50ng/mL IFNg plus 50ng/mL TNFa or M2 macrophages (M2 Mac) by 10ng/mL IL4 plus 10ng/mL IL13.

treatment_protocol: M2 Mac were treated with different M1-type compounds or IFNg or DMSO for 24 hrs. M1 Mac were treated with different M2-type compounds or IL4 or DMSO for 24 hrs.

tag: macrophage

value: M1 Mac

tag: replicate


title: D19-144095


title: miRNA_Subject_1600451

tag: tissue


title: D17-7507


title: Bru-seq_control_rep3

description:
Sample_42732_293siNTC0h3
42732_TAGCTT

tag: cell type

tag: time point

tag: molecule subtype


title: miRNA_Subject_1600331

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)


title: miRNA_Subject_1600251

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)

tag: infarct (infarcted placenta) (0=absent, 1=present)

tag: placwt (placenta weight) (grams)


title: miRNA_Subject_1600381

tag: mage (age of mother) (years)

tag: bmi (body mass index)

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)


title: miRNA_Subject_1600662

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: D19-144092

tag: treatment

tag: macrophage


title: miRNA_Subject_1600351

tag: tissue


title: D19-144094

value: IFNg

value: M2 Mac

tag: replicate


title: miRNA_Subject_1600371


title: miRNA_Subject_1600151


title: D19-144091


title: miRNA_Subject_1600141


title: D19-144090

value: lovastatin


title: miRNA_Subject_1600131


title: miRNA_Subject_1600111


title: D19-144089


title: miRNA_Subject_1501301


title: miRNA_Subject_1501261


title: D19-144093


title: miRNA_Subject_1501171


title: miRNA_Subject_1501191


title: miRNA_Subject_1501141


title: D19-144087


title: D19-144086

value: Purmorphamine


title: D19-144083

value: Bisantrene dihydrochloride


title: D19-144084


title: D19-144082


title: D19-144085


title: D19-144081


title: miRNA_Subject_1501121

value: placenta


title: miRNA_Subject_1501021


title: miRNA_Subject_1501002


title: D19-144080

value: Regorafenib


title: D19-144088


title: D19-144077

value: Arcyriaflavin A


title: D19-144078


title: miRNA_Subject_1500981


title: D19-144079


title: miRNA_Subject_1500822


title: miRNA_Subject_1500931


title: miRNA_Subject_1500841


title: miRNA_Subject_1500911


title: D19-144075


title: miRNA_Subject_1500821


title: miRNA_Subject_1500782


title: D19-144074

value: Sorafenib


title: D19-144073


title: miRNA_Subject_1500781


title: miRNA_Subject_1500731


title: D19-144072


title: D19-144070

value: Dasatinib


title: D19-144069


title: miRNA_Subject_1500661


title: miRNA_Subject_1500491


title: D19-144068

value: Axitinib


title: D19-144067


title: miRNA_Subject_1500431


title: D19-144076


title: miRNA_Subject_1500391


title: D19-144065

value: QS 11


title: miRNA_Subject_1400061


title: miRNA_Subject_1301931


title: miRNA_Subject_1301592


title: D19-144062

value: JTE 013


title: miRNA_Subject_1301541


title: miRNA_Subject_1301591


title: D19-144061


title: D19-144071


title: miRNA_Subject_1301401


title: D19-144059

value: triptolide


title: miRNA_Subject_1500601


title: miRNA_Subject_1500681


title: miRNA_Subject_1301271


title: miRNA_Subject_1301132


title: miRNA_Subject_1301101


title: D19-144060


title: miRNA_Subject_1301131


title: D19-144056

value: NVP 231


title: D19-144055


title: D19-144057

value: DMSO


title: D19-144066

value: M1 Mac


title: miRNA_Subject_1301071


title: miRNA_Subject_1300672


title: D19-144052

value: Evodiamine


title: miRNA_Subject_1301031


title: D19-144051

value: M2 Mac


title: D19-144064

value: Bosutinib


title: D19-144063


title: D19-144053

value: Cucurbitacin I


title: D19-144049

value: thiostrepton


title: miRNA_Subject_1300542

value: placenta


title: miRNA_Subject_1300651


title: miRNA_Subject_1300571


title: D19-144058


title: miRNA_Subject_1300441


title: D19-144048

value: Fenbendazole


title: D19-144046

value: Diphenyleneiodonium chloride


title: D19-144045


title: D19-144047


title: miRNA_Subject_1300412


title: miRNA_Subject_1300362


title: D19-144043


title: D19-144044


title: D19-144054


title: D19-144042


title: D19-144041


title: miRNA_Subject_1300232


title: miRNA_Subject_1300301


title: miRNA_Subject_1300231


title: D19-144050


title: D19-144040

value: Niclosamide


title: miRNA_Subject_1300221


title: miRNA_Subject_1300541


title: D19-144039


title: D19-144036

value: SCH 79797 dihydrochloride


title: miRNA_Subject_1300171


title: miRNA_Subject_1300201


title: D19-144037

value: MITOXANTRONE HCL


title: D19-144038


title: miRNA_Subject_1300391


title: miRNA_Subject_1300113


title: miRNA_Subject_1300161


title: D19-144034

value: Cantharidin


title: miRNA_Subject_1300361


title: D19-144035


title: miRNA_Subject_1300011


title: miRNA_Subject_1200741


title: miRNA_Subject_1300111


title: D19-144032

value: SMER 3


title: miRNA_Subject_1300071


title: D19-144031


title: miRNA_Subject_1200731


title: miRNA_Subject_1200692


title: miRNA_Subject_1200671


title: D19-144030

value: Taxol


title: D19-144027

value: Penfluridol


title: D19-144026


title: D19-144029


title: miRNA_Subject_1200561


title: miRNA_Subject_1200522


title: miRNA_Subject_1200691


title: miRNA_Subject_1200571


title: miRNA_Subject_1200441


title: D19-144023

value: Alprostadil


title: D19-144028


title: miRNA_Subject_1200352


title: D19-144024


title: D19-144021

value: DMSO


title: miRNA_Subject_1200351


title: D19-144025


title: miRNA_Subject_1200521


title: D16-45

treatment_protocol: Macrophages were treated with different chemicals or cytokines for 24 hrs.

value: IFN-g


title: miRNA_Subject_1200321


title: D19-144022

value: M2 Mac


title: D16-43

value: mocetinostat


title: D16-41

value: niclosamide


title: miRNA_Subject_1200282


title: miRNA_Subject_1200281


title: D16-38

value: fluvoxamine


title: D16-37

value: chlorhexidine


title: D16-36

value: thiostrepton


title: miRNA_Subject_1200232

value: placenta


title: miRNA_Subject_1200261


title: D16-35

value: fenbendazole


title: miRNA_Subject_1200201


title: miRNA_Subject_1200192


title: miRNA_Subject_1200191


title: D16-33

value: alsterpaullone


title: D16-31


title: miRNA_Subject_1200172


title: miRNA_Subject_1200021


title: miRNA_Subject_1200011


title: miRNA_Subject_1200182


title: miRNA_Subject_1200181


title: miRNA_Subject_1200031


title: miRNA_Subject_1200171


title: D16-44


title: miRNA_Subject_1101161


title: miRNA_Subject_1101171


title: miRNA_Subject_1200251


title: AML-relapse-mouse4

first: David

last: Scadden

address: 7 Divinity Ave, Sherman Fairchild Research Building #201

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using STAR and cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq, genecount values are provided.

source_name: AML-relapse

growth_protocol: GFP+ acute myeloid leukemia cells were sorted from mouse bone marrow for total RNA extraction

extract_protocol:
For RNA-seq, total RNAs were extracted using RNeasy micro kit (Qiagen).
RNA-sequencing libraries were generated using library prep kits (NEB) according to the manufacturer’s instructions.

tag: genotype/variation

value: MLL-AF9 transgenic

value: 10 days (relapse group) after completion of the chemotherapy

value: bone marrow

tag: cell type

value: GFP+ acute myeloid leukemia cells (MLL-AF9-driven AML)


title: capStarr-seq_Input

city: Macclesfield

first: Muhammad

middle: Ahmad

last: Maqbool

address: Alderley Park

department: Cancer Research UK Manchester Institut

description: capStarr-seq

data_processing:
Library strategy: CapStarr-seq
All sequencing reads were aligned to the mm9 genome assembly using Bowtie2 or TopHat2 (allowing 2 mismatches, keeping uniquely aligned reads only).
For ChIP-seq experiments, all samples were input subtracted and signals were scaled to reads per million so that the same number of units appeared in each experiment after merging of the replicates.
For RNA-seq experiments, reads that aligned to + or - strand were seperated and processed seperately to produce WIG files with strand specific enrichment scores.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2). Reads were aligned using Bowtie (v1.2.2) with the settings -a -m 1 --best --strata. Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Genome_build: mm9
Supplementary_files_format_and_content: BEDGRAPH, WIG

growth_protocol: Primary DN cells were isolated from thymus of Rag2-/- mice. Primary DP and DN3 cells were sorted from the Thymus of WT C57/Bl6 mice. Naïve CD4+ and CD8+ cells were sorted from Spleen and Lymph nodes of WT C57/Bl6 mice. TH1, TH2 and TH17 cells were generated by in vitro differentiation of Naive CD4+ cells.

extract_protocol:
ChIP DNA was extracted using the Phenol:Chloroform extraction followed by QiaQuick PCR Purification kit using standard protocol. RNA was extracted using TriZol reagent and ethanol precipitation. CapStarr-seq RNA was extracted as described by Vanhille et al. 2015 (Nature Communications). 4C material was extracted as described by Ben Zouari et al. 2020 (Frontiers in Genetics)
ChIP-seq libraries were prepared with Illumina's ChIP Sample Prep Kit according to standard protocol. RNA-seq Libraries were prepared either with ScriptSeq V2 Total RNA Library Prep Kit (EpiCenter, USA) by using manufacturer's recommended protocol. 4C libraries are generated directly during the extraction process.

tag: cell line

value: T Cells


title: TH17_total_RNAseq_rep2

description: Total RNAseq

data_processing:
All sequencing reads were aligned to the mm9 genome assembly using Bowtie2 or TopHat2 (allowing 2 mismatches, keeping uniquely aligned reads only).
For ChIP-seq experiments, all samples were input subtracted and signals were scaled to reads per million so that the same number of units appeared in each experiment after merging of the replicates.
For RNA-seq experiments, reads that aligned to + or - strand were seperated and processed seperately to produce WIG files with strand specific enrichment scores.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2). Reads were aligned using Bowtie (v1.2.2) with the settings -a -m 1 --best --strata. Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Genome_build: mm9
Supplementary_files_format_and_content: BEDGRAPH, WIG

source_name: TH17 Cells

value: TH17 Cells


title: capStarr-seq_rep1

description: capStarr-seq


title: capStarr-seq_rep2

description: capStarr-seq


title: miRNA_Subject_1101142

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)


title: AML-relapse-mouse3


title: AML-relapse-mouse2


title: TH2_total_RNAseq_rep2

description: Total RNAseq

source_name: TH2 Cells

value: TH2 Cells


title: D16-32

value: bosutinib


title: TH2_total_RNAseq_rep1

description: Total RNAseq


title: miRNA_Subject_1101131

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)


title: D19-144033

value: Cantharidin

value: M2 Mac


title: AML-relapse-mouse1


title: miRNA_Subject_1101092

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)

tag: infarct (infarcted placenta) (0=absent, 1=present)


title: TH1_total_RNAseq_rep2

description: Total RNAseq

source_name: TH1 Cells

value: TH1 Cells


title: TH1_total_RNAseq_rep1

description: Total RNAseq


title: miRNA_Subject_1101091

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)


title: AML-iCT-mouse3

source_name: AML-iCT

value: induction chemotherapy (doxorubicin+cytarabine) at 3 days (iCT group)


title: AML-iCT-mouse2


title: miRNA_Subject_1101081

source_name: Placenta of infants born at low gestational age

tag: bmi (body mass index)

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)


title: DN_total_RNAseq_rep2

description: Total RNAseq

source_name: CD4-/CD8- Thymic T Cells (DN)

value: CD4-/CD8- Thymic T Cells (DN)

tag: genotype


title: DP_total_RNAseq_rep1

description: Total RNAseq

source_name: CD4+/CD8+ Thymic T Cells (DP)

value: CD4+/CD8+ Thymic T Cells (DP)


title: AML-iCT-mouse1

tag: treatment


title: miRNA_Subject_1101042

tag: tissue

value: placenta

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: TH17_total_RNAseq_rep1

description: Total RNAseq


title: miRNA_Subject_1101041


title: CD4_total_RNAseq_rep2

description: Total RNAseq

source_name: CD4+ Naive T Cells (Naïve)

value: CD4+ Naive T Cells (Naive)


title: AML-vehicle-mouse5

source_name: AML-vehicle

tag: genotype/variation

value: vehicle


title: TH17_Input_rep2

description: Sonicated input DNA

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: chip antibody

value: none (Input DNA)


title: DN_total_RNAseq_rep1

description: Total RNAseq


title: AML-vehicle-mouse4

value: MLL-AF9 transgenic


title: TH17_Input_rep1

description: Sonicated input DNA


title: TH17_H3K79me2_rep2

description: Chromatin IP against H3K79me2


title: TH17_H3K79me2_rep1

description: Chromatin IP against H3K79me2


title: TH17_H3K27ac_rep2

description: Chromatin IP against H3K27ac


title: TH17_H3K27ac_rep1

description: Chromatin IP against H3K27ac


title: miRNA_Subject_1100901

tag: asthma (0=absent, 1=present, 2=data not obtained)


title: AML-vehicle-mouse3

value: bone marrow


title: miRNA_Subject_1101001

tag: birthweight (grams)


title: AML-vehicle-mouse2

value: GFP+ acute myeloid leukemia cells (MLL-AF9-driven AML)


title: TH17_H3K27me3_rep2

description: Chromatin IP against H3K27me3


title: DP_total_RNAseq_rep2

description: Total RNAseq


title: CD4_total_RNAseq_rep1

description: Total RNAseq


title: miRNA_Subject_1100891

tag: sex (0=female, 1=male)


title: AML-vehicle-mouse1


title: TH17_H3K27me3_rep1

description: Chromatin IP against H3K27me3


title: miRNA_Subject_1100881

tag: chorioamnionitis (0=absent, 1=present)


title: TH17_PolII_rep2

description: Chromatin IP against RNA Pol II

value: PolII (sc899x (N20))


title: TH17_PolII_rep1

description: Chromatin IP against RNA Pol II

value: TH17 Cells


title: TH17_H3K4me3_rep2

description: Chromatin IP against H3K4me3


title: CK2αfl/fldLck-Cre Replicate 1

city: New York

first: Wei

last: Yang

state: NY

address: Belfer Research Building,Room 760B,413 E. 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

data_processing:
Genewiz took the sequenced reads and trimmed to remove possible adapter sequences and nucleotides with poor quality bases (error rate < 0.05) at the ends. After trimming, sequence reads shorter than 30 nucleotides were discarded.
Genewiz took the remaining sequence reads and aligned to the Mus musculsus genome with CLC Genomics Server program. Gene hit counts were measured and RPKM values were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts of each genes for each samples

source_name: CD4+ T Isolated from Rag with colitis

growth_protocol: CD4+CD25-CD45RBhi T-cells from CK2αfl/fl or CK2αfl/fldLck-Cre mice were transferred into Rag1-/- mice.

extract_protocol:
CD4+ T were collected, centrifuged and washed for 3 times. Then RNA was isolated using the miRNeasy Mini Kit
RNA was sent to Genewiz for their standard library construction

treatment_protocol: CD4+CD25-CD45RBhi T-cells from CK2αfl/fl or CK2αfl/fldLck-Cre mice were transferred into Rag1-/- mice for 6 weeks.

value: CD4+ T cell

tag: conditions

value: colitis


title: TH17_H3K4me3_rep1

description: Chromatin IP against H3K4me3


title: CK2αfl/fldLck-Cre Replicate 2


title: TH17_H3K4me1_rep2

description: Chromatin IP against H3K4me1


title: TH17_H3K4me1_rep1

description: Chromatin IP against H3K4me1


title: miRNA_Subject_1100853

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)

tag: infarct (infarcted placenta) (0=absent, 1=present)


title: TH2_Input_rep2

description: Sonicated input DNA

value: TH2 Cells


title: CK2αfl/fl Control Replicate 2


title: miRNA_Subject_1101141

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)


title: miRNA_Subject_1100852

tag: bmi (body mass index)

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)


title: TH2_Input_rep1

description: Sonicated input DNA


title: CK2αfl/fl Control Replicate 1


title: miRNA_Subject_1100841


title: TH2_H3K27ac_rep1

description: Chromatin IP against H3K27ac


title: TH2_H3K27ac_rep2

description: Chromatin IP against H3K27ac


title: miRNA_Subject_1100791


title: Extracellular Vesicle small RNAseq

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing: Adapter sequences were trimmed with Cutadapt and simple repeat sequences trimmed with PrinSeq. This resulted in RNA with a peak sequence length of 19 nucleotides (nt) dropping off to zero reads around 55 nt. Adapter trimming and sequence alignment was conducted in the sRNAnalyzer. Sequences were searched against, miRBase version 21. FASTA files for C. elegans transcriptome and genome sequences were retrieved from NCBI genome database (assembly WBcel235). The FASTA files were transformed with bowtie-index files. All the alignments to microRNAs, RNAs and DNAs were performed under 0 to 2 mismatch allowance.

organism: Caenorhabditis elegans

source_name: EV derived from C. elegans

growth_protocol: C. elegans was cultured and maintained using standard methods.

extract_protocol:
EVs were isolated from young adult N2 animals. Briefly, conditioned media from ~500,000 developmentally synchronized young adult animals are incubated in S Basal for 24 hours. The conditioned media is then processed with filtering, exclusion chromatography, and ultrafiltration.
To quantify EV-associated RNA samples were processed with Total exosome protein and RNA isolation kit (Invitrogen, Carlsbad CA, USA, Cat # 4478545). We then characterized the abundance and size of the eluates on an Agilent 2200 TapeStation (Agilent, Santa Clara CA, USA; Cat # G2991AA) using high-sensitivity screen tape (Agilent, Santa Clara USA Cat # 5067-5579) along with a small RNA calibration ladder (Agilent, Santa Clara CA, USA; Cat # 5067-1550).  The vesicle samples displayed substantial small RNAs as well as 16s and 28s rRNA species at the expected sizes. To determine what RNA species are packaged into EVs we conducted RNAseq. We used a Qiagen small RNA Sample Preparation kit to prepare a cDNA library from our EV-associated RNA (Qiagen Germantown MD, USA Cat # 331502) while an Illumina MiSeq v2 kit (300 cycles) was used to prepare the sequencing library with 5’ adapter sequences (San Diego USA; Cat# MS-102-2002). The sample was then submitted to single-end sequencing on an Illumina MiSeq desktop sequencer.

value: Extracellular Vesicle

tag: strain


title: TH2_H3K27me3_rep2

description: Chromatin IP against H3K27me3


title: TH2_H3K27me3_rep1

description: Chromatin IP against H3K27me3


title: TH2_H3K79me2_rep1

description: Chromatin IP against H3K79me2


title: miRNA_Subject_1100872

tag: tissue


title: Male TRAP-seq M4_IP

city: Richardson

first: Diana

last: Tavares-Ferreira

address: 800 W. Campbell Road

department: School of Behavioral and Brain Sciences

institute: University of Texas at Dallas

description:
Male TRAP-seq
rRNA depleted RNA associated with ribosmes (eGFP-RPL10a in Nav1.8+ DRG neurons)

data_processing:
RNA-seq read files (fastq files) were checked for quality by FastQC and read trimming was done based on the Phred score and per-base sequence content
Trimmed Reads were then mapped against the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR v2.2.1
Relative abundances in Transcripts Per Million (TPM) for every gene of every sample was quantified by stringtie v1.3.5
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 5
Supplementary_files_format_and_content: TAR packaging followed by a GNU zip (gzip), tab separated text files with columns for gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all coding genes

source_name: Dorsal root ganglia (DRG)

growth_protocol: Rosa26fsTRAP mice were generated (P. Zhou et al, Proc Natl Acad Sci U S A 110, 15395 (Sep 17, 2013)) and purchased from Jackson Laboratory (Stock number: 022367). Transgenic mice expressing Cre recombinase under the control of the Scn10a (Nav1.8) promoter were obtained initially from Professor John Wood (University College London) but are commercially available from Infrafrontier (EMMA ID: 04582). Nav1.8cre mice on a C57BL/6J genetic background were maintained and bred at the University of Texas at Dallas. Upon arrival, Rosa26fstrap mice were crossed to Nav1.8cre to generate the Nav1.8-trap mice that express a fused EGFP-L10a protein in Nav1.8 expressing neurons. All experiments were carried out using male and female littermates aged 8 to 12 weeks old.

extract_protocol:
RNA was eluted from all samples using the Direct-zol kit (Zymo Research) according to the manufacturer’s instructions
cDNA libraries were prepared with total RNA Gold library preparation (with ribosomal RNA depletion) for all samples according to the manufacturer’s instructions (Illumina)

value: Nav1.8Cre/Rosa26fstrap mice on C57BL/6J genetic background

tag: specific tissue

value: Nav1.8-positive DRG neurons

tag: trap - immunoprecipitation

value: Incubated with anti-GFP antibodies


title: miRNA_Subject_1100711

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: Male TRAP-seq M3_IP


title: TH2_PolII_rep1

description: Chromatin IP against RNA Pol II

tag: cell type

tag: chip antibody


title: TH2_H3K4me3_rep2

description: Chromatin IP against H3K4me3


title: TH2_H3K4me3_rep1

description: Chromatin IP against H3K4me3


title: TH2_H3K4me1_rep2

description: Chromatin IP against H3K4me1


title: TH2_PolII_rep2

description: Chromatin IP against RNA Pol II


title: miRNA_Subject_1100691

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)


title: Male RNA-seq M4_IN

description:
Male RNA-seq
rRNA depleted RNA (whole DRG)

value: whole DRG


title: Male RNA-seq M3_IN


title: TH2_H3K4me1_rep1

description: Chromatin IP against H3K4me1


title: TH2_H3K79me2_rep2

description: Chromatin IP against H3K79me2


title: miRNA_Subject_1100611

value: placenta

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)


title: TH1_Input_rep1

description: Sonicated input DNA

value: TH1 Cells


title: Male RNA-seq M2_IN


title: Male TRAP-seq M2_IP


title: miRNA_Subject_1100601

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)


title: miRNA_Subject_1100751

tag: infarct (infarcted placenta) (0=absent, 1=present)


title: miRNA_Subject_1100551

tag: placwt (placenta weight) (grams)


title: TH1_Input_rep2

description: Sonicated input DNA


title: TH1_H3K79me2_rep1

description: Chromatin IP against H3K79me2


title: miRNA_Subject_1100521

tag: mage (age of mother) (years)


title: TH1_H3K27ac_rep2

description: Chromatin IP against H3K27ac


title: Male RNA-seq M1_IN


title: miRNA_Subject_1100511

tag: bmi (body mass index)


title: TH1_H3K27ac_rep1

description: Chromatin IP against H3K27ac


title: Female TRAP-seq F4_IP

description:
Female TRAP-seq
rRNA depleted RNA associated with ribosmes (eGFP-RPL10a in Nav1.8+ DRG neurons)


title: Female RNA-seq F4_IN

description:
Female RNA-seq
rRNA depleted RNA (whole DRG)


title: miRNA_Subject_1100462

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)


title: TH1_PolII_rep2

description: Chromatin IP against RNA Pol II


title: TH1_H3K79me2_rep2

description: Chromatin IP against H3K79me2


title: TH1_H3K27me3_rep1

description: Chromatin IP against H3K27me3


title: TH1_PolII_rep1

description: Chromatin IP against RNA Pol II


title: Female TRAP-seq F3_IP

tag: strain


title: miRNA_Subject_1100461

tag: tissue


title: Bladder carcinoma (BCa) tumor tissue circRNA 4

city: Harbin

first: Yang

state: Heilongjiang

address: No. 23 Youzheng Street

country: China

institute: Harbin Medcial University

description: circRNA expression bladder carcinoma(BCa) tumor tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: Bladder carcinoma(BCa) tumor tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: BCa and matched non-tumor bladder tissues

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

treatment_protocol: Tissues from BCa surgury and promptly frozen in liquid nitrogen.

tag: gender

value: Male

tag: age

value: BCa tissue

tag: molecule subtype

value: circRNA


title: Female RNA-seq F3_IN

tag: specific tissue

tag: trap - immunoprecipitation


title: miRNA_Subject_1100391

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: Female TRAP-seq F2_IP


title: Bladder carcinoma (BCa) tumor tissue circRNA 1


title: TH1_H3K4me3_rep2

description: Chromatin IP against H3K4me3

tag: cell type

tag: chip antibody


title: Bladder carcinoma (BCa) tumor tissue circRNA 2

value: Female


title: Male TRAP-seq M1_IP


title: bladder normol tissue circRNA 4

description: circRNA expression data from Homo sapiens bladder

source_name: Bladder normol tissue

value: normol bladder tissue from BCa


title: miRNA_Subject_1100361

tag: birthweight (grams)

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)


title: miRNA_Subject_1100381

tag: infarct (infarcted placenta) (0=absent, 1=present)

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)

tag: bmi (body mass index)


title: Female RNA-seq F2_IN

tag: strain


title: TH1_H3K4me3_rep1

description: Chromatin IP against H3K4me3


title: miRNA_Subject_1100471

tag: tissue

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)


title: Female TRAP-seq F1_IP

tag: specific tissue


title: TH1_H3K4me1_rep2

description: Chromatin IP against H3K4me1


title: Female RNA-seq F1_IN

tag: trap - immunoprecipitation


title: TH1_H3K4me1_rep1

description: Chromatin IP against H3K4me1


title: miRNA_Subject_1100111

tag: asthma (0=absent, 1=present, 2=data not obtained)


title: miRNA_Subject_1100112

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: CD4_Input_rep2

description: Sonicated input DNA

tag: cell type

value: CD4+ Naive T Cells (Naive)

value: none (Input DNA)


title: CD4_Input_rep1

description: Sonicated input DNA

tag: chip antibody


title: Bladder carcinoma (BCa) tumor tissue circRNA 3

tag: gender

tag: age

tag: molecule subtype


title: WT-4

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

institute: The University of Chicago

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Statistical tests for differential expression were performed using sleuth.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual transcripts for each sample as well as statistical results for differential gene abundance between genotypes.

source_name: colon

extract_protocol:
Mice were euthanized and colons dissected. Colons were placed in Trizol and homogenized. The Direct-zol kit (Zymo) was used to isolate total RNA.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on a NextSeq High Output Run.

value: 2 wks

tag: genotype

value: Wildtype

value: colon


title: WT-5


title: WT-3


title: CD4_H3K79me2_rep2

description: Chromatin IP against H3K79me2


title: bladder normol tissue circRNA 1


title: CD4_H3K79me2_rep1

description: Chromatin IP against H3K79me2


title: CD4_H3K27ac_rep2

description: Chromatin IP against H3K27ac


title: WT-2


title: bladder normol tissue circRNA 3


title: bladder normol tissue circRNA 2


title: MM58592

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

data_processing:
Illumina  software used for basecalling (Illumina HiSeq 2500)
Potential ribosomal RNA was removed using STAR v2.4
Unmapped reads were aligned ti hg19 human reference using GENCODE v19
Cufflinks v2.2.1 was run to create de novo transcriptome assembly specific to each sample
Cufflinks outputs for all the samples were merged with themselves and GENCODE database using cuffmerge. R and GNU parallel were used to analysis.
Coding potential of each transcript was checked using phyloCSF
Each sample was annotated to the merged transcript annotation using subread featureCounts
Counts were normalized to library-size using number of mapped reads to each sample by DESeq2, and converted into Transcripts-per-million (TPM)
Genome_build: GENCODE hg19 (v19)

source_name: Myeloma plasma cell

extract_protocol:
Bone marrow from 38 newly diagnosed MM patients were extracted and purified by cytometry with CD138+ positive magnetic system. Total RNA was isolated using TRIzol® Reagent
Strand specific RNA libraries were multiplexed (6 samples per lane) and the sequencing was done with Illumina HiSeq 2500 (Illumina) as 50 base paired-end runs

value: Bone marrow; multiple myeloma plasma cell

tag: Sex


title: MM58281


title: MM58410


title: C_4028: 21wk subject 4028

city: Jyväskylä

first: Maarit

last: Lehti

address: Rautpohjankatu 8

country: Finland

institute: LIKES Research Cetre for Physical Activity and Health

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized using quantile-normalization with affy package of Bioconductor in R.

label: biotin

source_name: PBMCs

label_protocol: Biotinlabeled cRNA was prepared with an Illumina RNA amplification kit (Ambion)

extract_protocol: Total RNA from mononuclear cells was extracted using Trizol reagent

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from the fasting venous blood samples using Becton Dickinson Vacutainer Cell Preparation Tubes with sodium citrate.

tag: diagnosis

value: coronary artery disease

value: lymphomonocytes

value: male


title: WT-1


title: C_4022: 21wk subject 4022


title: C_4015: 21wk subject 4015


title: C_4025: 21wk subject 4025


title: MM58177


title: C_4012: 21wk subject 4012


title: CD4_H3K27me3_rep2

description: Chromatin IP against H3K27me3


title: MM58183


title: C_4014: 21wk subject 4014


title: MM58166


title: MM57802


title: CD4_H3K27ac_rep1

description: Chromatin IP against H3K27ac


title: A_4025: 0wk subject 4025


title: C_4006: 21wk subject 4006


title: R1ko-5


title: A_4028: 0wk subject 4028


title: R1ko-6


title: CD4_H3K27me3_rep1

description: Chromatin IP against H3K27me3


title: MM58105


title: R1ko-4


title: R1ko-3


title: MM58089


title: CD4_PolII_rep2

description: Chromatin IP against RNA Pol II

value: PolII (sc899x (N20))


title: R1ko-2


title: R1ko-1


title: MM57991


title: A_4014: 0wk subject 4014


title: A_4022: 0wk subject 4022


title: BC121206_Treg1 [lib444]

first: Daniel

middle: J

last: Campbell

state: Washington

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

description:
processed data file:
raw_counts.csv
norm_counts.csv

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed with the program Casava.
One 3'-end base was removed from all reads, followed by quality-based trimming from both ends until minimum base quality for each read was >= 30.
Tophat aligned reads to GRCh38, using Ensembl annotation release number 77 and the read counts per Ensembl gene ID were computed with featureCounts.
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38.77
Supplementary_files_format_and_content: raw _counts.txt: Raw counts of the mapped reads.
Supplementary_files_format_and_content: norm_counts.txt: Lowly expressed genes and non-protein coding genes were filtered out and the ensembl gene IDs mapped to HGNC gene symbols. Count data was normalized using TMM (Robinson & Oshlack, 2010)

molecule: polyA RNA

source_name: Treg1 (CD127-CD25+CD45RA-CXCR3+CCR6-)

extract_protocol: requested; to be updated

value: blood

tag: population

value: Treg

tag: subset

tag: median cv coverage

tag: fastq total reads


title: Old Flu R5 [20_O_F]

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

data_processing:
Reads were demultiplexed using bcl2fastq version 2.19.1
Quality of reads was assessed with FastQC and trimmed with Trimmomatic version 0.36
Trimmed reads were aligned to Mus musculus genome (mm10, version 78) with STAR version 2.6.0
Aligned reads were associated with genes and counted with HTSeq count version 0.9.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw htseq count.

source_name: Old Flu_sorted muscle macrophages

extract_protocol:
RNA was harvested following manufactures directions for Arcturus PicoPure RNA isolation kit
RNA-seq libraries were prepared from 0.5 ng total RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit

tag: strain

tag: treatment

value: 60 days post influenza A virus infection

value: 18 months

value: Sorted muscle macrophages


title: MM57075

tag: tissue

value: Female


title: Old Flu R4 [19_O_F]


title: CD4_H3K4me3_rep2

description: Chromatin IP against H3K4me3


title: CD4_PolII_rep1

description: Chromatin IP against RNA Pol II


title: BC121206_Treg2 [lib442]


title: BC121206_Treg1_17 [lib443]


title: BC121206_Treg22 [lib441]


title: MM56965


title: MM57224


title: CD4_H3K4me1_rep2

description: Chromatin IP against H3K4me1


title: Old Flu R1 [16_O_F]


title: Old Flu R3 [18_O_F]


title: MM56945

value: Male


title: Young Flu R4 [15_Y_F]

source_name: Young Flu_sorted muscle macrophages

value: 4 months


title: DP_Input_rep2

description: Sonicated input DNA

value: CD4+/CD8+ Thymic T Cells (DP)

value: none (Input DNA)


title: DP_H3K79me2_rep1

description: Chromatin IP against H3K79me2


title: A_4006: 0wk subject 4006


title: Old Flu R2 [17_O_F]


title: DP_H3K79me2_rep2

description: Chromatin IP against H3K79me2


title: BC121206_Treg17 [lib440]


title: BC121206_NaiveNaive [lib439]

source_name: Naïve (CD127+CD25-CD45RA+)

value: Naive


title: CD4_H3K4me3_rep1

description: Chromatin IP against H3K4me3

value: CD4+ Naive T Cells (Naive)


title: BC121206_Th1 [lib438]

source_name: Th1 (CD127+CD25-CD45RA-CXCR3+CCR6-)

value: Th


title: DP_H3K27ac_rep2

description: Chromatin IP against H3K27ac


title: MM56525

value: Bone marrow; multiple myeloma plasma cell


title: MM56766


title: Young Flu R3 [13_Y_F]


title: MM56605


title: Young Flu R2 [12_Y_F]


title: CD4_H3K4me1_rep1

description: Chromatin IP against H3K4me1


title: MM56878


title: BC121206_Th1_17 [lib437]


title: DP_H3K4me1_rep2

description: Chromatin IP against H3K4me1


title: MM56417


title: BC121206_Th2 [lib436]


title: MM56357


title: BC121206_Th22 [lib435]


title: A_4015: 0wk subject 4015

value: coronary artery disease

value: lymphomonocytes


title: A_4012: 0wk subject 4012

value: male


title: MM55706


title: DN_Input_rep1

description: Sonicated input DNA

source_name: CD4-/CD8- Thymic T Cells (DN)

value: CD4-/CD8- Thymic T Cells (DN)


title: Young Naïve R4 [09_YN_864]

source_name: Young Naïve_sorted muscle macrophages

value: naïve


title: BC121206_Th17 [lib434]

value: blood


title: MM55658


title: DN_H3K27ac_rep2

description: Chromatin IP against H3K27ac


title: DN_H3K79me2_rep1

description: Chromatin IP against H3K79me2


title: MM55624


title: DP_H3K27ac_rep1

description: Chromatin IP against H3K27ac

source_name: CD4+/CD8+ Thymic T Cells (DP)


title: BC120926_Treg1 [lib433]

value: Treg


title: Young Naïve R3 [08_YN_863]

value: Sorted muscle macrophages


title: Young Naïve R2 [07_YN_862]


title: Y305A TASOR comp H3K9me3 rep2

city: Lund

first: Christopher

last: Douse

address: Sölvegatan 17

department: Medicine

country: Sweden

institute: Lund University

data_processing:
Read alignment with bowtie2 (v2.3.4.3) --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
For CUT&RUN, conversion to bedgraph format and normalization was done with bedtools genomecov (v2.27.1; -bg -scale), where the scale factor was 1e4 divided by the number of reads mapping to the yeast spike-in genome (R64-1-1). Peaks were called in SEACR (v1.1; stringent, norm options) for experimental samples against IgG controls. The RUVseq package (v1.20) was used to remove unwanted variation prior to differential binding analysis with edgeR (v3.28.1). TASOR-regulated H3K9me3 peaks were defined as those under a cutoff in the MA plot (log2 fold-change < -1) of KO vs control cells (n=4).
For CUT&Tag, PCR duplicates were removed from bam files (Picard) and coverage tracks generated with bamCoverage (deepTools v3.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with normalized coverage plots
Supplementary_files_format_and_content: bed file listing 393 TASOR-regulated H3K9me3 loci

source_name: HeLa cells

growth_protocol: HeLa and HEK293T cells (ECACC) were grown in IMDM or DMEM plus 10% fetal calf serum (FCS) and penicillin/streptomycin (100 U/mL). Cell lines were routinely tested for mycoplasma contamination using the MycoAlert detection kit (Lonza). Exogenous expression of TASOR variants was done with lentiviral vectors pHRSIN-pSFFV-HA-TASOR-WPRE-pPGK. Lentivirus was generated through the triple transfection of HEK 293T cells with the lentiviral transfer vector plus the two packaging plasmids pCMVΔR8.91 and pMD.G using TransIT-293 transfection reagent (Mirus) as recommended by the manufacturer. Viral supernatant was typically harvested 48 h post-transfection, cell debris removed using a 0.45 µm filter, and TASOR KO HeLa cells transduced by spin infection at 800 g for 1 h.

extract_protocol:
DNA was cleaved by antibody-directed MNase (CUT&RUN) or Tn5-transposase (CUT&Tag) treatment of digitonin-permeabilised cells and purified from the cell supernatant
For CUT&RUN, KAPA Hyperprep kit was used as per instructions. For CUT&Tag, libraries were directly PCR amplified following tagmentation and cleanup. Final cleanup was done with 1.1x KAPA SPRI beads

tag: cell line

value: HeLa

value: TASOR KO with expression of Y305A HA-TASOR

tag: antibody

value: rabbit anti-H3K9me3 abcam ab8898

tag: protocol

value: CUT&RUN


title: BC120926_Treg1_17 [lib432]


title: Young Flu R1 [11_Y_F]

value: 60 days post influenza A virus infection

value: 4 months

tag: cell type


title: MM55576

value: Male


title: MM55389


title: Young Naïve R1 [06_YN_861]


title: Old Naïve R5 [05_ON_860]

source_name: Old Naïve_sorted muscle macrophages

value: 18 months


title: BC120926_Treg2 [lib431]


title: WT TASOR comp IgG rep2

value: TASOR KO with expression of WT HA-TASOR

value: guinea pig anti-rabbit IgG CSB-PA00150E1Gp


title: BC120926_Treg22 [lib430]


title: Young Naïve R5 [10_YN_865]


title: MM55338

value: Bone marrow; multiple myeloma plasma cell

value: Female


title: Old Naïve R4 [04_ON_859]


title: MM55282


title: BC120926_Treg17 [lib429]


title: BC120926_NaiveNaive [lib428]

value: Naive


title: Old Naïve R3 [03_ON_858]

value: naïve


title: Old Naïve R2 [02_ON_857]


title: TASOR KO H3K9me3 rep2

value: Reporter clone with TASOR KO


title: MM55220


title: DN_H3K27ac_rep1

description: Chromatin IP against H3K27ac

value: CD4-/CD8- Thymic T Cells (DN)

tag: chip antibody


title: Control H3K9me3 rep2

value: Clone bearing HUSH-repressed GFP transgene reporter


title: Old Naïve R1 [01_ON_856]

tag: age

value: Sorted muscle macrophages


title: MM55051


title: BC120926_Th1_17 [lib426]

value: blood

value: Th


title: BC120926_Th2 [lib425]


title: MM54847


title: BC120926_Th22 [lib424]


title: RiNLE1-2 [DEX-128-2]

city: WAGENINGEN

first: Peng

address: Hoevestein 239 12B007

country: Netherlands

institute: Wageningen university

data_processing:
CLC 10.0 was used for mapping, calculating TPM, identifiying DEGs and making PCA plot
Genome_build: Medicago genome 4.0
Supplementary_files_format_and_content: Expression Browser

organism: Medicago truncatula

source_name: RiNLE1 overexpression_Roots

growth_protocol: Medicago hairy roots transformed DEX-RiNLE1 and DEX-EV construct

extract_protocol:
RNA isolation kits
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 uM DEX treat for 20 hours

tag: genotype/variation

value: roots


title: RiNLE1-1 [DEX-128-1]


title: EV-3

value: DEX-EV


title: MM54746


title: WT TASOR comp H3K9me3 rep2

value: HeLa

tag: genotype

value: rabbit anti-H3K9me3 abcam ab8898

value: CUT&RUN


title: BC120926_Th17 [lib423]


title: BC120607_Treg1 [lib422]

value: Treg


title: MM54639

tag: Sex


title: EV-2


title: MM54647


title: BC120607_Treg1_17 [lib421]


title: MM53225

value: Male


title: EV-1


title: BC120607_Treg2 [lib420]


title: MM55138

value: Bone marrow; multiple myeloma plasma cell


title: MM52305

value: Female


title: BC120926_Th1 [lib427]


title: BC120607_Treg22 [lib419]


title: CR IgG TASOR KO rep2

value: guinea pig anti-rabbit IgG CSB-PA00150E1Gp


title: MM48086


title: BC120607_Treg17 [lib418]


title: RiNLE1-3 [DEX-128-3]


title: MM51078


title: 6b-All_Nuclei

city: Stanford

first: Inma

last: Cobos

state: California

address: 300 Pasteur Drive, Lane Building, L235

institute: STANFORD UNIVERSITY MEDICAL SCHOOL

description: polyA mRNA (nuclear)

data_processing:
Sequencing data quality check. Performed with Illumina SAV.
Demultiplexing. Performed with Illumina Bcl2fastq2 v 2.19 program.
Alignment and filtering. Performed with Cellranger v3.0.1; cellranger count function, default parameters.
Barcode and UMI counting. Performed with Cellranger v3.0.1; cellranger count function, default parameters.
Genome_build: GRCh38 1.2.0 (10x Cellranger)
Supplementary_files_format_and_content: Matrices in the Hierarchical Data Format (HDF5 or H5). Obtained with Cellranger v3.0.1; cellranger count function, default parameters.

source_name: Brain, prefrontal cortex, Brodmann area 9 (BA9); Postmortem, fresh frozen

extract_protocol:
Comparison of single transcriptomes from neuronal nuclei versus somas, isolated using the pan-neuronal markers NeuN (nuclear) and MAP2 (cytoplasmic): Tissue from the prefrontal cortex (Brodmann area 9; BA9) of an AD Braak stage VI patient (case # 6) was thawed on ice, and the cortical ribbon spanning all cortical layers was micro-dissected. Dissociation of individual nuclei used mechanical force and a detergent (0.1% triton); dissociation of individual somas used gentle mechanical force. Immunostaining and FACS using the pan-neuronal markers NeuN or MAP2 was used to collect three populations: MAP2+, NeuN+, and All nuclei (NeuN+ and NeuN-). RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 assay. The generated paired-end libraries were sequenced on Illumina Novaseq 6000.
Single-cell RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 assay according to the manufacturer’s user manual. The numbers of cells loaded ranged from 1,400–11,000 to capture the maximum number of cells up to an upper limit of ~5,000 cells per sample (for an expected cell capture efficiency of ~40%). For cDNA amplification, the number of PCR cycles was 13–15 (adjusted to the targeted cell recovery). For library construction, the number of cycles for the sample index PCR reaction was 12–13 (adjusted to the quantified cDNA input). The generated paired-end libraries were sequenced on an Illumina Novaseq 6000 (2 × 100); 26 bp for read 1 (cell barcode and UMI), 8 bps for the i7 index, and 98 bps for read 2.

value: brain

tag: number of cells sequenced

tag: gender

value: F

tag: pmi (hr)

tag: rin

tag: brain weight (gr)

tag: brain region

value: Brodmann area 9 (BA9)

tag: disease

value: Alzheimer's disease

tag: ad stage

value: NIH-AA score A3B3C3; Braak VI

tag: other pathology


title: BC120607_NaiveNaive [lib417]

tag: tissue

value: blood

tag: population

value: Naive

tag: subset

tag: median cv coverage

tag: fastq total reads


title: blood_Tcm_6

data_processing:
Base-calling and demultiplexing were performed automatically on BaseSpace (Illumina) to generate FASTQ files.
The FASTQ files were processed in order to remove reads of zero length (fastq_trimmer v.1.0.0), remove adapter sequences (fastqmcf tool v.1.1.2) and perform quality trimming from both ends until a minimum base quality ≥ 30 (FASTQ quality trimmer tool v.1.0.0).
Reads were aligned to the human reference genome (build hg38) with TopHat (v.1.4.0) and read counts per Ensembl gene ID were quantified with htseq-count (v.0.4.1).
Quality metrics for the FASTQ and BAM/SAM files were generated with FastQC (v.0.11.3) and Picard (v.1.128).
Processing of FASTQ and BAM/SAM files was executed on the Galaxy workflow platform of Globus genomics.
Samples with a total number of fastq reads below 10^6, mapped reads below 70% or median CV coverage > 1 were excluded from further analysis.
gene_counts.txt: Gene counts as determined by htseq-count. Ensembl Gene IDs were mapped to HGNC gene symbols using biomaRt (GRCh38.p10). Genes with low counts as well as non-protein coding genes were removed for downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: gene_counts.txt

source_name: blood

extract_protocol:
Human PBMCs were isolated using Ficoll-Hypaque (GE-Healthcare; GE17-1440-02) gradient separation. For RNAseq CD4+ T cells were enriched using CD4 microbeads (Miltenyi; 130-045-101) and 4x106 cells/ml were resuspended in RPMIc with 50 U/ml IL-2 (Immunotools; 11340023) in a 24-well and rested for 20h prior to staining and cell sorting. For isolation of skin T cells, subcutaneous fat was removed before skin was minced with dissection scissors and surgical scalpel. Approximately 1cm^2 of skin was digested overnight in 5%CO2 at 37°C with 3ml of digestion mix containing 0.8mg/ml Collagenase Type 4 (Worthington; #LS004186) and 0.02mg/ml DNase (Sigma-Aldrich; DN25) in RPMIc. Samples were filtered, washed with RPMI and PBS and stained for flow cytometry/cell sorting.
500 cells per population were sorted into lysis buffer using a BD FACSARIA III or FACSFUSION instruments (BD Biosciences), and cDNA was prepared using the SMARTSeq v4 Ultra Low Input RNA Kit for Sequencing (Takara).
Library construction was performed using the NexteraXT DNA sample preparation kit (Illumina) using half the recommended volumes and reagents.
sequencing run: Dual-index, single-read sequencing of pooled libraries was run on a HiSeq2500 sequencer (Illumina) with 58-base reads and a target depth of 5 million reads per sample.

tag: cell type

value: CLA+CD4+ T cells

tag: cell population

value: CM

tag: acquisition site

value: Salzburg

tag: donor


title: BC120607_Th1 [lib416]

value: Th


title: 6b-NeuN

description: polyA mRNA (nuclear)

tag: number of cells sequenced

tag: age

tag: gender


title: MCF10DCIS cells treated with TGFβ1-4th

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

description: growth factor treated

hyb_protocol: Hybridization to the reporter and capture probes ensued in a thermal cycler for 16 hours at 65°C. Washing and cartridge immobilization were performed on the nCounter® PrepStation

scan_protocol: The cartridge was scanned at 550 fields of view (FOV) on the nCounter Digital Analyzer, and  the raw data: .RCC files containing the raw counts for each microRNA were used for  data analysis

data_processing: The array data were obtained using nSolver4.0. Normalization was done with R package NanoStringDiff.  Limma package was used for differential analysis.

label: miRNA tag

source_name: breast cancer cell line

label_protocol: One hundred nanograms of total RNA was used for miRNA tag annealing and ligation using stringent temperatures to ensure tagging specificity following the manufacturer’s protocol

growth_protocol: MCF10DCIS cells were cultured in DMEM:F12 media supplement with 5% horse serum, CaCl2, Pen/Strep, insulin, EGF and hydrocortisol

extract_protocol: Total RNA was extracted using miRNaesy Kit (Qiagen) following manufacturer’s protocol

treatment_protocol: MCF10DCIS cells were treated with recombinant human TGFβ1 (10 ng/µl) or DMSO for 72 hours

tag: cell line

value: breast cancer

tag: condition

value: TGFB treatment


title: blood_Tem_6

value: EM


title: blood_Tem_5


title: BC120607_Th2 [lib414]


title: BC120607_Th1_17 [lib415]


title: skin_Tcm_4

source_name: skin

value: skin


title: MCF10DCIS cells treated with TGFβ1-2nd

description: growth factor treated


title: MCF10DCIS cells treated with TGFβ1-3rd

description: growth factor treated


title: MCF10DCIS cells treated with DMSO-4th

description: DMSO treated

value: control


title: MCF10DCIS cells treated with TGFβ1-1st

description: growth factor treated


title: MCF10DCIS cells treated with DMSO-3rd

description: DMSO treated


title: BC120607_Th17 [lib412]


title: skin_Tem_4


title: blood_Tem_3

value: Seattle


title: 8-AT8

description: polyA mRNA (nuclear-enriched)

extract_protocol:
Methods for high-throughput isolation and profiling of single cells with neurofibrillary tangles (NFTs) and neighboring tangle-free neurons from fresh-frozen postmortem human brain: Tissue from the prefrontal cortex (Brodmann area 9; BA9) of Braak stage VI AD patients was thawed on ice, and the cortical ribbon spanning all cortical layers was micro-dissected. Gentle mechanical dissociation without detergents or enzymatic digestion followed by sucrose-iodixanol gradient centrifugation was used to purify cells with relatively well-preserved somas. Immunostaining and fluorescence-activated cell sorting using an antibody to detect pathological hyperphosphorylated tau (AT8) and the pan-neuronal marker MAP2 was used to collect two single-cell populations: AT8+ (either positive or negative for MAP2) and MAP2+/AT8-.  RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 assay. The generated paired-end libraries were sequenced on Illumina Novaseq 6000.
Single-cell RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 assay according to the manufacturer’s user manual. The numbers of cells loaded ranged from 1,400–11,000 to capture the maximum number of cells up to an upper limit of ~5,000 cells per sample (for an expected cell capture efficiency of ~40%). For cDNA amplification, the number of PCR cycles was 13–15 (adjusted to the targeted cell recovery). For library construction, the number of cycles for the sample index PCR reaction was 12–13 (adjusted to the quantified cDNA input). The generated paired-end libraries were sequenced on an Illumina Novaseq 6000 (2 × 100); 26 bp for read 1 (cell barcode and UMI), 8 bps for the i7 index, and 98 bps for read 2.

value: brain

value: M

tag: pmi (hr)

tag: rin

tag: brain weight (gr)

tag: brain region

tag: disease


title: BC120607_Th22 [lib413]

tag: tissue

tag: population

tag: subset


title: 7-AT8

description: polyA mRNA (nuclear-enriched)

value: F

value: Brodmann area 9 (BA9)

tag: ad stage

tag: other pathology

value: cardiovascular disease


title: Sc MMS 3

city: Nutley

first: Erika

last: Shor

state: New Jersey

address: 111 Ideation Way, , CDI

institute: Center for Discovery and Innovation

data_processing:
Raw data was trimmed with fastp version 0.20.0 with the following params: -w 8 --detect_adapter_for_pe-W 4 -M 10 --cut_by_quality3 --length_required 15
Reads were aligned to the transcriptome derived from sacCer3 using STAR version 2.5.1b with default parameters
Read counts for each transcript was measured using featureCounts from subread-1.6.2 package
Differentially expressed genes were determined using DESeq2 and a cut-off of 0.05 on adjusted p-value (corrected for multiple hypotheses testing)
GSEA was performed on normalized gene expression counts, using gene permutations for calculating p-value
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab-delimited text files with raw expression counts for each sample, Excel file reporting log2ratio(MMS/noMMS)

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: YPD 30°C (S. cerevisiae), YPD 37°C (C. glabrata)

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit according to manufacturer instructions
The libraries were made using NEBNext Ultra RNA Library Preparation Kit for polyA selection according to manufacturer instructions

treatment_protocol: 0.1% MMS for 1 hour

tag: strain

tag: treatment


title: 8-MAP2

description: polyA mRNA (nuclear-enriched)

tag: number of cells sequenced

value: Alzheimer's disease

value: NIH-AA score A3B3C3; Braak VI


title: MCF10DCIS cells treated with DMSO-1st

description: DMSO treated

tag: cell type


title: skin_Tem_3

value: CLA+CD4+ T cells

tag: cell population

tag: acquisition site

tag: donor


title: 7-MAP2

description: polyA mRNA (nuclear-enriched)

tag: age

tag: gender

tag: pmi (hr)


title: 6-AT8

description: polyA mRNA (nuclear-enriched)

tag: rin

tag: brain weight (gr)

tag: brain region


title: Sc MMS 2


title: skin_Tcm_2

tag: tissue

value: CM


title: Sc MMS 1


title: 6-MAP2

description: polyA mRNA (nuclear-enriched)

tag: disease


title: 6b-MAP2

description: polyA mRNA (nuclear-enriched)

tag: ad stage


title: 5-AT8

description: polyA mRNA (nuclear-enriched)

tag: other pathology


title: Sc no MMS 2

tag: strain

value: no MMS control


title: Sc no MMS 1

tag: treatment


title: Leptin treated mouse 4

city: Lausanne

first: Claudiane

last: Guay

address: Du Bugnon 9

institute: University of Lausanne

hyb_protocol: hybridization was performed according to microRNA Labeling & Hybridization Kit

scan_protocol: After hybridization and washing the arrays were scanned with an Agilent microarray scanner G2505B using high dynamic range settings as specified by the manufacturer.

data_processing: Agilent Feature Extraction Software v 10.7.3.1 was used to extract the data. Quantile normalization was applied to the Total Gene Signal intensity values, using the function normalize.quantiles from the R Bioconductor package preprocessCore.

source_name: ob/ob leptin treated islets, biological replicate 4

label_protocol: 100ng of total RNA was submitted to microRNA Labeling & Hybridization Kit

extract_protocol: total RNA was extracted with miRNeasy kit QIAGEN following manufacturer's instructions

treatment_protocol: Pancreatic islets were isolated from ob/ob mice, 21 days after leptin or saline (Ctl) infusion.

value: pancreatic islets

value: male

tag: agent

value: leptin


title: MCF10DCIS cells treated with DMSO-2nd

description: DMSO treated

tag: cell line

tag: cell type

value: breast cancer

tag: condition


title: Leptin treated mouse 2

source_name: ob/ob leptin treated islets, biological replicate 2


title: 5-MAP2

description: polyA mRNA (nuclear-enriched)

tag: number of cells sequenced


title: J13

city: X

first: Igor

last: Lobo

address: X

country: France

institute: X

data_processing:
Image analyses and base calling were performed using the Illumina HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.17). The quality of data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then the de novo transcriptome was assembled using Trinity v2.2.0, with parameters --seqType fq --max_memory 150G --trimmomatic --quality_trimming_params TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 LEADING:15 TRAILING:15 MINLEN:50
Transcripts per million (TPM) were calculated throughout RSEM software after mapping reads on de novo transcriptome.
Genome_build: de novo assembling
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Colossoma macropomum

source_name: Trunk

extract_protocol:
Twenty juveniles were selected based on their sizes (21 to 33 mm standard length), desensitized on ice, sacrificed by medullary section and immersed in RNA later (Qiagen®; Hilden, Germany) immediately after the removal of the head. Total RNA was isolated by the Guanidinium-acid-phenol method (Trizol; Life Technologies®; Carlsbad, USA). Ten best RNA samples were selected based on the quality of the material and the libraries  were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: trunk

tag: size

tag: genotype

value: wild type


title: J12


title: 4-AT8

description: polyA mRNA (nuclear-enriched)

tag: age

tag: gender

tag: pmi (hr)


title: Leptin treated mouse 1

source_name: ob/ob leptin treated islets, biological replicate 1


title: Control mouse 3

source_name: ob/ob control islets, biological replicate 3

value: NaCl


title: blood_Tem_1

value: blood

tag: cell population

value: EM

tag: acquisition site

value: Seattle

tag: donor


title: J11

tag: tissue


title: skin_Tem_1

value: skin


title: Control mouse 2

source_name: ob/ob control islets, biological replicate 2


title: skin_Tem_2


title: Leptin treated mouse 3

source_name: ob/ob leptin treated islets, biological replicate 3


title: 4-MAP2

description: polyA mRNA (nuclear-enriched)

value: brain

value: M

tag: rin

tag: brain weight (gr)

tag: brain region

value: Brodmann area 9 (BA9)

tag: disease

tag: ad stage

tag: other pathology


title: blood_Tcm_1

tag: cell type

value: CLA+CD4+ T cells


title: Control mouse 1

source_name: ob/ob control islets, biological replicate 1

tag: agent


title: blood_Tcm_2

value: CM


title: 3-AT8

description: polyA mRNA (nuclear-enriched)

tag: number of cells sequenced

value: Alzheimer's disease

value: NIH-AA score A3B3C3; Braak VI


title: 3-MAP2

description: polyA mRNA (nuclear-enriched)


title: blood_Tem_2


title: J9

tag: size

tag: genotype


title: J8


title: 2-AT8

description: polyA mRNA (nuclear-enriched)

tag: age

tag: gender

value: F


title: J6


title: ob/ob EGA islets, biological replicate 4

source_name: ob/ob EGA islets

treatment_protocol: Pancreatic islets were isolated from ob/ob mice, 28 days after sham or EGA surgery.

tag: strain

value: leptin-deficient (ob/ob)

tag: treatment

value: EGA

value: pancreatic islets

value: male


title: ob/ob EGA islets, biological replicate 3


title: ob/ob EGA islets, biological replicate 5


title: 2-MAP2

description: polyA mRNA (nuclear-enriched)

tag: pmi (hr)


title: J4

tag: tissue

value: trunk

value: wild type


title: ob/ob EGA islets, biological replicate 2


title: 1-AT8

description: polyA mRNA (nuclear-enriched)

tag: rin

value: cardiovascular disease


title: WTC_Nsi

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

institute: NINDS/NIH

description:
WTC iPSC line transfected with negative control siRNA (Nsi)
processed data files: Cross_Sample_*.txt

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Post CASAVA deplexing, .fastq files generated per library were import into the CLCbio Genomics Workbench (www.clcbio.com) and QC inspected, adaptor clipped, low quality trimmed, filtered, then mapped. Per quality trimming, 15bp from the 5' end of each read was globally removed along with 1bp from the 3' end. Bases with a call accuracy < 95% were trim-removed thereafter. Per filtering, reads having more than two ambiguities were discarded along with those having read length <15bp post quality trimming. Per mapping, the "RNA-Seq" tool supported in the Workbench was used to locally align reads by library against the human genome (GRCh38/hg38) without masking; keeping only those mapped reads with >= 80% reference identity for >=80% read length. Post mapping, the number of reads falling in known annotated transcripts (Ensembl) were enumerated and the counts converted into "Transcript per Million mapped reads" ("TPM") expression values. TPM expression values were next imported into R (https://cran.r-project.org/). Where, TPM expression values were pedestalled by 2, Log2 transformed, filtered to remove transcripts not having at least one transformed value >1, then quantile normalized. Normalized values for remaining transcripts were then used to confirm the absence of library-level outliers via Tukey box plot, covariance-based PCA scatter plot, and pearson correlation heat map. After, normalized expression was noise modeled using LOWESS (CV~mean) and transcripts not having at least one normalized value > 3.25 removed as noise-biased and non-informative. For transcripts not discarded, differential expression between Ei and Nsi treatment was tested for using ANCOVA while correcting for iPSC line type. Transcripts having an uncorrected P < 0.05 by this test and an absolute difference of corrected means >=1.5X were subsequently deemed to be differentially expressed between Ei and Nsi. Transcript annotations and corresponding enriched pathways and functions were obtained using the Ingenuity Pathway Analysis "IPA" tool (www.qiagen.com).
Post adaptor clipped and QC trimmed sequence files used in the reference mapping process are provided per sample in .fastq format.
Genome_build: hg38
Supplementary_files_format_and_content: TPM_Expression_Enumeration_*.txt: Tab-delimited text file per sample that details RPKM enumerated expression for each RepeatMasker annotated HERV region in hg38.
Supplementary_files_format_and_content: Cross_Sample_*.txt: Tab-delimited text files describe the cross sample RPKM expression before normalization, after normalization (pre-noise filtering), and after noise filtering.

source_name: iPSC

growth_protocol: To determine the genes and pathways that are regulated by HERV-K Env, three different iPSC cell lines ("PAU", "NC5" and "WTC", Miyaoka et al., 2014) were cultured on Matrigel-coated 6 well plates in E8 medium for 24 hrs; achieving 30-50% confluence.

extract_protocol:
RNA extraction and purification were performed 24hrs post siRNA transfection using a total RNA extraction and purification kit (Norgen, Thorold, ON, Canada) following the manufacturer’s suggested instructions.
Libraries for each RNA extracted were prepared using 10ug in conjunction with the Illumina paired-end stranded Total RNA-Seq ribosome depletion kit. Post preparation, libraries were paired-end sequenced (1550bp) for 40-50M reads each (Illumina HiSeq).

treatment_protocol: Cultured iPSCs were transfected for 24hrs using either a siRNA designed to target HERV-K Env ("Ei") or a negative control siRNA ("Nsi"). Per transfection reagent, TransIT-siQUEST (Mirus Bio, Madison, WI, USA) was mixed for 30mins with each siRNA respectively (100 mM stock, 125 nM final concentration) before treatment.

tag: iPS cell line

value: WTC

tag: sirna transfection

value: Nsi


title: PAU_Ei

description:
PAU iPSC line transfected with siRNA designed to target HERV-K Env (Ei)
processed data files: Cross_Sample_*.txt

value: PAU

value: Ei


title: WTC_Ei

description:
WTC iPSC line transfected with siRNA designed to target HERV-K Env (Ei)
processed data files: Cross_Sample_*.txt


title: PAU_Nsi

description:
PAU iPSC line transfected with negative control siRNA (Nsi)
processed data files: Cross_Sample_*.txt


title: ob/ob EGA islets, biological replicate 1


title: J3


title: NC5_Nsi

description:
NC5 iPSC line transfected with negative control siRNA (Nsi)
processed data files: Cross_Sample_*.txt


title: 1-MAP2

description: polyA mRNA (nuclear-enriched)

value: brain

tag: brain weight (gr)

tag: brain region

value: Brodmann area 9 (BA9)

tag: disease


title: J2


title: ob/ob sham islets, biological replicate 3

source_name: ob/ob sham islets

value: Sham


title: ob/ob sham islets, biological replicate 2


title: ob/ob sham islets, biological replicate 1


title: NC5_Ei

description:
NC5 iPSC line transfected with siRNA designed to target HERV-K Env (Ei)
processed data files: Cross_Sample_*.txt


title: J1


title: CT-20T

status: Public on Aug 04 2020

city: Bunkyo ku

first: Akihiko

last: Miyanaga

state: Tokyo

address: 1-1-5 Sendagi,

department: Department of Pulmonary Medicine and Oncology, Graduate School of Medicine

country: Japan

institute: Nippon Medical School

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized on the GeneChip® Human Exon 1.0 ST Array using  the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Transcriptome Analysis Console v4.0 using Thermo Fisher Scientific default analysis settings and global scaling as normalization method. The trimmed mean was used with normalized data.

source_name: lung tissue

label_protocol: cDNA synthesis, amplification and labeling were performed with The Ambion® WT Expression Kit and Affymetrix® GeneChip® WT Terminal Labeling Kit

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit columns (Qiagen) according to the manufacturer’s protocol.

value: lung carcinoid

value: Male

tag: histological subtype

value: Atypical carcinoid

tag: 8th pstage

value: IIB

tag: relapse

value: Relapsed


title: CT-17T

value: Typical carcinoid

value: IA

value: not relapsed


title: CT-19T

value: Female


title: CT-22T


title: CT-23T


title: CT-5T