title: H37Rv_DMSO_6h_repC

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 0.12.7 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome (M. tuberculosis H37Rv, from NCBI).
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
Count data were analyzed using R version 3.4.1 and the Bioconductor package DESeq2 version 1.18.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. Two independent analyses have been performed to study H37RV and 041195 strains  Separately.
Genome_build: M. tuberculosis H37Rv, from NCBI

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis

growth_protocol: Three replicates of each Mycobecterium tuberculosis strain were cultured in 140 ml Middlebrook 7H9 broth supplemented with 10% OADC (Oleic acid-Albumin-Dextrose-Catalase) at 37°C until early-exponential phase (optical density 0.1).

extract_protocol:
Cell pellets were re-suspended in TRIzol reagent and subjected to three cycles of 1 minute bead-beating (0.5 mm silica/zirconia beads) followed by RNA extraction using the Direct-zol RNA Kit (Zymo research) according to the manufactures’ protocol. DNA was removed by TURBO DNase (Ambion) until no genomic DNA was detected by PCR. The quality and integrity of the total RNA was checked on the Bioanalyzer system (Agilent).
Ribosomal RNA depletion was performed using the Bacteria RiboZero kit (Illumina). From rRNA-depleted RNA, directional libraries were prepared using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). Libraries were checked for quality on Bioanalyzer DNA chips (Agilent). More precise and accurate quantification was performed with the fluorescent-based quantitation Qubit® dsDNA HS Assay Kit (ThermoFisher). 65 bp single read sequences were generated on the Hiseq2500 sequencer according to manufacturer’s instructions (Illumina). The multiplexing level was 10 samples per lane.
Directional libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit following the manufacturer’s instructions (Illumina). Libraries were checked for quality on Bioanalyzer DNA chips (Agilent). 65 bp single read sequences  Were generated on the Hiseq2500 sequencer according to manufacturer’s instructions (Illumina). The  multiplexing level was 10 samples per lane.

treatment_protocol: Each culture was split and supplemented with dimethyl sulfoxide (DMSO) or 3 µg/ml delamanid (Otsuka). Samples of 20 ml were collected (15 min, 4000 g) at the start and 6h and 24h after addition of the drug.

tag: strain name

tag: strain origin

value: Laboratory

tag: compound

value: DMSO

tag: time of sampling (after addition compound)


title: Cortical brain, B3675

status: Public on Oct 31 2019

type: SRA

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse genome mm10 using the STAR aligner version 2.5.2b
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq Version 2.1.1 (Kalari et al., 2014)
In order to correct for GC bias and gene length differences and obtain similar quantile-by-quantile distributions of gene expression levels across samples, we performed conditional quantile normalization (CQN) on the raw gene counts (Hansen et al., 2012). According to the bimodal distribution of the CQN-normalized and log2-transformed reads per kb per million (RPKM) gene expression values, genes with average log2 RPKM of 2 or more in at least one group were considered expressed above detection threshold.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text file including raw counts for all samples

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Mouse cortical samples were treated with TRIzol RNA Isolation Reagents (Thermo Fisher Scientific, 15596026), and total RNAs were subsequently extracted from samples using DNase (QIAGEN, 79254) and an RNeasy mini kit (QIAGEN, 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: 55 days

tag: genotype

value: control

tag: stimulus

value: LPS

tag: tissue

value: brain


title: Cell37_Skininnervating

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 77 Massachusetts Ave

department: Chemistry

institute: Massachusetts Institute of Technology

data_processing:
Pooled libraries were demultiplexed using bcl2fastq (v2.17.1.14) with default settings, and aligned using STAR  to the mouse UCSC genome reference (version mm10), and a gene expression matrix was generated using RSEM (v1.2.3) in paired-end mode. Read counts were normalized to transcripts-per-million (TPM). Single-cell libraries with fewer than 3,000 unique genes and fewer than 17% of reads mapping to transcriptomic regions were excluded from subsequent analysis, resulting in a final dataset of 52 LN-innervating neurons collected from 8 mice, and 31 skin-innervating neurons collected from 4 mice.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a tab delimited text file containing a TPM-corrected gene expression matrix with the number of TPM for each gene (rows) and cell (columns). The 2-8th row represent metadata defined in column 1, including mouse number, cell collection date, innervation target, sequencing batch, and reads, gene count, and % transcriptomic alignment per library

molecule: polyA RNA

source_name: Dorsal root ganglion single neuron

growth_protocol: All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols of Harvard Medical School.

extract_protocol:
Single-cell libraries were generated according to the Smart-Seq2 protocol (Picelli et al. Nature Methods 2014 and Trombetta et al. Current Protocols in Molecular Biology 2014). Each fluorescent cell was pipetted up and down the micropipette three times to remove unwanted contamination before being ejected into 10 μl of cold RLT Buffer (Qiagen) supplemented with 1% β-mercaptoethanol in a 96-well plate, and snap-frozen on dry ice and stored at -80ºC. RNA from single-cell lysates was purified using AMPure RNA Clean Spri beads (Beckman Coulter) at a 2.2x volume ratio.
Following AMPure Bead cleanup, RNA was eluted in water and mixed with oligo-dT primer (SmartSeq2 3’ Oligo-dT Primer), dNTPs, and RNase inhibitor at 72ºC for 3 minutes on a thermal cycler to anneal the 3’ primer to polyadenylated mRNA. Reverse transcription was carried out in a master mix of Maxima RNaseH-minus RT enzyme and buffer, MgCl2, Betaine, RNase inhibitor, and a 5’ template switch oligonucleotide using the following protocol: 42ºC for 90 minutes, followed by 10 cycles of 50ºC for 2 minutes, 42ºC for 2 minutes, and followed by inactivation at 70ºC for 15 minutes. Whole transcriptome amplification was achieved by addition of KAPA HiFi HotStart ReadyMix and IS PCR primerto the reverse transcription product and amplification on a thermal cycler using the following protocol: 98ºC for 3 minutes, followed by 21 cycles of 98ºC for 15 seconds, 67ºC for 20 seconds, 72ºC for 6 minutes, followed by a final 5-minute extension at 72ºC. Libraries were purified using AMPure XP SPRI beads at a volume ratio of 0.8x followed by 0.9x. Library size was assessed using a High-Sensitivity DNA chip (Agilent Bioanalyzer), confirming the expected size distribution of ~1000-2000 bp. Tagmentation reactions were carried out with the Nextera XT DNA Sample Preparation Kit (Illumina) using 250 pg of cDNA per single cell as input, with modified manufacturer’s instructions as described. Libraries were purified twice with AMPure XP SPRI beads at a volume ratio of 0.9x, size distribution assessed using a High Sensitivity DNA chip (Agilent Bioanalyzer) and Qubit High-Sensitivity DNA kit. Libraries were pooled and sequenced using NextSeq500/550 High Output v2 kits (75 cycles, Illumina) using 30-30 paired end sequencing with 8-mer dual indexing

tag: innervation target

value: Skin

tag: mouse number


title: H37Rv_DMSO_6h_repB


title: Cell36_Skininnervating


title: Cell30_LNinnervating

value: LN


title: 13872_EDTA TRIzol LS replicate 1

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: 13872_EDTA TRIzol LS 1

hyb_protocol: cRNA was hybridized to SurePrint G3 Human GE v2 8x60K microarrays (Agilent Technologies) following manufacturer's instructions

scan_protocol: Slides were scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and R script v3.3 software was used to conduct the preliminary data filtration and statistical analysis.

organism: Homo sapiens

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

label_protocol: Total RNA (200ng) was used as starting material, which was amplified using the Low Input Quick Amp Two-Color Kit (Agilent Technologies).The labelled cRNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: RNA purchased from vendor.

tag: reference

value: Agilent's Universal Human Reference RNA

source_name: Whole blood

extract_protocol:
[Collection protocol] Blood was collected and preserved in five tubes, namely, PAXgene™ RNA tubes, RNAgard® Blood Tubes, BD Vacutainer™ tubes with ACD-A and K2EDTA and CPT (LeukoLOCK) tubes from five healthy volunteers. In parallel, PBMCs were isolated from EDTA, CPT and ACD-A tubes following the manufacturer’s instructions.
[Extract protocol] See 'extraction methodology' in the Channel 2 Characteristics section above. All extractions were performed following manufacturer's instructions.

tag: biological replicate

value: 1 of 3

tag: blood storage

value: Whole Blood collected in EDTA tube

tag: extraction methodology

value: RNA extracted using TRIzol LS reagent

tag: blood component

value: whole blood

tag: individual

value: donor 13872

tag: disease state

value: healthy


title: 13872_ACD-A TRIzol LS replicate 3

description: 13872_ACD-A TRIzol LS 3

value: 3 of 3

value: Whole Blood collected in ACD-A tube


title: H37Rv_DMSO_6h_repA

tag: strain name

value: Laboratory


title: 13872_ACD-A TRIzol LS replicate 2

description: 13872_ACD-A TRIzol LS 2

value: 2 of 3


title: Cortical brain, B3680

value: 55 days


title: H37Rv_DLM_6h_repC

tag: strain origin

value: Delamanid


title: H37Rv_DLM_6h_repB

tag: compound


title: Cell34_LNinnervating


title: H37Rv_DLM_6h_repA

tag: time of sampling (after addition compound)


title: Cortical brain, B3640

tag: age


title: Cell32_LNinnervating

tag: genotype


title: H37Rv_DMSO_24h_repC

value: DMSO


title: Cell27_LNinnervating


title: Cortical brain, B3638

tag: stimulus

value: LPS

value: brain


title: 13872_ACD-A _ACK lysing replicate 3

description: 13872_ACD-A _ACK lysing 3

value: RNA extracted using ACK lysing buffer/miRNeasy Mini kit


city: Fukuoka

first: Akiko

last: Fujimura

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Cancer Therapy and Research

country: Japan

institute: Graduate School of Medical Sciences Kyushu University

description: SAMPLE 1

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: activated human lymphocyte-transfected control vector, healthy volunteer

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: source cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: cell type

value: activated human lymphocyte

tag: transfected with

value: control vector


title: H37Rv_DMSO_24h_repA


description: SAMPLE 2

source_name: activated human lymphocyte-transfected shPTPN3, healthy volunteer


title: Cell31_LNinnervating

tag: innervation target

value: LN

tag: mouse number


title: Cell25_LNinnervating


title: H37Rv_DLM_24h_repC


title: Cortical brain, B3669

value: 57 days

value: control

tag: tissue


title: Cell23_LNinnervating


title: 13872_ACD-A _ACK lysing replicate 2

description: 13872_ACD-A _ACK lysing 2

tag: reference

value: Agilent's Universal Human Reference RNA

tag: biological replicate

tag: blood storage

tag: extraction methodology

value: whole blood

value: donor 13872

value: healthy


title: Cell29_LNinnervating


title: H37Rv_DLM_24h_repB

tag: strain name

value: Laboratory


title: Cortical brain, B3667


title: Cortical brain, B3660

value: 56 days


title: Cell28_LNinnervating


title: Cortical brain, B3659


title: Cortical brain, B3632


title: Cell21_LNinnervating


title: Cell20_LNinnervating


title: Cortical brain, B3612


title: 13872_ACD-A _ACK lysing replicate 1

description: 13872_ACD-A _ACK lysing 1

value: 1 of 3

value: Whole Blood collected in ACD-A tube

tag: blood component

tag: individual

tag: disease state


title: Cortical brain, B3634

tag: age


title: ITM-04-1195_DMSO_6h_repC

tag: strain origin

value: clinical (BCCMTM Collection, TB-TDR-0078)

tag: compound

value: DMSO

tag: time of sampling (after addition compound)


title: Cell26_LNinnervating

tag: genotype


title: Cell17_LNinnervating


title: Cell16_LNinnervating


title: ITM-04-1195_DMSO_6h_repB


title: Cortical brain, B3633

tag: stimulus

value: LPS

value: brain


title: Cell24_LNinnervating

tag: innervation target


title: Cortical brain, B3603

value: 55 days


title: Cell22_LNinnervating

tag: mouse number


title: H37Rv_DLM_24h_repA

value: Delamanid


title: ITM-04-1195_DLM_6h_repC


title: Cortical brain, B3621

value: 54 days

tag: tissue


title: H37Rv_control_0h_repC


title: Cortical brain, B3622


title: Cortical brain, B3602


title: ITM-04-1195_DLM_6h_repB


title: H37Rv_control_0h_repB


title: Cortical brain, B3620


title: Cell19_LNinnervating

value: LN


title: ITM-04-1195_DLM_6h_repA


title: H37Rv_control_0h_repA


title: Cell18_LNinnervating


title: Cell12_LNinnervating


title: Cortical brain, B3611


title: ITM-04-1195_DMSO_24h_repB


title: ITM-04-1195_DMSO_24h_repA


title: Cortical brain, B3610


title: Cell14_LNinnervating


title: Cortical brain, B3609

value: control


title: ITM-04-1195_DMSO_6h_repA


title: Cell9_LNinnervating


title: Cell15_LNinnervating


title: Cell13_LNinnervating


title: Cortical brain, B3498

value: 58 days


title: ITM-04-1195_DMSO_24h_repC


title: Cell10_LNinnervating


title: Cell11_LNinnervating


title: ITM-04-1195_DLM_24h_repC


title: ITM-04-1195_DLM_24h_repA


title: Cell8_LNinnervating


title: Cell6_Skininnervating

value: Skin


title: Cell7_Skininnervating


title: SIRT6KO_PRO-seq_repA

city: Newark

first: Jean-Pierre

last: Etchegaray

state: NJ

address: 225 University Ave

department: Biological Sciences

institute: Rutgers University

description:
biotin labeled nascent RNA isolated from mESC permeabilized cells
small RNA-seq (hidrolysis fractionation)
mm9_mESC_PROseq_KO_N3_dedup_F.bw
mm9_mESC_PROseq_KO_N3_dedup_R.bw

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
PRO-seq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt, for adapter using cutadapt 1.14, pairs containing reads trimmed shorter than 20 nt filtered
PRO-seq mapped to index composed of spike-in genome (dm3), successfully aligned pairs filtered, remaining mapped to reference (mm9) using bowtie 1.2.2 retaining uniquely mappable pairs only, allowing 2 mismatches; ChIP-seq mapped using bowtie 1.1.1 retaining uniquely mapped pairs only, allowing 2 mismatches
PROseq strand-specific bedGraphs generated using custom scripts based on 3' mapping location of end 1 reads only, with all replicates combined
Genome_build: mm9 (PRO-seq), dm3 (PRO-seq)
Supplementary_files_format_and_content: PRO-seq: bedGraph containing combined count of end 1 3' mapping locations for all replicates for a given treatment

source_name: mouse embryonic stem cells

extract_protocol:
nascent biotin-labeled RNA was isolated from permeabilized cells using Total RNA Purification kit (Norgen Biotek Corp.)
Custom library preparation
PROseq experiments: nascent biotin-labeled RNA was isolated from permeabilized cells using Total RNA Purification kit (Norgen Biotek Corp.).
PRO-seq experiments: custom Small RNA library preparation compatible with TruSeq Small RNA (Illumina), with 5% S2 cells spike-in RNAs.

treatment_protocol:
mESC SIRT6-KO cells
PRO-seq: Biological replicates were generated using WT (3 replicates) mESC cells, SIRT6-KO (3 biological replicates) and Glucose deprivation (2 replicates).

tag: cell line

value: mESC cells

tag: treatment

value: SIRT6-Knock Out

tag: sample type

value: nascent RNA


title: Cell2_Skininnervating


title: ITM-04-1195_control_0h_repC


title: Cell5_Skininnervating


title: ITM-04-1195_control_0h_repB


title: ITM-04-1195_control_0h_repA


title: 5_rep2

city: Columbus

first: David

last: Brigstock

state: Ohio

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
Each sample was aligned to the GRCh38.p6 assembly of the human reference from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000001405.32_GRCh38.p6) using version 2.5.1b of the RNA-Seq aligner STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15)
Features were identified from the GFF file that came with the assembly from NCBI
Feature coverage counts were calculated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
Differentially expressed features were calculated using DESeq2 (http://genomebiology.com/2014/15/12/550).
Genome_build: GRCh38.p6
Supplementary_files_format_and_content: Excel spreadsheet containing normalized read counts and differential expression data for each comparison

source_name: Hepatoma cell line HepG2

growth_protocol: HepG2 cells were maintained in the complete medium supplemented with 10% FBS and 1% Pen/Step.

extract_protocol:
Total RNA was extracted with a QIAGEN RNAeasy kit and treated with DNase I
The library was prepared from first strand cDNA using ScriptSeq v2 RNA-Seq library preparation kit (Epicentre Biotechnologies,WI). Sequencing was performed using the Illumina HiSeq 4000 platform.

treatment_protocol: Cells were inoculated with gradient purified HEV in 4 replicates in the presence of 4% PEG8000 for 4 hr, followed by washing with PBS for 3 times

tag: passages

tag: infection/virus type

value: HEV Kernow C1 P6 (genotype 3)


title: Cell3_Skininnervating


title: Cell1_LNinnervating


title: M14

city: Budapest

first: Gábor

middle: Nándor

last: Than

address: Magyar tudósok krt. 2

department: Institute of Enzymology

country: Hungary

institute: Research Centre for Natural Sciences

data_processing:
Read quality data was assessed using FastQC.
RNA-seq reads were aligned to the GRCh38 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 include read count values for genes with ENSEMBL identifiers for each sample.

source_name: First trimester placental tissue

extract_protocol:
Tissue samples were rinsed with sterile saline and examined under a lightbox for content confirmation and selection of molar tissue or chorionic villi. Samples were then stored in RNAlater RNA stabilization reagent (approximately 10 μL reagent per 1mg of tissue, Qiagen, Germantown, MD, USA) at 37 °C for a maximum of 24 h until collected for dissection. Samples were then dissected into ~1 g tissue aliquots and stored at -80 °C. Stored samples were then thawed at room temperature and homogenized with electric homogenizer. Total RNA was isolated using the protocol provided with the Qiagen RNeasy Mini Kit. RNA quantity was measured by a Nanodrop ND-8000 analyzer (Thermo Scientific, Waltham, MA, USA). Samples were then stored at −80 °C until used.
Library preparation and paired-end sequencing were performed by the USC Epigenome Core Laboratory. Double-stranded cDNA fragments were synthesized from mRNA, ligated with adapters, and size-selected for library construction according to Illumina protocol. RNA sequencing was carried out on Illumina Genome Analyzer (Illumina, San Diego, CA, USA).

value: First trimester placental tissue

tag: gestational age


title: Cell4_Skininnervating


title: MW17

source_name: Complete hydatidiform mole tissue

value: Complete hydatidiform mole tissue


title: SIRT6KO_PRO-seq_repB


title: WTNoGlucose_PRO-seq_repB

description:
biotin labeled nascent RNA isolated from mESC permeabilized cells
small RNA-seq (hidrolysis fractionation)
mm9_mESC_PROseq_NG_N2_dedup_F.bw
mm9_mESC_PROseq_NG_N2_dedup_R.bw

treatment_protocol:
mESC cells were glucose deprived
PRO-seq: Biological replicates were generated using WT (3 replicates) mESC cells, SIRT6-KO (3 biological replicates) and Glucose deprivation (2 replicates).

value: Wild-type Glucose deprivation


title: M21


title: WTNoGlucose_PRO-seq_repA


title: 5_rep3


title: 5_rep4


title: ITM-04-1195_DLM_24h_repB

tag: strain name

value: clinical (BCCMTM Collection, TB-TDR-0078)


title: SIRT6KO_PRO-seq_repC


title: WT_PRO-seq_repC

description:
biotin labeled nascent RNA isolated from mESC permeabilized cells
small RNA-seq (hidrolysis fractionation)
mm9_mESC_PROseq_WT_N3_dedup_F.bw
mm9_mESC_PROseq_WT_N3_dedup_R.bw

treatment_protocol:
mESC wild-type cells
PRO-seq: Biological replicates were generated using WT (3 replicates) mESC cells, SIRT6-KO (3 biological replicates) and Glucose deprivation (2 replicates).

value: Wild-type


title: MW11


title: WT_PRO-seq_repB


title: M5_rep4

value: mock-infected


title: M5_rep3


title: WT_PRO-seq_repA


title: 5_rep1


title: MW6


title: ExSed 3

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

description: counts.txt

data_processing:
Illumina proprietary software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence
Transcript abundance quantified by Salmon version 0.11.3, and gene-level count matrices created by importing transcript quantification data using tximport package
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text file includes gene-level raw counts for each sample

source_name: LSK sorted from all long bones and pelvic bone

extract_protocol:
mRNA was isolated from FACS-purified cells using the NucleoSpin RNA XS kit (Takara Bio), according to the manufacturers’ protocols. RNase-free DNase Set (Qiagen) was used for DNase digestion during RNA purification. RNA quality was assessed with the Agilent RNA 6000 Pico kit (Agilent Technologies) on the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To purify LSK, a PE-lineage depletion was performed with MACS columns (130-042-401, Miltenyi Biotec), according to the manufacturer’s protocol. Briefly, single cell suspensions were stained with a lineage cocktail of PE-conjugated antibodies: CD3 (100206), CD4 (130310), CD8 (100708), CD49b (108908), CD90.2 (140308), CD19 (115508), B220 (103208), NK1.1 (108708), TER119 (116208), CD11b (101208), CD11c (117308), Gr1 (108408; all 1:150, BioLegend), followed by incubation with anti-PE microbeads (130-048-801, Miltenyi Biotec). Lineage-depleted bone marrow cells were then stained with CD48-AF700 (103426), CD150-PerCP/Cy5.5 (115922), c-kit-PE/Cy7 (105814), Sca-1-BV605 (108133; all 1:150, BioLegend) and FAC-sorted using a FACSAria II cell sorter (BD Biosciences).

tag: strain

tag: gender

value: male

tag: age at harvest

value: 16-17  weeks

tag: sample group

value: housed with exercise wheel for 6 weeks followed by 3 weeks with igloo (ExSed)

tag: cell type


title: M5_rep1


title: ExSed 2

description: counts.txt

value: LSK sorted from all long bones and pelvic bone


title: M5_rep2


title: ExSed 1

description: counts.txt


title: Ex 1

description: counts.txt

value: housed with exercise wheel (Ex)


title: Ex 2

description: counts.txt


title: Sed 3

description: counts.txt

value: housed with igloo (Sed)


title: Ex 3

description: counts.txt


title: Sed 1

description: counts.txt


title: Day 21 Tumor-Bearing TB21_27

city: College Park

first: Robert

middle: Smith

last: Oakes

address: 8278 Paint Branch Drive

department: Bioengineering

institute: University of Maryland, College Park

description:
Day 21 Tumor-Bearing
Test

data_processing:
Gene expressions from OA was screened to identify genes of interest during disease course. First, genes with insufficient data within synthetic niche samples (missing greater than 4/14 per cohort or 2/3 per time-point) were dropped from the study, resulting in 559 genes for full analysis. Next the 16 reference genes were ranked according to their expression stability compared to each other and as a function of experimental design (NormFinder Algorithm)49, which led to the selection of Gapdh, Tbp, Ywhaz, Hmbs, and Ubc. ΔCq values were calculated against the average of the reference genes, centered on median of time-matched healthy controls, then standardized for cluster and multivariate statistical analysis. From ΔCq data fold change, significance (uncorrected p and false-discovery rate corrected q), at Days 7, 14, and 21 were calculated.
For the normalization it uses the average of five reference genes: Gapdh, Hmbs , Tbp, Ubc, Ywhaz.
Target gene signals normalized to reference genes; 2^-ΔCq, where ΔCq = (Cq_Target − Cq_Reference)
Diseased versus Healthy Control fold changes at Days 7, 14, and 21 were computed as ΔΔCq based fold-change calculations from the uploaded raw threshold cycle data; 2^-ΔΔCq, where -ΔΔCq = -(ΔCqDiseased -ΔCqHealthyControl)
Matrix normalized worksheet reports normalized signal (against reference genes).
Fold Change worksheet reports diseased/healthy control ratios at Days 7, 14, and 21

label: FAM

source_name: Synthetic niche tissue infiltrate

label_protocol: Generation of first strand cDNA was performed through reverse transcription via the SuperScript™ VILO™ cDNA Synthesis Kit. For all RT-qPCR of synthetic niche, RT was performed with an RNA concentration of 200 ng/μL. Gene expression was analyzed with Applied Biosystems™ TaqMan™ OpenArray™ (OA) Mouse Inflammation Panel (Cat. No. 4475393). cDNA from synthetic niches biopsied from tumor-free healthy controls (n=14 total healthy) and tumor-bearing mice (n=14 total diseased) across the three time points of 7 (n=3), 14 (n=8), and 21 (n=3) days were mixed with 2X TaqMan® OA Real-Time Master Mix then loaded onto the OA panels via a robotic OA AccuFill™ System in an order that staggered conditions and time points across the panels analyzed. The OA RT-qPCR run was performed on a QuantStudio 12K Flex Real-Time PCR System.

growth_protocol: 4T1 tumor cells were expanded in RPMI 1640 supplemented with 10% FBS to prepare for tumor inoculation.

extract_protocol: Frozen surgically biopsied scaffolds were immersed in TRIzol® reagent, then homogenized with a rotor stator homogenizer. Samples were then centrifuged at 10,000g to remove particulate, and the TRIzol® containing genomic content from the scaffold was then processed with the Direct-zol™ RNA Miniprep Plus with DNase I treatment to isolate total RNA. Concentration and purity of the RNA isolation was assessed via a NanoDrop 2000c. Additionally, RNA integrity number (RIN) analysis was obtained through RNA fragment analysis ranged from 8.2-9.7.

treatment_protocol: BALB/c mice implanted with microporous PCL polymer scaffolds, which develop into synthetic niche, were inoculated with 4T1 tumor cells to monitor the changes in the synthetic niche during cancer disease course.

value: BALB/c

value: Female

tag: tumor cell line

tag: days following tumor inoculation

value: Immune, stromal, and epithelial cell infiltrate into microporous PCL implant

tag: panel barcode

tag: condition at time of analysis

value: Tumor-bearing


title: Day 21 Healthy Control HC21_25

description:
Day 21 Healthy Control
Control

tag: tissue

value: Healthy


title: Day 21 Tumor-Bearing TB21_26

description:
Day 21 Tumor-Bearing
Test


title: Day 21 Tumor-Bearing TB21_28

description:
Day 21 Tumor-Bearing
Test


title: 6-Chd7-3

city: MONTREAL

first: ERIC

last: SAMARUT

state: QC

address: 900 St DENIS

department: NEUROSCIENCES

country: Canada

institute: CRCHUM

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.19 allowing 1 mismatch in the 6pb index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Ensembl version 87
Expression values were also computed using RSEM version 1.2.28 based on Ensembl version 87 transcript annotations
Genome_build: GRCz10
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

organism: Danio rerio

source_name: dissected larval brain

growth_protocol: E3 medium

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA RNA Stranded PolyA

value: AB

value: brain

tag: age

tag: genotype


title: 5-Chd7-2


title: Day 21 Healthy Control HC21_24

description:
Day 21 Healthy Control
Control


title: Sed 2

description: counts.txt


title: Day 21 Healthy Control HC21_23

description:
Day 21 Healthy Control
Control


title: Day 14 Tumor-Bearing TB14_22

description:
Day 14 Tumor-Bearing
Test


title: 4-Chd7-1


title: 3-WT3

value: wild type


title: Day 14 Tumor-Bearing TB14_21

description:
Day 14 Tumor-Bearing
Test


title: Day 14 Tumor-Bearing TB14_18

description:
Day 14 Tumor-Bearing
Test


title: 2-WT2


title: 1-WT1


title: sa37_16hpf_2

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

institute: Kanazawa University

data_processing:
Illumina RTA software was used for base-calling.
Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio (danRer10) using the Burrows-Wheeler Aligner (BWA) and HiSAT2 software.
Tags per million (TPM) were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5.
Genome_build: danRer10
Supplementary_files_format_and_content: Tab-delimited text files include tags per million (TPM) values for each sample.

source_name: whole embryo

extract_protocol:
Total RNAs were extracted from staged embryos using RNeasy Mini Kit (QIAGEN).
2?g of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit (DNAFORM). 5'caps of RNAs are biotinylated after reverse transcription. RNA-cDNA hybirds were then captured by streptavidin-conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5? linker, which includes the three nucleotide barcodes, followed by 3? linker ligation. Second-strand synthesis was performed using the nAnT-iCAGE second primer, creating the final double-stranded DNA product.
Cap analysis gene expression (CAGE) sequencing

value: whole embryo

value: 16 hours post-fertilization


title: Day 14 Tumor-Bearing TB14_19

description:
Day 14 Tumor-Bearing
Test


title: Day 14 Tumor-Bearing TB14_20

description:
Day 14 Tumor-Bearing
Test


title: Day 14 Tumor-Bearing TB14_16

description:
Day 14 Tumor-Bearing
Test


title: Day 14 Tumor-Bearing TB14_15

description:
Day 14 Tumor-Bearing
Test


title: Day 14 Tumor-Bearing TB14_17

description:
Day 14 Tumor-Bearing
Test


title: WT_16hpf_2


title: sa37_12hpf_2

value: 12 hours post-fertilization


title: WT_12hpf_2


title: Day 14 Healthy Control HC14_13

description:
Day 14 Healthy Control
Control


title: Day 14 Healthy Control HC14_14

description:
Day 14 Healthy Control
Control


title: gabrg2-/- HM3

data_processing:
Sequencing was performed with the Illumina NextSeq500 using the SBS Reagent Kit v3 (80 cycles, paired-end) with 1.6 nM of the pooled library.
Basecalling was performed using Illumina RTA 2.4.11 and sequences were demultiplexed using bcl2fastq 2.20.
Cluster density was targeted at around 800k clusters/mm2. Between 86 and 100 million reads were generated for each sample.
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 (Bolger et al., 2014) and aligned to the reference genome version GRCz10 (gene annotation from Ensembl version 87) using STAR version 2.5.1b (Dobin et al., 2013).
Gene expression were obtained as readcounts directly from STAR.
Differential gene expression analysis was assessed by DeSeq2 package using R software.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

source_name: TL background

extract_protocol:
Total RNA was extracted from whole brains of 5 dpf gabrg2 -/- and +/+ larvae using picopure RNA extraction kit (Thermo Fisher Scientific) following the manufacturer’s standard protocol.
Library preparation was performed using the Truseq RNA (Illumina). 13 PCR cycles were required to amplify cDNA libraries. Libraries were quantified by Nanodrop and BioAnalyzer. All libraries were diluted to 10 nM and normalized with the Miseq SR50 v2. Libraries were pooled to equimolar concentration and multiplexed by 6 samples per lane.  RNAseq (poly-A purification)

value: whole brain

value: 5 dpf

tag: background strain

value: TL


title: gabrg2+/+ WT3

value: WT


title: Day 14 Healthy Control HC14_12

description:
Day 14 Healthy Control
Control


title: Day 14 Healthy Control HC14_10

description:
Day 14 Healthy Control
Control


title: Day 14 Healthy Control HC14_11

description:
Day 14 Healthy Control
Control


title: gabrg2+/+ WT2


title: gabrg2-/- HM2


title: Day 14 Healthy Control HC14_09

description:
Day 14 Healthy Control
Control


title: Day 14 Healthy Control HC14_07

description:
Day 14 Healthy Control
Control


title: Day 14 Healthy Control HC14_08

description:
Day 14 Healthy Control
Control


title: gabrg2-/- HM1


title: tail-PS-vc4

city: Braunschweig

first: Joana

last: Sabino Pinto

address: Mendelsohnstrasse 4

country: Germany

institute: Technische Universität Braunschweig, Zoologisches Institute

description: Gene expression from tail clip from a Pond-originated larvae translocated/kept in a Stream

hyb_protocol: Agilent Low Input Quick Amp Labelling kit for â€˜One-Color Microarray-Based Gene Expression Analysisâ€™

scan_protocol: Agilent DNA Microarray Scanner (type C)

data_processing: feature extraction software (Agilent)

organism: Salamandra salamandra

source_name: Tail clip, Transferred, Pond-Stream

label_protocol: Cyanine-3 (Cy3)

growth_protocol: Larvae were captured and placed in the containers on 11 May 2015 for a reciprocal transplant experiment between ponds and streams, the experiment lasted 14 days.

extract_protocol: The total RNA was extracted using the Thermo Fisher TRIzol protocol

treatment_protocol: At the end of the experiment, larvae were tail-clipped. Tail-clips were stored in RNA-later and kept at −20 °C, until further analysis.

tag: sampleID

value: tail clip

tag: treatment

value: PS

tag: origin

value: KoV

tag: destination

value: KoGc

value: larva

tag: location

value: Kottenforst, Germany


title: tail-SP-be5

description: Gene expression from tail clip from a Stream-originated larvae translocated/kept in a Pond

source_name: Tail clip, Transferred, Stream-Pond

value: SP

value: KoGb

value: KoE


title: tail-PP-ee4

description: Gene expression from tail clip from a Pond-originated larvae translocated/kept in a Pond

source_name: Tail clip, Transferred, Pond-Pond

value: PP


title: tail-S-c9

description: Gene expression from tail clip from a free-swimming Stream-originated larvae

source_name: Tail clip, Free-swimming, Stream

value: S


title: tail-SP-ce4


title: tail-SS-cc4

description: Gene expression from tail clip from a Stream-originated larvae translocated/kept in a Stream

source_name: Tail clip, Transferred, Stream-Stream

value: SS


title: tail-PP-ve4


title: tail-PS-vb4


title: tail-PS-ec4


title: gabrg2+/+ WT1


title: tail-SS-bc4


title: Day 7 Tumor-Bearing TB07_06

description:
Day 7 Tumor-Bearing
Test

tag: strain

value: BALB/c

tag: gender

value: Female

value: Immune, stromal, and epithelial cell infiltrate into microporous PCL implant

value: Tumor-bearing


title: TAPBPR_2nd-round-neg-2ugmlDd-10nMP18_R1

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

description:
plasmid DNA
Synthetic coding sequences

library_source: genomic

data_processing:
Library strategy: mutational scan
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script: python Paired_read_fuser.py --path output/ --read1 TAPBPR_R2.fastq --read2 TAPBPR_R1.fastq --wtseq GGTGCGCACCGTGGAGCTCTCGCCAGCAGTGAGGAC --read1_overlap_start 22 --read1_overlap_end 58 --read2_overlap_start 34 --read2_overlap_end 70 --mode B
Aligner script:python Fused_read_aligner.py --path output/ --infile TAPBPR_R2.fast_B_qc1 --referenceDNA GGTGCGCACCGTGGAGCTCTCGCCAGCAGTGAGGAC --referenceAA GAHRGALASSED --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
MapCounts script: python mapCounts.py --path output/ --infile TAPBPR_R2.fast_B_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path ratios/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: python mapParts.py --path ratios/ --infile mapratios_sorted_library --mode mutations:1
Unlink script:  python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size 12
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

molecule: genomic DNA

organism: synthetic construct

source_name: Second round of sorting (negative selection): TAPBPR library stained with  2 ug/ml H2-Dd in presence of 10 nM P18 peptide

growth_protocol: Yeast (strain EBY100) were cultured in SDCAA medium overnight at 30 deg C, then protein expression was induced at a density of OD(600nm) = 0.5 in SGCAA for 2 days at 24 deg C.

extract_protocol:
Plasmid DNA was harvested from unsorted and sorted cells.  The scoop loop region was PCR amplified in 2 steps; in the first, primer overhangs added sequences for annealing to the Illumina sequencing primers, and in the second, primer overhangs added unique barcodes and Illumina adaptors.
Primer pair for 1st round of PCR: Illumina_TAPBPR_111F (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGACTGTTTCCTGGTGAAGG) and Illumina_TAPBPR_229R (TCTTTCCCTACACGACGCTCTTCCGATCTCCTTGGAAATCGGTGAAGTC)
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors): MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a HiSeq 4000 using a 2x150 nt paired end protocol.

treatment_protocol: Yeast were electroporated with a TAPBPR scoop loop library, in which the TAPBPR ectodomain was fused to Aga2p for yeast surface display.  Saturation mutagenesis on the scoop loop (residues G27-D38) was by overlap extension PCR, generating a library expressing all possible single amino acid substitutions within the TAPBPR scoop loop.  Induced yeast were incubated with 500 ng/ml or 2 ug/ml murine H2-Dd tetramers (loaded with P18 peptide) conjugated to APC.  Yeast were co-incubated with anti-myc-FITC to detect surface expression levels based on a C-terminal c-myc epitope tag.  After washing, cells were FACS sorted based on expression (collected cells were positive in the FITC channel) and based on H2-Dd binding (positive selection for the highest 7.5% in the APC channel in the first round of sorting, and negative selection for the lowest 7.5% in the APC channel in the second round of sorting).

tag: protein

value: human TAPBPR

tag: sort gate

value: Yeast are positive for TAPBPR expression, but have low signal (bottom 7.5%) for bound H2-Dd tetramer


title: Day 7 Healthy Control HC07_02

description:
Day 7 Healthy Control
Control

tag: tumor cell line

value: Healthy


title: Day 7 Tumor-Bearing TB07_05

description:
Day 7 Tumor-Bearing
Test

tag: days following tumor inoculation


title: Day 7 Healthy Control HC07_03

description:
Day 7 Healthy Control
Control

tag: panel barcode


title: TAPBPR_2nd-round-neg-2ugmlDd-100nMmotif_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: Second round of sorting (negative selection): TAPBPR library stained with  2 ug/ml H2-Dd in presence of 100 nM motif peptide


title: TAPBPR_2nd-round-neg-2ugmlDd-100nMP18_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: Second round of sorting (negative selection): TAPBPR library stained with  2 ug/ml H2-Dd in presence of 100 nM P18 peptide


title: Day 7 Healthy Control HC07_01

description:
Day 7 Healthy Control
Control

tag: condition at time of analysis


title: Day 7 Tumor-Bearing TB07_04

description:
Day 7 Tumor-Bearing
Test

tag: tissue


title: tail-PS-eb4

value: tail clip

value: PS

tag: age


title: TAPBPR_pre-2nd-round-sort_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: TAPBPR library after positive selection for binding 2 ug/ml H2-Dd, followed by recovery in growth medium for a second round of negative selection.


title: TAPBPR_2nd-round-neg-2ugmlDd-10nMmotif_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: Second round of sorting (negative selection): TAPBPR library stained with  2 ug/ml H2-Dd in presence of 10 nM motif peptide


title: TAPBPR_1st-round-pos-2ugmlDd-10nMmotif_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: TAPBPR library sorted for binding 2 ug/ml H2-Dd in presence of 10 nM motif peptide

value: Top 7.5% of yeast that both express TAPBPR and bind H2-Dd tetramers


title: tail-P-e8

description: Gene expression from tail clip from a free-swimming Pond-originated larvae

source_name: Tail clip, Free-swimming, Pond

value: P

value: larva

value: Kottenforst, Germany


title: tail-SP-cv6

value: SP

value: KoGc

value: KoV


title: tail-PP-ev3

value: PP

value: KoE


title: TAPBPR_1st-round-pos-2ugmlDd-100nMmotif_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: TAPBPR library sorted for binding 2 ug/ml H2-Dd in presence of 100 nM motif peptide


title: TAPBPR_naive_library_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: TAPBPR Naive Library


title: TAPBPR_WT_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: Wildtype TAPBPR: Control for sequencing errors


title: TAPBPR_1st-round-pos-500ngmlDd_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: TAPBPR library sorted for binding 500 ng/ml H2-Dd


title: tail-SS-bb4

value: SS

value: KoGb


title: tail-PP-ve3


title: tail-P-v8


title: tail-PP-ee3


title: tail-PS-vc3


title: TAPBPR_1st-round-pos-2ugmlDd_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: TAPBPR library sorted for binding 2 ug/ml H2-Dd


title: tail-SP-be3


title: tail-S-c8

value: S


title: TAPBPR_1st-round-pos-2ugmlDd-10nMP18_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: TAPBPR library sorted for binding 2 ug/ml H2-Dd in presence of 10 nM P18 peptide

value: human TAPBPR


title: macrophages_modified PEEK_rep2

city: Shenzhen

first: ANG

last: GAO

state: Guangdong

address: 1068 Xueyuan Avenue, Shenzhen University Town

country: China

institute: Shenzhen Institutes of Advanced Technology,Chinese Academy of Sciences

description: Gene expression data from macrophages cultured on modified PEEK for 3 days

hyb_protocol: Following labeling, cDNA was hybridized on a Affymetrix Mouse Clariom S Array.

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

label: biotin

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: The RAW264.7 cells were maintained in the high-glucose dulbecco's modified eagle medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS; Corning) and 1% penicillin-streptomycin (Invitrogen) at 37 °C in humidified 5% CO2 incubator. The cells were seeded onto different samples with an initial density of 1 × 10 5 cells/well with the 24-well tissue culture plate as holders.

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

treatment_protocol: The RAW264.7 cells were seeded on pristine PEEK surface (Control) and modified PEEK surface (Sample) in triplicate and cultured for 3 days.

tag: culture substrate

value: modified PEEK


title: tail-PS-ec3

source_name: Tail clip, Transferred, Pond-Stream


title: macrophages_modified PEEK_rep3

source_name: macrophages cultured on modified PEEK for 3 days


title: tail-PS-vb3


title: tail-SS-bc3


title: tail-SP-ce3

source_name: Tail clip, Transferred, Stream-Pond


title: macrophages_pristine PEEK_rep3

description: Gene expression data from macrophages cultured on pristine PEEK for 3 days

value: pristine PEEK


title: macrophages_pristine PEEK_rep1

source_name: macrophages cultured on pristine PEEK for 3 days


title: macrophages_modified PEEK_rep1


title: TAPBPR_1st-round-pos-2ugmlDd-100nMP18_R1

description:
plasmid DNA
Synthetic coding sequences

source_name: TAPBPR library sorted for binding 2 ug/ml H2-Dd in presence of 100 nM P18 peptide


title: macrophages_pristine PEEK_rep2


title: tail-SS-cb5

source_name: Tail clip, Transferred, Stream-Stream

value: tail clip


title: tail-P-v7


title: iMAC-Ni

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

country: South Korea

institute: Korea National Institute of Health

description:
sample name in processed data file:
iMAC_D60-3 (GroupA), iMAC (GroupB)
GroupA_vsd.txt, GroupB_vsd.txt

data_processing:
RNA-seq reads were aligned to the hg38 reference genome assembly using STAR v2.6.0
The raw counts were normalized using variance stabilizing transformation (VST) method after excluded a minimum count of 1.0 in all of the samples.
Differentiall expressed genes were calculated using DESeq package in R
Genome_build: hg38 (GRCh 38)
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts

source_name: Embryonic stem cell

growth_protocol: The H9 hESC line was obtained from WiCell (Madison, WI, USA) and cultured in feeder-free TeSR-E8 or mTeSR-1 medium (STEMCELL Technologies, Vancouver, Canada) on tissue culture plates coated with Vitronectin (Gibco, Grand Island, NY, USA) or Matrigel hESC-qualified Matrix (Corning Inc., Corning, NY, USA), and were mechanically passaged. For differentiation into macrophage-like cells, hESCs were transitioned into Growth Factor-Reduced Matrigel (Corning Inc.) in mTeSR-1 medium at a density of 5–8 colonies/35-mm dish. Mesodermal differentiation was induced with APEL2 medium supplemented with 1× insulin-transferrin-selenium-X (Gibco) and BMP4. HSPC production was induced by treatment with APEL2 medium containing VEGF4 and SCF for 2 days, followed by SCF, IL-3 and IL-6 and TPO and Flt-3L. After 12-20 days, floating HSPCs were further differentiated into iMAC using macrophage M-CSF and RPMI1640 medium supplemented with 10% fetal bovine serum.     THP-1 pro-monocyte cells were maintained in RPMI1640 containing 10% FBS and 5% penicillin/streptomycin. For differentiation into macrophages, THP-1 cells were treated with phorbol 12-myristate 13-acetate (PMA, 100 ng/ml for 48 h). To generate hMDMs, we sorted CD14+ blood monocytes from hPBMCs using magnetic CD14 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and cultured the cells in the presence of M-CSF (100 ng/ml).

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Briefly, cells were homogenized and transferred directly into a spin column. Tubes were centrifuged 2 min at maximum speed. Homogenized lysate were then transfered into spin column and centrifuged for 30min at 8000g, and save the flow-through and add 1 volume of 70% EtOH. Transfer 700 ul of sample into RNeasy spin column and centrifuged for 15s at 8000g. After 15s, 700 ul RPE buffer was added to spin column and centrifuged 15s at 8000g. Next, 500 ul RPE buffer was added to spin column and centrifuged 2min at 8000g. After 2min, transfer spin column in a new 1.5 ml collection tube and added 50ul RNase free water directly to the membrane and centrifuged for 1min at 8000g.
The library was prepared using Truseq stranded mRNA prep kit (Illumina, San Diego, CA, USA) and run on a HiSeq2500 sequencer (Illumina) with a 101-bp paired-end read length. Raw data were processed using STAR v.2.6 to align genome reads against human Reference genome (hg38) and differentially expressed genes were identified using DESeq21 after raw count data were normalized using variance stabilizing transformation (VST) method. Multidimensional scaling (MDS) and clustering analysis were calculated based on Poisson model. Spearman correlation coefficients between pairs of samples were computed.

treatment_protocol: Macrophages were infected with H37Rv-GFP Mtb at the desired multiplicity of infection (MOI) for 2h with mild shacking (120 rpm) at 37°C. For the high-throughput screening, a MOI of 5 was used. Infected cells were washed twice with fresh medium.

tag: cell type

value: human ES-derived macrophage

tag: infection status

value: not infected


title: H9-2

description:
sample name in processed data file:
H9-2
GroupA_vsd.txt

value: human ES


title: iMAC-Moi

description:
sample name in processed data file:
iMAC_TB
GroupB_vsd.txt

value: infected with H37Rv-GFP Mtb


title: tail-S-b8

source_name: Tail clip, Free-swimming, Stream

tag: sampleID

tag: treatment

value: larva

value: Kottenforst, Germany


title: tail-PP-ve2

source_name: Tail clip, Transferred, Pond-Pond

tag: origin

tag: destination


title: tail-P-e7

value: P

tag: location


title: tail-PP-ee2


title: THP1-2

description:
sample name in processed data file:
THP1-2
GroupA_vsd.txt

source_name: monocyte

value: THP-1 macrophages


title: tail-PP-vv2

value: PP

value: KoV


title: H9-1

description:
sample name in processed data file:
H9-1
GroupA_vsd.txt


title: tail-SS-bb3

value: SS


title: THP1-1

description:
sample name in processed data file:
THP1-1
GroupA_vsd.txt


title: tail-PP-ev2

value: KoE


title: tail-SP-ce2

value: SP

value: KoGc


title: tail-SP-be2

value: KoGb


title: tail-S-c7

value: S


title: tail-PS-eb3

value: tail clip

value: PS


title: tail-SS-bb2


title: tail-SP-bv2


title: tail-PS-eb2


title: tail-PS-vc2


title: tail-S-b7


title: tail-PS-ec2


title: tail-PS-vb2


title: GOLNL7dR2

city: Wuhan

first: Jianda

last: Shi

state: Hubei

address: Hube

institute: HZAU

data_processing:
Quality control
Comparative analysis: Hisat2 tools soft were used to map with reference genome.
The gene expression analyses were performed with StringTie
Supplementary_files_format_and_content: tab-delimited list file includes FPKM values for each Sample and infromatiom of new genes...

organism: Solanum lycopersicum

source_name: tomato leaf

growth_protocol: During the culture, the plants were grown under light conditions at an average photosynthetic photon-flux density of 300 μmol m-2·s-1. The day and night temperatures of the growth chamber were 28°C and 18°C, respectively, and its day relative humidity was 75%.

extract_protocol:
RNA prep Pure Plant Kit (No. DP441; Tiangen Co. Ltd, China)
NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: The plants were grown under hydroponic conditions in a growth chamber, and were grown in full-strength Hoagland solution containing normal N (9 mM) or low N (1 mM)

tag: time

value: 7 day

value: Low Nitrogen

tag: cultivar

value: Guozhen No.1

value: leaf


title: tail-PP-ev1

value: larva

value: Kottenforst, Germany


title: tail-SP-cv2


title: tail-SP-ce1


title: tail-SP-be1


title: tail-PS-vc5


title: GOLNL7dR3


title: tail-SS-bc1


title: tail-SS-cc1


title: tail-SS-bc5


title: tail-PP-vv6


title: tail-PP-ev4


title: tail-PS-ec1


title: tail-PP-vv4


title: tail-PP-ve5


title: tail-PS-eb1


title: tail-S-c6


title: tail-PP-ve1


title: tail-P-v9

source_name: Tail clip, Free-swimming, Pond

value: P


title: tail-PP-ee1

value: PP


title: tail-SS-cb1


title: tail-S-b6


title: tail-PS-vc1

value: KoV


title: tail-SP-bv1


title: tail-PS-ec5


title: GOLNL7dR1


title: tail-PS-vb1


title: tail-SP-bv9


title: GOLNR7dR3

source_name: tomato root

value: root


title: GOLNR7dR2


title: PF-2.5uM-2

first: Marc

last: Wein

address: 15 Fruit Street

department: Massachusetts General Hospital, Department of Medicine

institute: Harvard Medical School

description: Control cells with 2.5M PF treatment

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9

source_name: Ocy454, osteocytes

extract_protocol: Total RNA was collected from cultured cells using QIAshredder (QIAGEN) and PureLink RNA mini kit (InvitrogenTM) following the manufacture’s instructions. Lysis buffer with 2-mercaptoethanol was added to cold PBS washed cells and collected into QIAshredder, then centrifuged at 15,000g for 3 minutes. The flow-through was collected into a new tube and RNA isolation was carried out with PureLink RNA mini kit following the manufacturer’s instructions.

value: mouse long bone derived osteocytes

tag: genotype

value: Original cells

value: 2.5uM PF562271 treatment for 4 hours


title: PF-2.5uM-1

description: Control cells with 2.5M PF treatment


title: STATIC_NT2

description: Control cells with static condition

value: STATIC for 3 hours


title: PF-0uM-2

description: Control cells with 0M PF treatment

value: 0uM PF562271 treatment for 4 hours


title: GOCNL7dR3

value: CK


title: GOLNR7dR1


title: tail-P-e6

value: tail clip

value: KoE


title: GOCNL7dR1

value: 7 day


title: GOCNL7dR2

value: Guozhen No.1


title: PF-0uM-1

description: Control cells with 0M PF treatment


title: STATIC_NT1

description: Control cells with static condition


title: GOCNR7dR3


title: LG-Cont1

description: Control cells with control lenti vector(LV)

value: Control LV infected cells


title: tail-P-v6

value: larva


title: GOCNR7dR1


title: LG-Cont2


title: GULNL7dR3

value: Low Nitrogen

value: Guizhen No.1

value: leaf


title: GOCNR7dR2


title: FFSS350_NT1

description: Control cells with FFSS

value: Fluid Flow Shear Stress (FFSS) for 3 hours


title: S_siTFAP2C1_1

city: London

last: Sahai

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: TFAP2C knockdown vs. control

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCh30-release-86 transcriptome
The “--forward-prob” parameter was set to “0” and all other parameters were kept as default
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

growth_protocol: Human vulval carcinoma fibroblasts (VCAF8) were isolated from patient samples and immortalised with lentiviral HTERT as described in Gaggioli, C., et al. Cells were selected using 400 μg mL-1 hygromycin and maintained in DMEM (Invitrogen), 10% FCS (PAA Labs), 1% ITS (insulin–transferrin–selenium; #41400-045; Invitrogen) supplement.

extract_protocol:
RNA was extracted from fibroblasts using RNeasy Plus Micro Kit (Cat No: 74034, Qiagen) as per manufacturers  instructions.
Total RNA libraries were prepared using KAPA HyperPrep with RiboErase in accordance with the manufacturers guidelines. Libraries were amplified with 8 cycles of PCR and QC’d using the TapeStation before sequencing on the Illumina HiSeq platform.

treatment_protocol: Vulval carcinoma fibroblasts (VCAF8) were transfected with 50nM siRNA using Dharmafect 3 (Dharmacon) as per the manufacturer’s instructions in Gibco™ Opti-MEM™ Reduced Serum Media supplemented with 10% FCS. Cells were maintained for 48 hrs for full knock-down before RNA extraction.

tag: cell line

value: human vulval carcinoma fibroblast

tag: transfection

value: siRNA against TFAP2C (siTFAP2C1)


title: GULNL7dR1


title: S_siTFAP2C1_2

description: TFAP2C knockdown vs. control


title: FAK-FFSS2

description: FAK knockout with FFSS

value: mouse long bone derived osteocytes

value: FAK gene deletion


title: FFSS350_NT2

description: Control cells with FFSS

value: Original cells


title: c31-input (ChIP-seq)

city: Shanghai

first: Guofeng

last: Meng

address: Jinke 3528

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
The adaptors were cut using Ngmerge
Pair-end reads were aligned to hg38 genome using bowtie2 under default parameter setting
The TF binding sites were detected by macs2
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

source_name: brain prefrontal cortex region tissues

extract_protocol:
Chromatin was sonicated by Bioruptor (Diagenode, Belgium) under the condition as follows: 20 cycles of 30 s on, 60 s off. The sonicated chromatin was spun down at 12,000 rpm for 10 min at 4 °C to collect the chromatin. Add antibody (10 μg) to the soluble chromatin (80 μg), and incubate at 4 °C with rotation overnight. Protein A/G Dynabeads (10 μl of beads per 1 μg of antibody, Life Tech, 10004D) were washed three times with Low Salt Wash Buffer. The washed Dynabeads were added to the soluble chromatin and antibodies, incubated at 4°C for 4 h with rotation. The magnetic Dynabeads were pelleted by placing the tubes in a magnetic rack and were sequentially washed once with Low Salt Wash Buffer, once with High-salt Wash Buffer, once with LiCl Wash Buffer. Wash the beads three times with TE buffer. Remove any supernatant remaining after the last washing. The beads were resuspended in 150 μl of Elution Buffer (50 mM Tris•Cl pH 8.0, 10 mM EDTA, 1% SDS), followed by incubation for 15 min at 65 °C. Repeat step 7 again, combine the elution, then you have 300 μl of the eluted DNA solution. Add 1 μl of high concentration RNase A (10 mg/ml) to the eluted DNA solution and the Input samples (500 μl), respectively. Incubate them at 37 ℃ for 1 h. Reverse formaldehyde crosslinks by respectively adding 12.5 μl or 55 μl of 5 M NaCl to the eluted DNA solution and the Input samples to a final concentration of 0.2 M. Incubate samples at 65 ℃ (650 rpm) for more than 8 h (less than 16 h).  Add both 80.5 μl of ddH2O and 5 μl of 20 mg/ml Proteinase K to the eluted DNA solution, and just 5 μl of Proteinase K to the Inputs. Incubate at 56 ℃ for 2 h. Extract once with 400 μl of phenol/chloroform/isoamyl alcohol, and once with 400 μl of chloroform/isoamyl alcohol (optional). Transfer 355 μl of supernatant to a new tube. Add 55 μl or 40 μl of 3 M NaAc (pH 5.2, 0.3 M final) to the Input samples and eluted DNA solution, 5 μl of glycogen each sample and mix well. Add 800 μl (two-fold volume) of absolute ethanol. Precipitate at -20 ℃ overnight or at -80 ℃ for 4 h. Centrifuge at 14000 rmp for 20 min at 4 ℃. Wash once with 75% ethanol and store at -20 ℃.
The library is constructed under the protocol of Iillumina

tag: disease state

value: normal

tag: Sex

value: male

tag: braak

tag: chip antibody

value: brain prefrontal cortex region tissues


title: c13-input (ChIP-seq)

tag: age

tag: tissue


title: GULNL7dR2


title: ad16-input (ChIP-seq)

value: AD

value: female


title: GULNR7dR3

value: 7 day

value: root


title: FAK-FFSS1

description: FAK knockout with FFSS

tag: cell type


title: ad11-input (ChIP-seq)


title: S_CtrlTfn_1

description: TFAP2C knockdown vs. control

value: mock (Ctrl_Tfn)


title: LG-FFSS1

description: LV cells with FFSS

value: Control LV infected cells


title: FAK-Cont2

description: FAK knockout with static condition

value: STATIC for 3 hours


title: LG-FFSS2

description: LV cells with FFSS


title: GULNR7dR1

value: Low Nitrogen

value: Guizhen No.1


title: FAK-Cont1

description: FAK knockout with static condition


title: GUCNL7dR2

value: CK

value: leaf


title: GUCNL7dR3


title: ATAC_Panc1_SB

city: New York

first: Joan

last: Massague

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

description:
ATACSeq
Sample_Chr2434-Panc1-SB-AT-A11-GGACTCCT.tdf

data_processing:
QC: FastQC v0.11.5
Alignment: STAR2.5.2b for RNASeq, Bowtie2 for ChIPseq
RNAseq annotation: HTSeq v0.6.1p1
RNAseq normalization: DESeq2 v3.4
ChIPseq sorting, normalization, and visualization: Sam Tools & HOMER
Genome_build: mm10, hg19
Supplementary_files_format_and_content: RNASeq: Normalized Counts in .csv; ChIPSeq/ATACSeq: genome browser tracks in .tdf

source_name: pancreatic ductal adenocarcinoma

growth_protocol: High glucose DMEM + 10% FBS

extract_protocol:
Total RNA was collected using Qiagen's Rneasy Mini Kit (74106) and assessed for RNA integrity number >9.5. For ChIP-seq, cells were fixed, quenched, sonicated to ~250 bp in 1% SDS lysis buffer, and incubated with Protein A Dynabeads (Novex 10008) and 5 µg of the indicated antibody. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. After wash, treatment with RNAse A and Proteinase K, DNA was eluted and purified with Qiagen's PCR purification kit (28106).For ATACSeq, cell nuclei were prepared from 5x104 cells and incubated with 2.5 μL transposase (Illumina) in a 50 μL reaction for 30 minutes at 37°C.
For RNASeq, library construction was performed using TruSeq RNA Sample Prep Kit v2 (Illumina) following manufacturer’s instructions. For ChIPSeq, DNA quality was checked using Agilent Technologies 2200 TapeStation and quantified using PicoGreen. Library construction was performed using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina  according to manufacturer's conditions. Samples were pooled and submitted to New York Genome Center for SE50 sequencing. For ATACSeq, following purification of transposase-fragmented DNA, the library was amplified  by PCR and subjected to PE50 high-throughput sequencing.

treatment_protocol: Cells were plated at 300k per 15 cm plate in 2.5 µM MK2206 (ChemieTek CT-MK2206) 12h prior to treatment with 2.5 µM SB505124 (Sigma S4696) or 100 pM TGFβ (R&D 101-B1). Where indicated, doxycycline at 1 µg/mL at plating.

tag: timepoint


title: S_CtrlAllS_1

description: TFAP2C knockdown vs. control

value: human vulval carcinoma fibroblast

value: non-targeting control siRNA (Ctrl_AllS)


title: GUCNR7dR1

tag: treatment


title: GUCNR7dR3


title: GUCNL7dR1


title: S_CtrlTfn_2

description: TFAP2C knockdown vs. control


title: GOLNL1dR3

value: 1 day

value: Guozhen No.1


title: GUCNR7dR2


title: GOLNL1dR2


title: GOLNL1dR1


title: Cyanobacteria_environmental_station19_depth36

city: Stockholm

first: Marcus

last: Stenegren

address: Svante Arrhenius vag 20A

department: Ecology Environment and Plant Sciences

country: Sweden

institute: Stockholm University

description: Gene expression of cells filtered from a mixed plankton community at sea

hyb_protocol: A total of 600 ng Cyanine 3-CTP labelled cRNA were hybridized to Agilent custom designed 8x15K microarray and incubated under rotation at 65° C for 17 h.

scan_protocol: After hybridization, arrays were washed according to manufacturer’s protocol, and the slides were immediately scanned using Agilent DNA microarray scanner G2505C at 5 µm resolution, for one-color microarray and 8x15K format slides.

data_processing:
The fluorescence intensities of the scanned images were extracted and preprocessed using the Agilent Feature Extraction Software (version 10.7.3.1) with grid IS-15744-8-V1_8x15K_Gx_EQC_V20060608, and mean signals were calculated from the probe replicates
Normalized signal intensity averages from 15 probe replicates

organism: seawater metagenome

label_protocol: Each sample, with a total RNA of 50-100 ng, was labelled and amplified with Cy3-dCTP using the Agilent Low Input Quick Amp WT Labelling kit according to the manufacturer’s protocol.

growth_protocol: Environmental sample

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen, Germany) following the manufacturer’s protocol with a few modifications. All samples were treated with a 1 hour DNAse treatment with the Qiagen RNase-free DNase kit, and the final elution volume was 20 µl.

treatment_protocol: Filtered whole water within 30 min of collection, submerged in RNAlater and flash frozen in liquid nitrogen and stored for later analysis

tag: diazotrophs

value: Richelia intracellularis and Calothrix rhizosoleniae

tag: genomes

value: RintRC01, RintHH01, RintHM01, CalSC01

tag: station

tag: depth

value: western tropical North Atlantic


title: Cyanobacteria_environmental_station2_depth21

tag: location


title: GULNR7dR2

tag: time

tag: cultivar


title: GOLNR1dR3


title: Cyanobacteria_environmental_station2_depth11


title: Cyanobacteria_environmental_station20_depth1_day

data_processing:
The fluorescence intensities of the scanned images were extracted and preprocessed using the Agilent Feature Extraction Software (version 10.7.3.1) with grid IS-15744-8-V1_8x15K_Gx_EQC_V20060608, and mean signals were calculated from the probe replicates
Normalized signal intensity averages from 18 probe replicates

value: 1 m

tag: time sampled

value: South China Sea


title: Cyanobacteria_environmental_station2_depth30


title: Cyanobacteria_environmental_station19_depth21


title: Cyanobacteria_environmental_station2_depth4

value: 4 m


title: S_CtrlAllS_2

description: TFAP2C knockdown vs. control

tag: cell line

tag: transfection


title: GOLNR1dR2

value: root


title: GOCNL1dR3


title: Cyanobacteria_environmental_station18_depth37_day


title: Cyanobacteria_environmental_station18_depth1_day


title: Cyanobacteria_environmental_station17_depth25_night


title: GOCNL1dR1


title: Cyanobacteria_environmental_station17_depth21_day


title: GOCNR1dR3


title: GOCNR1dR2


title: Cyanobacteria_environmental_station11_depth20_day


title: Cyanobacteria_environmental_station19_depth2

value: 2 m


title: Cyanobacteria_environmental_station21_depth21_night


title: Cyanobacteria_environmental_station17_depth1_day


title: GULNL1dR3


title: GULNL1dR2


title: Cyanobacteria_environmental_station20_depth25_day


title: Cyanobacteria_environmental_station17_depth1_night


title: GULNL1dR1


title: GULNR1dR2


title: Cyanobacteria_environmental_station10_depth21_night


title: GULNR1dR3


title: GULNR1dR1


title: Cyanobacteria_environmental_station10_depth1_night


title: GUCNL1dR3


title: GOCNL1dR2


title: GOLNR1dR1


title: Cyanobacteria_environmental_station11_depth1_day


title: Cyanobacteria_environmental_station9_depth1_day


title: GUCNL1dR2


title: Cyanobacteria_environmental_station19_depth5_night

value: 5 m


title: Cyanobacteria_environmental_station8_depth4_night


title: GOCNR1dR1


title: Cyanobacteria_environmental_station8_depth10_night


title: Cyanobacteria_environmental_station19_depth10_night


title: GUCNL1dR1


title: GUCNR1dR3


title: GUCNR1dR1


title: GUCNR1dR2


title: Cyanobacteria_environmental_station19_depth23_night


title: Cyanobacteria_environmental_station19_depth27_night


title: CAP-H2 shRNA [ML-ED15_S15]

status: Public on Oct 30 2019

city: Cleveland

first: Michelle

middle: Suzanne

last: Longworth

state: OH

address: 9500 Euclid Ave NE20

department: Molecular Genetics

institute: Cleveland Clinic Foundation

data_processing:
Reads were trimmed with Trim Galore! (v.0.3.7) with FastQC enabled for quality control
Samples were run on two lanes. Reads from the two lanes were combined for each sample before alignment.
Combined reads were aligned to the human genome (GRCh38/hg38) using STAR (v.2.5.3a) in gene counting mode (--quantMode GeneCounts) with Gencode (v.27) annotations.
After first-pass alignment, splice junctions were combined and filtered to remove non-canonical junctions and junctions covered by < 10 reads prior to second-pass alignment.
Second-pass counts were loaded into R (v.3.3.3) and analyzed with DESeq2 (v.1.14.1).
To offset uneven sample variance, fdrtool was used to reestimate false discovery rates where p-values were not uniformly distributed outside of the low-p-value peak that includes DE genes.
Genes with adjusted P-value < 0.05 and fold change > 2 were deemed to be differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts and regularized log2 counts as excel spreadsheets

source_name: Human colon adenocarcinoma (HT-29) cells

growth_protocol: HT-29 cells were cultured in RPMI-1640 media with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. 200,000 cells were seeded on a 6 well plate and alllowed to attach overnight. Cells were then treated with IPTG for 48 hours to induce shRNA expression

extract_protocol:
RNA was isolated from HT-29 cellsusing the Qiagen Mini RNeasy Kit
cDNA libraries (50 base pair, single end) were made at the University of Chicago Genomics Core and sequenced on an Illumina HiSeq2500, according to standard protocols.

treatment_protocol: Cells were treated with 50uM menadione (or an equal volume of DMSO) for 30 minutes prior to harvesting.

value: DMSO


title: CAP-H2 shRNA [ML-ED14_S14]


title: Cyanobacteria_environmental_station8_depth25_night


title: CAP-D3 shRNA [ML-ED11_S11]

value: 50uM Menadione


title: CAP-H2 shRNA [ML-ED13_S13]


title: CAP-D3 shRNA [ML-ED10_S10]


title: CAP-D3 shRNA [ML-ED12_S12]


title: CAP-D3 shRNA [ML-ED9_S9]


title: CAP-D3 shRNA [ML-ED8_S8]


title: CAP-D3 shRNA [ML-ED7_S7]


title: Non Target shRNA [ML-ED6_S6]


title: Non Target shRNA [ML-ED5_S5]


title: Non Target shRNA [ML-ED1_S1]


title: 293FlpIN_pcDNA5_NS1A_pDox_Spt5PO4_Rep1

city: Aurora

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

description: Spt5-PO4 ChIP-seq

data_processing:
Libraries that were sequenced multiple times were combined into a single fastq file
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: BigWig

source_name: HEK293 Flp-in T-REx pcDNA5 HA-NS1A

growth_protocol: DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep

extract_protocol:
Cross-linked chromatin was sonicated with a Bioruptor or Covaris Ultrasonicator
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

tag: growth conditions

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline

tag: antibody

value: rabbit anti phospho-Spt5 this work

value: NS1A  expression was induced with 2ug/ml doxycycline for 24 hrs,


title: 293FlpIN_pcDNA5_NS1A_mDox_Spt5PO4_Rep1

description: Spt5-PO4 ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin

value: control without doxycycline induction


title: Non Target shRNA [ML-ED2_S2]


title: 293FlpIN_pcDNA5_NS1A_mDox_PolII_Rep2

description: Pol II ChIP-seq

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)


title: 293FlpIN_pcDNA5_NS1A_mDox_Spt5_Rep1

description: Spt5 ChIP-seq

value: rabbit anti Spt5 (Glover-Cutter et al NSMB 15:71-78, 2008)


title: 293FlpIN_pcDNA5_NS1A_pDox_Spt5_Rep1

description: Spt5 ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_20_Spt5

description: Spt5 ChIP-seq

source_name: HEK293 Flp-in T-REx pcDNA5 HA-Xrn2 D235AshXrn2

value: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 20 min.


title: 293FlpIN_pcDNA5_NS1A_pDox_PolII_Rep1

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_20_PolII

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_20_Spt5PO4

description: Spt5-PO4 ChIP-seq

source_name: HEK293 Flp-in T-REx pcDNA5  HA-Xrn2 WT shXrn2

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 20 min.


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_20_Spt5

description: Spt5 ChIP-seq


title: Hap1_PSMG1_pA-MT_PolII_Rep1

description: Pol II ChIP-seq

growth_protocol: IMDM 10% FCS,

value: IMDM 10% FCS,

value: no treatment


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_20_Spt5PO4

description: Spt5-PO4 ChIP-seq


title: Hap1_PolII_Rep1

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_20_PolII

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_30_PolII_Rep2

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline +triptolide

value: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 30 min.


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_20_PolII_Rep2

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_5_PolII_Rep2

description: Pol II ChIP-seq

value: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 5 min.


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_PolII_Rep2

description: Pol II ChIP-seq

value: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs,


title: Non Target shRNA [ML-ED4_S4]


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_5_PolII_Rep2

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +triptolide

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 5 min.


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_PolII_Rep2

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs,


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_20_PolII_Rep2

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_30_PolII_Rep2

description: Pol II ChIP-seq

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 30 min.


title: Non Target shRNA [ML-ED3_S3]

value: DMSO


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_10_PolII_Rep2

description: Pol II ChIP-seq

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 10 min.


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_15_PolII_Rep1

description: Pol II ChIP-seq

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)

value: Xrn2 D235A  expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 15 min.


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_10_PolII_Rep1

description: Pol II ChIP-seq

value: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 10 min.


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_15_PolII_Rep1

description: Pol II ChIP-seq

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, Triptolide (10 mM) was added for 15 min.


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_PolII_Rep1

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin, +DRB


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_5_PolII_Rep1

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_PolII_Rep1

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +DRB


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_5_PolII_Rep1

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2_WT_Dox_Trip_10_PolII_Rep1

description: Pol II ChIP-seq


title: 293FlpIN_pcDNA5_Xrn2D235A_DRB_WashOut_T10_PolII

description: Pol II ChIP-seq

value: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr. then washed out for 10 min


title: 293FlpIN_pcDNA5_Xrn2D235A_DRB_PolII

description: Pol II ChIP-seq

value: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr.


title: 293FlpIN_pcDNA5_Xrn2D235A_DRB_WashOut_T5_PolII

description: Pol II ChIP-seq

value: Xrn2 D235A  expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr. then washed out for 5 min


title: 293FlpIN_pcDNA5_Xrn2_WT_DRB_WashOut_T15_PolII

description: Pol II ChIP-seq

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr. then washed out for 15 min


title: 293FlpIN_pcDNA5_Xrn2_WT_DRB_WashOut_T10_PolII

description: Pol II ChIP-seq

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr. then washed out for 10 min


title: 293FlpIN_pcDNA5_Xrn2D235A_Dox_Trip_10_PolII_Rep2

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline +triptolide


title: 293FlpIN_pcDNA5_Xrn2_WT_DRB_WashOut_T5_PolII

description: Pol II ChIP-seq

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr. then washed out for 5 min


title: 293FlpIN_pcDNA5_Xrn2_WT_DRB_PolII

description: Pol II ChIP-seq

value: Xrn2 expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr.


title: nonAligned_1901_R2

description: Aligned vs. non-aligned phenotype

growth_protocol: Human fibroblasts were isolated from patient samples and immortalised with lentiviral HTERT as described in Gaggioli, C., et al. Cells were selected using 400 μg mL-1 hygromycin and maintained in DMEM (Invitrogen), 10% FCS (PAA Labs), 1% ITS (insulin–transferrin–selenium; #41400-045; Invitrogen) supplement.

treatment_protocol: The fibroblast derived matrix assay was performed as described in Franco-Barraza, J., et al. Cells were maintained for 6 days on gelatin coated mattek dishes changing the media every two days.

value: human breast carcinoma fibroblast

tag: matrix alignment

value: not aligned


title: nonAligned_1901_R1

description: Aligned vs. non-aligned phenotype


title: nonAligned_MAF2_5C

description: Aligned vs. non-aligned phenotype

value: human metastatic melanoma fibroblast


title: aligned_CerCAF_4B

description: Aligned vs. non-aligned phenotype

value: CerCAF

value: human cervical carcinoma fibroblast

value: aligned


title: aligned_CerCAF_4A

description: Aligned vs. non-aligned phenotype


title: aligned_VCAF2B_R1

description: Aligned vs. non-aligned phenotype

value: human vulval carcinoma fibroblast


title: aligned_OCAF1_3A

description: Aligned vs. non-aligned phenotype

value: human oral carcinoma fibroblast


title: aligned_VCAF2B_1C

description: Aligned vs. non-aligned phenotype


title: aligned_OCAF1_3B

description: Aligned vs. non-aligned phenotype


title: aligned_VCAF8_R1

description: Aligned vs. non-aligned phenotype


title: 293FlpIN_pcDNA5_Xrn2D235A_DRB_WashOut_T15_PolII

description: Pol II ChIP-seq

value: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +DRB

value: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)

value: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr. then washed out for 15 min


title: nonAligned_MAF2_5A

description: Aligned vs. non-aligned phenotype


title: aligned_CerCAF_4C

description: Aligned vs. non-aligned phenotype


title: aligned_VCAF8_2B

description: Aligned vs. non-aligned phenotype


title: Sample_MB135_stranded_nodox_1

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Stranded RNA-seq libraries were aligned using TopHat version 2.1.1 with Bowtie version 2.2.9 and the iGenomes UCSC gene transfer format file with the following options: --read-mismatches 8 --read-edit-dist 8.
For repeat counting in our stranded, ribosome-depleted RNA-seq dataset we used the TEtranscripts script from TEtoolkit package with the multi-mode option and a custom GTF file which was made from the current (07-Nov-2016 release) of Dfam non-redundant repeat matches.
We performed differential expression analysis on the resulting count table with DESeq2 using default options.
Genome_build: hg38
Supplementary_files_format_and_content: SuppFile2.xls contains DESeq2 differential expression results for -/+DOX of TEtranscripts output counts table.

source_name: Human MB135 myoblast cells with inducible DUX4

growth_protocol: Myoblasts were cultured in F10 medium (Gibco/ThermoFisher Scientific) supplemented with 20% FBS (GE Healthcare Life Sciences) and 1% penicillin/streptomycin (Gibco/ThermoFisher Scientific), 10.0 ng/ml recombinant human FGF (Promega) and 1.0 μM dexamethasone (Sigma-Aldrich).

extract_protocol:
RNA was isolated using TRIzol reagent (ThermoFisher Scientific) according to manufacturer’s instructions.
Stranded total RNA-seq libraries were made from 1.0 μg of MB135-DUX4i RNA using the KAPA stranded RNA-seq kit with RiboErase (HMR) and following the manufacturer’s instructions.

treatment_protocol: Cells were grown for approximately 18 hours in the presence of 1.0 μg/ml of doxycycline hyclate (Sigma-Aldrich).

value: -Doxycycline

tag: replicate


title: Sample_MB135_stranded_nodox_2


title: Sample_MB135_stranded_dox_4

value: +Doxycycline


title: Sample_MB135_stranded_dox_3


title: aligned_VCAF2B_1A

description: Aligned vs. non-aligned phenotype

tag: cell type


title: aligned_OCAF1_3C

description: Aligned vs. non-aligned phenotype


title: Sample_mouse_IgG_rep2_wDOX

description: nonspecific control

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads aligned to hg38 using BWA version 0.7.12 with the option -n 6.
peaks were called by comparison to the IgG background control condition using MACS2 version 2.1.0 using the options: --broad, --broad-cutoff 0.01, -q 0.01. We then used Diffbind version 2.3.8 to differentially call dsRNA enrichment between +/- DOX conditions with “minOverlap” set at 0.5, which treated J2 and K1 antibodies as biological replicates for comparison purposes. The significance threshold was set at 1e-10.
We filtered our list of enriched dsRNAs to eliminate dsRNAs which overlapped known rRNAs, tRNAs and snRNAs (obtained from UCSC table browser repeatMasker track filter repclass: “snRNA OR rRNA OR tRNA OR snoRNA”) using bedtools “intersect”
For repeat counting we used the TEtranscripts script from TEtoolkit package with the multi-mode option and a custom GTF file which was made from the current (07-Nov-2016 release) of Dfam non-redundant repeat matches. We performed differential expression analysis on the resulting count table with DESeq2 using default options.  We performed the above analysis in K1 or J2 versus IgG in doxycycline-treated samples.
Genome_build: hg38
Supplementary_files_format_and_content: SuppFile1.xls contains the diffBind differential expression analysis of regions enriched for dsRNA
Supplementary_files_format_and_content: SuppFile3.xls contains DESeq2 differential expression results of +DOX K1 or J2 vs. IgG from TEtranscripts output counts table.

extract_protocol:
RNA was isolated using TRIzol reagent (ThermoFisher Scientific) according to manufacturer’s instructions.
Ribosomal RNA depletion was performed using the NEBNext rRNA depletion kit (New England Biolabs). First strand synthesis was achieved using SuperScript III reverse transcriptase (ThermoFisher Scientific) with random hexamers and using the following thermocycler conditions: 25°C 10min, 50°C 30min, 55°C 30min and 85°C 5min. Second strand synthesis was achieved using the NEB second strand cDNA synthesis kit, following manufacturer’s recommendations. The double-stranded cDNA was fragmented to approximately 250 bp average size using a Diagenode Bioruptor sonicator in 120 μl total volume for three 10-minute intervals on medium intensity at 4°C, 20s on/off, replenishing with pre-cooled water between each interval. Libraries were made from the AmpureXP (Beckman Coulter) purified cDNA using the Ovation Ultralow system V2 kit and following the manufacturer’s instructions. Stranded total RNA-seq libraries were made from 1.0 μg of MB135-DUX4i RNA using the KAPA stranded RNA-seq kit with RiboErase (HMR) and following the manufacturer’s instructions.

value: IgG


title: Sample_mouse_IgG_rep3_wDOX

description: nonspecific control


title: Sample_mouse_IgG_rep3_noDOX

description: nonspecific control


title: Sample_mouse_IgG_rep2_noDOX

description: nonspecific control


title: aligned_VCAF8_2C

description: Aligned vs. non-aligned phenotype


title: Sample_mouse_IgG_rep1_wDOX

description: nonspecific control


title: Sample_K1_rep3_noDOX

description: dsRNA immunoprecipitation


title: Sample_K1_rep3_wDOX

description: dsRNA immunoprecipitation


title: Sample_mouse_IgG_rep1_noDOX

description: nonspecific control


title: Sample_K1_rep2_wDOX

description: dsRNA immunoprecipitation


title: Sample_K1_rep1_wDOX

description: dsRNA immunoprecipitation


title: Sample_K1_rep1_noDOX

description: dsRNA immunoprecipitation


title: Sample_J2_rep3_noDOX

description: dsRNA immunoprecipitation


title: Sample_J2_rep3_wDOX

description: dsRNA immunoprecipitation


title: Sample_J2_rep2_noDOX

description: dsRNA immunoprecipitation


title: Sample_J2_rep2_wDOX

description: dsRNA immunoprecipitation


title: Sample_J2_rep1_wDOX

description: dsRNA immunoprecipitation


title: Small RNAs from ovaries of CCR4/CCR4 rep2

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

description:
CCR4_sRNA_homo_rep2.2
ccr4_homo2.2.sRNA

data_processing:
Small RNAs: The reads with clipped 3'-adapter were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Chrom-bound RNAs: After removal of Illumina 3’adapter, rRNA reads were filtered out; the remaining reads were mapped on the genome assembly of Drosophila (BDGP assembley R6/dm6) by bowtie 2.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited files include the frequencies of clipped read occurrences in each library.

organism: Drosophila melanogaster

source_name: Small RNAs from ovaries of CCR4/CCR4

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
small RNAs: Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt); chromatin bound RNA: Nuclear RNA was extractred as descirbed in (Chen et al 2016, PMID: 27292797).
small RNAs: Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012); chromatin bound RNAs: cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Reaction of tagmentation was performed in according to previously published protocol (Picelli et al. 2014) using in-house produced Tn5 charged with oligonucleotides compatible with the Illumina system. Reaction products were cleaned using Clean Mini (Evrogen), PCR amplified and sequenced on the Illumina HiSeq 2500.

tag: genotype/variation

tag: tissue

value: ovaries

tag: biological replica

tag: technical replica


title: Sample_J2_rep1_noDOX

description: dsRNA immunoprecipitation

tag: treatment


title: Small RNAs from ovaries of CCR4/CCR4 rep1

description:
CCR4_sRNA_homo_rep2.1
ccr4_homo2.sRNA


title: Small RNAs from ovaries of CCR4/+ rep1

description:
CCR4_sRNA_het_rep2.1
ccr4_het2.sRNA

source_name: Small RNAs from ovaries of CCR4/+

extract_protocol:
small RNAs: Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt); chromatin bound RNA: Nuclear RNA was extractred as descirbed in (Chen et al 2016, PMID: 27292797).
chromatin-bound RNAs: Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012); chromatin bound RNAs: cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Reaction of tagmentation was performed in according to previously published protocol (Picelli et al. 2014) using in-house produced Tn5 charged with oligonucleotides compatible with the Illumina system. Reaction products were cleaned using Clean Mini (Evrogen), PCR amplified and sequenced on the Illumina HiSeq 2500.

value: twin +/-


title: Small RNAs from ovaries of CCR4/+

description:
CCR4_sRNA_het_rep1
ccr4_het.sRNA


title: Small RNAs from ovaries of CCR4/+ rep2

description:
CCR4_sRNA_het_rep2.2
ccr4_het2.2.sRNA


title: Small RNAs from ovaries of CCR4/CCR4

description:
CCR4_sRNA_homo_rep1
ccr4_homo.sRNA


title: Sample_K1_rep2_noDOX

description: dsRNA immunoprecipitation


title: Peripheral-8mm-rpe-cho-donor-2

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

description: Sample 5

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg19 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
Experiment 1:  Relates to donors 1-3 (Samples 1-6).  The six samples were collectively aggregated with the cellranger aggr function with the following parameter: --normalized=mapped.  Cells were then filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 300 (to remove cells with poor read quality) or greater than 6000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). Aggregated reads were normalized and clustered in Seurat (v3.0.2) with the following commands: seurat_obj <- NormalizeData(seurat_obj, normalization.method = "LogNormalize", scale.factor = 10000); seurat_obj <- FindVariableFeatures(seurat_obj, selection.method = "mvp", nfeatures = 2000); all.genes <- rownames(seurat_obj); seurat_obj <- ScaleData(seurat_obj, features = all.genes); seurat_obj <- RunPCA(Seurat_obj, features = VariableFeatures(object = seurat_obj)); seurat_obj <- FindNeighbors(seurat_obj, dims = 1:14); seurat_obj <- FindClusters(seurat_obj, resolution = 0.175).
Experiment 2:   Relates to donors 4-7 (Samples 7-14).  Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 500 (to remove cells with poor read quality) or greater than 7000 (to remove cells likely to be doublets) were removed. Cells with greater than 60% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-"). For each of the eight libraries, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands: donor_x_region <- NormalizeData(donor_x_region, normalization.method = "LogNormalize", scale.factor = 10000); donor_x_region <- FindVariableFeatures(donor_x_region, selection.method = "vst", nfeatures = 2000).  Integration anchors from the first 20 dimensions of the canonical correlation analysis were used to integrate data with the following commands: CD31.anchors <- FindIntegrationAnchors(object.list = c(donor_4_macula, donor_5_macula, donor_6_macula, donor_7_macula, donor_4_peripheral, donoro_5_peripehral, donor_6_peripheral, donor_7_peripheral), dims=1:20); CD31.combined <- IntegrateData(anchorset = CD31.anchors, dims = 1:20).  Data scaling, principal component analysis, and clustering were performed with the following commands: CD31.combined <- ScaleData(CD31.combined, verbose = FALSE); CD31.combined <- RunPCA(CD31.combined, npcs = 30, verbose = FALSE); CD31.combined <- RunUMAP(CD31.combined, reduction = "pca", dims = 1:20); CD31.combined <- FindNeighbors(CD31.combined, reduction = "pca", dims = 1:20); CD31.combined <- FindClusters(CD31.combined, resolution = 0.5).
Genome_build: hg19
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format. Log-normalized expression values (from GetAssayData(object = seurat_object) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values.

source_name: RPE-choroid

extract_protocol:
In experiment 1, an 8-mm macular centered and an 8-mm peripheral punch of RPE/choroid from the inferotemporal region were acquired from three human donors (Donors 1-3). Tissue was dissociated using the Papain Dissociation System (Worthington Biochemical Corporation, Lakewood NJ). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Single-cell RNA libraries were prepared for sequencing using standard 10X genomics protocols. Briefly, cryopreserved samples from donors 1-3 were thawed, and single cells were captured and barcoded using the Chromium System with the v3 single cell-reagent kit (10x Genomics, Pleasanton CA). Cryopreserved cells from donors 4-7 were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) of the CD31+ cell fraction. The positive cell fraction was passed two times through a 40 mm filter to remove aggregates before immediate single cell capturing and barcoding as described above. Sequencing was performed on pooled libraries using the Illumina HiSeq 4000 platform (San Diego, CA), generating 150 base pair paired-end reads.

tag: enrichment

value: unenriched

tag: donor

value: RPE-choroid

value: periphery

tag: punch-size


title: Peripheral-8mm-rpe-cho-donor-3

description: Sample 6

tag: location


title: Macula-8mm-rpe-cho-donor-2

description: Sample 2

value: macula


title: Macula-8mm-rpe-cho-donor-3

description: Sample 3


title: Macula-8mm-rpe-cho-donor-1

description: Sample 1