title: 201496860040_R03C01

description: normal blood sample


title: N7-2 RNA-Seq

status: Public on May 19 2020

type: SRA

city: SHENYANG

first: Yixin

last: Chen

address: No.36 Sanhao Street, Heping District

country: China

institute: SHENGJING HOSPITAL OF CHINA MEDICAL UNIVERSITY

library_source: transcriptomic

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

molecule: total RNA

organism: Homo sapiens

source_name: Pericardium

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: tissue

value: Pericardium

tag: age (y)

tag: Sex

value: Female

tag: cause (operation)

value: aortic stenosis (aortic valve replacement)


title: 201496860042_R03C01

type: genomic

city: London

first: Oliver

last: Robinson

state: London

address: St Mary's Campus, Norfolk Place

department: School of Public Health

country: United Kingdom

institute: IMPERIAL COLLEGE LONDON

description: normal blood sample

hyb_protocol: Then, bisulfite-converted DNA was used for hybridization on the Infinium HumanMethylation EPIC BeadChip, following the Illumina Infinium HD Methylation protocol. Briefly, a whole genome amplification step was followed by enzymatic end-point fragmentation and hybridization to HumanMethylation EPIC BeadChips at 48°C for 17 h, followed by single nucleotide extension. The incorporated nucleotides were labelled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP).

scan_protocol: the BeadChip was scanned using the Illumina HiScan SQ scanner. The intensities of the images were extracted using in-house software written for the R statistical computing environment. The methylation score for each CpG was represented as a β-value according to the fluorescent intensity ratio representing any value between 0 (unmethylated) and 1 (completely methylated).

data_processing:
DNA methylation (DNAm) data were pre-processed and normalized using in-house software written for the R statistical computing environment, including background and color bias correction, quantile normalization, and Beta MIxture Quantile dilation (BMIQ) procedure to remove type I/type II probes bias, as described elsewhere (Fiorito et al., 2017). DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values). Cross-reactive and polymorphic probes - with minor allele frequency greater than 0.01 in Europeans (Y. A. Chen et al., 2013) - were excluded. Methylation measures were set to missing if the detection p-value was greater than 0.01. Samples with the bisulfite conversion control fluorescence intensity lower than 10,000 for both type I and type II probes and those with total call rate lower than 95% were excluded. Finally, samples were excluded if the predicted sex (based on chromosome X methylation) did not match that self-reported.
DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values).

molecule: genomic DNA

source_name: blood samples

extract_protocol: bisulphite conversion of 500 ng of each DNA sample was performed using the EZ DNA Methylation-Lightning Kit according to the manufacturer’s protocol (Zymo Research, Orange, CA).

tag: age

value: M

tag: person id

tag: disease state

value: normal


title: 201496860040_R02C01

description: normal blood sample

label: biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP)

label_protocol: Illumina Infinium HD Methylation protocol

value: F


title: WTCHG_265188

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

description:
2 lanes
WTCHG_345854_265188
WTCHG_348065_265188

data_processing:
Fastq quality was evaluated using FastQC (0.11.2) and contamination by other organisms was excluded using FastQ Screen (0.4.4). Files were not trimmed.
Transcripts per million (TPM) and counts tables were obtained using Salmon (0.8.2 [40]) with kmer size option 31 and index option fmd. Salmon results were imported into R using tximport (1.10.0 [41]).
Genome_build: hg38
Supplementary_files_format_and_content: TPM tables from salmon

molecule: polyA RNA

source_name: iPSC-derived motor neurons

growth_protocol: iPSCs were grown on Matrigel until confluency, then neural induction was started using DMEM/F12:Neurobasal 1:1, N2, B27,  ascorbic acid (0.5 mM), 2-mercaptoethanol, compound C (3 µM) and Chir99021 (3 µM). After 4 days in culture, RA (1 µM) and SAG (500 nM) were added to the medium. On the next day, Chir99021 and compound C were removed from the medium, and the cells were cultured for another 4–5 days. After that, cells were split 1:3 on approximately day 10. Subsequently, the medium was supplemented with growth factors BDNF (10 ng/ mL), GDNF (10 ng/mL), N-[N-(3,5-Difluorophenacetyl)-L-ala- nyl]-S-phenylglycine t-butyl ester (DAPT) (10 mM), and laminin (0.5 mg/mL). After 7 days, DAPT and laminin were removed from the medium, and the neurons were allowed to mature until day 25-30.

extract_protocol:
RNA was extracted from whole iPSMN cultures at day 30.
Library preparation was carried out using the Illumina TruSeq RNA Sample Prep Kit v2 by the Oxford Centre for Human Genomics. RNA sequencing was performed on the Illumina HiSeq4500 platform over 75 cycles. Sequences were paired-end. Fastq files were generated from the sequencing platform using the manufacturer’s proprietary software.

tag: cell line

tag: cell type

value: iPSC-derived motor neurons

tag: cell type background

value: iPSC line derived from a C9orf72-HR positive ALS patient

tag: genotype/variation

value: edited samples

tag: date

value: AUG

tag: operator


title: 201496860019_R08C01

description: normal blood sample


title: 201496860040_R01C01

description: normal blood sample


title: N6-1 RNA-Seq

value: Male

value: coronary artery bypass grafting


title: 6wk_VipSCN_nuc019

city: Charlottesville

first: John

middle: N

last: Campbell

state: VA

address: 485 MCCORMICK RD, GILMER HALL ROOM 229 PO BOX 400328

department: Biology

country: USA

institute: University of Virginia

description: 6wk old male (tissue pool from 2 mice)

data_processing:
Demultiplexing by bcl2fastq2 v2.20.0.
Alignment to mouse genome by HISAT2 v2.1.0 (using “-k 2”)
BAM conversion of aligned reads by SAMtools v1.8.063
Duplicate and low-quality read removal by Picard 2.17.0
Reads assigned to features (genes) using the feature Counts from the Subread package v1.6.0 (using recommended setting and a custom meta-annotation that merges overlapping isoforms)
Genome_build: Mus musculus, build: mm10, GRCm38
Supplementary_files_format_and_content: CSV of gene expression counts with rows of genes and columns of samples

organism: Mus musculus

source_name: suprachiasmatic nucleus

growth_protocol: Six-week old (juvenile; n = 2) and 10 week-old (adult, n = 1) VIP-IRES-Cre::H2b-TRAP male siblings were bred from the same VIP-IRES-Cre x H2b-TRAP mouse line and raised on a 12 hrs light/dark cycle with food and water available ad libitum

extract_protocol:
The following morning, the RNAlater-preserved tissue samples were processed into single-nuclei suspensions according to the sNuc-Seq method of Habib et al.38. Briefly, the two SCN tissue samples (juvenile, adult) were dounce homogenized (Wheaton tissue grinders, catalog # 357538) and separated by density gradient centrifugation as described in the published protocol38. Each pellet was then re-suspended in 0.5 ml sNuc-Seq resuspension buffer38 and filtered through a 20 μm mesh (Miltenyi Biotec pre-separation filters, catalog # 130-101-812) to remove clumped nuclei and larger debris. Nuclei were counterstained with two drops of NucBlue Live ReadyProbes Reagent (ThermoFisher Scientific catalog # R37605) per ml of nuclei. Nuclei were sorted by MoFlo Astrios EQ cell sorter (Harvard Bauer core facility), gating for NucBlue+/mCherry+ singlets and distributing them individually to wells of 96-well plates containing 5 μl per well of nuclei capture buffer (1% beta-mercaptoethanol in Qiagen Buffer TCL; catalog # 1031576). Each plate was loaded with equal numbers of samples from juvenile and adult SCN tissue. Loaded plates were centrifuged for 5 min at 2,500 xg and 4degC to ensure nuclei reached the capture buffer and frozen at -80degC for up to 4 weeks until use.
Sample plates were transferred to an RNA-dedicated PCR cabinet, thawed quickly, and immediately purified with RNA-Clean XP (Beckman Coulter, catalog # A63987; 2.5:1 ratio of RNA-Clean XP to sample volume), eluting in 4μl Smart-seq2 buffer (2 μl Smart-seq2 cell lysis buffer, 1 μl 100 μM oligo-dT primer, and 1 μl 10 mM dNTP mix)61. cDNA was then generated and amplified as described in the Smart-Seq2 protocol61, except that 22 PCR cycles were used for the amplification step. After the PCR step, 10 μl of each sample was transferred to new 96-well plates for subsequent processing. Amplified cDNA was purified with two rounds of SPRIselect   (Beckman Coulter, catalog # B23318; 0.8:1 ratio of SPRIselect to sample volume), eluting in ultrapure water. cDNA concentration was measured by Qubit fluorometry in a microplate format, each well containing 2 μl of cDNA sample and 98 μl of Qubit working solution (ThermoFisher Scientific, catalog # Q32854). Qubit readings were collected with a fluorescence microplate reader (Molecular Devices SpectraMax M5; Harvard Medical School ICCB-Longwood core facility) and used to calculate DNA concentrations by comparing each sample’s Qubit reading to standards in a 50% dilution series (n=8 standards; range, 0.25 ng/μl to 0.01 ng/μl plus a negative control, 0.0 ng/μl). cDNA samples were then diluted to 0.15 ng/ μl with ultrapure water and processed into sequencing libraries with sample-specific indices using the Nextera DNA Sample Prep Kit and Nextera XT Index Kit v2 sets A-D (Illumina, catalog #s FC-131-1096, FC-131- 2001, FC-131-2002, FC-131-2003, FC-131-2004, respectively). Nextera XT was used at 1/4 reaction volumes but otherwise according to manufacturer’s instructions. Sequencing libraries were purified with two rounds of SPRIselect (0.8:1 ratio of SPRIselect to sample volume) and eluted in a single volume of ultrapure water. Library pool concentration was measured by Qubit according to the manufacturer’s instructions sized using Agilent BioAnalyzer high sensitivity kit, and then diluted with ultrapure water to a size-corrected concentration of 2 nM. The diluted library pool was denatured and further diluted to 2 pM loading concentration according to Illumina NextSeq recommendations, then sequenced with a NextSeq 500 v2 75cycle sequencing kit (Illumina, catalog # FC-404-2005).

treatment_protocol: One hour after light cycle onset, the VIP-IRES-Cre::H2b-TRAP mice were removed from their home cage and rapidly decapitated in order to minimize stress related changes in gene expression. Brains were extracted quickly, chilled briefly in ice cold DMEM/F12 media, and then sectioned coronally at 1 mm intervals in a chilled stainless-steel brain matrix. The brain sections containing and neighboring the SCN were collected in ice-cold RNAlater (Qiagen catalog # 76106). Each section was imaged by a fluorescence stereoscope (Zeiss Discovery V8) in order to visualize fluorescently labeled cells in the SCN for dissection. Dissected tissue was pooled across mice by age group (juvenile, adult) and placed into ice-cold RNAlater overnight in the dark at 4degC.

tag: gender

value: male

tag: genotype

value: single mCherry+ cell nucleus

tag: sample time

value: sample collected at 7am


title: 6wk_VipSCN_nuc018

description: 6wk old male (tissue pool from 2 mice)


title: N3-1 RNA-Seq

value: infective endocarditis(aortic valve replacement


title: 201496860019_R07C01

description: normal blood sample


title: CP2-2 RNA-Seq

value: idiopathic constrictive pericarditis


title: 201496860019_R04C01

description: normal blood sample


title: 6wk_VipSCN_nuc017

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc021

description: 6wk old male (tissue pool from 2 mice)


title: 201496860040_R05C01

description: normal blood sample


title: 6wk_VipSCN_nuc016

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc015

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc020

description: 6wk old male (tissue pool from 2 mice)


title: 201496860019_R03C01

description: normal blood sample


title: C2-3 RNA-Seq

value: Pericardium


title: C4-1 RNA-Seq


title: 6wk_VipSCN_nuc014

description: 6wk old male (tissue pool from 2 mice)


title: 201496860015_R08C01

description: normal blood sample


title: 201496860019_R06C01

description: normal blood sample


title: 201496860019_R01C01

description: normal blood sample


title: 201496860015_R06C01

description: normal blood sample


title: 201496860015_R05C01

description: normal blood sample


title: 6wk_VipSCN_nuc027

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc012

description: 6wk old male (tissue pool from 2 mice)


title: 201496860015_R07C01

description: normal blood sample


title: 201496860015_R03C01

description: normal blood sample


title: 201496860015_R04C01

description: normal blood sample


title: 201496860015_R02C01

description: normal blood sample


title: 201496860019_R02C01

description: normal blood sample


title: Proliferating NSC culture untreated rep3

type: RNA

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalized using quantile normalization with beadarray (version 2.34.0) in R/BioConductor. Probes were assigned to Entrez GeneIDs using the illuminaMousev2.db package (version 1.26.0). Unmapped genes were removed and replicate expression data for the same GeneID were also removed, retaining only the gene with the highest mean.

label: biotin

source_name: Adherent neural stem cell culture

label_protocol: Amplification and biotin labeling with the TotalPrep™ RNA Amplification Kit (Illumina)

growth_protocol: Cells were cultured on poly-D-lysine/laminin-coated plates in Neurobasal media supplemented with 2 % B27, GlutaMAX,  20 ng/ml bFGF and 20 ng/ml EGF

extract_protocol: Cells were lysed on the culture dish and total RNA was prepared using the Qiagen RNeasy micro kit.

treatment_protocol: After withdrawal of bFGF and EGF to induce differentiation, the treatment group was grown in the presence of 25 μM quercetin. Cells were harvested 4 days later.

value: Adherent neural stem cell culture

tag: culture conditions

value: Proliferation

tag: treatment

value: Control


title: Proliferating NSC culture quercetin-treated rep1

value: quercetin


title: Proliferating NSC culture quercetin-treated rep3


title: 201496860014_R08C01

description: normal blood sample

value: F

value: normal


title: Proliferating NSC culture quercetin-treated rep2


title: 201496860014_R07C01

description: normal blood sample

value: M


title: 6wk_VipSCN_nuc011

description: 6wk old male (tissue pool from 2 mice)

tag: tissue


title: 6wk_VipSCN_nuc010

description: 6wk old male (tissue pool from 2 mice)


title: 201496860014_R06C01

description: normal blood sample

tag: Sex


title: 201496860014_R05C01

description: normal blood sample


title: 201496860014_R04C01

description: normal blood sample


title: 6wk_VipSCN_nuc009

description: 6wk old male (tissue pool from 2 mice)


title: 201496860014_R03C01

description: normal blood sample


title: 201496860014_R02C01

description: normal blood sample


title: 201496860015_R01C01

description: normal blood sample


title: 6wk_VipSCN_nuc013

description: 6wk old male (tissue pool from 2 mice)


title: Proliferating NSC culture untreated rep1


title: Differentiating NSC culture quercetin-treated rep3

value: Differentiation


title: Differentiating NSC culture quercetin-treated rep2


title: 6wk_VipSCN_nuc007

description: 6wk old male (tissue pool from 2 mice)


title: 201496850204_R08C01

description: normal blood sample


title: 201496850204_R07C01

description: normal blood sample


title: Differentiating NSC culture untreated rep3


title: 201496850204_R05C01

description: normal blood sample


title: Differentiating NSC culture quercetin-treated rep1


title: 6wk_VipSCN_nuc006

description: 6wk old male (tissue pool from 2 mice)


title: 201496850204_R04C01

description: normal blood sample


title: Proliferating NSC culture untreated rep2


title: 201496850204_R06C01

description: normal blood sample


title: 6wk_VipSCN_nuc005

description: 6wk old male (tissue pool from 2 mice)


title: Differentiating NSC culture untreated rep2


title: 201496850204_R03C01

description: normal blood sample


title: 6wk_VipSCN_nuc004

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc008

description: 6wk old male (tissue pool from 2 mice)


title: 6wk_VipSCN_nuc003

description: 6wk old male (tissue pool from 2 mice)


title: Differentiating NSC culture untreated rep1


title: 201496850204_R01C01

description: normal blood sample


title: 201496850203_R08C01

description: normal blood sample


title: 201496860014_R01C01

description: normal blood sample


title: 201496850203_R06C01

description: normal blood sample


title: 201496850204_R02C01

description: normal blood sample


title: 201496850203_R05C01

description: normal blood sample


title: 6wk_VipSCN_nuc002

description: 6wk old male (tissue pool from 2 mice)


title: WT_PDL1_possorted (scRNA-seq)

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
RNA-Seq data mapped with STAR and read counting performed using HT-seq
BAM to bedgraph performed using bedtools and bedgraph to bigwig performed using bedGraphToBigWig v4
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files, count table files (txt), genes-barcodes (tsv file) matrices (matrix file)

source_name: mouse tumor infiltrating T cells

extract_protocol: Total RNA was extracted using an RNeasy mini kit (Qiagen, Valencia, CA) and cDNA was synthesized using the iScript cDNA Synthesis Kit (BioRad, Hercules, CA).

treatment_protocol: T cell activation was determined at 72h by flow cytometry. In selected wells, T cells were treated with PD-1 Fc or control IgG Fc (2.5 ug/ml; R&D). In other experiments, T cells were treated with an _PD-L1 mAb (10 ug/ml, 10F.9G2) or Rat IgG2b_ (both Biolegend). FACS-sorting was performed on the SY3200 (Sony, Tokyo, Japan). Cell pellets were re-suspended and cell labeling was performed after blocking Fc_RIII/II with an anti-CD16/CD32 mAb (eBioscience, San Diego, CA) by incubating 1x106 cells with 1ug of fluorescently conjugated mAbs directed against mouse CD45 (30-F11).

value: PDL1 floxed/WT-CD4Cre

value: no treatment

tag: FACS-sorted from mouse pancreatic tumors

value: tumor infiltrating T cells


title: 201496850203_R07C01

description: normal blood sample

tag: age


title: WT_possorted (scRNA-seq)

value: WT


title: 201496850203_R04C01

description: normal blood sample

tag: person id


title: 6wk_VipSCN_nuc001

description: 6wk old male (tissue pool from 2 mice)

value: male

value: single mCherry+ cell nucleus


title: POL1_Flox_possorted (scRNA-seq)

value: PDL1 floxed/floxed-CD4Cre


title: 201496850203_R03C01

description: normal blood sample

tag: disease state


title: 201496850203_R02C01

description: normal blood sample


title: 201496850203_R01C01

description: normal blood sample


title: 201496850202_R06C01

description: normal blood sample


title: 201496850202_R05C01

description: normal blood sample


title: CD4CRE (scRNA-seq)


title: PDL1_Fc_3 (RNA-seq)

source_name: mouse splenic T cells

value: anti-mouse CD3/CD28 + PD1 Fc

tag: negatively enriched by magneting beading

value: splenic T cells


title: PDL1_Fc_2 (RNA-seq)

tag: cell type


title: PDL1_possorted (scRNA-seq)

value: PDL1 floxed/floxed


title: 201496850202_R02C01

description: normal blood sample


title: 201496850202_R03C01

description: normal blood sample


title: 201496850176_R08C01

description: normal blood sample


title: 201496850176_R07C01

description: normal blood sample


title: PDL1_Fc_1 (RNA-seq)


title: 201496850202_R07C01

description: normal blood sample


title: Input (NelfA)

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

library_source: genomic

data_processing:
detailed data analysis file: ChIP-Seq analsyis done by Active Motif (Data Explain file attached in Pdf format)
Sequence analysis: The 75-nt sequence reads ("tags") identified by the sequencing service (using NextSeq 500) are mapped to the genome using BWA algorithm. Alignment information for each tag is stored in BAM format. Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Fragment density: Since the 5'-ends of the tags represent the end of a ChIP/IP-fragments, the tags are extended in silico (using Active motif software)at their 3' -ends to a length of 150-250 bp, depending on the average fragemtn length in the size selected library. To identify the density of fragemnts (extendend tags) along the genome, the genome is divided into 32 nt bins and the number of fragments in each bin is determined. This information is stored in a bigWig file that can be reviewed in a browser such as Affymetrix' Integrated Genome Browser (IGB).
peak finding: An interval is a discrete genomic region, defined by the chromosome number and a start and end coordinate. Intervals represent the locations of the fragment density peaks. Two main peak callers used by active motif are MACS and SICER. Both look for significant enrichments in the ChIUP/IP data file when compared to Input data file
active region: To compare peak metrics between two samples, overlapping intervals are grouped into"Active regions', which are defined by the start coordinate of the most upstream interval and the end coordinate of the most downstream interval (=union of overlapping Intervals). In locations where only one sample has an interval, this interval defines the Active Region. Active regions are useful to consider because the location and the lenghts of the intervals are rarely exactly the same when comparing different samples.
Genome_build: mm10

source_name: whole Heart

extract_protocol: ChIP, Library construction and Illumina sequencing performed by Active Motif, Inc

treatment_protocol: C57Bl/6 mice (12wks, ~26gms, male) were subjecetd to transaortic coartation (standard protocol described in detail in related publications Sayed et al, 2013; Sayed et al  2015) for 4-7days before hearts were extracted for analysis.

value: pooled from normal and TAC hearts

tag: strain


title: 201496850202_R01C01

description: normal blood sample


title: 201496850176_R05C01

description: normal blood sample


title: 201496850176_R06C01

description: normal blood sample


title: PD1_Fc_3 (RNA-seq)

value: anti-mouse CD3/CD28 + PDL1 Fc


title: 201496850176_R04C01

description: normal blood sample


title: 201496850176_R03C01

description: normal blood sample


title: PD1_Fc_2 (RNA-seq)


title: NelfA_ChIP-Seq Sham

source_name: Whole Heart

value: Normal Heart:12wk old male mice subjected to sham operations (n=3)

tag: antibody

value: anti-NelfA (Santacruz sc 23599))


title: 201496850176_R02C01

description: normal blood sample

value: F

value: normal


title: 201496850202_R08C01

description: normal blood sample

value: M


title: PD1_Fc_1 (RNA-seq)


title: Ctrl_Fc_3 (RNA-seq)

value: anti-mouse CD3/CD28 + control Fc


title: 201496850175_R07C01

description: normal blood sample


title: 201496850175_R05C01

description: normal blood sample


title: NelfA_ChIP-Seq TAC

value: Hypertrophied hearts:12wk old male mice subjected to sham operations (n=3)

value: anti-NelfA (Santacruz sc23599)


title: 201496850175_R03C01

description: normal blood sample


title: Ctrl_Fc_1 (RNA-seq)

value: WT


title: 201496850175_R04C01

description: normal blood sample


title: Control_3 (RNA-seq)

value: anti-mouse CD3/CD28 only


title: Ctrl_Fc_2 (RNA-seq)


title: 201496850175_R06C01

description: normal blood sample


title: 201496850176_R01C01

description: normal blood sample


title: CTB 20h rep3

city: Vienna

first: Martin

last: Knöfler

address: Währinger Gürtel 18-20, 5Q,

department: Department of Obstetrics and Gynaecology, Reproductive Biology Unit

country: Austria

institute: Medical University of Vienna

description:
MK-4_16
vCTB-20h_S2

data_processing:
Read quality data was assessed using FastQC.
RNA-seq reads were aligned to the UCSC GRCh38/hg38 genome assembly using  HISAT2 version 2.1.0 with default parameters.
Aligned BAM files were indexed and sorted with Samtools version 0.1.18.
Read count matrices were obtained using featureCounts version 1.5.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files contain read count values for genes with GRCh38 gene symbols for each sample.

source_name: placenta pool 3

growth_protocol: Cells were seeded on fibronectin (20 µg/mL) coated cell culture dishes and were cultivated in DMEM/Ham's F12 with GlutaMAX-I/10% fetal bovine serum/0.05 mg/mL gentamicin/0.5µg/mL fungizone

extract_protocol:
RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity  DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen). Pooled libraries were  sequenced on a NextSeq500 instrument (Illumina) in 1x75bp single-read sequencing mode.

tag: gestational week

value: 6-7th week of gestation

tag: differentiation stage

value: vCTB

tag: time poiont

tag: protocol

value: ibronectin-coated cell culture dish


title: BPH342PrF_Via

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

description:
Samples were sequenced on the Illumina NextSeq 500 and the Illumina NovaSeq 6000
Viable cells from normal human prostate tissue transition zone

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 3.1.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 3.1.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Viable human prostate transition zone

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)

treatment_protocol: Populations of single-cells dissociated from diseased prostates from BPH patients were isolated by FACS

tag: patient phenotype

value: BPH Glandular

tag: prostatic zone

value: Transition Zone

tag: digestion enzyme

value: 5mg/mL Collagenase I 4hr

tag: facs ab profile

value: Via-


title: CTB 72h rep3

description:
MK-4_17
vCTB-72h_S18

value: STB


title: 201496850167_R08C01

description: normal blood sample

tag: Sex


title: 201496850167_R07C01

description: normal blood sample


title: 201496850175_R01C01

description: normal blood sample


title: CTBs 72h rep2

description:
MK-4_14
vCTB-72h_S11

source_name: placenta pool 2


title: Control_2 (RNA-seq)

tag: genotype

tag: treatment

value: splenic T cells


title: 201496850175_R02C01

description: normal blood sample

tag: age

tag: person id


title: 201496850167_R06C01

description: normal blood sample

tag: disease state


title: Control_1 (RNA-seq)

tag: negatively enriched by magneting beading

tag: cell type


title: 201496850167_R05C01

description: normal blood sample

value: F


title: 201496850167_R04C01

description: normal blood sample

value: normal


title: 201496850167_R03C01

description: normal blood sample

value: M


title: 201496850175_R08C01

description: normal blood sample


title: anti-ETO2 U937_ETO2

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

data_processing:
Base-calling performed with Illumina analysis pipeline.
ChIP-Seq reads were aligned to the human hg19 genome using STAR (2.5.2).
ChIP-Seq reads were further analyzed using HOMER (4.9) with default settings.
BedGraph files were generated with the “makeUCSCfile” tool accompanying the HOMER package.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: BedGraph files showing ChIP-Seq binding signals.

source_name: human AML cells

growth_protocol: Kasumi-1 and U937 cells were maintained in RPMI 1640 with 10% fetal bovine serum (FBS). CD34+ HSPCs were purified from umbilical cord blood of unidentified human donors (STEMCELL Technologies) and cultured in IMDM supplemented with 20% FBS, FLT3L (100 ng/ml), SCF (100 ng/ml), TPO (100 ng/ml), IL-6 (20 ng/ml), GM-CSF (20 ng/ml), and IL-3 (50 ng/ml) (PeproTech).

extract_protocol:
ChIP was performed using SimpleChIP® Enzymatic Chromatin IP Kits (Magnetic Beads, Cell Signaling Technology #9003) following the manufacturer’s instructions.
Libraries were constructed following instructions accompanying the library preparation kit designed for Illumina sequencing.

treatment_protocol: U937 cells were transduced with lentiviruses expressing ETO2. Transduced cells were selected with Puromycin.

tag: cell line

value: human AML cells

tag: chip antibody

value: ETO2 (Santa Cruz, SC-9741)

tag: transduced with

value: lentiviruses expressing ETO2


title: 201496850167_R02C01

description: normal blood sample


title: CTBs 72h rep1

description:
MK-4_11
vCTB-72h_S1

source_name: placenta pool 1

tag: gestational week

tag: differentiation stage

tag: time poiont


title: U937_ETO2 INPUT


title: CTBs 20h rep1

description:
MK-4_10
vCTB-20h_S12

tag: protocol


title: 201496850167_R01C01

description: normal blood sample


title: S18-1069

city: Guangzhou

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina HiSeq2500 software used for basecalling.
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: nasopharyngeal carcinoma cells

growth_protocol: The S18 and LACTB knocked-down cells were cultured in Dulbecco’S Modified Eagle’S Medium (DMEM) supplemented with 10% FBS at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells and tissue specimens using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: lowly metastatic ability

value: nasopharyngeal carcinoma cells

tag: knockdown

value: LACTB-knocked down using shRNA1069


title: S18-581

value: LACTB-knocked down using shRNA 581


title: 201496850166_R05C01

description: normal blood sample

tag: Sex


title: 201496850166_R04C01

description: normal blood sample


title: 201496850166_R06C01

description: normal blood sample


title: 201496850166_R02C01

description: normal blood sample


title: 27C2  rep1

description:
MK-1_06-41620664
27C2_S2

source_name: JEG-3 choriocarcinoma

growth_protocol: Cell lines are cultivated in DMEM/ 2mM L-glutamine/ 10% fetal bovine serum/ 0.5µg/mL Puromycin dihydrochloride/ 100 U/mL Penicillin Streptomycin

treatment_protocol: YAP knock out was performed using CRISPR-Cas9 genome editing

tag: genotype

value: wilde type


title: H11TMS1 (Pt11-RT)

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

description: V3 library prep protocol

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0 for v2 samples and version 3.1.0 for v3 samples, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0 for v2 samples and version 3.1.0 for v3 samples, 10X Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: Csv files including gene expression matrix from all samples

source_name: Human trabecular meshwork, 65 y/o M

extract_protocol:
The trabecular meshwork was dissected in Ames' medium, digested in papain, and manually triturated into single cell suspensions in ovomucoid solution. The cells were resuspended in 0.04% non-acetylated BSA in Ames to solutions of ~1000 cells/uL and loaded into Chromium Single Cell Chips for a targeted recovery of 6,000 cells.
Single cell libraries were made with Chromium 3’ v2 or v3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
Chromium 3’ v2 or v3 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: Human eyes were retrieved approximately 6 hours after death and transferred to the lab in a humid chamber on ice. The entire globe was then transferred to Ames' medium (Sigma-Aldrich; equilibrated with 95% O2/5% CO2) for dissections.

tag: tissue

value: Human trabecular meshwork


title: 27C1  rep1

description:
MK-1_05-41610714
27C1_S3


title: 201496850166_R01C01

description: normal blood sample

tag: age


title: S18-Neg

value: highly metastatic ability

value: Scrambled control


title: 201496850166_R03C01

description: normal blood sample

tag: person id


title: 27C1  rep2

description:
MK-1_11-41610716
27C1_S10


title: CTBs 20h rep2

description:
MK-4_13
vCTB-20h_S15

value: 6-7th week of gestation

value: vCTB

value: ibronectin-coated cell culture dish


title: 201496850152_R06C01

description: normal blood sample

tag: disease state


title: 201496850152_R08C01

description: normal blood sample


title: 201496850152_R05C01

description: normal blood sample


title: H4TMS1 (Pt4-LT)

description: V2 library prep protocol

source_name: Human trabecular meshwork, 64 y/o M


title: 27_7  rep2

description:
MK-1_10-41618683
27-7_S17

value: YAP knock out


title: H9RimS1 (Pt9-LT)

description: V2 library prep protocol

source_name: Human corneoscleral segment, 56 y/o F

value: Human corneoscleral segment

value: F


title: 201496850166_R08C01

description: normal blood sample

source_name: blood samples

value: M

value: normal


title: 201496850152_R04C01

description: normal blood sample


title: 27_7  rep1

description:
MK-1_04-41616711
27-7_S12


title: 201496850166_R07C01

description: normal blood sample


title: H3TMS1 (Pt3-RT)

description: V2 library prep protocol

source_name: Human trabecular meshwork, 60 y/o M


title: 27C2  rep2

description:
MK-1_12-41613722
27C2_S18


title: 201496860019_R05C01

description: normal blood sample


title: 201496850152_R03C01

description: normal blood sample


title: 27_6  rep2

description:
MK-1_03-41612724
27-6_S11


title: 201496850152_R02C01

description: normal blood sample


title: 201496850084_R08C01

description: normal blood sample


title: 27_6  rep1

description:
MK-1_09-41608727
27-6_S7


title: 201496850152_R01C01

description: normal blood sample


title: H2TMS2 (Pt2-LT)

description: V2 library prep protocol

source_name: Human trabecular meshwork, 78 y/o M, left eye


title: H2TMS1 (Pt2-RT)

description: V2 library prep protocol

source_name: Human trabecular meshwork, 78 y/o M, right eye


title: 27_5  rep2

description:
MK-1_02-41603797
27-5_S4


title: 201496850084_R05C01

description: normal blood sample


title: 201496850084_R06C01

description: normal blood sample


title: 27_5  rep1

description:
MK-1_08-41616707
27-5_S1


title: Caco2 organoid Omni ATAC rep2

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data were analyzed using ENCODE pipeline https://github.com/kundajelab/atac-seq-pipeline
Genome_build: hg19
Supplementary_files_format_and_content: bw

source_name: Caco2 organoid Omni ATAC

growth_protocol: Cells were grown in indicated medias using standard methods

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were construced using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purfied with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion

value: Human intestinal epithelial cells


title: 201496850084_R07C01

description: normal blood sample


title: 201496850152_R07C01

description: normal blood sample


title: 201496850084_R03C01

description: normal blood sample


title: H1TMS1 (Pt1)

description: V2 library prep protocol

source_name: Human trabecular meshwork, 74 y/o M


title: Caco2 organoid Omni ATAC rep1


title: 201496850083_R07C01

description: normal blood sample


title: 201496850083_R05C01

description: normal blood sample


title: 201496850084_R01C01

description: normal blood sample


title: 201496850083_R06C01

description: normal blood sample


title: Caco2 Omni ATAC rep2

source_name: Caco2 Omni ATAC


title: 201496850084_R02C01

description: normal blood sample


title: 201496850083_R04C01

description: normal blood sample


title: CTBs pcDNA rep3

description:
MK-4_7
vCTBs-pcDNA_S8

source_name: placenta pool 3

growth_protocol: Trophoblast cells were seeded on fibronectin (20 µg/mL) coated cell culture dishes and were cultivated in DMEM/ Ham's F12 with GlutaMAX-I/ 10% fetal bovine serum/ 0.05 mg/mL gentamicin/ 0.5µg/mL fungizone

treatment_protocol: Trophoblasts were transfected with either pcDNA 3.1(-) (empty control plasmid) or pCMV-flag YAP2-5SA

value: 6-8th week of gestation

tag: plasmid dna

tag: gene

value: ctrl.


title: 18_4  rep1

description:
MK-1_01-41619685
18-4_S8


title: 201496850083_R08C01

description: normal blood sample


title: 201496850083_R03C01

description: normal blood sample


title: CTBs YAP 5SA rep2

description:
MK-4_5
vCTBs-YAP-5SA_S5

value: pCMV-flag YAP2 -5SA


title: Caco2 Omni ATAC rep1

tag: cell type


title: Human intestinal organoid Omni ATAC rep2

source_name: Human intestinal organoid Omni ATAC


title: 201496850083_R01C01

description: normal blood sample


title: 201496850056_R08C01

description: normal blood sample


title: CTBs YAP 5SA rep1

description:
MK-4_2
vCTBs-YAP-5SA_S13


title: 201496850056_R06C01

description: normal blood sample


title: Human intestinal organoid Omni ATAC rep1


title: CTBs pcDNA rep2

description:
MK-4_4
vCTBs-pcDNA_S6

source_name: placenta pool 2


title: 201496850084_R04C01

description: normal blood sample


title: ML-110

data_processing:
Sequences were mapped to the hg38 human genome with Bowtie version:  2.2.6.0
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Genome_build: hg38
Supplementary_files_format_and_content: csv files include read count values for each Sample

source_name: Human intestinal organoid

growth_protocol: The protocol of Miyoshi et. al. for colon organoid sub-culture and expansion, was used with minor modifications. Tissue samples were obtained from the Department of Surgical Pathology at the Cleveland Clinic under IRB protocol (#17-1167). Adjacent normal intestinal crypts were harvested from surgical resections of patients with adenocarcinoma. Briefly, tissue was first rinsed in HBSS (Hank’s buffered saline solution), and blotted to remove excess mucus. Colonic mucosal strips (~4) were cut from tissue, placed in 60mm dishes, and minced with scissors such that they could pass through a 1 ml pipette tip. Tissue fragments were then suspended in a collagenase solution (2 mg/ml Type I collagenase and 50 mg/ml gentamicin in wash media [DMEM F/12 containing 10% FBS, 1% Pen/Strep and 1% L-glutamine]) and digested at 37oC until colonic crypts were liberated (~30-40 minutes). The crypts were then washed in wash media, counted and plated in 15ul Matrigel to have ~5000 crypts per Matrigel bead, in 24 well tissue culture plates. Intestinal stem cells were then cultured at 37oC in 50% L-WRN cell conditioned media containing 10mM Y-27632 and 500nM A-83-01. To passage organoids, dissociation buffer (1mM DTT, 0.5M EDTA in PBS) was added to break up Matrigel beads, following which organoids were trypsinized for one minute at 37oC. Wash media was added to neutralize trypsin, organoids were washed twice and then plated in Matrigel and cultured with conditioned media. Typically, organoids were passaged 1:3 every week. Fresh medium was added to wells every other day.

extract_protocol:
Organoids culture harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -800C under ethanol. 1ug RNA was used for RNA-seq library preparation.
Directional cDNA libraries made from cellular mRNAs were generated from the samples using the Illumina TruSeq RNA library kit and sequenced (paired-end sequencing of 100 bp reads) in the Genomics Core at the University of Chicago on an Illumina HiSeq2500, according to standard Illumina protocols.

value: Primary human intestinal organoids


title: CTBs pcDNA rep1

description:
MK-4_1
vCTBs-pcDNA_S7

source_name: placenta pool1


title: 201496850056_R05C01

description: normal blood sample


title: ML-111


title: 18_2  rep2

description:
MK-1_07-41621695
18-2_S13


title: 201496850083_R02C01

description: normal blood sample


title: 201496850048_R08C01

description: normal blood sample


title: 201496850056_R04C01

description: normal blood sample


title: PT5

city: Lund

first: Göran

last: Jönsson

address: Medicon Village

country: Sweden

institute: Lund University

data_processing:
Raw sequencing read data were demultiplexed and collated by library barcode into sample data sets.
TopHat 2.0.13 was used to align reads to the human reference genome hg38 together with 104,133 transcript annotations from the UCSC knownGenes table.
Cufflinks 2.2.1 was used to calculate FPKM.
Gene expression data were collapsed on 30,865 unique gene symbols by the sum of FPKM values of the individual transcripts.
Genes were reduced to 18,418 protein-coding genes as defined by HGNC.
The TCGA SKCM RNAseq data (n=472) was used as a reference set. We applied the quantile distribution of the quantile-normalized and log-transformed TCGA data of 17,075 common genes to each sample of the present data, and centered each gene by subtracting the median gene value of the TCGA data.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing FPKM values, that have undergone quantile normalization, log-transformation and centering using the large TCGA SKCM RNAseq set as reference.

source_name: Melanoma

extract_protocol:
Tumor DNA and RNA was extracted from snap frozen tumor fragments using AllPrep DNA/RNA Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
RNAseq strategy encompasses the performance of paired end sequencing of 75 bp reads on an Illumina NextSeq 500 instrument

value: Tumor

value: Primary tumor region 5


title: CTRL Nuc #1

city: Ipswich

first: Eric

last: Wolf

email: ewolf@neb.com, ericjwolf1@gmail.com

address: 240 County Road

department: RNA Division

institute: New England Biolabs

description: Poly (A) selected RNA

data_processing:
Transcript quantification was performed utilizing Salmon utilizing an index built from Refseq anotated transcripts (command: quant --validateMappings)
Gene level abundances were computed utilizing Tximport
FPKM calculations and fold changes were calculated utilizing DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 FPKM calcualtions

source_name: HEK293 Flp-In-TReX cells

growth_protocol: HEK293 Flp-In-TReX cells were grown in DMEM media supplemented with 10% FBS and 5% Pen-Strep

extract_protocol:
Control and MKRN2-depleted cells were harvested, fractionated using detergent, and RNA from these fractions was isolated using TRIZOL and Ambion PureLink kit (ThermoScientific)
RNA was poly(A)+ selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S), and libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep kit (NEB, E7765S). We used NEBNext Multiplex Oligos for Illumina (Index Primers #1 - #24) (NEB, E7335S and E7500S) as the unique index primers.

treatment_protocol: Two independent siRNA transfections were used to deplete MKRN2

tag: condition

value: C

tag: fraction

value: N


title: 201496850056_R03C01

description: normal blood sample


title: CTRL Cyto #1

description: Poly (A) selected RNA


title: 201496850056_R07C01

description: normal blood sample


title: CTRL Total #1

description: Poly (A) selected RNA

value: T


title: 201496850056_R02C01

description: normal blood sample


title: 201496850048_R02C01

description: normal blood sample


title: 201496850056_R01C01

description: normal blood sample


title: PT2

value: Primary tumor region 2


title: 201496850048_R07C01

description: normal blood sample


title: 201496850048_R06C01

description: normal blood sample


title: 201496850048_R05C01

description: normal blood sample


title: IT7

value: In-transit metastatic lesion 7


title: 201496850048_R01C01

description: normal blood sample


title: 201496850048_R03C01

description: normal blood sample


title: 201496850046_R08C01

description: normal blood sample


title: MKRN2 Total #2

description: Poly (A) selected RNA


title: MKRN2 Cyto #2

description: Poly (A) selected RNA


title: 201496850048_R04C01

description: normal blood sample


title: MKRN2 Nuc #2

description: Poly (A) selected RNA


title: 201496850046_R07C01

description: normal blood sample


title: IT6

value: In-transit metastatic lesion 6


title: Normal

source_name: Normal skin

value: Normal

value: Normal skin


title: PT4

value: Primary tumor region 4


title: CTBs YAP 5SA rep3

description:
MK-4_8
vCTBs-YAP-5SA_S9

tag: gestational week


title: ML-109


title: CTRL Cyto #2

description: Poly (A) selected RNA


title: PT3

value: Primary tumor region 3


title: 201496850046_R06C01

description: normal blood sample

value: F

value: normal


title: 201496850046_R05C01

description: normal blood sample

value: M


title: 201496850046_R03C01

description: normal blood sample


title: IT5

value: In-transit metastatic lesion 5


title: CTRL Nuc #2

description: Poly (A) selected RNA


title: 201496850037_R07C01

description: normal blood sample


title: 201496850037_R08C01

description: normal blood sample


title: CTRL Total #2

description: Poly (A) selected RNA


title: 201496850037_R04C01

description: normal blood sample


title: 201496850046_R01C01

description: normal blood sample


title: IT3

value: In-transit metastatic lesion 3


title: 201496850037_R06C01

description: normal blood sample


title: 201496850046_R02C01

description: normal blood sample


title: MKRN2 Cyto #1

description: Poly (A) selected RNA


title: MKRN2 Nuc #1

description: Poly (A) selected RNA


title: MKRN2 Total #1

description: Poly (A) selected RNA


title: IT1

value: Tumor

value: In-transit metastatic lesion 1


title: 201496850037_R05C01

description: normal blood sample


title: IT2

value: In-transit metastatic lesion 2


title: 201496850037_R03C01

description: normal blood sample


title: 201496850037_R02C01

description: normal blood sample


title: RYGB_6 POST9

city: Baton Rouge

first: Wagner

middle: S.

last: Dantas

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: Human – GRCh38.77
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

source_name: skeletal muscle (vastus lateralis)

extract_protocol:
Skeletal muscle were removed, fresh frozen on liquid nitrogen and RNA was harvested using Trizol and Rneasy Mini Kit (Cat#ID-74104).
Quant-Seq  3' mRNA-Seq Library Prep Kit
indexed and pooled samples, 50bp forward read

treatment_protocol: RYGB surgery combined (or not) with exercise training were used as a treatment in this study.

tag: group

value: RYGB POST SURGERY

value: skeletal muscle (vastus lateralis)

tag: bmi

tag: gender

value: female


title: 201496850037_R01C01

description: normal blood sample


title: EGFP-MKRN2 (iCLIP) Rep 3

description: iCLIP isolated RNA

data_processing:
Reads were deduplicated and trimmed to remove adapter sequences
Reads were aligned to the genome utilizing Hisat2
Crosslinking sites were called utilizing PureCLIP
Genome_build: hg38
Supplementary_files_format_and_content: Genomic coordinates of PureCLIP enriched crosslinking sites

extract_protocol:
Cell pellets were lysed, a stringent EGFP IP was performed and RNA was isolated utilizing an iCLIP protocol
Libraries were prepared from isolated RNA utilizing a circularization, restriction digestion and PCR protocol

treatment_protocol: Cells were UV crosslinked with 150 mJ/cm2, harested and flash frozen on dry ice

tag: cell line

value: HEK293 Flp-In-TReX cells

tag: rip antibody

value: EGFP


title: 201496710224_R07C01

description: normal blood sample

data_processing:
DNA methylation (DNAm) data were pre-processed and normalized using in-house software written for the R statistical computing environment, including background and color bias correction, quantile normalization, and Beta MIxture Quantile dilation (BMIQ) procedure to remove type I/type II probes bias, as described elsewhere (Fiorito et al., 2017). DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values). Cross-reactive and polymorphic probes - with minor allele frequency greater than 0.01 in Europeans (Y. A. Chen et al., 2013) - were excluded. Methylation measures were set to missing if the detection p-value was greater than 0.01. Samples with the bisulfite conversion control fluorescence intensity lower than 10,000 for both type I and type II probes and those with total call rate lower than 95% were excluded. Finally, samples were excluded if the predicted sex (based on chromosome X methylation) did not match that self-reported.
DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values).

extract_protocol: bisulphite conversion of 500 ng of each DNA sample was performed using the EZ DNA Methylation-Lightning Kit according to the manufacturer’s protocol (Zymo Research, Orange, CA).

tag: Sex


title: 201496710224_R08C01

description: normal blood sample


title: 201496710224_R06C01

description: normal blood sample


title: 201496710224_R05C01

description: normal blood sample


title: IT4

value: In-transit metastatic lesion 4


title: RYGB_6 PRE

value: RYGB PRE SURGERY


title: EGFP-MKRN2 (iCLIP) Rep 2

description: iCLIP isolated RNA


title: 201496710224_R04C01

description: normal blood sample


title: RYGB_5 POST9


title: EGFP-MKRN2 (iCLIP) Rep 1

description: iCLIP isolated RNA


title: RYGB_4 POST9


title: RYGB_5 PRE


title: 201496710224_R02C01

description: normal blood sample


title: RYGB_4 PRE


title: 201496710220_R06C01

description: normal blood sample


title: 201496710220_R08C01

description: normal blood sample


title: 201496710220_R07C01

description: normal blood sample


title: 201496710224_R03C01

description: normal blood sample


title: 201496710224_R01C01

description: normal blood sample


title: 201496710220_R04C01

description: normal blood sample


title: RYGB_3 POST9


title: RYGB_3 PRE


title: 201496710220_R05C01

description: normal blood sample


title: Hs578T_siASAP1_3

city: Leiden

first: Jichao

last: He

address: Einsteinweg 55

department: Drug Discovery and Safety

country: Netherlands

institute: Leiden University

data_processing:
Processing of sequencing data was conducted using Illumina’s BCL2FASTQ software employing default parameter settings. Sequencing data were demultiplexed to generate fastq files.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome corresponding to the gene panel used in the assay, allowing up to 2 mis-matches.
Normalization and differential expression were performed using the DESeq2 package. Each treatment condition was paired with the appropriate control and the counts for each sample were then normalized using the DESeq2 estimateSizeFactors function. Differential expression of each treatment relative to its respective control (Log2 FC, Log2 fold change) was measured using the Wald test.
Log2 FC of 1 used as cut-off for differentially expressed genes.
Data normalised to control siRNA (siCtrl)
Genome_build: pseudogenome (indexed probe fasta file reflecting the 50 nt sequences targeted by the detector oligos)
Supplementary_files_format_and_content: comma-delimited text file (csv) with read count per gene

source_name: Hs578T triple-negative breast cancer cell line

growth_protocol: All cell lines were maintained in RPMI-1640 medium (Gibco, ThermoFisher Scientific,  Breda, The Netherlands)supplemented with 10% FBS (Thermo Fisher Scientific; 10270106) and 25 IU/ml Penicillin and 25 μg/ml Streptomycin (ThermoFisher  Scientific; 15070-063). Cells were cultured in a humidified incubator at 37oC, 5% CO2.

extract_protocol:
Cells were washed with 1X PBS, then lysed in 1X Lysis Buffer (BioSpyder Technologies, Inc.). Lysates were frozen at − 80 °C and shipped to BioSpyder technologies on dry ice for human whole transcriptome targeted RNA sequencing TempO-Seq analysis.
In TempO-Seq, each Detector Oligo consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. Detector Oligos were qualified by functional testing using denatured gDNA as an equimolar target source for intraexonic Detector Oligos, as well as a variety of human reference RNAs and tissue total RNAs. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing.

treatment_protocol: Cells were seeded overnight in 96-well plate and transfected with 50 nM siRNA by transfection reagent INTERFERin (Polyplus-Transfection SA, Illkirch-Graffenstaden, France) according to the manufacturer’s instructions.

tag: treatment


title: Hs578T_siCtrl_3


title: 201496710220_R03C01

description: normal blood sample

source_name: blood samples


title: RYGB_2 PRE

tag: tissue


title: Hs578T_siASAP1_2


title: Hs578T_siCtrl_2


title: 201496710220_R02C01

description: normal blood sample

tag: age


title: RYGB_2 POST9


title: Hs578T_siASAP1_1


title: 201496710220_R01C01

description: normal blood sample

tag: person id


title: 201496710207_R05C01

description: normal blood sample

tag: disease state


title: 201496710207_R04C01

description: normal blood sample


title: BT549_siCtrl_2

source_name: BT549 triple-negative breast cancer cell line


title: 201496710207_R03C01

description: normal blood sample


title: 201496710207_R02C01

description: normal blood sample


title: 201496710207_R01C01

description: normal blood sample


title: 201496710207_R07C01

description: normal blood sample


title: BT549_siASAP1_3


title: BT549_siASAP1_2


title: 201496710207_R08C01

description: normal blood sample


title: BT549_siCtrl_3


title: 201496710207_R06C01

description: normal blood sample


title: RYGB_1 PRE


title: Hs578T_siCtrl_1


title: 201496710200_R08C01

description: normal blood sample


title: RYGB + exercise training_5 POST9

value: RYGB + exercise training POST SURGERY


title: 201496710200_R07C01

description: normal blood sample


title: 201496710200_R06C01

description: normal blood sample


title: 201496710200_R05C01

description: normal blood sample


title: RYGB + exercise training_5 PRE

value: RYGB + exercise training PRE SURGERY


title: 201496710200_R03C01

description: normal blood sample


title: BT549_siCtrl_1


title: RYGB + exercise training_4 POST9


title: 201496710200_R01C01

description: normal blood sample


title: RYGB_1 POST9


title: 201496710189_R07C01

description: normal blood sample


title: SUM149PT_siCtrl_1

source_name: SUM149PT triple-negative breast cancer cell line


title: BT549_siASAP1_1


title: SUM149PT_siCtrl_3


title: 201496710200_R04C01

description: normal blood sample

value: F


title: RYGB + exercise training_6 POST9


title: 201496710200_R02C01

description: normal blood sample

value: normal


title: RYGB + exercise training_4 PRE


title: 201496710189_R05C01

description: normal blood sample


title: SUM149PT_siCtrl_2


title: 201496710189_R08C01

description: normal blood sample


title: RYGB + exercise training_6 PRE


title: 201496710189_R02C01

description: normal blood sample

value: M


title: 201496710189_R06C01

description: normal blood sample


title: 201496710189_R04C01

description: normal blood sample


title: 201496710189_R01C01

description: normal blood sample


title: RYGB + exercise training_3 POST9


title: 201496710189_R03C01

description: normal blood sample


title: SUM149PT_siASAP1_2


title: SUM149PT_siASAP1_1


title: RYGB + exercise training_2 PRE


title: 201496710171_R08C01

description: normal blood sample


title: 201496710171_R07C01

description: normal blood sample


title: 201496710171_R03C01

description: normal blood sample


title: RYGB + exercise training_1 POST9


title: 201496710171_R02C01

description: normal blood sample


title: SRRM4_2

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

data_processing:
STAR version 2.5.3a is used to align reads to reference genome.
Fragments Per Kilobase Million (FPKM) and Transcripts Per Kilobase Million (TPM) were calculated using RSEM (v1.2.31).
Genes with read counts greater than 30 in at least one third cases were kept for subsequent analyses.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression

growth_protocol: Cells were cultured in RPMI 1640 with 10% FBS.

extract_protocol:
Phenol/chloroform phase separation (Trizol)
Illumina TruSeq Library Preparation Kit

treatment_protocol: Cells were transfected with Lipofectamine 2000 (Thermo Fisher Scientific). Media was changed after 6 hours.

value: LNCaP

value: Immortal cell line derived from prostate cancer lymph node metastasis

tag: passages

tag: genotype/variation

value: Transfected with SRRM4 coding plasmid


title: 201496710171_R01C01

city: London

first: Oliver

last: Robinson

address: St Mary's Campus, Norfolk Place

institute: IMPERIAL COLLEGE LONDON

description: normal blood sample


title: RYGB + exercise training_1 PRE


title: lean control_6

value: lean control


title: RYGB + exercise training_3 PRE


title: 201496710171_R06C01

description: normal blood sample


title: 201496710168_R06C01

description: normal blood sample


title: 201496710168_R08C01

description: normal blood sample


title: 201496710171_R05C01

description: normal blood sample


title: LSD1_2

tag: cell type

value: Transfected with LSD1 coding plasmid


title: lean control_5


title: lean control_4


title: 201496710168_R04C01

description: normal blood sample


title: SRRM4_3


title: SRRM4_1


title: 201496710168_R05C01

description: normal blood sample


title: 201496710168_R01C01

description: normal blood sample


title: SUM149PT_siASAP1_3


title: lean control_3


title: lean control_2


title: 201496710142_R08C01

description: normal blood sample


title: lean control_1


title: 201496710168_R07C01

description: normal blood sample


title: 8a_2

value: Transfected with LSD1+8a coding plasmid


title: 8a_3


title: RYGB + exercise training_2 POST9

value: skeletal muscle (vastus lateralis)


title: 201496710142_R05C01

description: normal blood sample


title: N7-2 miRNA-Seq

city: SHENYANG

first: Yixin

last: Chen

address: No.36 Sanhao Street, Heping District

institute: SHENGJING HOSPITAL OF CHINA MEDICAL UNIVERSITY

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads.
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression.
In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin.
The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned
Genome_build: miRBase v21
Supplementary_files_format_and_content: tab-delimited fastq files include TPM values for each Sample

source_name: Pericardium

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies)
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).

value: Pericardium

tag: age (y)

value: Female

tag: cause (operation)

value: aortic stenosis (aortic valve replacement)


title: 201496710142_R06C01

description: normal blood sample


title: 8a_1


title: 201496710142_R07C01

description: normal blood sample


title: LSD1_1


title: 201496710142_R01C01

description: normal blood sample


title: N3-1 miRNA-Seq

value: Male

value: infective endocarditis(aortic valve replacement)


title: 201496710119_R08C01

description: normal blood sample


title: 201496710119_R06C01

description: normal blood sample


title: EV_1

value: Transfected with empty vector


title: 201496710142_R03C01

description: normal blood sample


title: CP2-2 miRNA-Seq

value: idiopathic constrictive pericarditis


title: EV_3


title: 201496710142_R02C01

description: normal blood sample

value: F


title: C4-1 miRNA-Seq


title: 201496710092_R08C01

description: normal blood sample

value: normal


title: N6-1 miRNA-Seq

value: coronary artery bypass grafting


title: sample9_young_mice_infected_plus_set_3_S3 (young infected biological replicate 3)

city: Buffalo

first: Elsa

last: BouGhanem

address: 955 Main Street

department: Microbiology and Immunology

institute: University at Buffalo

data_processing:
Per-cycle basecall (BCL) files generated by the Illumina HiSeq2500 were converted to per-read FASTQ files using bcl2fastq version 2.20.0.422 using default parameters.
The quality of the sequencing was reviewed using FastQC version 0.11.5. Detection of potential contamination was done using FastQ Screen version 0.11.1.
FastQC and FastQ Screen quality reports were summarized using MultiQC version 1.5.
Sequence alignments were compressed and sorted into binary alignment map (BAM) files using samtools version 1.3. Counting of mapped reads for genomic features was performed using Subread featureCounts version 1.6.2 using the parameters -s 2 –g gene_id –t exon –Q 60, the annotation file specified with –a was the NCBI GRCh38 reference provided by Illuminas iGenomes. Alignment statistics and feature assignment statistics were again summarized using MultiQC. Differentially expressed genes were detected using the Bioconductor package DESeq2 version 1.20.0.
Genome_build: Genomic alignments were performed using HISAT2 version 2.1.0 using default parameters. NCBI reference GRCh38 was use for the reference genome and gene annotation set.
Supplementary_files_format_and_content: normalizedCounts, featureCounts

source_name: young infected

growth_protocol: Cells were freshly isolated from bone marrow of mice and were treated with PMN negative selection kit from StemCell (#19762) and were incubated in RPMI media with 10%FBS on ice till challenged with S. pneumoniae

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen) and DNA was digested using Invitrogen kit (AM1907). Total RNA concentration and integrity assessed using Agilent 2100 Bioanalyser
Total RNA was enriched for mRNA using poly-A-selection (Illumina). Standard Illumina protocols were used to generate cDNA adapted with sequencing primers and sample barcodes, size selected and PCR enriched.

treatment_protocol: Approximately, a million of neutrophils of each type were either mock infected or infected with S. pneumoniae TIGR4 strain at MOI of 4 at 37 degrees for approx 40 minutes.

tag: strain background

value: Wild type

tag: sample group

tag: tissue/cell type

value: Bone marrow neutrophils


title: EV_2

value: LNCaP

value: Immortal cell line derived from prostate cancer lymph node metastasis


title: ubp12ubp13_HTA9_H2Aub1_1

city: Uppsala

first: Claudia

last: Köhler

address: Almas Allé 5

department: Plant Biology

institute: SLU

data_processing:
Low quality ends (phred of <20) and adapter sequences were removed with Trimmomatic (version 0.38)
Reads with low average quality were discarded too (phred <25 for the H2Aub1/H2A.Z ChIP-seq experiment, and <28 for the H3K27me3 and REF6 experiments).
For all experiments, reads were mapped to the Arabidopsis reference TAIR10 genome using bowtie2 (version 2.2.9), unpaired mode for the H2Aub1/H2A.Z experiment, and paired mode for the H3K27me3 and REF6 experiments. For the latter two, 50 bp was taken as the minimum distance between mates and 500 bp the maximum distance.
After mapping duplicated reads were removed with Picardtools.
ChIP-seq experiment fragment length was estimated with R function estimate.mean.fraglen for H2Aub/H2A.Z experiment. After that original fragments were reconstructed using either the estimated fragment lengths (for the first experiment) or both mates of a pair (for second and third experiments).
Genome was divided in 50bp bins, and the number of reconstructed fragments in these bins were obtained.
The number of fragments (+1) was divided by the total base coverage (in billion bases). The latter value was obtained by adding up the lengths of all reconstructed fragments.
For each bin the mean was taken of the values in the two replicates.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Plants were grown on 1/2 MS MES agar for 15 days, then transferred to soil where they grew for 2 more weeks. Grown under LD conditions.

extract_protocol:
Rosette leaves were harvested one hour before darkness. ChIP was performed as described before [Villar and Köhler 2010, Plant Cromatin Immunoprecipitation], with the following modifications: no vacuum infiltration with DMA was performed. Vacuum infiltration with formaldehyde was performed for 2x5min. For quenching the formaldehyde, the solution was poured off, after which 0.125 M glycine was added and another 5-min vacuum infiltration was performed. Vacuum infiltration was performed at room temperature. Around 300 and 500 mg cross-linked plant material was used for nuclei extraction for the H2Aub1 and H3K27me3 experiment, respectively. Sonication of the chromatin was done for eight 30-s ON, 30-s OFF cycles. Overnight antibody binding was performed directly after sonication, followed by addition of washed protein A dynabeads (Thermofisher) to each ChIP aliquot. For bead washing, the LiCl wash step was skipped. De-crosslinking and subsequent DNA recovery steps performed using the Ipure kit v2 (Diagenode, Liège, Belgium). The MicroPlex Library Preparation kit v2 (Illumina) was used for library preparation
The MicroPlex Library Preparation kit v2 (Illumina) was used for library preparation.

value: rosette leaves

tag: ecotype

tag: genotype

tag: chip antibody

value: anti-HTA9 (AS10 718, Agrisera, Vännäs, Sweden)


title: 201496710168_R03C01

description: normal blood sample

tag: Sex


title: 201496710168_R02C01

description: normal blood sample

value: M


title: ubp12ubp13_HTA9_H2Aub1_2


title: 201496710119_R07C01

description: normal blood sample


title: 201496710092_R06C01

description: normal blood sample


title: 201496710119_R05C01

description: normal blood sample


title: sample6_young_mice_uninfected_set_4_S2 (young uninfected biological replicate 3)

source_name: young uninfected


title: 201496710119_R04C01

description: normal blood sample


title: wt_HTA9_H2Aub1_1

value: wt


title: 201496710092_R05C01

description: normal blood sample


title: 201496710092_R02C01

description: normal blood sample


title: 201496710119_R03C01

description: normal blood sample


title: 201496710119_R02C01

description: normal blood sample


title: sample32_CD73_KO_infected_plus_set_5_S17 (CD73KO infected biological replicate 3)

source_name: CD73KO infected

value: Lacking CD73 gene


title: wt_HTA9_H2Aub1_2


title: 201496710092_R04C01

description: normal blood sample


title: 201496710092_R01C01

description: normal blood sample


title: 201496710092_R07C01

description: normal blood sample


title: C2-3 miRNA-Seq

value: Pericardium

value: Female


title: 201496710119_R01C01

description: normal blood sample


title: ubp12ubp13_H2Aub1_H2Aub1_2

data_processing:
For RNA-seq adapters were removed with cutadapt v1.18 (Martin, 2011), and only reads longer than 25 nt were kept for mapping.
For the H2Aub1 ChIP-seq experiment (single end sequencing including H2Aub1, H3) adapter trimming and low quality read filtering was done with reaper (Davis et al., 2013). Reads with Phred <30 or shorter than 10nt were discarded.
For the H3K27me3 ChIP-seq experiment (paired-end sequencing including H3K27me3, H3) low quality ends were trimmed, and low quality reads were filtered with Trimmomatic v 0.38 (Bolger, 2012), removing ends with phred <20, removing reads with average phred <28, and removing reads with length <20.
For ChIP-seq experiments, alignment of reads to the TAIR10 genome was performed with Bowtie2 (Langmead and Salzberg, 2012), with the default minimum score threshold. For RNA-seq the program tophat v2.11 (Kim 2013) was used, and only reads with mapping quality over 30 were kept.
For the RNA-seq experiment, raw read counts per gene were obtained using Htseq v0.11.1 (Anders, 2014), and are provided.
For H3K27me3 ChIP-seq all duplicate reads were removed with Picard Tools
For H2Aub1 ChIP-seq experiment mean fragment/insert length was estimated using the R function estimate.mean.fraglen.
For both the H2Aub1 and H3K27me3 ChIP-seq experiment peaks were called using MACS2 in broad mode. The direct output (.broadPeak files) of MACS2 is provided.
For both the H2Aub1 and H3K27me3 ChIP-seq experiment genome-wide coverage in 50bp bins was calculated using Deeptools multiBamSummary and scaled by calculating the median coverage across all bins, dividing the coverage value in all bins by that median value, and then multiplying it by 50. Then the H3 coverage was subtracted from the H2Aub1 or H3K27me3 coverage.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNAseq data is provided in raw read counts for each gene. ChIP-seq data is provided as bigwigfiles that list median-scaled read count in 50bp bins of H2Aub1 or H3K27me3 minus median-scaled read count for H3. For the ChIP-seq data also the broadPeak output from MACS2 has been provided. A bed file with regions with significantly gained H2Aub1 in both replicates has been provided as well.

extract_protocol:
Rosette leaves were harvested one hour before darkness. ChIP was performed as described before [Villar and Köhler 2010, Plant Cromatin Immunoprecipitation], with the following modifications: no vacuum infiltration with DMA was performed. Vacuum infiltration with formaldehyde was performed for 2x5min. For quenching the formaldehyde, the solution was poured off, after which 0.125 M glycine was added and another 5-min vacuum infiltration was performed. Vacuum infiltration was performed at room temperature. Around 300 and 500 mg cross-linked plant material was used for nuclei extraction for the H2Aub1 and H3K27me3 experiment, respectively. Sonication of the chromatin was done for eight 30-s ON, 30-s OFF cycles. Overnight antibody binding was performed directly after sonication, followed by addition of washed protein A dynabeads (Thermofisher) to each ChIP aliquot. For bead washing, the LiCl wash step was skipped. De-crosslinking and subsequent DNA recovery steps performed using the Ipure kit v2 (Diagenode, Liège, Belgium).
The MicroPlex Library Preparation kit v2 (Illumina) was used for library preparation

value: anti-H2Aub1 #8240S, Cell signalling technology, Danvers, MA lot no #0002


title: 201496710042_R04C01

description: normal blood sample


title: 201496710092_R03C01

description: normal blood sample


title: sample29_old_PMN_minus_set_5_S15 (old uninfected biological replicate 3)

source_name: old uninfected


title: wt_H2Aub1_H2Aub1_2

value: WT


title: ubp12ubp13_H3_H2Aub1_1

description: UBP_R1R2_H3_fromH2Aub_genomecov_covscale.bw

value: anti-H3 07-690, Merck Millipore, Burlington, MA, USA lot no #2716572


title: sample5_young_mice_uninfected_set_3_S1 (young uninfected biological replicate 2)


title: wt_H2Aub1_H2Aub1_1


title: ubp12ubp13_H2Aub1_H2Aub1_1


title: ubp12ubp13_H3_H2Aub1_2


title: 201496710042_R08C01

description: normal blood sample

value: F


title: sample26_CD73_KO_infected_plus_set_4_S12 (CD73KO infected biological replicate 2)


title: sample30_old_PMN_infected_plus_set_5_S16 (old infected biological replicate 3)

source_name: old infected


title: 201496710042_R07C01

description: normal blood sample

value: normal


title: sample24_CD73_KO_infected_plus_set_2_S11 (CD73KO infected biological replicate 1)


title: 201496710042_R05C01

description: normal blood sample


title: 201496710042_R06C01

description: normal blood sample


title: sample28_young_PMN_infected_plus_set_5_S14 (young infected biological replicate 2)


title: 201496710042_R02C01

description: normal blood sample


title: 201492570236_R07C01

description: normal blood sample


title: 201492570236_R01C01

description: normal blood sample


title: wt_H3_H2Aub1_2

description: Col_R1R2_H3_fromH2Aub_genomecov_covscale.bw


title: 201492570236_R08C01

description: normal blood sample


title: 201492570236_R05C01

description: normal blood sample


title: 201496710042_R01C01

description: normal blood sample


title: ubp12ubp13_RNA_3

source_name: whole seedlings

growth_protocol: Plants were grown on 1/2 MS MES agar for 15 days. Grown under LD conditions.

extract_protocol:
whole seedlings were harvested between 6 and 8 hours after dark to light transition. RNA was isolated with the MagJET plant RNA purification kit (Thermo Fisher Scientific; Waltham, MA, USA)
libraries were prepared with the TRUseq RNA sample preparation kit v2 (Illumina; San Diego, CA, USA)

value: whole seedlings


title: sample18_old_mouse_infected_plus_set_4_S8 (old infected biological replicate 2)

value: Wild type


title: wt_H3_H2Aub1_1


title: 201496710042_R03C01

description: normal blood sample


title: ubp13_RNA_3


title: 201492570236_R03C01

description: normal blood sample


title: ubp12ubp13_RNA_2


title: ubp13_RNA_2


title: 201492570236_R02C01

description: normal blood sample


title: ubp12ubp13_RNA_1


title: 201492570236_R06C01

description: normal blood sample


title: sample21_CD73_KO_uninfected_set_3_S9 (CD73KO uninfected biological replicate 1)

source_name: CD73KO uninfected

value: Bone marrow neutrophils


title: 201490030230_R02C01

description: normal blood sample


title: sample14_old_mouse_uninfected_set_4_S6 (old uninfected biological replicate 2)


title: 201490030230_R07C01

description: normal blood sample


title: LSD1_3

tag: cell line

value: LNCaP

value: Transfected with LSD1 coding plasmid


title: 201490030230_R01C01

description: normal blood sample


title: 201490030230_R06C01

description: normal blood sample


title: 201490030230_R05C01

description: normal blood sample


title: 200551600067_R08C01

description: normal blood sample


title: sample10_young_mice_infected_plus_set_4_S4 (young uninfected biological replicate 1)


title: 201490030230_R03C01

description: normal blood sample


title: 201492570236_R04C01

description: normal blood sample


title: 200551600067_R05C01

description: normal blood sample


title: sample17_old_mouse_infected_plus_set_3_S7 (old infected biological replicate 1)


title: ubp13_RNA_1

tag: tissue


title: 200551600067_R04C01

description: normal blood sample

tag: age


title: 201490030230_R08C01

description: normal blood sample

tag: person id


title: 200551600067_R03C01

description: normal blood sample

tag: disease state


title: 200551600067_R06C01

description: normal blood sample


title: ubp12_RNA_2


title: ubp12_RNA_1


title: X VAR (rep 1)

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

data_processing:
Illumina adapter sequence and low quality bases were trimmed using Trimmomatic. FastQC reports were generated.
Trimmed data mapped to the mouse genome using tophat2.
Read counts mapped to each gene were obatined using featureCounts.
Raw read counts were normalized and differential expression analysis was performed using DESeq2
Samples were normalized and FPKMs were generated using cufform and cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: gene count file generated by Feature counts. Values represent raw read counts mapped to each gene
Supplementary_files_format_and_content: normalized cuffnorm file. Values are obatined by cuffnorm tool.
Supplementary_files_format_and_content: FPKM file. Values denote FPKM enerated by cuffdiff.

source_name: striatum

extract_protocol:
Bilateral striatum were removed and placed into RNAlater.  RNA was extracted using the Qiagen Rneasy Mini Kit. The libraries were made with the Illumina TruSeq RNA Sample Prep Kit. The pool of libraries was sequenced on the Illumina HiSeq Rapid Run with 150 nt single read sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were assigned to 2 groups: SAL (Saline) or VAR (2 mg/kg varenicline). To examine the effect of varenicline on ethanol consumption and gene expression we used a 2-day Drinking-in-the-Dark (DID) procedure. Briefly, naïve male mice were repeatedly tested in three 2-day DID sessions. On day 1, the water bottle was removed and a single 20% ethanol tube was presented 3 hours into the dark cycle. The volume of ethanol in the tube was read to the closest 0.1 ml and was recorded at the beginning of the session and at 30 min, 1 h, and 2 h into the drinking session. After the 2-hour drinking session, the ethanol tube was removed and water was returned. On the second day, mice were given an acute injection of saline 30 min before the DID session. After the first 2-day DID cycle, mice were assigned to treatment with either saline or 2 mg/kg varenicline such that average ethanol consumption was equal between groups. During the next 2 DID cycles, the animals were treated based on their group assignment 30 minutes prior to the day 2 ethanol session based on prior research. At the end of the final DID session mice were euthanized by cervical dislocation and the striatum was dissected.

tag: strain

value: Male

tag: treatment

value: 2 mg/kg varenicline


title: ubp12_RNA_3


title: 200551600067_R02C01

description: normal blood sample

value: M


title: W SAL (rep1)

value: saline


title: U SAL (rep1)


title: wt_RNA_3


title: 200551600067_R01C01

description: normal blood sample


title: S VAR (rep 1)


title: injured + apobec2 KD 1

city: Ann Arbor

first: Daniel

last: Goldman

address: 109 Zina Pitcher Place

institute: University of Michigan

description: inj apobec2 regulated genes MG.txt

data_processing:
Illumina Casava software for basecalling
Quality control with FASTC
TOPHAT and BOWTIE2 to quantify known transcriptsand align reads
CUFFDIFF2 to identify differentially expressed genes
Genome_build: ZV9
Supplementary_files_format_and_content: tab delimited text file includes RPKM values

organism: Danio rerio

source_name: Retina

growth_protocol: Fish were maintained in aquaria at 28 degrees centrigrade

extract_protocol:
Two days post injury, control uninjured and injured retinas were isolated, dissociated and GFP+ Muller glia purified by FACS. RNA was harvested with Trizol.
RNA libraries prepared using standard Illumina  protocols

treatment_protocol: Retinas received needle poke injury with and without apobec2a/apobec2b morpholino.

value: Retina

value: Adult

tag: transgenic fish


title: sample13_old_mouse_uninfected_set_3_S5 (old uninfected biological replicate 1)

tag: genotype/variation


title: Q VAR (rep 1)


title: wt_RNA_2


title: M SAL (rep1)


title: 45_S45_L004

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing reads from rat VTA were mapped to rn6 using HISAT2v2.1.0.
Counts of reads mapping to genes were obtained using featureCounts against Ensembl v90 annotation.
Differential expression analysis was done using the DESeq2 package (v1.6.3) at a p-value cutoff of 0.05.
Genome_build: rn6
Supplementary_files_format_and_content: Counts in tab delimited text file generated using featureCounts

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
VTA tissue punches were homogenized in Trizol (Thermo Fisher), and RNA was isolated on RNeasy Microcolumns (Qiagen) following manufacturer’s instructions. RNA concentrations were assessed using a nanodrop spectrophotometer and RNA 260/280 and 260/230 ratios were confirmed at >1.8.
Following RNA purification, RNA-seq libraries were prepared according to Illumina protocols and sequenced on an Illumina HiSeq 4000 (or equivalent) sequencer.

treatment_protocol: Cocaine Self-Administration (SA) Prior to jugular catheterization, animals were food restricted (20 g per day; 3-4 days) and trained to respond to the “active” lever on a fixed ratio (FR) schedule 1 of reinforcement for food pellets (1 hr sessions per day). Following successful learning (~100 pellets per session), animals were implanted with jugular catheters and then given 5 days to recover before cocaine SA. Catheter patency was tested with 1 mg methohexital sodium (Brevital; Sigma-Aldrich, St. Louis, MO) the day prior to cocaine SA. Animals were then trained to respond on an “active” lever for cocaine hydrochloride diluted in 0.9% sterile saline, 1mg/kg/infusion IV (0.1 ml injection volume delivered over 4 s), with a 20 s timeout in between each infusion, which was indicated by a cue light located directly above the “active” lever; responding on the lever was recorded but without consequence.   Rodents were trained on this paradigm at a FR 1 (2 days), FR3 (1 day) and then FR5 (2 days; 1 hr sessions). Following completion of successful learning at FR5 (~15 rewards total), rodents were allowed extended access (6 hr sessions) cocaine for 10 days, with each cocaine infusion resulting in delivery of 0.5mg/kg/infusion of cocaine. Additionally, a separate group of rodents were put through the same paradigm but were only allowed to respond for saline (0.9%) (non-reinforcement controls). For RNA-seq analyses, cocaine vs. saline animals were infected intra-VTA with lentiviruses expressing either empty vector (RFP) or H3.3 WT controls vs. H3.3Q5A 24 hr after drug taking, and then euthanized following 30 days of withdrawal.

tag: self-administration

value: Cocaine

tag: virus

tag: region

value: Ventral tegmental area


title: sample22_CD73_KO_uninfected_set_4_S10 (CD73KO uninfected biological replicate 2)

tag: strain background

value: Lacking CD73 gene

tag: sample group

tag: tissue/cell type


title: injured 2

description: inj apobec2 regulated genes MG.txt


title: control uninjured 1

description: inj apobec2 regulated genes MG.txt


title: injured 1

description: inj apobec2 regulated genes MG.txt


title: Sample 11_∆hel2; Biorep 3

city: st louis

first: Liewei

middle: Leo

address: 1 brookings dr.

institute: Washington University in St Louis

data_processing:
RNA-seq reads were then aligned to the Ensembl release 76 (GCA_000146045.2) with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
Genome_build: Ensembl release 76 (GCA_000146045.2)
Supplementary_files_format_and_content: gene counts

organism: Saccharomyces cerevisiae

source_name: ∆hel2_whole cell

growth_protocol: Cells were grown in YPD to OD~0.5.

extract_protocol:
RNA was extracted using hot phenol followed by chloroform extraction and ethanol precipitation.
polyA enriched libraries were prepared from total RNA using Oligo-dT beads. Samples were prepared according to library kit manufacturer’s protocol

treatment_protocol: Cells were treated with MMS for 90 min at 30 degrees C.


title: Sample 10_Wild-type;MMS treated;Biorep 3

source_name: Wild-type_MMS treated_whole cell

value: wild type

value: methyl methanesulfonate (MMS) for 90min


title: Sample 12_∆hel2; MMS treated;Biorep 3

source_name: ∆hel2_ MMS treated_whole cell


title: wt_RNA_1

tag: ecotype

tag: genotype

value: WT


title: control uninjured 2

description: inj apobec2 regulated genes MG.txt


title: K SAL (rep1)

tag: Sex


title: 42_S42_L004

value: RFP


title: 41_S41_L004


title: Sample 9_Wild-type;Biorep 3

source_name: Wild-type_whole cell


title: Sample 7_∆hel2; Biorep 2


title: 43_S43_L004


title: injured + apobec2 KD 2

description: inj apobec2 regulated genes MG.txt

tag: tissue


title: 44_S44_L004


title: J VAR (rep 1)


title: A SAL (rep1)


title: 34_S34_L003


title: MouseTMS2

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software( version 3.0.2, 10X Genomics)
Sample alignment with the count function from Cell Ranger software (version 3.0.2,10X Genomics)
Genome_build: mm10
Supplementary_files_format_and_content: Csv files including gene expression matrix from mouse samples

source_name: Mouse anterior segment, 10-12 wk old

extract_protocol:
Tissues were dissected in Ames' medium, digested in papain, and manually triturated into single cell suspensions in ovomucoid solution. The cells were resuspended in 0.04% non-acetylated BSA in Ames to solutions of ~1000 cells/uL and loaded into Chromium Single Cell Chips for a targeted recovery of 6,000 cells.
Single cell libraries were made with Chromium 3’ v3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.

treatment_protocol: CD1 mice were used. Eyes were enculeated and transferred immediately to Ames' medium (Sigma-Aldrich; equilibrated with 95% O2/5% CO2).

value: eye

value: corneoscleral segments

tag: age

value: 10-12 weeks


title: 40_S40_L004

value: Saline


title: Sample 4_∆hel2; MMS treated;Biorep 1


title: Sample 6_Wild-type;MMS treated;Biorep 2


title: Sample 8_∆hel2; MMS treated;Biorep 2


title: I VAR (rep 1)

value: Male


title: F VAR (rep 1)

value: 2 mg/kg varenicline


title: 37_S37_L004


title: 36_S36_L003


title: 39_S39_L004


title: B SAL (rep1)


title: 28_S28_L003


title: 35_S35_L003


title: galectin-1-treated BMDMs_rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: BMDMs with stimulation with galectin-1

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: BMDMs added galectin-1

extract_protocol:
Total RNA from murine samples was extracted using a RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: BMDMs derived from wild type mice were seeded on 24-well tissue culture plates (1×10^6cells/well) at 37℃ in an incubator with 5% CO₂. Then, BMDMs were stimulated by lipopolysaccharide (LPS) 1 μg/ml for 1 hour and cultured with recombinant mouse galectin-1 (R&D) or phosphate-buffered saline (PBS) as a control for 24 hours.

value: Bone marrow

tag: cell type

value: Bone marrow derived macrophages (BMDMs)

value: recombinant mouse galectin-1 for 24hrs


title: 33_S33_L003


title: 27_S27_L003


title: 32_S32_L003


title: Sample 5_Wild-type;Biorep 2


title: 31_S31_L003


title: vehicle-treated BMDMs_rep2

description: BMDMs without stimulation with galectin-1

source_name: BMDMs added PBS

value: phosphate-buffered saline (PBS) as a control for 24 hrs


title: 23_S23_L002

value: Cocaine


title: 30_S30_L003

value: Ventral tegmental area


title: MouseTMS1


title: 29_S29_L003


title: Sample 3_∆hel2; Biorep 1


title: 38_S38_L004


title: 21_S21_L002


title: 26_S26_L003


title: Set4_Control

first: Elham

last: Azizi

institute: Memorial Sloan Kettering Cancer Center

data_processing:
read alignment: TopHat
transcript assembly: Cufflinks
differential expression analysis: DESeq
Genome_build: mm9
Supplementary_files_format_and_content: raw counts per gene in .txt format

source_name: Ovarian surface epithelium

growth_protocol: The ID8 IP2 cell line was cultured in DMEM with 10% FBS, 1% ITS Liquid Media Supplement, and 1% penicillin-streptomycin.

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104) and the RNase-Free DNase Set (QIAGEN, 79254)
libraries were created using Illumina TruSeq kit according to manufacturer's recommendations

treatment_protocol: ID8 IP2 cells were infected with virus derived from a pCCL vector encoding an HA-tagged Notch3 intracellular domain (codons 1664-2318) followed by an IRES-GFP (Notch3IC) or empty pCCL vector (Control).

value: Ovarian surface epithelium

tag: cell line

value: ID8 IP2


title: galectin-1-treated BMDMs_rep1

description: BMDMs with stimulation with galectin-1


title: 25_S25_L003


title: 18_S18_L002


title: Set3_Notch3IC


title: Sample 1_Wild-type; Biorep 1

value: wild type


title: 24_S24_L002


title: 22_S22_L002

value: WT


title: 20_S20_L002

value: RFP


title: 15_S15_L002


title: Set4_Notch3IC


title: 19_S19_L002


title: vehicle-treated BMDMs_rep1


title: Set2_Control


title: 9_S9_L001


title: 16_S16_L002


title: Sample 2_Wild-type;MMS treated;Biorep 1

value: methyl methanesulfonate (MMS) for 90min


title: 14_S14_L002


title: 12_S12_L001


title: 10_S10_L001


title: 13_S13_L002


title: 8_S8_L001


title: Set1_Control


title: 6_S6_L001


title: sample27_young_PMN_minus_set_5_S13 (young uninfected biological replicate 1)

source_name: young uninfected

value: Wild type

value: Bone marrow neutrophils


title: 7_S7_L001