title: AM2045-4_S4: High-fat rep4

value: 16 Weeks diet-fed

value: DIO


title: AM2045-6_S6: Low-fat rep2

status: Public on Jan 28 2020

type: SRA

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
quality controls of paired-end reads were assessed using FastQC tools
Adapter sequences and low-quality bases were trimmed using Cutadapt Alignment was performed by using HISAT2
Uniquely mapped paired-end reads were used for subsequent StringTie for abundance estimation
Ballgown was employed for DEA
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix, raw count, tab delimited

molecule: total RNA

organism: Mus musculus

source_name: DC-restricted progenitors from BM

growth_protocol: DC-restricted progenitors (Lin-/c-kit(int)/Sca1(lo)/CD115+/Flt3+; ~50,000 cells) from bone marrow (BM) compartment of high fat (60kcal % fat) & control chow (10 kcal%fat)-fed mic (n=4 per group) were flow-sorted and RNA was isolated.

extract_protocol:
DC-restricted progenitors were flow-sorted directly into lysis buffer and RNA was harvested using Arctus PicoPure RNA isolation kit, quality tested by Bioanalyzer (Agilent)for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NuGen Ovation Solo RNA-Seq System (Mouse part no 0501) protocols

treatment_protocol: The whole transcriptome was amplified and library was constructed using NuGen Ovation Solo RNASeq System; and evaluated on high-sensitivity DNAchip (Agilent) and sequenced on a HiSeq 3000 platform

tag: strain background

tag: age

value: age-&diet-matched control

tag: genotype

value: DIO-Control

tag: tissue

value: DC-restricted progenitors from bone marrow


title: AM2045-3_S3: High-fat rep3


title: AM2045-2_S2: High-fat rep2


title: AM2045-1_S1: High-fat rep1


title: AM2045-5_S5: Low-fat rep1


title: M754_St [A2_St_M754]

city: Munich

first: Tatsiana

last: Aneichyk

address: Josef-Frankl-Strasse 5A

country: Germany

institute: Independent Data Lab

data_processing:
Quality control (QC) assessment of sequence reads was performed using fastQC (v. 0.10.1 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were aligned to mouse reference genome GRCm38 (v. 83) using STAR (v. 2.4.2) with its default parameter settings and --quantMode GeneCounts to generate gene counts
Genome_build: GRCm38 (v. 83)
Supplementary_files_format_and_content: Processed data files consist ENSEMBL gene ID and raw RNA-seq gene counts

molecule: polyA RNA

growth_protocol: All animal procedures were in accordance with the University of Miami Institutional Animal Care and Use Committee and followed the NIH Guidelines, ‘Using Animals in Intramural Research’. Mbd5+/GT and wild-type littermate control mice, on a C57BL/6 genetic background, were housed 2–4 per cage in a temperature- and humidity-controlled room with 12-h light/dark cycle (lights on at 6 am, off at 6 pm). Food and water was available ad libitum.

extract_protocol:
Mouse tissue samples were collected from the cortex, cerebellum and striatum of heterozygous Mbd5+/GT mice and wild-type controls at 8-weeks. Tissues that were previously frozen at -80oC were thawed overnight at -20oC submerged in RNAlater®-ICE Frozen Tissue Transition Solution (ThermoFisher Scientific) enabling easy cutting and extraction of high-quality RNA. RNA from tissues was obtained by lysing in 1mL of Trizol (Invitrogen) using metallic pellets (Qiagen) and a tissue lyser, then mixed with 1/5th volume of chloroform and centrifuged at 200g for 5 minutes. The aqueous phase was collected and mixed with isopropanol and centrifuged to obtain a pellet that was then washed with 75% ethanol and air dried and resuspended in RNAse-free water. Each tissue type was collected on the same day to avoid batch effects.
The RNAseq library was prepared as previously described (Aneichyk et al 2018).

treatment_protocol: A C57BL/6 background mouse model carrying an insertional mutation in the Mbd5 locus (B6;CB-Mbd5Gt(pU-21B)205Imeg) was previously generated at the Institute of Resource Development and Analysis (IRDA), Kumamoto University, using a gene-trap construct pU-21B that randomly inserted into the second intron in embryonic stem cells from the line Ayu21-B205. The insertional mutation creates a hypomorphic allele with (Figure 1A) Mbd5 expression reduced  sufficiently to produce neurodevelopmental abnormalities in heterozygous mice and perinatal lethality in homozygous mice  (Camarena et al, 2014). For this study, we used 10 Mbd5+/GT mice and 8 wild-type mice at 8 weeks of age.

tag: litter

tag: gender

value: F

value: wild type (wt)

value: striatum (St)


title: M757_St [D2_St_M757]


title: M755_St [B2_St_M755]

value: Mbd5 heterozygous deletion (het)


title: M756_St [C2_St_M756]


title: M753_St [C1_St_M753]

value: M


title: M757_Cx [H6_Cx_M757]

value: cortex (Cx)


title: M752_St [B1_rep_St_M752]


title: M755_Cx [F6_Cx_M755]


title: M751_St [A1_rep_St_M751]


title: M756_Cx [G6_Cx_M756]


title: M753_Cx [G5_Cx_M753]


title: M754_Cx [E6_Cx_M754]


title: K562-HiCoP1

status: Public on Jan 29 2020

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

country: China

institute: Southern Medical University

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
CoP, ATAC-seq and HiCoP rawdata were filtered by fastp(version 0.19.6) with default parameters.
CoP and ATAC-seq reads were mapped to the hg19 (or mm10) genome assembly using bowtie2 (version 2.20.8) with parameters (-X 2000, --sensitive);
Uniq mapped CoP and ATAC-seq reads pairs were got after pcr duplication removing by Picard (version version 2.20.8) and samtools (version 1.3.1);
RPKM normalized BigWig files of CoP and ATAC-seq were generated by BEDtools (version 2.26.0);
BroadPeaks of CoP and ATAC-seq were called from Bam file by using MACS2 (version 2.1.3.3) with parameters (--nomodel, --extsize 147, -q 0.01).
HiCoP reads were aligned to the hg19 genome assembly and filtered by using HiCPro (version 2.11.1) with default parameters;
Hic file of HiCoP were transfer from HiCPro result by using Juicertools (version 1.13.02);
HiCoP interactive loops were identified by FitHiC (version 2.0.7)  with parameters (distUpThres=1000000, disLowThres=20000, noofBins=100, noOfPasses=2) at resolution 10kb.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: bigwig files; broakpeak file (bed format); hic file;

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Jurkat cells were grown in RPMI-1640 medium containing 10% fetal bovine serum at 37°C and 5% CO2. K562 cells were grown in IMDM medium containing 10% fetal bovine serum at 37°C and 5% CO2, and HL-60 cells were grown in IMDM medium containing 20% fetal bovine serum at 37°C and 5% CO2.

extract_protocol:
For mouse CoP, thymus, spleen and kidney were removed,cells were filtered through nylon mech. Red cells were lysed in AcK buffer.Cells were crosslinked,lysates of CoP sample were clarified from sonicated nuclei and open chromatin were isolated with DNA purification column.
For K562 CoP, cells were crosslinked,open chromatin were isolated with DNA purification column from sonicated nuclei.
For K562 Hi-CoP, cells were crosslinked,digested and ligated. After sonication, open chromatin were isolated with DNA purification column.
For mouse ATAC, thymus was removed,cells were filtered through nylon mech. Red cells were lysed in AcK buffer.Cells were perforated and dealed with Tn5, open chromatin were isolated with DNA purification column.
The CoP libraries were prepared by either Tn5 tagmentation or linker ligation. Tagmentation was done with TransNGS Tn5 DNA Library Prep kit for Illumina following the manufacturer’s recommendations. The reaction was incubated 5 min at 55 ºC followed by adding 30μl of 2x Tn5 Digestion Mix and incubated 5min at 55ºC, then purified with MagicPure Size Selection DNA Beads and elution in21 μL of water. After that, library (20 μL)was amplified by using TransNGS Library Amplification SuperMix. Alternatively, end repair and dA tailing were done with VAHTSTM Universal End preparation Module for Illumina. DNA was purified with VAHTS DNA Clean beads. Added adapter by Quick ligase, then library was amplified with PCR amplification kit. After 5 cycles of amplification, qPCR was done to determine additional cycle number. After library amplification, purification and size selection, library concentration was detected by Qubit. The libraries were sequenced by HiseqXten-PE150 Illumina sequencing platform in Novogene Corporation Inc.
Hi-CoP libraries were prepared using in-situ HiC protocol. Dynabeads MyOne Streptavidin C1 beads was washed once with 1×Tween Washing Buffer. The beads were added to HiCoP DNA and incubated at RT for 15 min with rotation. The beads were washed by adding 200μl of 1×TWB. Heat the tubes on a Thermomixer at 55°C for 2 min with mixing. The beads were reclaimed using a magnet, supernatant was discarded. Repeat washing. End-repair and dA tailing following the in situ Hi-C protocol, adapters were added to DNA fragments. PCR amplification was performed with thirteen to nineteen cycles using Illumina primers.
ATAC library was prepared according to Vazyme's instructions accompanying the TruePrep DNA Library Prep Kit V2 for Illumina (#TD501).

tag: strain

value: Cell line

value: wild type


title: M751_Cx [E5_Cx_M751]


title: d3IR2

city: Ann Arbor

first: Amanda

middle: Katherine

last: Huber

state: MI

address: 1000 Wall Street

department: Computational Medicine and Bioinformatics

institute: University of Michigan

description: Tibialis anterior was harvested 3 days after injury, and digested using type I collagenase and dispase. Total cellular isolates were submitted for sequencing.

data_processing:
Cell Ranger Single Cell Software Suite 1.3 was used to perform sample de-multiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core
A total of ~200 million reads were generated from the 10X Genomics sequencing analysis for each of the replicates. The sequencing data was first pre-processed using the 10X Genomics software Cell Ranger (10x Genomics Inc., Pleasanton, CA, USA) and aligned to mm10 genome. For quality control, genes expressed in fewer than 10 cells, and cells expressing fewer than 500 genes per cell, or more than 20% mitochondrial UMI content, or UMI content >60,000 were filtered out. Replicates from the same group (condition) were pooled together for downstream analysis. The case group consisted of 7718 cells and 14466 genes (before quality control, 7718 cells and 19333 genes), while the control group consisted of 2760 cells and 12636 genes (before quality control, 3520 cells and 17730 genes). Downstream analysis steps were performed using Seurat pipeline. The downstream analysis steps for each sample type include normalization, scaling, dimensionality reduction (PCA, and t-SNE), unsupervised clustering, cluster consolidation via centroid rank correlation analysis, discovery of differentially expressed cluster specific markers, and marker enrichment.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger mtx

source_name: day 3 IR/CTX injury

extract_protocol:
Day 0 and post-surgery day 3,  the tibialis anterior was harvested tissue samples were digested for 45 minutes in 0.3% Type 1 Collagenase and 0.4% Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation at 120rpm. Digestions were subsequently quenched with 10% FBS RPMI and filtered through 40μm sterile strainers. Cells were then washed in PBS with 0.04% BSA, counted and resuspended at a concentration of ~1000 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were processed for further sequencing.
Single-cell 3’ library generation was performed on the 10x Genomics Chromium Controller following the manufacturers protocol for the v2 reagent kit (10X Genomics, Pleasanton, CA, USA). Cell suspensions were loaded onto a Chromium Single-Cell A chip along with reverse transcription (RT) master mix and single cell 3’ gel beads, aiming for 2000-6000 cells per channel. In this experiment, 8700 cells were encapsulated into emulsion droplets at a concentration of 700-1200 cells/ul which targets 5000 single cells with an expected multiplet rate of 3.9%. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting Post GEM-RT product was cleaned up using DynaBeads MyOne Silane beads (ThermoFisher Scientific, Waltham, MA, USA).  The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA, USA) cleaned and quantified then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup is performed after end repair and A-tailing.  Another single-sided cleanup is done after adapter ligation.  Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by Kapa qPCR for Illumina Adapters (Roche) and size was determined by Agilent tapestation D1000 tapes. Read 1 primer sequence are added to the molecules during GEM incubation. P5, P7 and sample index and read 2 primer sequence are added during library construction via end repair, A-tailing, adaptor ligation and PCR. Libraries were generated with unique sample indices (SI) for each sample.
Libraries were sequenced on a HiSeq 4000,  (Illumina, San Diego, CA, USA) using a HiSeq 4000 PE Cluster Kit (PN PE-410-1001) with HiSeq 4000 SBS Kit (100 cycles, PN FC-410-1002)reagents, loaded at 200 pM following Illumina’s denaturing and dilution recommendations.   The run configuration was 26 x 8 x 98 cycles for Read 1, Index and Read 2, respectively.

treatment_protocol:
10ul of cardiotoxin (3mg/mL) were injected from proximal to distal along the length of the left tibialis anterior muscle. Superficial femoral artery and vein were isolated from the nerve just distal to the profunda femoris and clamped for 3 hours with an Ackland clamp. After 3 hours the clamps were removed and incisions formally closed.
Mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. The left leg and groin were de-epilated using Nair ointment and cleansed. 10ul of cardiotoxin (3mg/mL) were injected from proximal to distal along the length of the left tibialis anterior muscle. An incision was made at the groin crease and groin fat pad retracted to exposed the femoral vessels. Superficial femoral artery and vein were isolated from the nerve just distal to the profunda femoris takeoff and occluded with an Ackland clamp. The incision was closed temporarily and mice were kept in a warmed anesthetic chamber for 3 hours at which point clamps were removed and incisions formally closed.

tag: agent

value: 10ul of cardiotoxin (3mg/mL)

value: Tibialis anterior

tag: group

value: day 3 IR/CTX injury


title: d0IR1

description: Tibialis anterior was harvested and digested using type I collagenase and dispase. Total cellular isolates were submitted for sequencing.

source_name: day 0 control

treatment_protocol:
Day 0 controls. No treament was performed
Mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. The left leg and groin were de-epilated using Nair ointment and cleansed. 10ul of cardiotoxin (3mg/mL) were injected from proximal to distal along the length of the left tibialis anterior muscle. An incision was made at the groin crease and groin fat pad retracted to exposed the femoral vessels. Superficial femoral artery and vein were isolated from the nerve just distal to the profunda femoris takeoff and occluded with an Ackland clamp. The incision was closed temporarily and mice were kept in a warmed anesthetic chamber for 3 hours at which point clamps were removed and incisions formally closed.

value: day 0 control


title: d0IR2


title: d3IR1


title: 14209X11

city: Salt Lake City

first: Edwin

last: Lin

address: 50 N medical dr

institute: University of Utah

data_processing:
FASTQC
KALLISTO
TAXONOMER
DESEQ2
Genome_build: Ensembl human cDNA transcripts (release 91)
Supplementary_files_format_and_content: txt.gz read counts

extract_protocol:
Pure FFPET RNA Isolation kit (Roche, Indianapolis, IN).
Illumina TruSeq Stranded Total RNA Sample Prep protocol prior to cDNA library preparation
An Illumina HiSeq 2500 instrument was used to sequence the PCR amplified libraries using 50-cycle single-read chemistry.

tag: subject id

tag: subject status

value: control

value: lung


title: M757_Cb [F4_Cb_M757]

value: cerebellum (Cb)


title: M755_Cb [D4_Cb_M755]


title: M754_Cb [C4_Cb_M754]


title: d3IR3


title: 14209X8


title: 14209X7


title: M768_St [H1_St_M768]


title: M764_St [D1_St_M764]


title: M752_Cb [D3_Cb_M752]


title: M766_St [F1_St_M766]


title: M765_St [E1_St_M765]


title: M752_Cx [F5_Cx_M752]


title: 14209X9

value: Eosinophilic granulomatosis with polyangiitis (EGPA)


title: M751_Cb [C3_Cb_M751]


title: 14209X3


title: M768_Cx [D6_Cx_M768]


title: 14209X1


title: M756_Cb [E4_Cb_M756]


title: M767_Cx [C6_Cx_M767]


title: M766_Cx [B6_Cx_M766]


title: M766_Cb [H3_Cb_M766]


title: M764_Cx [H5_Cx_M764]


title: M768_Cb [B4_Cb_M768]


title: M765_Cx [A6_Cx_M765]


title: M753_Cb [E3_Cb_M753]


title: M765_Cb [G3_Cb_M765]


title: M764_Cb [F3_Cb_M764]


title: M767_Cb [A4_Cb_M767]


title: M760_St [G2_St_M760]


title: M762_St [A3_St_M762]


title: M763_St [B3_St_M763]


title: M759_St [F2_St_M759]


title: M767_St [G1_St_M767]


title: 14209X6


title: M758_St [E2_St_M758]


title: M761_St [H2_St_M761]


title: M760_Cx [C7_Cx_M760]


title: M763_Cx [F7_Cx_M763]


title: M763_Cb [D5_Cb_M763]


title: M761_Cx [D7_Cx_M761]


title: M762_Cb [C5_Cb_M762]


title: M759_Cx [B7_Cx_M759]


title: M758_Cx [A7_Cx_M758]


title: M760_Cb [A5_Cb_M760]


title: M758_Cb [G4_Cb_M758]


title: M761_Cb [B5_Cb_M761]


title: N2A + LbCas12a + mouse Optimization Library

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
FASTQ files were pre-processed to extract Cas9 or Cas12a guide sequence using a bespoke Perl script.
The Cas12a guide was extracted from read1 files as the 23 bases preceeding 'ATCTAC', while Cas9 guide sequence was extracted from read2 files as the 20 bases proceeding 'GTTT'.
Trimmed FASTQ files were then aligned to the appropriate FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> -2 <trimmed_read2.fastq> aligned.sam
The number of reads aligning to each dual-guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Dual-guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.

source_name: dual-guide amplicon

growth_protocol: Human HAP1 cells were maintained in low glucose (10 mM), low glutamine (1 mM) DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin. Human hTERT-RPE1 cells were maintained in DMEM with high glucose and pyruvate supplemented with 10% FBS and 1% Penicillin/Streptomycin. CGR8 mouse embryonic stem cells (mESC) were grown in gelatin-coated plates in GMEM supplemented with 100 μM β-mercaptoethanol, 0.1 mM nonessential amino acids, 2 mM sodium pyruvate, 2 mM L-glutamine, 5,000 units/mL penicillin/streptomycin, 1,000 units/mL recombinant mouse LIF and 15% ES fetal calf serum. Mouse neuroblastoma Neuro-2A (N2A) cells were grown in DMEM with high glucose supplemented with 10% FBS, sodium pyruvate, non-essential amino acids, and penicillin/streptomycin.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega).
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared in two PCR steps, the first to enrich guide-RNA regions from the genome, and the second to amplify guide-RNA and attach Illumina TruSeq adapters with i5 and i7 indices.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: non-treated; 2.5 mM thymidine; 6 µM 6-thioguanine; Torin1 treatment was performed at a concentration that causes a 60% reduction in cell growth (i.e. IC60).

tag: cell line

tag: cas protein

tag: crispr library

value: CHyMErA Mouse Optimization Libary

tag: treatment

value: non-treated

tag: library file

tag: annotation file


title: CGR8 + AsCas12a + mouse Optimization Library


title: DE3

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: EAU retinal endothelial cells pool 3

data_processing:
The multiplexed libraries were loaded, and sequences were produced using a TruSeq PE cluster and SBS-kit on a HiSeq 1500 (Illumina).
Approximately 25 million paired-end reads/sample were mapped against the mouse reference genome (NCBI Build 37/ UCSC mm9) using STAR software to generate read alignments for each sample.
Expression levels were quantified using the featureCounts(9) tool and the UCSC RefSeq gene annotation as a reference (exons only, genes as meta features).
Differential analysis between groups was performed using the EdgeR package (quasi-likelihood F-tests). Normalized expression levels were estimated using the EdgeR rpm function and converted to log2 FPKM (fragments per kilobase of exon per million mapped reads) after resetting low FPKMs to 1.
Genome_build: NCBI Build 37/ UCSC mm9
Supplementary_files_format_and_content: Excel file include CPM values (Log2) for each sample

source_name: Retinal endothelial cells

extract_protocol:
RNA extraction was performed using the MiRNeasy MicroKit (Qiagen) according to the manufacturer’s recommendations and a DNase step to avoid DNA contamination.
Indexed cDNA libraries were prepared using the Ovation SoLo RNAseq system (Nugen).

tag: disease state

value: Experimental autoimmune uveitis

value: Retina

tag: cell type

value: Retinal endothelial cells


title: DE4

description: EAU retinal endothelial cells pool 4


title: M762_Cx [E7_Cx_M762]

value: F

tag: genotype

value: wild type (wt)


title: NE3

description: Naive retinal endothelial cells pool 3

value: Naive

tag: tissue


title: DE1

description: EAU retinal endothelial cells pool 1


title: DE2

description: EAU retinal endothelial cells pool 2


title: NE2

description: Naive retinal endothelial cells pool 2


title: DR4

description: EAU retinal cells pool 4

source_name: Total retinal cells

value: Total retinal cells


title: NE1

description: Naive retinal endothelial cells pool 1


title: CGR8 + LbCas12a + mouse Optimization Library


title: Knockdown 2% O2, rep3

city: Helsinki

first: Juha

middle: Mikael

last: Saarikettu

address: Viikinkari 1

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

data_processing:
BGI (Beijing Genome Institute, Hong Kong) internal software SOAPnuke was used to remove adaptor reads, reads that contain more than 5% unknown bases and low quality reads. The impurities in the raw data were removed, including 5' primer contaminants, no-insert tags, oversized insertion tags, low quality tags, poly-A tags and small tags, and tags without 3' primer.
The resulting reads in FASTQ format were aligned  to the Drosophila melanogaster genome (genome assembly BDGP6.92) using TopHat2.
Quantification of reads per gene was performed using the HTseq tool.
Cufflinks was used for retrieving the FPKM values
Genome_build: BDGP6.92
Supplementary_files_format_and_content: Excel files including FPMK values for each sample.

organism: Drosophila melanogaster

source_name: Whole fly

growth_protocol: The flies were maintained on a standard mashed potato diet at 25°C

extract_protocol:
Trizol extraction
The total-RNA samples were purified using poly-dT oligo attached magnetic beads. The mRNA was cleaved using elevated temperature and divalent cations and reverse transcribed to first strand cDNA followed by second strand cDNA synthesis using DNA polymerase I and RNAse H. The synthesized cDNA was subjected to end-repair and then 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments and the fragments were PCR amplified. Samples were pooled together to make a single strand DNA circle (ssDNA circle), giving the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process.  The libraries were sequenced at BGI (Beijing Genome Institute, Hong Kong) using BGISEQ-500 instrument.

treatment_protocol: The flies were exposed to either 2% or 6% oxygen for 6 hours, or kept at normal atmospheric oxygen

value: w;;Da-GAL4/UAS-Tudor-SN RNAi

tag: RNAi line

value: Bloomington #34865

value: female

tag: age

value: 1-5 days


title: M759_Cb [H4_Cb_M759]

tag: litter

tag: gender


title: MEFdT

type: genomic

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

description: MEFdT_MeDIP_ChIP array

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Agilent Scanner G2505C scanner according to manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for NimbleScan v2.5 ChIP data extraction.
scaled, log2 (ChIP/Input) ratio

source_name: Thymidine-induced MEFs by CD45 sorting

label_protocol: The purified DNA was quantified using a nanodrop ND-1000, labeled by the NimbleGen Dual-Color DNA labeling Kit and array hybridized according to the manufacturer’s protocol (Nimblegene Systems, Inc., Madison, WI, USA)

growth_protocol: Mouse embryonic fibroblasts (MEFs) were obtained at E14.5 embryos and supplied with Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) with 15% FBS, 100 μg/ml streptomycin and 100 U/ml penicillin. Potential hematopoietic progenitor cells (CD45+CD41+CD31+c-Kit+) were negatively selected with Biotin labeled anti-CD45, anti-CD31, anti-CD41 and anti-c-Kit antibodies by magnetic beads.Hereafter, treated MEFs are referred to as 4neg MEFs for initiation of induction.

extract_protocol: DNA samples were sheared into 200-1000 bp fragments by Bioruptor sonicator (Diagenode). Sonicated genomic DNA was immunoprecipitated by anti-5-methylcytosine antibody (Diagenode) followed by purification using Qiagen MinElute columns.

treatment_protocol: 4neg MEFs were seeded on mitomycin (MMC)-treated MEFs as feeder cells and cultured in DMEM with 15% FBS, 100  μg/ml streptomycin, 100 U/ml penicillin, 2 mM L-glutamine, 0.1 mM non-essential amino acids and 100 μM thymidine as induction medium for 2 days

value: MEFs

tag: agent

value: thymidine

tag: anti-body

tag: strain

source_name: mouse embryonic fibroblasts

tag: chip antibody

value: none, input


title: DR3

description: EAU retinal cells pool 3


title: Knockdown 6% O2, rep3


title: RPE1 + LbCas12a + ExonDeletion Library

tag: cell line

tag: cas protein

value: CHyMErA Exon-Deletion Library


title: DR1

description: EAU retinal cells pool 1


title: RPE1 + LbCas12a + DualTargeting Library

tag: crispr library

value: CHyMErA Dual-Targeting & Paralog Library

tag: treatment


title: Knockdown 2% O2, rep1


title: Knockdown 6% O2, rep2


title: NR3

description: Naive retinal cells pool 3


title: HAP1 + LbCas12a + DualTargeting Library + Torin1

tag: library file

tag: annotation file


title: NR2

description: Naive retinal cells pool 2

tag: disease state

tag: cell type


title: HAP1 + LbCas12a + DualTargeting Library

value: non-treated


title: Knockdown 6% O2, rep1

tag: genotype


title: Knockdown normoxia, rep3

tag: RNAi line


title: HAP1 + LbCas12a + Optimization Library + Thymidine Block

value: CHyMErA Human Optimization Libary

value: double thymidine block


title: Knockdown normoxia, rep2

tag: age


title: NR1

description: Naive retinal cells pool 1

tag: tissue

value: Retina


title: HAP1 + LbCas12a + Optimization Library


title: Control 2% O2, rep3

value: w;;+/UAS-Tudor-SN RNAi

tag: gender


title: DR2

description: EAU retinal cells pool 2

value: Experimental autoimmune uveitis


title: Knockdown 2% O2, rep2


title: Knockdown normoxia, rep1


title: Control 2% O2, rep2


title: Control 2% O2, rep1


title: NR4

description: Naive retinal cells pool 4

value: Naive


title: Control 6% O2, rep2


title: Control normoxia, rep3


title: Control 6% O2, rep3


title: Control 6% O2, rep1


title: Control normoxia, rep2


title: Control normoxia, rep1


title: HAP1 + AsCas12a + Optimization Library


title: Liver Snd1 KO rep 3

data_processing:
The data processing was done at the Beijing Genome Institute (BGI), Hong Kong.
The impurities in the raw data were removed, including 5' primer contaminants, no-insert tags, oversized insertion tags, low quality tags, poly-A tags and small tags, and tags without 3' primer.
Bowtie tool was used to map the reads to the reference genome.
Genome_build: GRCm38.92
Supplementary_files_format_and_content: Excel files including TPM values for each sample and chromosomal locations for the non-annoated sequences (named novel_*) .

source_name: Liver, left lobe

growth_protocol: Samples were collected at around noon. The mice were not fasted.

extract_protocol:
Trizol extraction followed by DNA-free DNA removal kit.
The total-RNA was Polyacrylamide separated to obtain 18-30 base RNA fragments. Library preparation included 5’-adenylated, 3’-blocked single-stranded DNA adaptor ligation to 3' end of the RNAs, reverse primer annealing and cross-linking to the 3’-adaptor, and 5’-adaptor ligation. The library was reverse transcribed, PCR amplified and size separated using a polyacrylamide gel for fragment size of 100-120 bp. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA were formatted as the final library. The library was constructed and sequenced at the Beijing Genome Institute (BGI), Hong Kong.

value: Male

value: 8-12 week-old


title: Liver Snd1 KO rep 4


title: Mediterranean_diet_subject_11

city: Seattle

first: Corbin

middle: Scott Clarke

last: Johnson

state: WA

address: 330 Guthrie Hall

department: Department of Psychology

institute: University of Washington

data_processing:
Illumina Generate FASTQ version 1.35.0 used for base calling.
RNA-seq reads were aligned to the Macaca fascicularis reference genome (Macaca_fascicularis_5.0, v 93, Ensembl) assembly using HiSat2 version 2.1.0.
Reads were converted to a sample-by-gene read count matrix using featureCounts within the subread package version 1.6.0.
Genes with median reads per kilobase per million (RPKM) < 1 were removed for further analyses.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for each sample.

organism: Macaca fascicularis

source_name: CD14+ PBMC

extract_protocol:
Blood was collected into EDTA-containing tubes, mixed with an equal amount of PBS without calcium or magnesium, and overlaid on a 90% Ficoll-Paque Plus/10% PBS solution in LeucoSep tubes followed by centrifugation at 800 x g for 20 min. Isolated PBMCs were then immediately used for the collection of CD14+ monocytes by positive selection using a Miltenyi bead-based protocol following manufacturer’s instructions (Miltenyi Biotec, Bergisch Gladbach, Germany). After assessing cell viability and numbers, CD14+ monocytes were stored in 85% FBS, 15% DMSO sterile freezing media at -80°C and transferred to liquid nitrogen for storage until RNA extraction. RNA was extracted from monocytes using the AllPrep DNA/RNA Mini Kit (Qiagen, Inc., Hilden, Germany).
RNA libraries were prepared for sequencing by the Cancer Genomics Shared Resource (Wake Forest University, Winston-Salem, NC) using the TruSeq-stranded total RNA kit (Illumina), which includes a ribosomal depletion step.

value: Peripheral blood

tag: selection

value: CD14 positive selection

tag: estimated age

value: 10 years

tag: diet

value: Mediterranean


title: Western_diet_subject_19

value: 10.2 years

value: Western


title: Mediterranean_diet_subject_12

value: 10.3 years


title: Mediterranean_diet_subject_13

value: 11.2 years


title: Mediterranean_diet_subject_15


title: Western_diet_subject_20


title: Mediterranean_diet_subject_10

value: 10.7 years


title: Mediterranean_diet_subject_14

value: 10.9 years


title: Western_diet_subject_17


title: Mediterranean_diet_subject_6

value: 9.8 years


title: Western_diet_subject_18


title: Western_diet_subject_16

value: 11.8 years


title: Mediterranean_diet_subject_7

value: 10.1 years


title: Mediterranean_diet_subject_8


title: Liver Snd1 KO rep 2

tag: strain


title: Liver Snd1 KO rep 1


title: Western_diet_subject_13


title: Liver WT rep 4


title: Western_diet_subject_15


title: Liver WT rep 3


title: Western_diet_subject_14

value: 11.6 years


title: Liver WT rep 2


title: Western_diet_subject_12

value: 11.7 years


title: Mediterranean_diet_subject_9

value: 12.2 years


title: Mediterranean_diet_subject_4

value: 10.8 years


title: Mediterranean_diet_subject_3

value: Peripheral blood


title: Western_diet_subject_10

value: CD14 positive selection


title: Western_diet_subject_11


title: Western_diet_subject_9


title: Liver WT rep 1

value: Male

value: 8-12 week-old


title: Mediterranean_diet_subject_5

value: 12.3 years

value: Mediterranean


title: Western_diet_subject_5

value: Western


title: Western_diet_subject_6


title: Western_diet_subject_7


title: Control cells with FFSS 1

city: Boston

first: Marc

last: Wein

state: MA

address: 15 Fruit Street

department: Massachusetts General Hospital, Department of Medicine

institute: Harvard Medical School

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
Supplementary_files_format_and_content: htseq_output.txt

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.
Methods per BGI

value: mouse long bone derived osteocytes

value: original cells

value: Fluid Flow Shear Stress (FFSS)

tag: time point

value: 3 hours


title: DKO cells with FFSS 3

value: HDAC4 and HDAC5 deletion cells


title: DKO cells with FFSS 1


title: input DNA

data_processing:
ChIP-seq was performed using a BGISEQ-500 platform.ChIP-seq analysis was completed by BGI company(Shenzhen,China)
Genome_build: mm10
Supplementary_files_format_and_content: MACS-peaks, peak-gene

source_name: ISC cells

growth_protocol: Primary Lgr5+ ISCs were isolated from tamoxifen treated Srcapflox/flox; Lgr5-Cre+ mice (Srcap KO) and Srcap+/+; Lgr5-Cre+ mice (Srcap WT). No in vitro culture were done.

extract_protocol:
Sheared chromatin (sonicated to 200–500 bp) from ISCs (5×105) fixed in 1% formaldehyde was incubated with 4 μg antibody overnight at 4℃ followed by immunoprecipitation with salmon sperm DNA/protein agarose beads. After washing, elution and cross-link reversal, DNA from each ChIP sample and corresponding input sample were purified and prepared followed by library construction and sequenced on  BGISEQ-500 platform (BGI America Co., Cambridge, MA).
Construction of ChIP-seq library was completed by BGI company (Shenzhen,China).

treatment_protocol: Crypts were isolated from Lgr5GFP mice.For ISC isolation, the crypts were dissociated into individual cells with 1x TrypLE express supplemented with 0.8 kU/ml DNaseI (Roche) followed by sorting according to GFP intensity

value: Intestinal stem cell


title: DKO cells with static condition 2

value: STATIC


title: Mediterranean_diet_subject_2

value: 10.2 years


title: Western_diet_subject_8

value: 10.9 years


title: DKO cells with static condition 3


title: Control cells with FFSS 3


title: Western_diet_subject_4

value: 10.3 years


title: Control cells with FFSS 2


title: DKO cells with FFSS 2


title: Mediterranean_diet_subject_1

value: Peripheral blood


title: Western_diet_subject_3

value: CD14 positive selection

value: 11.7 years


title: Control cells with static condition 2


title: SRCAP_ChIPSeq

tag: chip antibody

value: SRCAP (Kerafast, Cat# ESL104


title: Western_diet_subject_1

value: 10.1 years


title: Control cells with static condition 1


title: CRC2M

status: Public on Jan 27 2020

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

description: rRNA depleted RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
Gene annotated in GencodeV25 were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Liver metastasis colon cancer

extract_protocol:
Tissue RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using ribosomal RNA depleted RNA-seq protocols

value: Liver metastasis colon cancer tissue


title: CRC3N

description: rRNA depleted RNA

source_name: Matched normal colon

value: Matched normal colon tissue


title: CRC2T

description: rRNA depleted RNA

source_name: Primary colon cancer

value: Primary colon cancer tissue


title: CRC1N

description: rRNA depleted RNA


title: CRC1M

description: rRNA depleted RNA


title: PC9_4D_72H_R2

city: Amsterdam

first: Evert

last: Bosdriesz

address: De Boelelaan 1111

department: Computer Science

country: Netherlands

institute: VU University Amsterdam

description: 4177_4_pc9_treated_4_drug_combo_72h_rep_2_20-9-2016_GTCCGCA

data_processing:
Reads were mapped using TopHat 2.1 with the following versions/parameters: bowtie 1.1.0, samtools 0.1.19, Library type: fr-firststrand##, transcriptome-index, prefilter-multihits
Gene expression was quantified using HTSeq-count
Genome_build: hg38
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: human NSCLC cell line

growth_protocol: PC9 cells were routinely generated by re-plating twice a week (typically 2–3 × 106 cells into a 15cm dish). Cells were cultured in RPMI medium (Gibco 21875034) supplemented with 10% FBS (Serana), 1% penicillin/streptomycin (Gibco 15140122) and 2 mM L-glutamine (Gibco 25030024). Cells were cultured at 37°C and with 5% CO2.

extract_protocol: Cells were harvested in trizol and RNA was isolated.

treatment_protocol: 2E6 PC9 cells were plated in a 10cm dish and after overnight attachment cells were treated with 7nM gefitinib, 250 nM LY3009120, 8nM trametinib and 250nM SCH772984 (in the case of the treated samples) for the indicated time periods.

tag: driver mutation

value: EGFR

tag: passages

tag: cell line

value: Treated for 72 hrs (7nM gefitinib, 250 nM LY3009120, 8nM trametinib and 250nM SCH772984)


title: CRC2N

description: rRNA depleted RNA


title: CRC3T

description: rRNA depleted RNA


title: CRC1T

description: rRNA depleted RNA


title: PC9_4D_48H_R1

description: 4177_1_pc9_treated_4_drugs_combo_48h_1-9-2016_AGTTCCG

tag: treatment

value: Treated for 48 hrs (7nM gefitinib, 250 nM LY3009120, 8nM trametinib and 250nM SCH772984)


title: DKO cells with static condition 1

value: mouse long bone derived osteocytes

value: HDAC4 and HDAC5 deletion cells

value: 3 hours


title: Control cells with static condition 3

value: original cells

value: STATIC


title: BG3-c2_MNase_med_illumina

city: Planegg-Martinsried

first: Sandro

last: Baldi

address: Großhaderner Strasse 9

department: BMC Molecular Biology

institute: LMU Munich

data_processing:
base-calling for nanopore sequencing: Albacore software
mapping of nanopore reads: Graphmap v0.3.0
mapping of Illumina reads: bowtie 1.1.1, -X=1500
conversion from bam files to .bed files: 1. BEDtoools v2.22.0: bamToBed -bedpe 2. Reduce .bed file to chr/start/stop columns
Genome_build: dm3
Supplementary_files_format_and_content: .bed files were generated by converting the mapped reads in .bam format to .bed intervals

source_name: medium MNase concentration used for digest

growth_protocol: BG3-c2  cells were cultured at 26°C in Schneider’s Drosophila Medium (Gibco) including 10% fetal calf serum (FCS), Penicillin-Streptomycin (and for BG3-c2 cells also 10 µg/ml human insulin)

extract_protocol:
1-2 x 108 cells were harvested by centrifugation (500 x g, 5 min), washed in 15 ml cold PBS, and resuspended in 1 ml lysis buffer (15 mM HEPES pH 7.6, 0.1 mM EGTA, 1 mM EDTA, 0.15 mM spermine, 0.5 mM spermidine, 1x Protease Inhibitor cocktail (Roche)). After 1 min incubation on ice, 176 µl of 10% NP-40 was added, gently vortexed, and the cells again incubated on ice for 5 min. The released nuclei were spun down at 4°C and 1000 rpm (100 x g) for 10 min. They were then washed with 1 ml MNase buffer (10 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 2 mM CaCl2, 0.15 mM spermine, 0.5 mM spermidine) and centrifuged again (4°C, 100 x g, 10 min). The nuclei were resuspended in 1 ml MNase buffer, and distributed into five aliquots of 200 µl. Different amounts of MNase (Sigma-Aldrich) were added to the five tubes. The exact amounts depend on MNase batches and conditions and should be determined empirically. In a typical experiment, we prepared a stock solution of 1.2 x 10-3 U MNase/µl and added 1, 2, 4, 8 or 16 µl of this stock solution to the 200 µl aliquots. The chromatin was then digested for 20 min at 37°C. Digestion was stopped by transferring the tubes to ice and adding 5 µl 0.5 M EGTA. To digest proteins, 12 µl of 10% SDS and 100 µg of Proteinase K (Bioline) were added and the chromatin was incubated at 50°C for 1 h. After nucleic acids were extracted with 1 volume of phenol-chloroform-isoamyl alcohol mixture (PVA, 25:24:1, Invitrogen), 50 µg RNase A was added to digest RNA at 37°C for 30 min. DNA was extracted with 1 volume of PVA. DNA was precipitated in presence of 10 µg glycogen (Roth) by adding 1/10 volume of 3 M NaOAc and 2.5 volume. EtOH and incubation for 1h or overnight at -20°C. The precipitated DNA was pelleted at 4°C and 16,000 x g for 30 min and washed with 300 µl 70% EtOH. Pellets were shortly dried (5 min) and dissolved in 21 µl TE buffer.  1 µl of each sample was run on an Agilent Bioanalyzer 1000 DNA chip to determine degree of digestion.
Nanopore sequencing: Partially MNase-digested chromatin retaining contiguous oligonucleosomes was used for generation of libraries for nanopore sequencing. 1 µg of purified DNA was end-repaired and A-tailed with the NEBnext UltraII end repair module (New England Biolabs, Ipswich, USA), purified with Ampure XP beads (Beckman-Coulter, Brea; USA) and ligated to AMX adapter from the Oxford Nanopore 1D sequencing Kit (SQK-LSK108, Oxford Nanopore Technologies, Oxford, UK) using NEB Blunt/TA ligase mastermix. Excess adapters were removed by adding 0.5 volumes of Ampure XP beads and washing with ABB buffer from the 1D sequencing kit. Illumina sequencing: 10 µl of DNA from partially MNase-digested chromatin was run on an 11 cm 1.2 % agarose gel in 0.5x TAE buffer at 70 V and stained with ethidium bromide. The tetranucleosomal band was cut out and purified (Gel and PCR Clean Up Kit, Macherey-Nagel). 80 ng DNA was used for library preparation with the Diagenode iDeal library preparation kit.

value: larval L3, central nervous system

tag: molecule subtype

value: total MNase-digested chromatin


title: PC9_4D_48H_R2

description: 4177_5_pc9_treated_4_drug_combo_48h_rep_2_19-9-2016_GTGAAAC


title: BG3-c2_MNase_high_illumina

source_name: high MNase concentration used for digest


title: PC9_UNT_R1

description: 4177_2_pc9_untreated_48h_1-9-2016_ATGTCAG

value: Untreated


title: BG3-c2_MNase_low_nanopore

source_name: low MNase concentration used for digest


title: BG3-c2_gDNA_nanopore

source_name: total genomic DNA purified with Qiagen Blood & Tissue Kit

value: total genomic DNA  (without histones)  digested with micrococcal nuclease


title: PC9_4D_72H_R1

description: 4177_3_pc9_treated_4_drugs_combo_72h_2-9-2016_CCGTCCC


title: Western_diet_subject_2

value: Peripheral blood

value: CD14 positive selection

value: 10.9 years

value: Western


title: BG3-c2_MNase_high_nanopore


title: BG3-c2_MNase_low_illumina


title: BG3-c2_MNase_med_nanopore


title: CRC3M

description: rRNA depleted RNA

value: Liver metastasis colon cancer tissue


title: PC9_UNT_R2

description: 4177_6_pc9_untreated_48h_rep_2_19-9-2016_ATCACGA

value: EGFR


title: CW99-003-F-33

status: Public on Jan 26 2020

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Environmental and Occupational Health

institute: University of Pittsburgh

data_processing:
FASTQ TO BAM
FEATURECOUNTS
EDGER
Genome_build: hg38
Supplementary_files_format_and_content: batch corrected counts from featureCounts

source_name: brain

extract_protocol:
All samples were provided by the University of Pittsburgh Alzheimer’s Disease Research Center (ADRC) brain bank and the Sanders-Brown Center on Aging at the University of Kentucky. Braak staging was performed on Bielschowsky-stained sections. APOE allelic polymorphism was determined by a PCR-based assay. Gray matter samples of APOEε2/3, APOEε3/3, APOEε3/4, and APOEε4/4 genotypes from the right inferior parietal lobule were dissected and used for further processing.
RNA isolation and purification were performed using RNeasy mini kit (Qiagen). To increase sample purity, rRNA was removed with Ribo-Zero Gold rRNA Removal Kit (Illumina) and libraries were generated using mRNA Library Prep Reagent Set (Illumina) with the incorporation of barcodes for multiplexing. A targeted size selection was performed using Pippin Prep (Sage Science), the quality of the libraries was assessed on a 2100 Bioanalyzer (Agilent) and sequenced on Illumina HiSeq 2000 at the Functional Genomics Core, University of Pennsylvania, Philadelphia, PA.

value: brain

tag: Sex

value: F

tag: apoe


title: CW98-030-F-33


title: CW97-041-F-34


title: CW95-044-F-44


title: CW15-023-M-34

value: M


title: CW13-020-F-34


title: CW14-012-M-44


title: CW13-018-M-34


title: CW15-020-M-34


title: CW13-002-M-33


title: CW12-004-F-33


title: CW11-002-M-44


title: CW12-002-F-34


title: CW02-016-F-33


title: CW10-016-M-33


title: CW04-017-M-44


title: CW06-017-M-34


title: 866-M-23


title: CW13-014-M-34


title: CW06-013-M-33


title: CW01-031-F-34


title: CW01-004-M-33


title: 983-F-33


title: CW98-037-F-34


title: DR5

description: EAU retinal cells pool 5

source_name: Total retinal cells

tag: disease state

value: Experimental autoimmune uveitis

value: Retina

tag: cell type

value: Total retinal cells


title: CW15-021-F-34

tag: tissue


title: 1244-F-23


title: 1253-F-23


title: 1222-M-23


title: 1212-M-34


title: 1213-M-34


title: CW00-019-M-33


title: 1202-F-34


title: 1200-F-23


title: 1199-M-34


title: 1196-F-34


title: 1185-F-44


title: 1168-F-33


title: 1174-M-23


title: 1068-F-23


title: BMP9 overexpression [CV-6pos]

city: Montreal

first: claire

last: viallard

state: QC

address: 5690 rosemont boulevard

institute: HMR

description: IonXpress_031.CV-6pos.2019-09-12T16_12_50Z

data_processing:
Ion Proton sequencing platform
Gene expression levels were calculated using Torrent-Suite 5.12.0 software
Genome_build: mm10
Supplementary_files_format_and_content: RPM values for each Sample

source_name: BMP9 overexpression_LLC tumors

growth_protocol: To initiate tumors, LLC (control or BMP-overexpressing) cells were  injected subcutaneously into the lateral flank of C57/Bl6 mice

extract_protocol:
After 2 week, tumors were removed, dissociated and stained with CD31. CD31 cells were isolated by FACS.  RNA was harvested using PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific)
Libraries were prepared for sequencing using the Ion AmpliSeq Transcriptome Mouse Gene Expression Kit for Ion Torrent (Thermo Fisher Scientific)
Ampli-Seq Gene Expression Panel

tag: host strain

tag: source cell type

value: Lewis Lung Carcinoma (LLC) cells

tag: genotype/variation

value: BMP9 overexpression

value: LLC tumors

value: CD31 positive cells


title: Control [CV-2pos]

description: IonXpress_024.CV-2pos.2019-09-12T13_26_08Z

source_name: Control_LLC tumors

value: Control


title: Control [CV-3pos]

description: IonXpress_027.CV-3pos.2019-09-12T13_26_08Z


title: BMP9 overexpression [CV-5pos]

description: IonXpress_029.CV-5pos.2019-09-12T16_12_50Z


title: N2A + AsCas12a + mouse Optimization Library

source_name: dual-guide amplicon

tag: cas protein

tag: crispr library

value: CHyMErA Mouse Optimization Libary

value: non-treated

tag: library file

tag: annotation file


title: Control [CV-1pos]

description: IonXpress_020.CV-1pos.2019-09-12T13_26_08Z


title: 1064-F-23


title: BMP9 overexpression [CV-4pos]

description: IonXpress_021.CV-4pos.2019-09-12T13_26_08Z


title: STARR B73 DNA scaled

status: Public on Jan 25 2020

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Library strategy: STARR-seq
STARR-seq: analysis was performed by bowtie1.2.2 and bedtools
Genome_build: Zea mays assembly AGP.v4 reference genome
Supplementary_files_format_and_content: STARR tab delimited text file, see "STARR_column_header_descriptions.txt" for column headers

organism: Zea mays

source_name: B73 leaf

growth_protocol:
There are two separate growth protocols—one for the second leaf and one for the ear primordia.  For both samples, plants were grown from seed collected from field-grown ears grown during the summer of 2017 in Athens, Georgia.
Second leaf protocol: kernels were sown in Sungro Horticulture professional growing mix (Sungro Horticulture Canada Ltd., 52130 RR 65, P.O. Box 189, Seba Beach, AB T0E 2B0 Canada) approximately 0.5 inches below the soil surface.  Soil was saturated with tap water and placed under a 50/50 mixture of 4100K (Sylvania Supersaver Cool White Delux F34CWX/SS, 34W) and 3000K (GE Ecolux w/ starcoat, F40CX30ECO, 40W) light.  The photoperiod was 16 hours of light, eight hours of dark.  The temperature was approximately 25°C during light hours. The relative humidity was approximately 54%.  Seedlings were grown for approximately six days and harvested from four to six hours after photoperiod dawn.  Seedlings were harvested when the V1 leaf had emerged two to three centimeters above the apical tip of the coleoptile. The seedlings were cut approximately three millimeters above the coleoptile-mesocotyl boundary, excluding the shoot apical meristem, and the V2 leaf was removed from within the sheath of the V1 leaf.  Only the inner V2 leaves were used for experiments.
Ear primordia protocol: Plants were grown in greenhouse or field conditions.  Plants were harvested approximately one month after sowing and ear primordia were dissected from shoots. Ear primordia were harvested from any node of the shoot if they were within the desired size range: between 3 to 8 millimeters from the base to the apical tip of the ear.

extract_protocol: STARR-seq libraries were prepared as described in the main text.

tag: line

value: 7-day-old 2nd leaf


title: STARR B73 RNA


title: 1219-F-33


title: STARR B73 DNA high


title: HiChIP B73 leaf H3K4me3

data_processing:
Library strategy: HiChIP-seq
HiChIP-seq: analysis was performed by HiC-pro v2.8.0 and FitHiChIP v7.1
Genome_build: Zea mays assembly AGP.v4 reference genome
Supplementary_files_format_and_content: HiChIP tab delimited text file, see "HiChIP_column_header_descriptions.txt" for column headers

extract_protocol: HiChIP libraries were prepared following the HiChIP protocol described in (Mumbach et al. 2016) with modifications described in the main text.


title: 1209-M-44


title: HiChIP B73 leaf H3K27me3

data_processing:
Library strategy: HiChIP-seq
HiChIP-seq: analysis was performed by HiC-pro v2.8.0 and FitHiChIP v7.2
Genome_build: Zea mays assembly AGP.v4 reference genome
Supplementary_files_format_and_content: HiChIP tab delimited text file, see "HiChIP_column_header_descriptions.txt" for column headers


title: GDPOL1-5-100m

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

description: Whole Genome Sequencing

data_processing:
bowtie2 (version 2.2.3) was used to align paired-end fastq files to the S. cerevisiae reference genome
sam files were converted to bam files using samtools then reads were sorted
bam files were converted to bed files using bedtools paired end function and PCR duplicates were removed
Printed columns for the chromosome, position of the start and stop of the read, and the strand information into output bed files
For whole genome sequencing files used bedtools genomecov to output genome coverage files
Genome_build: Yeast S288C, build R64-1-1
Supplementary_files_format_and_content: OEM_position_timing_fkh.xls, xls file, chromosome, position, calculated origin efficiencies for each replicate and each condition for each strain, timing of origin firing, forkhead status for each origin. This includes new replicates and forkhead status.
Supplementary_files_format_and_content: poorly_mapped_sites.xls, xls file, chromosome, start position (bp), end position (bp)
Supplementary_files_format_and_content: bed files, chromosome, start and end positions of mapped reads, strand information
Supplementary_files_format_and_content: genome coverage files, chromosome, position, number of reads spanning these positions

organism: Saccharomyces cerevisiae

growth_protocol: 30°C, grow overnight in YEP + 3% raffinose + 0.5% galactose until log phase then switched into various galactose concentrations + 3% raffinose for four hours

extract_protocol:
Lysed cells were sonicated then treated with proteinase K for 2hrs at 37 degrees Celsius. Samples were then phenol chloroform extracted and precipitated.
Libraries were generated using the Illumina TruSeq Nano DNA LT Kit.

treatment_protocol: Add alpha factor for 3hrs during sugar switch. Release into various galactose media at room temperature. Collected cells every 10 minutes post-release and used flow cytometry to identify the phase of the cell cycle. Samples from S phase were sequenced.

tag: strain background

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB


title: GDPOL1-5-80m

description: Whole Genome Sequencing


title: GDPOL1-50-0m

description: Whole Genome Sequencing


title: GDPOL1-5-120m

description: Whole Genome Sequencing


title: GDPOL1-14-110m

description: Whole Genome Sequencing


title: GDPOL1-50-100m

description: Whole Genome Sequencing


title: GDPOL1-14-90m

description: Whole Genome Sequencing


title: GDPOL1-50-80m

description: Whole Genome Sequencing


title: PBS.1WK.4 [94-5]

city: Durham

first: Syed Faaiz

last: Enam

state: NC

address: 308 Research Dr, Rm C-141 LSRC

department: Biomedical Engineering

institute: Duke University

data_processing:
Individual lanes were concatenated, adaptor trimming was performed with cutadapt (v2.4), quality was checked with FastQC (v0.11.8)
Kallisto (v0.46) index was created with GENCODE vM23 protein-coding transcripts and kallisto was run with 100 bootstraps; quality-check done by making dendrogram of tpms
Differential expression was assessed through Sleuth (v0.30) in R (v3.6.1) with Wald test and gene_mode=TRUE
Kallisto and sleuth data were combined, significantly differentially expressed genes were run in g:profiler, ranked gene lists were made for gene set enrichment analysis (GSEA)
Genome_build: GENCODE vM23
Supplementary_files_format_and_content: tab-separated values

extract_protocol:
Brains were harvested and the left hemisphere dissected. A 2-mm rectangular width of tissue around the injection site was cut and flash-frozen in liquid nitrogen. The tissue homogenized and processed through an Rneasy Lipid Tissue Kit (Qiagen) with Qiazol reagent to extract RNA.
RNA libraries were constructed using standard Illumina protocol.

tag: injury

value: Closed head injury

value: Phosphate-buffered Saline

value: brain; left cortex


title: SHAM.0 [95-3]

value: Sham

tag: treatment

value: No treatment


title: SHAM.1 [95-4]


title: GDPOL1-50-60m

description: Whole Genome Sequencing


title: WT-500-70m

description: Whole Genome Sequencing


title: WT-500-50m

description: Whole Genome Sequencing


title: PBS.1WK.2 [94-3]


title: WT-500-60m

description: Whole Genome Sequencing


title: GDPOL1-5-rep2

description: Okazaki Fragments

extract_protocol:
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438)
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438)

treatment_protocol: Add rapamycin for one hour


title: PBS.1WK.1 [94-2]


title: PBS.1WK.3 [94-4]


title: GDPOL1-5-rep1

description: Okazaki Fragments


title: GDPOL1-14-rep1

description: Okazaki Fragments


title: GDPOL1-14-rep2

description: Okazaki Fragments


title: PBS.1WK.0 [94-1]


title: MSC.1WK.4 [93-5]

value: Naïve mesenchymal stromal cell


title: GDPOL1-41-rep1

description: Okazaki Fragments


title: GDPOL1-50-rep1

description: Okazaki Fragments


title: MSC.1WK.3 [93-4]


title: GDPOL1-14-70m

description: Whole Genome Sequencing


title: GDPOL1-50-rep2

description: Okazaki Fragments


title: SUM159-Control-1

first: Michael

middle: Dale

last: Brooks

state: Michigan

address: 2800 Plymouth Rd Building 26 Rm 329S

department: Internal Medicine

data_processing:
Standard Illumina pipeline basecalling
Reads were mapped with STAR to the human GRCh37 genome build
Genome_build: GRCh37

growth_protocol: SUM159 were grown in F12 with 5% FBS, Insulin, and Hydrocortisone

extract_protocol:
Total RNA was extracted with Qiagen columns
Standard polyA RNA Illumina library construction

treatment_protocol: Cells were treated with either DMSO control or Doxycycline to induce siRNA knockdown of the SHARP gene

tag: cell line

value: Breast Cancer Cell Line

value: DMSO-Control


title: SUM159-Sharp-Knockdown-2

value: Doxycyclin


title: MSC.1WK.2 [93-3]


title: MSC.1WK.1 [93-2]


title: SUM159-Sharp-Knockdown-1


title: SUM159-Control-2


title: MSC.1WK.0 [93-1]


title: 125

first: Jennifer

last: Downs

address: 1300 York Ave.

institute: Weill Cornell Medicine

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using tophat v2.0.11.
Read counts were calculated using HTSeq-count v0.6.1.
Genome_build: hg19
Supplementary_files_format_and_content: txt file, raw read counts

source_name: blood

extract_protocol:
RNA extraction with Tempus Spin RNA Extraction kit (Invitrogen)
Libraries were prepared using Illumina TruSeq RNA Sample Preparation (Non-stranded and Poly-A selection).

tag: gender

value: Male

tag: s.haematobium infection status

value: Uninfected

value: blood


title: 128

value: Infected


title: 127


title: 132


title: 126


title: IL4.1WK.4 [92-5]

value: Interleukin-4 expressing MSC


title: 131


title: 124


title: IL4.1WK.2 [92-3]


title: 123


title: 129


title: IL4.1WK.3 [92-4]


title: GDPOL1-41-rep2

description: Okazaki Fragments


title: 122


title: 121


title: 120


title: 119

value: Female


title: SHAM.4 [90-5]


title: coconut oil 6

city: balice

first: Maria

last: Oczkowicz

state: malopolskie

address: krakowska 1

country: Poland

institute: National Reseach Institute of Animal Production

data_processing:
Quality control (fastQC)
Filtration of low quality reads (pred quality <20). Minimal length of reads set to 35. Removal of adaptors (Flexbar)
Mapping with default options (Tophat)
Counting reads to Ensembl GTF version 95 intervals (htseq-count) and differential expresion calculated with the use of Deseq2
Genome_build: Sus Scrofa 11.1

organism: Sus scrofa

source_name: Liver

growth_protocol: Animals were kept in individual straw-bedded pens with free access to water. The fattening experiment continued from about 60 kg to 118 kg of body weight (BW). All groups obtained diets with similar energy and protein concentrations covering the nutritional requirements of pigs,  but differed among groups in term of the type of fat used (rapeseed oil, beef tallow, coconut oil).

extract_protocol:
RNA was isolated with PureLink RNA Mini Kit (Thermofisher scientific)
Libraries were prepared using  QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer recommendations.

value: male

tag: breed

value: (Polish Landrace x Polish Large White) sows mated with (Duroc x Pietrain) boars


title: 118


title: 130


title: SHAM.2 [90-1]


title: SHAM.3 [90-2]


title: coconut oil 5

value: female


title: coconut oil 4


title: 116


title: PBS.3WK [89-5]

description: Excluded due to high tpm

value: Closed head injury

value: Phosphate-buffered Saline


title: 117


title: 115


title: coconut oil 2


title: PBS.3WK.2 [89-3]

value: brain; left cortex


title: IL4.1WK.1 [92-2]


title: 113


title: PBS.3WK.1 [89-2]


title: coconut oil 1


title: PBS.3WK.0 [89-1]


title: coconut oil 3


title: beef tallow 5


title: IL4.1WK.0 [92-1]


title: MSC.3WK.4 [88-5]


title: 112


title: beef tallow 4


title: 114


title: MSC.3WK.3 [88-4]


title: 109


title: 111


title: beef tallow 3


title: beef tallow 2


title: 110


title: beef tallow 1


title: MSC.3WK.2 [88-3]


title: 107


title: rapeseed oil 5


title: PBS.3WK.3 [89-4]


title: 106


title: MSC.3WK.0 [88-1]


title: MSC.3WK.1 [88-2]


title: IL4.3WK.2 [87-3]


title: rapeseed oil 2


title: IL4.3WK.3 [87-4]


title: rapeseed oil 3


title: 103


title: IL4.3WK.1 [87-2]


title: IL4.3WK.0 [87-1]


title: 101


title: 100


title: 108


title: NRHV193_stim

city: Manchester

first: Paul

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

country: United Kingdom

institute: Univeristy of Manchester

data_processing:
CellRanger (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
Quality control, normalization and scaling of nUMI and percentage of mitochondrial-associated genes were performed using Seurat (v2.3.0).
Two groups (unstimulated and IL-2 stimulated) were aligned using canonical correlation analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat object of the aligned donors. Clustered using 25 CCs from the CCA dimensionality reduction and a resoultion of 0.8. Antigen presenting cells, NKT cells and stessed cells were removed.

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood collected into EDTA-coated tubes using density gradient centrifugation.  Primary human NK cells were then isolated using negative magnetic bead selection
Single cell libraries were prepared using 10X Genomics Chromium 3' kit (v2).

tag: disease diagnosis

value: healthy

tag: cell type

value: NK cells

tag: group

value: 4hr IL-2 stimulated

tag: cmv status

value: CMV-negative


title: 102

tag: tissue


title: NRHV193_unstim

value: freshly isolated


title: NRHV187_stim


title: NHRV187_unstim


title: rapeseed oil 4


title: IL4.3WK.4 [87-5]


title: 104


title: 105


title: w17Md_48: 17 dpi wild type mycorrhizal rep3

city: Norwich

first: Catherine

last: Jacott

address: Colnet Lane

institute: John Innes Centre

data_processing:
Kallisto, version 0.44, kmser size 31
Genome_build: IBSC Morex v2 (PMID 28447635)
Supplementary_files_format_and_content: TSV containing counts and TPM values

organism: Hordeum vulgare

source_name: 17 dpi wild type mycorrhizal

growth_protocol: Germinated H. vulgare cv. Ingrid wild type and Hvmlo1-5 seedlings were transferred plates containing modified Fahraeus plant agar medium (ModFP) with Augmentin (50 μg/ml), grown in a controlled-environment room at 23°C (16-h photoperiod, and 300 mmol m-2 s-1) for 3 days, then transferred to 90% sterilized Terragreen/Sand  (1:1 mix of terragreen (Oil‐dry UK ltd) and sharp sand (BB Minerals))and 10% mycorrhizal inoculum (soil substrate containing Allium schoenoprasum roots exposed to Rhizophagus irregularis for 8 weeks). Plants were grown in a Weiss Technik growth cabinet at 35°C/20°C (35% RH day, 50 % RH night; 16-h photoperiod, and 500 μmol m-2 s-1, average temperature: 30°C) and harvested at 17 dpi and 26 dpi.

extract_protocol:
RNAs were extracted from root tissue (Plant RNeasy Kit, Qiagen) and was treated with DNase (RNase-Free DNase Set, Qiagen).
mRNA libraries were prepared with the Illumina TruSeq® Stranded mRNA HT technology with a paired-end 150 bp (PE 150) strategy.

treatment_protocol: Control: 100% Terragreen:Sand, mycorrhizal: 90% Terragreen/Sand and 10% Rhizophagus irregularis inoculum

tag: cultivar

value: Ingrid

value: Roots

tag: days post inoculation

value: 17 dpi

tag: genotype

value: wild type

value: mycorrhizal


title: w17Mb_46: 17 dpi wild type mycorrhizal rep2


title: m17Ca_49: 17 dpi Hvmlo1-5 control rep1

source_name: 17 dpi Hvmlo1-5 control

value: control


title: w17Cd_44: 17 dpi wild type control rep3

source_name: 17 dpi wild type control


title: w17Ma_45: 17 dpi wild type mycorrhizal rep1


title: w17Cb_42: 17 dpi wild type control rep2


title: m17Cb_50: 17 dpi Hvmlo1-5 control rep2


title: m26Ca_66: 26 dpi Hvmlo1-5 control rep1

source_name: 26 dpi Hvmlo1-5 control

value: 26 dpi


title: m17Mc_55: 17 dpi Hvmlo1-5 mycorrhizal rep2

source_name: 17 dpi Hvmlo1-5 mycorrhizal


title: w26Cd_60: 26 dpi wild type control rep3

source_name: 26 dpi wild type control


title: m26Me_74: 26 dpi Hvmlo1-5 mycorrhizal rep3

source_name: 26 dpi Hvmlo1-5 mycorrhizal


title: m17Mb_54: 17 dpi Hvmlo1-5 mycorrhizal rep1


title: m26Mc_72: 26 dpi Hvmlo1-5 mycorrhizal rep2


title: m26Mb_71: 26 dpi Hvmlo1-5 mycorrhizal rep1


title: w26Mc_63: 26 dpi wild type mycorrhizal rep2

source_name: 26 dpi wild type mycorrhizal


title: w26Cb_58: 26 dpi wild type control rep1


title: m26Cd_69: 26 dpi Hvmlo1-5 control rep3


title: m17Md_56: 17 dpi Hvmlo1-5 mycorrhizal rep3


title: m17Cd_52: 17 dpi Hvmlo1-5 control rep3


title: w26Cc_59: 26 dpi wild type control rep2


title: w26Me_65: 26 dpi wild type mycorrhizal rep3


title: m26Cc_68: 26 dpi Hvmlo1-5 control rep2


title: w26Ma_61: 26 dpi wild type mycorrhizal rep1


title: Control rep2

status: Public on Jan 24 2020

city: San Francisco

first: Todd

last: Nystul

state: CA

address: 513 Parnassus Ave, Box 0412

institute: UCSF

data_processing:
Read trimming using Scythe and Sickle
Reads aligned to Drosophila genome (BDGP 5.74) using TopHat2 (v 2.0.10)
Differential expression called using HTSeq-count (v 0.6.1) and DESeq2 (v 1.2.10)
Filtering differentially expressed genes for transcription factors present in Trusted TFs (v1) on FlyTF.org.
Genome_build: ENSEMBL BDGP 5.74
Supplementary_files_format_and_content: CSV table of differential expressed genes identified by DESeq2
Supplementary_files_format_and_content: CSV table of differential expressed transcription factors, including outcome of RNAi screen to knock down these transcription factors

source_name: Ovary follicle cells

growth_protocol: Juvenile flies reared at 18C to adulthood to avoid developmental effect.

extract_protocol:
RNAqueous-Micro Total RNA Isolation Kit + Oligo-dT pulldown
ScriptSeqv2 (Illumina SSV21106)

treatment_protocol: Adult flies transferred to 29C for 7-10 days prior to dissection.

value: Ovary follicle cells

tag: type

value: Control (UAS-CD8-GFP)


title: EGFR-activated rep2

value: EGFR-activated (UAS-EGFR-lambdatop + UAS-CD8-GFP)


title: Control rep1


title: EGFR-activated rep1


title: brain endo 2

city: La Jolla

first: Roeben

last: Munji

state: California

address: 9500 Gilman Dr.

department: Pharmacology

institute: University of California San Diego

description:
enriched brain endothelial cells
MunjiSoungDaneman RNAseq BBB Health Brain endo.txt

data_processing:
Alignment: Aligned to mouse genome build "mm9" using the program Tophat 2.0.13. Gene annotation (GTF file) used was Ensembl version 65. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search  --mate-inner-dist=150 --no-discordant --no-mixed
Reads to gene-level counts: Aligned reads were assigned to genes to arrive at per-gene counts using "featureCounts" (Liao et al., 2014), part of the Subread suite (http://subread.sourceforge.net/).
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: Raw per-gene count data table in plain text format, suitable for loading in Excel

source_name: Mouse brain endothelial cells

growth_protocol: Mice were raised in a barrier vivarium with 12-hour light and 12-hour dark cycle and food/water ad libitum

extract_protocol:
Papain digestion, mechanical dissociation, Collagenase and Dispase digestion, Myelin removal, FACS sorting, Nucleic acid purification by Trizol/chloroform, Qiagen RNAeasy using manufacturers protocols
Prepared at the Gladstone Genomics core: NuGEN Ovation RNA-seq V2 kit and NuGEN Ovation Ultralow kit wereused

treatment_protocol: Ten days prior to enrichment, Rosa-tdTomato; VE-Cadherin-CreERT2 mice were injected 100ul of 20mg/ml tamoxifen solubilized in corn oil for three consecutive days to induce expression of the tdTomato transgene

value: Rosa-tdTomato; VE-Cadherin-CreERT2

value: forebrain

tag: developmental stage

value: adult

tag: Sex

value: male

value: endothelial cells


title: w17Ca_41: 17 dpi wild type control rep1


title: brain endo 1


title: Neu_8d_injured_ipsi_3

status: Public on Jan 22 2020

city: London

first: Sara

middle: Elgaard

last: Jager

address: Hodgkin Building, Guy's Campus

institute: King's College London

description:
Sequenced over 2 lanes
DESeq2_values_8d_neu.txt
FPKM_values_neurons.txt

data_processing:
FastQ files were aligned to the UCSC mm10 build of the mouse genome using STAR.
Aligned BAM files from separate lanes were combined using the Merge BAM tool from SamTools
Fragments per kilobase per million (FPKM) estimates were obtained using Cufflinks
DESeq2 was used to determine the foldchange in gene expression between the following samples: naive SGCs vs naive DRG; SGCs 3 days after injury vs SGCs 3 days after sham; SGCs 14 days after injury vs SGCs 14 days after sham; nociceptors 8 days after injury vs nociceptors 8 days after sham
Genome_build: mm10
Supplementary_files_format_and_content: FPKM estimates for all samples in .txt format and DESeq2 data also in .txt format

source_name: MACS sorted neurons (ipsi) 8 days after partial sciatic nerve ligation

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

tag: strain

tag: age

value: 9-11 weeks

tag: extract protocol

value: L3-L5 DRGs were dissected, dissociated with enzymes, sorted with MACS Neuronal isolation kit (Miltenyi catalog no 130-115-389) and finally purified with Qiagen Rnease micro kit (catalog number 74004)


title: Neu_8d_injured_ipsi_4


title: RNA-seq of Human Umbilical Vein Endothelial Cell (HUVEC) treated with Sodium palmitate

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

data_processing:
Demultiplexing of raw reads were done using standard Illumina protocol
Demultiplexed fastq reads alignment using Tophat2 using Bowtie2 index
cufflinks based transcripts assembly
cuffdiff based differential gene expression
Genome_build: h38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

growth_protocol: HUVECs were cultured in EGM2 growth medium (Lonza)

extract_protocol:
Total RNA was isolated from the HUVECs and rRNA was removed using ribozero gold (Illumina). The rRNA depleted RNA was used for library preparation using TruSeq Directional RNAseq kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were treated with 250 µM of sodium palmitate for 24 hrs

tag: treatment

value: 250 uM of sodium palmitate for 24 hrs


title: Neu_8d_injured_contra_2

source_name: MACS sorted neurons (contra) 8 days after partial sciatic nerve ligation


title: rapeseed oil 1

tag: gender

value: female

value: (Polish Landrace x Polish Large White) sows mated with (Duroc x Pietrain) boars


title: Neu_8d_injured_contra_1


title: LEC 368 scRNAseq

status: Public on Jan 18 2020

city: Stanford

first: Menglan

last: Xiang

address: 450 Serra Mall

institute: Stanford University

data_processing:
FASTQ files were trimmed with Trim Galore (v0.4.4) followed by alignment of the data to the mouse reference genome (mm10-GRCm38) using TopHat (v2.1.1) and bowtie2 (v2.2.6.0). PCR duplicates were removed using SAMtools (v0.1.18). Counting of fragments aligning per gene was done using the featurecounts function of the Subread package (v1.4.6-p5).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file of raw count data

source_name: Inguinal lymph node

extract_protocol:
Inguinal LN digests from 20-week-old female Prox1-GFP/C57BL/6J mice were depleted for hematopoietic cells and stained with anti-CD31 PE-Cy7 (clone 390) , anti-Podoplanin AF660 (clone eBio8.11) antibodies (Thermo Fisher Scientific). Dump channel included anti-mouse TER-119 eFluor450 (clone Ter119), anti-mouse CD45 eFluor450 (clone 30-F11), anti-mouse CD11b eFluor450 (clone M1/70) and dead cell staining SYTOX™ Blue (Thermo Fisher Scientific). Triple positive live cells (GFP+ Pdpn+ CD31+) (LECs) were gated and sorted on a BD FACSAria III (BD Biosciences) (100 um nozzle, 20 psi) as single cells into a 384 well plate with lysis buffer.
scRNA-seq libraries were prepared using the SMART-seq2 protocol.

value: 20 weeks

value: Inguinal lymph node


title: LEC 375 scRNAseq


title: LEC 378 scRNAseq


title: LEC 381 scRNAseq


title: LEC 371 scRNAseq


title: LEC 370 scRNAseq


title: LEC 379 scRNAseq


title: LEC 384 scRNAseq


title: LEC 376 scRNAseq


title: LEC 380 scRNAseq


title: LEC 365 scRNAseq


title: LEC 372 scRNAseq


title: LEC 377 scRNAseq


title: LEC 366 scRNAseq


title: LEC 373 scRNAseq


title: LEC 383 scRNAseq


title: LEC 367 scRNAseq


title: LEC 364 scRNAseq


title: LEC 363 scRNAseq


title: RNA-seq of Human Umbilical Vein Endothelial Cell (HUVEC) PBS Control

value: PBS control


title: LEC 374 scRNAseq


title: LEC 362 scRNAseq


title: LEC 369 scRNAseq


title: LEC 361 scRNAseq


title: LEC 357 scRNAseq


title: LEC 359 scRNAseq


title: LEC 360 scRNAseq


title: LEC 358 scRNAseq


title: LEC 356 scRNAseq


title: LEC 354 scRNAseq


title: LEC 355 scRNAseq


title: LEC 353 scRNAseq


title: LEC 349 scRNAseq


title: LEC 352 scRNAseq


title: LEC 351 scRNAseq


title: LEC 347 scRNAseq


title: LEC 345 scRNAseq


title: LEC 346 scRNAseq


title: LEC 350 scRNAseq


title: LEC 348 scRNAseq


title: LEC 341 scRNAseq


title: LEC 342 scRNAseq


title: LEC 339 scRNAseq


title: LEC 338 scRNAseq


title: LEC 340 scRNAseq


title: LEC 343 scRNAseq


title: LEC 337 scRNAseq


title: LEC 334 scRNAseq


title: LEC 333 scRNAseq


title: LEC 336 scRNAseq


title: LEC 335 scRNAseq


title: LEC 332 scRNAseq


title: LEC 331 scRNAseq


title: LEC 329 scRNAseq


title: LEC 330 scRNAseq


title: LEC 382 scRNAseq


title: LEC 344 scRNAseq


title: LEC 326 scRNAseq


title: LEC 328 scRNAseq


title: LEC 325 scRNAseq


title: LEC 324 scRNAseq


title: LEC 322 scRNAseq


title: LEC 321 scRNAseq


title: LEC 320 scRNAseq


title: LEC 316 scRNAseq


title: LEC 318 scRNAseq


title: LEC 314 scRNAseq


title: LEC 317 scRNAseq


title: LEC 310 scRNAseq


title: LEC 319 scRNAseq


title: LEC 311 scRNAseq


title: LEC 315 scRNAseq


title: LEC 306 scRNAseq


title: LEC 309 scRNAseq


title: LEC 304 scRNAseq


title: LEC 303 scRNAseq


title: LEC 313 scRNAseq


title: LEC 312 scRNAseq


title: LEC 307 scRNAseq


title: LEC 308 scRNAseq


title: LEC 305 scRNAseq


title: LEC 300 scRNAseq


title: LEC 327 scRNAseq


title: LEC 301 scRNAseq


title: LEC 299 scRNAseq


title: LEC 295 scRNAseq


title: LEC 294 scRNAseq


title: LEC 298 scRNAseq


title: LEC 293 scRNAseq


title: LEC 297 scRNAseq


title: LEC 323 scRNAseq


title: LEC 296 scRNAseq


title: LEC 287 scRNAseq


title: LEC 288 scRNAseq


title: LEC 286 scRNAseq


title: LEC 285 scRNAseq


title: LEC 289 scRNAseq


title: LEC 284 scRNAseq


title: LEC 302 scRNAseq


title: LEC 281 scRNAseq


title: LEC 282 scRNAseq


title: LEC 283 scRNAseq


title: LEC 278 scRNAseq


title: LEC 277 scRNAseq


title: LEC 274 scRNAseq


title: LEC 275 scRNAseq


title: LEC 273 scRNAseq


title: LEC 271 scRNAseq


title: LEC 272 scRNAseq


title: LEC 291 scRNAseq


title: LEC 292 scRNAseq


title: LEC 267 scRNAseq


title: LEC 268 scRNAseq


title: LEC 264 scRNAseq


title: LEC 266 scRNAseq


title: LEC 270 scRNAseq


title: LEC 290 scRNAseq


title: LEC 269 scRNAseq


title: LEC 265 scRNAseq


title: LEC 279 scRNAseq


title: LEC 261 scRNAseq


title: LEC 276 scRNAseq


title: LEC 259 scRNAseq


title: LEC 262 scRNAseq


title: LEC 258 scRNAseq


title: LEC 257 scRNAseq


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title: LEC 185 scRNAseq


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title: LEC 209 scRNAseq


title: LEC 189 scRNAseq


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title: LEC 128 scRNAseq


title: LEC 131 scRNAseq


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title: LEC 146 scRNAseq


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title: LEC 125 scRNAseq


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title: LEC 41 scRNAseq


title: LEC 46 scRNAseq


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title: LEC 9 scRNAseq


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title: LEC 11 scRNAseq


title: LEC 8 scRNAseq


title: LEC 6 scRNAseq


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title: LEC 28 scRNAseq


title: LEC 3 scRNAseq


title: LEC 4 scRNAseq


title: LEC 1 scRNAseq


title: LEC 2 scRNAseq


title: PRC1CPM_TAM_Input_rep3

status: Public on Jan 08 2020

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford

data_processing:
Library strategy: DNA-seq
For cRNA-seq, first, paired-end reads were aligned using Bowtie 2 (with “--very-fast”, “--no-mixed” and “--no-discordant” options) against the concatenated mm10 and dm6 rDNA genomic sequence (GenBank: BK000964.3 and M21017.1) and reads mapping to rDNA were discarded. All unmapped reads were then aligned against the concatenated mm10 and dm6 genome sequences using STAR (Dobin et al., 2013). Finally, reads that failed to map using STAR were aligned against the mm10+dm6 concatenated genome using Bowtie 2 (with “--sensitive-local”, “--no-mixed” and “--no-discordant” options) to improve mapping of introns. Uniquely aligned reads from the last two steps were combined for further analysis. PCR duplicates were removed using Sambamba (Tarasov et al., 2015). For the corresponding gDNA-seq experiments, paired-end reads were aligned to the concatenated mm10+dm6 genome using Bowtie 2 (Langmead and Salzberg, 2012) with the “--no-mixed” and “--no-discordant” options. Only uniquely mapped reads after removal of PCR duplicates with Sambamba (Tarasov et al., 2015) were used for downstream analysis.
For visualisation of cRNA-seq data, uniquely aligned mouse reads were normalised using dm6 spike-in as described previously (Fursova et al., 2019). Briefly, mm10 reads were randomly subsampled based on the total number of spike-in reads in each sample. To account for any minor variations in spike-in cell mixing between replicates, we used the ratio of spike-in/mouse total read counts in the corresponding Input/gDNA-seq samples to correct the subsampling factors. After normalisation, read densities for individual biological replicates were compared across gene bodies using multiBamSummary and plotCorrelation from deepTools (Ramirez et al., 2014). For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.96, see Table S3) and were merged for downstream analysis.
For differential gene expression analysis, read counts from individual biological replicates prior to spike-in normalisation were obtained. A custom Perl script utilising SAMtools was used to annotate a custom-built non-redundant mm10 gene set (n = 20633) with read counts. The non-redundant gene set was derived from mm10 refGene genes by removing very short genes with poor sequence mappability and highly similar transcripts.
To identify significant changes, we used a custom R script that incorporates spike-in calibration into DESeq2 analysis (Love et al. 2014). In order to do this, we used read counts from the spike-in genome at a control set of unique dm6 refGene genes to calculate DESeq2 size factors for normalisation of raw mm10 read counts (as has been previously described in Taruttis et al., 2017 and Fursova et al., 2019). Prior to quantification, spike-in reads were pre-normalised using the spike-in/mouse read ratio derived from the corresponding genomic DNA-seq sample in order to account for minor variations in mixing of mouse and spike-in cells. For a change to be called significant, we applied a threshold of p-adj < 0.05 and fold change > 1.5, unless otherwise specified. To identify genes that were differentially affected by the removal of PRC1 or specifically PRC1 catalytic activity, we used two complementary approaches. First, we isolated genes that were expressed at significantly lower levels (p-adj < 0.05 and fold change > 1.5) in PRC1CPM as compared to PRC1CKO cells following tamoxifen treatment (PRC1CPM_OHTvsPRC1CKO_OHT). In addition, we also identified genes, for which the magnitude of expression changes following tamoxifen treatment was significantly smaller in PRC1CPM cells than in PRC1CKO cells, using the DESeq2 design that included the interaction term between the cell line and treatment factors (PRC1CPM_OHTtoUNTvsPRC1CKO_OHTtoUNT).
Genome_build: mm10
Supplementary_files_format_and_content: Stranded bigWig files were generated using genomeCoverageBed from BEDTools representing genome coverage of merged spike-in normalised biological replicates.
Supplementary_files_format_and_content: DESeq2 results table for differential gene expression analysis containing normalised read counts, estimated log2 fold changes and statistical significance levels for a non-redundant set of mm10 refGene genes.
Supplementary_files_format_and_content: Table with RefSeq IDs and MGI symbols for a selected group of genes described in the paper (related to Figure 7)

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr OHT), gDNA-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. ). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For cRNA-seq, 1 x 10^7 mouse ESCs (both untreated and following 72 hours OHT treatment) were mixed with 4 x 10^6 Drosophila SG4 cells in 600 ml PBS. For RNA extraction, 400 ml of cells was used (corresponding to 6.7 x 10^6 mouse ESCs), and for DNA extraction the remaining 200 ml of cells was used (corresponding to 3.3 x 10^6 mouse ESCs). RNA extraction was performed using RNeasy mini kit columns (Qiagen) following manufacturer’s guidelines, and 10 mg was subjected to Turbo DNase (ThermoFisher) treatment to remove any contaminating DNA. Quality of RNA was assessed using 2100 Bioanalyzer RNA 6000 Pico kit (Agilent). Next, RNA samples were depleted of rRNA using the NEBNext rRNA Depletion kit (NEB). To quantitate the consistency of spike-in cell mixing for each individual sample, a matched sample of cells was used to isolate genomic DNA using Quick-DNA miniprep kit (Zymo).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit (NEB). Libraries from gDNA were prepared using NEBNext Ultra II FS kit (NEB) following manufacturer’s guidelines. RNA and DNA libraries were sequenced as 80 bp paired-end reads on the Illumina NextSeq 500 platform.

treatment_protocol: To induce conditional removal of PRC1 or PRC1 catalytic activity in PRC1CKO and PRC1CPM ESC lines, cells were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 hours.

tag: cell line

tag: clone

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 72 hr

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line


title: Whole Mesenchyme Single Cell RNA-seq rep1

status: Public on Jan 17 2020

city: Boston

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
All bulk RNAseq data was analyzed using the VIPER pipeline
It was aligned to the mouse reference genome Mm10 using the STAR aligner
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger (3.0.2, 10X Genomics) was used to generate UMI matrix.

source_name: small intestine whole mesenchyme

extract_protocol: Cells were isolated from entire small intestinal tissues, muscle stripped, epithelium denuded via 20 minutes in warm 10 mM EDTA/HBSS (at 37degrees C), and tissue was further minced by fine scalpels. Digestion of tissue was performed using 1.5mg/ml collagenase II (Worthington) in 10%FBS/DMEM at 37 degrees C. Supernatants were collected every 20 minutes for one hour, and washed twice to remove debris. Antibody-labelling was performed prior to FACS.  GFP cells were FACS sorted at a ratio of 2:1 GFPlo to GFPhi. A manually estimated 8700 cells were loaded on a 10X Chromium Controller (10X Genomics) for targeting 5000 cells using the single cell 3' V2 assay. Reverse-transcription, cDNA amplification and library prep were compelted according to manufacturer's protocol. Sequencing of library was performed using a HiSeq4000 Illumina System.

tag: cell type

value: Whole Mesenchyme

tag: source

value: primary cells


title: PRC1CPM_TAM_Input_rep1

tag: genotype


title: PRC1CPM_UNT_Input_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq

value: 0 hr


title: PRC1CPM_UNT_Input_rep3


title: PRC1CPM_TAM_Input_rep2


title: Whole Mesenchyme Single Cell RNA-seq rep2