title: Control antago-miR rep3

city: Pisa

first: Federico

last: Cremisi

address: Piazza dei Cavalieri, 7

department: Science

country: Italy

institute: Scuola Normale

data_processing:
Transcripts were quantified using Salmon (REF:10.1038/nmeth.4197) in mapping-based mode (with its default "--validateMappings" flag) taking as a reference a decoy-aware version of the Ensembl mouse transcriptome (mm10; refgenomes.databio.org).
Read count analysis was performed using the R package NOISeq. Raw counts were normalized with the Trimmed Mean of M values (TMM) method. Low-count filtering was performed using the CPM method, with cpm=4 as threshold.
PCA exploration was carried out to confirm that the experimental samples were clustered according to the experimental design
Differential expression was calculated by the NOISeqBIO method and a significance threshold of q=0.95 was applied.
Genome_build: mm10
Supplementary_files_format_and_content: .csv data files (read counts, DE analysis)

source_name: Neural progenitor cells

growth_protocol: Murine ESC lines E14Tg2A (passages 25-38) were differentiated in Chemically defined minimal medium (CDMM) under Wnt and BMP inhibition for 11 days in vitro (DIV), from DIV0 to DIV11, and then maintained in culture in minimal medium until DIV17. CDMM composition: DMEM/F12 (21331-046, ThermoFisher Scientific), 2mM Glutamine, 1mM sodium Pyruvate, 0.1Mm NEAA, 0.05mM β-mercaptoethanol, 100 U/ml Penicillin/Streptomycin, N-2 Supplement (175020, ThermoFisher Scientific), B-27 Supplement minus Vitamin A (125870, ThermoFisher Scientific), 2.5μM 53AH Wnt inhibitor (C5324-10, Cellagen Technology),  0.25μM BMP inhibitor (SML0559, Sigma Aldrich). Minimal medium composition: Neurobasal (ThermoFisher Scientific), 2mM Glutamine, 1mM sodium Pyruvate, 0.1Mm NEAA, 0.05mM β-mercaptoethanol, 100 U/ml Penicillin/Streptomycin, B-27 Supplement.

extract_protocol:
miRNeasy Mini Kit (217004, QIAGEN)
RNA-seq libraries were prepared with the SMART-Seq® HT PLUS Kit (Takara) following manufacturer's instructions

treatment_protocol: Antago-miR transfection in mouse cortical cells was performed using Lipofectamine 2000 according to the manufacturer’s instructions. miRCURY LNA™ microRNA Inhibitor to miR-541-5p and control antago-miR were resuspended in TE buffer (10mM Tris pH 7.5, 1mM EDTA) to a final concentration of 50μM. Cells were transfected at DIV12 in 24-well plate using 25pmol of LNA diluted in 2.5 μL/well of Lipofectamine 2000 in a final volume of 0.5 mL/well OPTI-MEM. After transfection, cells were incubated at 37°C and 5% CO2 for 4-6 hours and then the medium was replaced with minimal medium. Cells were then cultured in minimal medium until DIV17.

value: ESC-derived neural progenitor cells

tag: strain

tag: Stage

value: control antago-miR transfection


title: Epi-HOTΔL2

status: Public on Apr 22 2021

type: SRA

city: Paris

first: Marina

last: Pinskaya

address: rue d'Ulm

country: France

institute: Institut Curie

description:
Epi cells transduced by the lentiviral construct expressing cDNA of truncated HOTAIR missing Lsd1 interacting domain
L2

library_source: transcriptomic

data_processing:
Reads were mapped with tophat version 2.0.6, with a tolerance of 3 mismatches
Only unique mapped reads were kept for further analysis
Reads were counted on genomic features with htseq-count version 0.6.1p1
The read counts on E1-tot, E2-tot, M1-tot and M2-tot were processed on gencode v19, and the read counts of the other cell lines were processed on gencode v26.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file reporting htseq counts

molecule: total RNA

organism: Homo sapiens

source_name: HEK-based cell line

growth_protocol: For each cell-line, cells were grown up to 90% confluence in 100 cm² square dishes in MEM-alpha medium supplemented with non-essential amino-acids and sodium pyruvate, at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted using Qiagen miRNeasy kit with a Trizol reagent.
all RNA-seq libraries were prepared with TruSeq Stranded Total RNA Sample Prep Kit (RS-122-2201, Illumina)

tag: cell line

value: Epi-HOT<delta>L


title: ChIP H3K27ac on FoxA Dev double null - sample 2

city: Philadelphia

first: Klaus

middle: H

last: Kaestner

state: PA

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Single-end sequencing reads were trimmed with Cutadapt and aligned to mouse genome (genome build mm9) using Bowtie2 version 2.3.4.1. PCR duplicates were removed using picard.jar tool and the command MarkDuplicates with the following flags:”REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT”. In order to compare differential binding between controls and FoxA double nulls in hyper- or isomethylated sites, we used DiffBind version 2.10.0 (Ross-Innes et al., 2012). Peaks were defined as ±250 base pairs from peak center. Bam files were converted to Bedgraph files after normalizing to 1 million reads per library using BEDtools (“genomecov”) and then converted to bigwig format using UCSC toolkit (“bedGraphToBigWig”). For control and FoxA triple null groups, an average bigwig file was also generated from the replicates (“bigWigMerge“).
Genome_build: mm9
Genome_build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: ChIP H3K27ac on FoxA Dev double null

extract_protocol:
130 mg of frozen liver was minced in 2 mL of cold 1X DPBS (Thermo Fisher 14080055). The volumes of liver slices were brought up to 10 mL of 1X DPBS and 1% formaldehyde and incubated at room temperature for 8 minutes with rotation. Reaction was brought to 0.125 M glycine for quenching and incubated for 5 minutes at room temperature with rotation. Samples were centrifuged at 2,500 RCF for 2 minutes at 4°C, the supernatants discarded, and pellets washed with 1X DPBS. The pellet was resuspended in 1 mL of cold ChIP cell lysis buffer (10 mM Tris- HCl pH 8.0, 10 mM NaCl, 3mM MgCl2, 0.5% IGEPAL CA-630, 1X cOmplete protease inhibitor cocktail) and transferred on ice to a 10 mL tissue grinder. The samples were homogenized 20 times with a smooth Teflon pestle and incubated at 4°C for 5 minutes. Following incubation the samples were centrifuged for 5 minutes at 17,000 RCF at 4°C, to pellet the nuclei. After the supernatant was discarded, and nuclei were resuspended in 1 mL of cold ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 5 mM EDTA, 1% SDS, 1X cOmplete protease inhibitor cocktail). Then, we performed two rounds of sonication using the Standard Biruptor (Diagenode UCD-200) with the following parameters: Intensity = High (H), Multitimer = OFF: 30 sec, ON: 30 sec, Total timer = 7.5 minutes with maintaining 4°C. Following sonication, samples were centrifuged at 17,000 RCF for 10 minutes at 4°C and supernatant was recovered. We isolated DNA from the sonicated chromatin to determine the amount of material required for precipitation. The DNA concentration was quantified using a NanoDrop-1000 (Thermo Fisher) and run on a BioAnalyzer High Sensitivity ChIP to estimate the length distribution. Then, 10 μg of sonicated chromatin was added to 1 mL of ChIP dilution buffer (16. mM Tris-HCl pH 8.0, 167 mM NaCl, 0.01% SDS, 1.1% Triton-X 100, 1X cOmplete protease inhibitor cocktail). 3 μg of the following antibodies, H3K27ac (Active Motif 39133) and HNF4a (Abcam ab181604), were added to the samples and the samples were incubated at 4°C overnight with rotation. 40 μL of recombinant protein G agarose beads (Thermo Fisher) were washed three times with 1 mL of ChIP dilution buffer. Next, the beads were resuspended in 75 μL of ChIP Dilution Buffer and 5 μL of BSA (New England BioLabs) and incubated at 4°C overnight with   rotation for blocking. Then chromatin samples were added to the blocked beads and incubated at 4°C for 1 hour with rotation. Samples were centrifuged at 100 RCF for 30 seconds and the supernatant was discarded. The beads were then washed sequentially with each of the following buffers by resuspending the beads in 1 mL of buffer, incubating beads at room temperature for 5 minutes with rotation, pelleting beads, and discarding supernatant: TSE I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), TSE II ( 20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), ChIP Buffer III (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% IGEPAL CA-630, 1% Sodium Deoxycholate), TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). After the washes, the beads were resuspended in 100 μL of elution buffer (0.1 M NaHCO3, 1% SDS) and incubated at room temperature for 15 minutes with rotation. 4 μL of 5M NaCl was added to the supernatant and then samples were incubated at 65°C overnight. Next, DNA was isolated from the samples using Minielute (Quiagen). Enrichment of IP samples was measured through qPCR using the following program: 95°C for 3 minutes, for 40 cycles, 95°C for 5 seconds, 60°C for 20 seconds.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were sequenced on the Illumina Hiseq 4000 with 50 bp single-end sequencing with a minimum of 20 million reads per sample.

tag: age

value: 8 weeks old

tag: tissue

value: Liver


title: XS8b.None.Vector.First.p4

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
The sequencing reads were mapped to hg38 reference using star/2.5.3a. Gene expression counts were further estimated using ESAT v1. Normalization was further applied as counts per million total reads. The mean of 3-5 replicates per evolution time-point sample was calculated based on the normalized counts and was used for calculating fold changes between samples.
Genome_build: hg38
Supplementary_files_format_and_content: integer count data in txt format

source_name: Human Mesencymal Progenitor

growth_protocol: Human mesenchymal progenitor cells were grown in the alpha-MEM medium (Gibco) supplemented with 10% FBS (HyClone FBS, Thermo Fisher Scientific) and Pen/Strep/Glutamine ( on 15-cm cell culture dishes (Corning); Cells from each growth timepoint were harvested by using 0.25% trypsin in a versene solution on the same day of each proliferation analysis timepoint.

extract_protocol:
Total RNA are exacted using RNeasy Mini Kit (Qiagen).
Standard Nextera tagmentation substituting P5NEXTPT5-bmc primer

treatment_protocol: Doxycycline was used for induction of Tet-on promoter at 1 µg/mL and the medium was changed every two days to ensure the efficacy of Doxycycline.

value: Human mesenchymal progenitor (hMPro cells)

tag: lentiviral library

tag: oncogene

value: Vector

tag: evolution experiment

value: First

tag: passage


title: Epi-HOTΔP2

description:
Epi cells transduced by the lentiviral construct expressing cDNA of truncated HOTAIR missing PRC2 interacting domain
P2

value: Epi-HOT<delta>P


title: Control antago-miR rep2

tag: cell type

tag: treatment


title: XS9a.26orf.EWS-FLI1.First.p8


title: XS7e.None.EWS-FLI1.First.p4


title: Epi-HOTΔP1

description:
Epi cells transduced by the lentiviral construct expressing cDNA of truncated HOTAIR missing PRC2 interacting domain
P1


title: XS7d.None.EWS-FLI1.First.p4


title: Epi-HOTΔL1

description:
Epi cells transduced by the lentiviral construct expressing cDNA of truncated HOTAIR missing Lsd1 interacting domain
L1


title: PID115star_HSC

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCh38.p10 genome assembly using STAR 2.7.0e with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 1.32.4
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

source_name: Blood

growth_protocol: Fresh human hematopoietic stem/progenitor cells were obtained from 123 blood samples of 18 patients with chronic and progressed PV and 21 controls with informed consent and approval of the local ethics committee (KEK-ZH-Nr: 2015-0564 with amendment PB_2019-00135; Clinical Hematology, University Hospital Zurich, Zurich Switzerland, and blood donation center SRK in Schlieren, Zurich).

extract_protocol:
Human CD34+ hematopoietic stem/progenitor cells were enriched from mononuclear cells using immunomagnetic beads according to manufacturer instructions (CD34 MicroBead Kit; Miltenyi Biotec). Fluorescence-activated cell sorting and antibodies specific for CD2, CD3, CD4, CD7, CD8, CD14, CD19, CD56, CD10, CD11b, CD20, CD235a, CD34, CD38, CD123, CD45RA were used to isolate the various cell types (HSC, CMP/MEP, CMP, GMP, MEP). 10'000 cells of each subpopulation were sorted into RNeasy lysis buffer containing beta-mercaptoethanol. Total RNA was purified according to manufacturer instructions using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using SmartSeq2-Picelli protocol.

treatment_protocol: High-risk PV patients (above age 60 and/or history of thromboembolic event) were treated with cytoreductive hydroxyurea, acetylsalicylic acid and phlebotomies. Low-risk patients (criteria for high risk not fulfilled) were treated with acetylsalicylic acid and phlebotomies. Phlebotomies were only performed when the hematocrit was above 45%.

value: hematopoietic stem/multipotent progenitor cells

tag: donor id

tag: patient vs control

value: patient

tag: cytoreductive treatment

value: hydroxyurea treatment

tag: disease progression status

value: not progressed

value: Blood


title: ChIP H3K27ac on FoxA1L/L;FoxA2L/L - sample 1

source_name: ChIP H3K27ac on FoxA1L/L;FoxA2L/L


title: Epi-HOT2

description:
Epi cells transduced by the lentiviral construct expressing cDNA of HOTAIR
H2

value: Epi-HOT


title: Control antago-miR rep1


title: XS8c.None.Vector.First.p4


title: XS7c.None.EWS-FLI1.First.p4


title: PID115star_CMP_MEP


title: Antago-miR-541 rep3

value: mmu-miR-451-5p antago-miR transfection


title: XS7b.None.EWS-FLI1.First.p4


title: Epi-HOT1

description:
Epi cells transduced by the lentiviral construct expressing cDNA of HOTAIR
H1


title: Haemo_GMP

value: granulocyte-macrophage progenitors

value: control

value: no cytoreductive treatment


title: PID115star_CMP

value: common myeloid progenitors


title: Haemo_MEP

value: megakaryocyte-erythrocyte progenitors


title: Antago-miR-541 rep1

value: ESC-derived neural progenitor cells


title: XS7a.None.EWS-FLI1.First.p4

value: Human mesenchymal progenitor (hMPro cells)


title: XS6e.26orf.Vector.First.p4

value: Vector


title: MUS_RNA_FLen_F2R2

city: Shenzhen

first: JING

last: LUO

email: luoj17@lzu.edu.cn, luojing9520@163.com

address: No 7,Pengfei Road,Dapeng District

country: China

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
Sequencing reads were trimmed by cutadapt (1.8.dev0).
Trimmed reads were mapped with bowtie2(version 2.1.0) to the mm9 with local alignment strategy.
Sam file and bam file processing were using samtools.
Genome_build: mm9
Supplementary_files_format_and_content: bed file include reads mapping information

source_name: mESCs

growth_protocol: Mouse embryo stem cells  which removed feeders were grown at 37 °C in a 5% CO2 incubator in DMEM supplemented with 15% fetal bovine serum (Gibco; 10099-141), Penicillin-Streptomycin, 0.1 mM nonessential amino acids(NEAA; 11140-050), 0.1 mM β-mercaptoethanol (Gibco; 21985-023), 1% Sodium pyruvate (Gibco; 11360-070), 1000 U/ml LIF (Millipore; ESG1107) and 2i inhibitors, on gelatin-coated(0.1% v/v) plates. The culture medium was changed daily. After three days of culture, the cells were lysed directly using TRIzol (Invitrogen; 15596026) for 5 min, and then directly to isolate RNA or store at -80 °C.

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the manufacturer’s protocol.
We recycle unmapped reads from standard RNA-seq data, and selected one of unmapped reads as a model. Then, we design specific reverse transcription primers to capture its both ends separately to produce the 5’ and 3’ end first strand cDNAs. Second strand cDNAs are synthesized and combined to ultrasonic disrupted. The fragments of double strand cDNAs were subjected to construct library follow the instruction of library preparation kit(Vazyme; ND607).

value: embryonic stem cell


title: XS6d.26orf.Vector.First.p4

value: First


title: IP_L1

description: A685C15.unique-W200-G1000-islands-summary-FDR0.05_filteredBR.bed

data_processing:
Reads were mapped with Bowtie2 version 2.1.0, with a tolerance of 1 mismatch in seed alignment
Only unique mapped reads were kept for further analysis.
Peak calling was performed using sicer, version 1.1, with redundancy threshold 1, gap 400, window 200, genome fraction 0.74, Evalue 100 and FDR 0.05. Input was given as control.
Peaks showing overlap with black regions were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: peaks files

growth_protocol: For each cell-line, cells were grown up to 90% confluence in 600 cm² square dishes in MEM-alpha medium supplemented with non-essential amino-acids and sodium pyruvate, at 37°C, 5% CO2.

extract_protocol:
First, cells were fixed for 10 min at 37°C by adding room temperature Crosslinking Buffer to culture medium (to final concentrations of 50 mM TrisHCl pH 8, 100 mM NaCl, 1 mM EDTA, 1% formaldehyde). Fixation was topped by adding Glycine to a final concentration of 250 mM and incubates 5 min at room temperature. After two washes of ice-cold PBS, cells were scraped twice in 30 ml and 15 ml PBS. Cells were pelleted for 10 min at 4000 rpm 4°C, washed in ice-cold PBS and resuspended in 10 ml Cell Lysis Buffer (10 mM TrisHCl pH 8, 25 mM KCl, 0.5% NP-40) supplemented with AEBSF. After incubating 10 min on ice, lysate was passed 10 times through a 20G needle and incubated again for 10 min on ice. Nuclei were pelleted for 15 min at 3500 rpm 4°C and resuspended in 3.4 ml Sonication Buffer (50 mM TrisHCl pH 8, 10 mM EDTA, 0.1% SDS) supplemented with AEBSF. Nuclei were then divided in 2 tubes and sonicated for 20 min at 4°C on the Diagenode Bioruptor Pico according to manufacturer’s instructions. Finally, poorly sonicated chromatin was pelleted for 10 min at 16 000g and supernatant was recovered and added to blocked Protein A beads (Ademtech, 04230) for pre-clearing of chromatin. After incubating for 3 hours at 4°C on a rotating wheel, 200 µl were taken as Input. The rest of the chromatin was incubated overnight at 4°C on a rotating wheel with IP antibodies: Lsd1 (Abcam ab195405). The next day, 50µl blocked protein A beads were added to the chromatin and incubated 4 hours at 4°C on a rotating wheel. They were then washed twice in FA150 buffer (50 mM HEPES pH 7.4, 1 mM EDTA, 1% Triton X-100, 150 mM NaCl, 0.1% NA-Deoxycholate, 0.1% SDS), twice in FA500 (50 mM HEPES pH 7.4, 1 mM EDTA, 1% Triton X-100, 500 mM NaCl, 0.1% Na-Deoxycholate, 0.1% SDS) and once in TE (10 mM TrisHCl pH 8, 1 mM EDTA). To elute chromatin, beads were resuspended in 100 µl ChIP Elution Buffer (50 mM TrisHCl pH 7.4, 10 mM EDTAs 1% SDS) and incubated for 1 hour at 65°C with 650 rpm shaking. Supernatant was then recovered, NaCl was added to a final concentration of 200 mM and incubated overnight in a 65°C waterbath to remove crosslinks. The next day, samples were treated with RNase for one hour at 37°C and with proteinase K for one hour at 45°C. DNA was then purified using Qiagen PCR Purification columns and quantified using Qubit dsDNA HS kit.
ChIP-seq libraries were prepared with TruSeq ChIP Sample Prep Kit (IP-202-1012, Illumina)

value: Epi-HOT<delta>L

tag: chip antibody

value: Lsd1 (Abcam, catalog# ab195405, lot# GR319278-1)

tag: fraction

value: IP DNA


title: IP_L2

description: A685C16.unique-W200-G1000-islands-summary-FDR0.05_filteredBR.bed


title: CTR1

description:
Epi cells transduced by the lentiviral construct expressing GFP
G1

value: Epi-CTR


title: Haemo_HSC

value: hematopoietic stem/multipotent progenitor cells

value: not progressed

value: Blood


title: Haemo_CMP_MEP


title: IP_P2

description: A685C14.unique-W200-G1000-islands-summary-FDR0.05_filteredBR.bed

value: Epi-HOT<delta>P


title: Priming.3.4

city: Boston

first: Michael

last: Wheeler

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
The data was demultiplexed using the inDrop pipeline (https://github.com/indrops/indrops) using the library index.
The reads were trimmed using Trimmomatic (v0.39) and the cell barcodes were checked against the cell barcode whitelist provided by the inDrop pipeline.
Reads were aligned to mouse (GRCm38) genome by bowtie.
The reads were quantified and expression of genes was calculated using the inDrop pipeline.
Genome_build: GRCm38
Supplementary_files_format_and_content: 10X format output including sparse matrix, barcode.tsv and gene.tsv

source_name: mCherry+ cells from Gfap-Cre;TVA-G(f/+) mice labeled with RabDG-mCherry-EnvA

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, labeled with Miltenyi anti-Dead Cell and anti-myelin kits, then magnetically purified and washed. Cells were sorted by flow cytometry based on mCherry fluorescence. Post-sort, cells were washed then processed by inDrop
Libraries were created according to the InDrop v3 protocol derived from Klein et al. Cell 2015.
inDrop scRNA-Seq

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

tag: strain

tag: Sex

value: Male


title: Priming.3.3

value: mCherry+ cells from Gfap-Cre;TVA-G(f/+) mice labeled with RabDG-mCherry-EnvA


title: XS6b.26orf.Vector.First.p4


title: PID106_GMP

value: granulocyte-macrophage progenitors

value: patient

value: hydroxyurea treatment


title: XS6a.26orf.Vector.First.p4

value: Human mesenchymal progenitor (hMPro cells)


title: PID106_HSC


title: Priming.3.2


title: IP_P1

description: A685C13.unique-W200-G1000-islands-summary-FDR0.05_filteredBR.bed

tag: cell line


title: Priming.3.1


title: CTR2

description:
Epi cells transduced by the lentiviral construct expressing GFP
G2


title: XS5e.26orf.EWS-FLI1.First.p4


title: PID106_CMP_MEP


title: Priming.2.4


title: Antago-miR-541 rep2

value: ESC-derived neural progenitor cells

tag: Stage

value: mmu-miR-451-5p antago-miR transfection


title: PID199_GMP

tag: tissue


title: IP_G2

description: A685C10.unique-W200-G1000-islands-summary-FDR0.05_filteredBR.bed


title: Haemo_CMP

value: common myeloid progenitors

value: control

value: no cytoreductive treatment


title: XS8a.None.Vector.First.p4

tag: lentiviral library

value: Vector

value: First


title: XS6c.26orf.Vector.First.p4

tag: oncogene


title: IP_H1

description: A685C11.unique-W200-G1000-islands-summary-FDR0.05_filteredBR.bed

value: Epi-HOT

value: Lsd1 (Abcam, catalog# ab195405, lot# GR319278-1)

value: IP DNA


title: Priming.2.3


title: XS5d.26orf.EWS-FLI1.First.p4

tag: evolution experiment


title: XS5b.26orf.EWS-FLI1.First.p4

tag: passage


title: IP_G1

description: A685C9.unique-W200-G1000-islands-summary-FDR0.05_filteredBR.bed

value: Epi-CTR


title: PID282_MEP

tag: cell type

value: megakaryocyte-erythrocyte progenitors

value: progressed

value: Blood


title: XS5c.26orf.EWS-FLI1.First.p4


title: Priming.2.2

value: Male

value: mCherry+ cells from Gfap-Cre;TVA-G(f/+) mice labeled with RabDG-mCherry-EnvA


title: PID282_GMP

value: granulocyte-macrophage progenitors

value: patient

value: hydroxyurea treatment


title: Input_L2

value: Epi-HOT<delta>L

value: Input DNA


title: PID282_CMP

value: common myeloid progenitors


title: Input_L1


title: IP_H2

description: A685C12.unique-W200-G1000-islands-summary-FDR0.05_filteredBR.bed


title: XS5a.26orf.EWS-FLI1.First.p4

value: Human mesenchymal progenitor (hMPro cells)


title: PID282_HSC

value: hematopoietic stem/multipotent progenitor cells


title: Priming.1.3


title: Priming.1.2


title: Input_P2

value: Epi-HOT<delta>P


title: PID282_CMP_MEP


title: XS4d.None.Vector.First.p1

value: Vector

value: First


title: Priming.1.1


title: PID92_GMP

value: not progressed


title: XS4c.None.Vector.First.p1


title: Input_P1


title: Input_H2

value: Epi-HOT


title: XS4b.None.Vector.First.p1


title: Input_H1


title: XS4a.None.Vector.First.p1


title: PID92_HSC


title: PID92_MEP

value: megakaryocyte-erythrocyte progenitors


title: XS3e.None.EWS-FLI1.First.p1


title: PID92_CMP

value: Blood


title: Priming.3.2_Rabid

value: Male


title: Priming.3.3_Rabid

value: mCherry+ cells from Gfap-Cre;TVA-G(f/+) mice labeled with RabDG-mCherry-EnvA


title: Priming.3.4_Rabid


title: Priming.2.1


title: XS3d.None.EWS-FLI1.First.p1


title: XS4e.None.Vector.First.p1


title: Input_G1

value: Epi-CTR


title: PID92_CMP_MEP

value: patient


title: Priming.3.1_Rabid


title: XS3c.None.EWS-FLI1.First.p1


title: PID757_GMP

value: granulocyte-macrophage progenitors

value: control

value: no cytoreductive treatment


title: Priming.2.4_Rabid


title: Priming.2.3_Rabid


title: Infected day 10, liver, fish 4

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Arrays were scanned with GenePix 4100 microarray scanner.

data_processing: Images were processed using GenePix Pro 6.0. After removal of flagged spots lowess normalization was performed.

organism: Salmo salar

source_name: Liver

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed.

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen).

value: Liver

tag: treatment

value: IPNV infection

tag: time point

value: Day 10

source_name: Liver, mixture of all samples

tag: sample type

value: Reference


title: Priming.2.2_Rabid


title: PID757_CMP_MEP

tag: donor id

tag: patient vs control

tag: cytoreductive treatment


title: XS3a.None.EWS-FLI1.First.p1

value: Human mesenchymal progenitor (hMPro cells)


title: PID94_GMP

tag: disease progression status


title: Priming.2.1_Rabid

tag: strain


title: Input_G2

tag: chip antibody

tag: fraction

value: Input DNA


title: Infected day 10, liver, fish 3


title: PID94_HSC

value: hematopoietic stem/multipotent progenitor cells

value: not progressed


title: PID94_CMP_MEP


title: Infected day 10, liver, fish 2


title: Priming.1.2_Rabid

tag: Sex


title: Priming.1.3_Rabid


title: XS2e.26orf.Vector.First.p1

tag: tissue

value: Vector

value: First


title: Infected day 10, liver, fish 1


title: XS2c.26orf.Vector.First.p1

tag: lentiviral library


title: PID81_GMP

value: hydroxyurea treatment

value: Blood


title: Priming.1.1_Rabid

value: Male

value: mCherry+ cells from Gfap-Cre;TVA-G(f/+) mice labeled with RabDG-mCherry-EnvA


title: PID81_CMP_MEP

value: patient


title: Infected day 8, liver, fish 4

value: Day 8


title: XS2b.26orf.Vector.First.p1

tag: oncogene


title: Infected day 8, liver, fish 2


title: XS3b.None.EWS-FLI1.First.p1

tag: evolution experiment


title: PID81_HSC


title: XS2a.26orf.Vector.First.p1

tag: passage


title: Infected day 6, liver, fish 5

value: Day 6


title: PID240_GMP

tag: cell type

value: granulocyte-macrophage progenitors

value: no cytoreductive treatment


title: Infected day 8, liver, fish 1

value: Liver

tag: treatment

value: IPNV infection


title: XS2d.26orf.Vector.First.p1

value: Human mesenchymal progenitor (hMPro cells)


title: PSPC1-0h-GFP-Ser2P-2

city: Beijing

first: Hai

last: Qi

address: Zhongguancun North Street

department: School of Medicine

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version
Reads obtained from ChIP-seq library sequencing were aligned to the mm9 genome assembly using bowtie2 program with default parameters.
Peaks were called using the MACS program (p < 10e-3).
Bigwig files were obtained by deeptools from mapped reads files.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files containing the sequencing signals of ChIP-seq

source_name: AID-FB(KI)-PSPC1 mESC (constructed from CJ9 mES cells) transiently express GFP

growth_protocol: ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
ChIP was done following previously protocol with modifications (Shen, 2008). Briefly, cells were crosslinked on plate with 1% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
Libraries were prepared by Tn5 according to the ChIPmentation protocols (Schmidl et al, 2015).
ChIP was done following previously protocol with modifications (Shen, 2008). Briefly, cells were crosslinked on plate with 3% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.

treatment_protocol: Cells were transfected with GFP.

value: embryonic stem cells

value: transfected with FLAG-tagged GFP 48 hrs prior to ChIP procedure

value: Pol II Ser2P (CST, 13499)

tag: affinity purification


title: PSPC1-3h-GFP-Ser2P-1

treatment_protocol: Cells were transfected with GFP. 48 hours post transfection, cells were treated by adding 1 mM IAA, and culture at 37℃ for 3 hours

value: transfected with FLAG-tagged GFP 48 hrs prior to ChIP procedure, 3 hours


title: PSPC1-3h-GFP-Ser2P-2


title: PID206_CMP_MEP

value: not progressed


title: XS1d.26orf.EWS-FLI1.First.p1

value: First


title: Infected day 6, liver, fish 4

tag: time point

tag: sample type

value: Reference


title: Infected day 6, liver, fish 3


title: PSPC1-3h-RRMmut-Ser2P-1

source_name: AID-FB(KI)-PSPC1 mESC (constructed from CJ9 mES cells) transiently express PSPC1-RRMmut

treatment_protocol: Cells were transfected with PSPC1-RRMmut. 48 hours post transfection, cells were treated by adding 1 mM IAA, and culture at 37℃ for 3 hours

value: transfected with FLAG-tagged PSPC1-RRMmut 48 hrs prior to ChIP procedure, 3 hours


title: XS1b.26orf.EWS-FLI1.First.p1


title: XS1c.26orf.EWS-FLI1.First.p1


title: Infected day 6, liver, fish 2


title: PID206_GMP

tag: donor id

tag: patient vs control

value: Blood


title: PSPC1-0h-GFP-Ser2P-1


title: PID115_GMP

value: patient

tag: cytoreductive treatment

tag: disease progression status


title: PSPC1-3h-RRMmut-Ser2P-2

tag: strain

tag: chip antibody


title: PID206_HSC

value: hematopoietic stem/multipotent progenitor cells


title: Control, liver, fish 4

value: Before infection


title: Infected day 4, liver, fish 4

value: Day 4


title: Infected day 4, liver, fish 3


title: XS1a.26orf.EWS-FLI1.First.p1


title: sRNA-RSV-Rep3

city: Ningbo

first: Cui

last: Weijun

address: Fenghua Road No. 818

institute: Ningbo University

description:
small RNA
RSV_derived small RNA_expression_all.txt

data_processing:
Genome_build: RSV genome sequence (Sequence ID：DQ333941.2,DQ333942.2,DQ333943.2,DQ333944.2)
mRNA-Seq: Illumina Casava1.8+ software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using in-house ACGT101(1.4) software. Clean reads were aligned to the N. benthamiana Genome transcripts v0.4.4 reference genome using the Bowtie package.Differential gene expression analysis were performed using ACGT101_DESeq(1.4). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam. Unique sRNA sequences were then obtained for each library. The sRNA sequence were mapped to the RSV genomic sequences to obtain RSV-derived siRNA with Botwtie.
Degradome-Seq: The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.1. Get some degradome data (RNA-seq reads from 5' ends of uncapped RNAs, where the 1st nt of the read represents the in vivo 5' end), free from adapter sequences. Map the degradome reads to the appropriate transcriptome using appropriate thresholds.Filter the mapped data, if required. Summarize the mapped degradome data into a "degradome density file" using script 'CleaveLand3_map2dd.pl'.Generate small RNA / mRNA alignments using 'targetfinder.pl'. Compare the degradome density file to the target predictions, and output significant hits using script 'CleaveLand3_analysis.pl'. Generate "t--plots" of the targets using script 'CleaveLand3_t-- plotter.pl'.The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Supplementary_files_format_and_content: transcript_expression_all.txt: tab-delimited text files include FPKM values of transcript for each Sample
RSV_derived small RNA_expression_all.txt: tab-delimited text files include TPM values of RSV-derived small RNA for each Sample
degradome_density_output.txt: tab-delimited text files include density values of genes (gene identifiers can be searched at ftp://ftp.solgenomics.net/genomes/Nicotiana_benthamiana/annotation/Niben044/Niben.genome.v0.4.4.transcripts.fasta)

organism:
Nicotiana benthamiana
Tenuivirus oryzaclavatae

source_name: leaves

growth_protocol: N. bentamiana plants were grown in a greenhouse at 23–25 °C, with a 16-h day/ 8-h night light cycle under well-watered conditions.

extract_protocol:
The six small RNA library was generated from the customer sample using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure

treatment_protocol: N. benthamiana plants at the six-leaf stage were mechanically inoculated with crude extracts from RSV-infected rice leaves.

tag: age

value: 7 days infection

value: RSV inoculated

tag: genotype

value: wild type


title: Control, liver, fish 1

tag: tissue

value: Liver


title: PSPC1-3h-WT-Ser2P-2

source_name: AID-FB(KI)-PSPC1 mESC (constructed from CJ9 mES cells) transiently express PSPC1-WT

treatment_protocol: Cells were transfected with wildtype PSPC1. 48 hours post transfection, cells were treated by adding 1 mM IAA, and culture at 37℃ for 3 hours

value: embryonic stem cells

value: transfected with FLAG-tagged PSPC1-WT 48 hrs prior to ChIP procedure; IAA, 3 hours


title: PSPC1-0h-RRMmut-Ser2P-1

treatment_protocol: Cells were transfected with PSPC1-RRMmut.

value: transfected with FLAG-tagged PSPC1-RRMmut 48 hrs prior to ChIP procedure

value: Pol II Ser2P (CST, 13499)


title: PSPC1-0h-RRMmut-Ser2P-2


title: PID115_MEP

value: megakaryocyte-erythrocyte progenitors

value: no cytoreductive treatment

value: not progressed


title: XS1e.26orf.EWS-FLI1.First.p1

value: Human mesenchymal progenitor (hMPro cells)

tag: lentiviral library

tag: oncogene

value: First


title: PSPC1-3h-trun-Ser2P-1

source_name: AID-FB(KI)-PSPC1 mESC (constructed from CJ9 mES cells) transiently express PSPC1-ΔLCS2

treatment_protocol: Cells were transfected with PSPC1-ΔLCS2. 48 hours post transfection, cells were treated by adding 1 mM IAA, and culture at 37℃ for 3 hours

value: transfected with FLAG-tagged PSPC1-ΔLCS2 48 hrs prior to ChIP procedure; IAA, 3 hours


title: Infected day 4, liver, fish 2

value: IPNV infection

value: Reference


title: Control, liver, fish 3

value: Before infection


title: mRNA-RSV-Rep2

data_processing:
Genome_build: N. benthamiana Genome transcripts v0.4.4 (ftp.solgenomics.net/genomes/Nicotiana_benthamiana)
mRNA-Seq: Illumina Casava1.8+ software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using in-house ACGT101(1.4) software. Clean reads were aligned to the N. benthamiana Genome transcripts v0.4.4 reference genome using the Bowtie package.Differential gene expression analysis were performed using ACGT101_DESeq(1.4). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam. Unique sRNA sequences were then obtained for each library. The sRNA sequence were mapped to the RSV genomic sequences to obtain RSV-derived siRNA with Botwtie.
Degradome-Seq: The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.1. Get some degradome data (RNA-seq reads from 5' ends of uncapped RNAs, where the 1st nt of the read represents the in vivo 5' end), free from adapter sequences. Map the degradome reads to the appropriate transcriptome using appropriate thresholds.Filter the mapped data, if required. Summarize the mapped degradome data into a "degradome density file" using script 'CleaveLand3_map2dd.pl'.Generate small RNA / mRNA alignments using 'targetfinder.pl'. Compare the degradome density file to the target predictions, and output significant hits using script 'CleaveLand3_analysis.pl'. Generate "t--plots" of the targets using script 'CleaveLand3_t-- plotter.pl'.The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Supplementary_files_format_and_content: transcript_expression_all.txt: tab-delimited text files include FPKM values of transcript for each Sample
RSV_derived small RNA_expression_all.txt: tab-delimited text files include TPM values of RSV-derived small RNA for each Sample
degradome_density_output.txt: tab-delimited text files include density values of genes (gene identifiers can be searched at ftp://ftp.solgenomics.net/genomes/Nicotiana_benthamiana/annotation/Niben044/Niben.genome.v0.4.4.transcripts.fasta)

extract_protocol:
Six transcriptome libraries were constructed using the Illumina mRNA-Seq sample preparation kit(Directional mRNA-Seq Sample Preparation Part # 15018460 Rev. A, October 2010.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure

value: 7 days infection


title: PID730_CMP

value: common myeloid progenitors

value: control

value: Blood


title: PSPC1-3h-trun-Ser2P-2

value: embryonic stem cells


title: mRNA-RSV-Rep3

value: RSV inoculated

value: wild type


title: PID115_CMP

value: patient


title: mRNA-RSV-Rep1


title: PID115_HSC

value: hematopoietic stem/multipotent progenitor cells


title: PSPC1-0h-trun-Ser2P-2

treatment_protocol: Cells were transfected with PSPC1-ΔLCS2.

value: transfected with FLAG-tagged PSPC1-ΔLCS2 48 hrs prior to ChIP procedure

value: Pol II Ser2P (CST, 13499)


title: PID115_CMP_MEP

value: no cytoreductive treatment

value: not progressed


title: PID64_GMP

value: granulocyte-macrophage progenitors


title: RSV-dgd

data_processing:
Library strategy: Degradome-Seq
Genome_build: N. benthamiana Genome transcripts v0.4.4 (ftp.solgenomics.net/genomes/Nicotiana_benthamiana)
mRNA-Seq: Illumina Casava1.8+ software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using in-house ACGT101(1.4) software. Clean reads were aligned to the N. benthamiana Genome transcripts v0.4.4 reference genome using the Bowtie package.Differential gene expression analysis were performed using ACGT101_DESeq(1.4). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam. Unique sRNA sequences were then obtained for each library. The sRNA sequence were mapped to the RSV genomic sequences to obtain RSV-derived siRNA with Botwtie.
Degradome-Seq: The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module. A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.1. Get some degradome data (RNA-seq reads from 5' ends of uncapped RNAs, where the 1st nt of the read represents the in vivo 5' end), free from adapter sequences. Map the degradome reads to the appropriate transcriptome using appropriate thresholds.Filter the mapped data, if required. Summarize the mapped degradome data into a "degradome density file" using script 'CleaveLand3_map2dd.pl'.Generate small RNA / mRNA alignments using 'targetfinder.pl'. Compare the degradome density file to the target predictions, and output significant hits using script 'CleaveLand3_analysis.pl'. Generate "t--plots" of the targets using script 'CleaveLand3_t-- plotter.pl'.The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Supplementary_files_format_and_content: transcript_expression_all.txt: tab-delimited text files include FPKM values of transcript for each Sample
RSV_derived small RNA_expression_all.txt: tab-delimited text files include TPM values of RSV-derived small RNA for each Sample
degradome_density_output.txt: tab-delimited text files include density values of genes (gene identifiers can be searched at ftp://ftp.solgenomics.net/genomes/Nicotiana_benthamiana/annotation/Niben044/Niben.genome.v0.4.4.transcripts.fasta)

extract_protocol:
For degradome-seq, mRNA was enriched using oligo-d(T) magnetic beads. The enriched mRNA was mixed with biotinylated random primers and were ligated to 5' adaptors. First-strand cDNA was reverse-transcribed from ligated mRNA products and then amplified with PCR.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure

value: a pool of 3 biological replicates of RSV-infected Nicothiana benthamiana


title: PID730_GMP


title: PSPC1-trun-ChIP-2

source_name: CJ9 mES cells transiently express FLAG-tagged PSPC1-ΔLCS2

extract_protocol:
ChIP was done following previously protocol with modifications (Shen, 2008). Briefly, cells were crosslinked on plate with 3% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.
Libraries were prepared by Tn5 according to the ChIPmentation protocols (Schmidl et al, 2015).
ChIP was done following previously protocol with modifications (Shen, 2008). Briefly, cells were crosslinked on plate with 3% FMA for 10 min, then quenched by 1/20 volume of 2.5 M glycine. after two times of ice cold PBS wash, cell were harvested by trypsin digestion, and lysis by 1 x nuclei lysis buffer. The lysate were further sonicated into average DNA size 200-500 bp. spin at 14000rpm for 15 min, transferred the supernatant into a new tube and diluted by adding 5 × volume of ChIP dilution buffer. Added 5 μg FLAG antibody, end to end rotate overnight at 4℃. The target were further captured by adding 20 ul Protein A/G UltraLink Resin, further rotated for 4 hours at 4℃. After thoroughly washing, the targeted DNA was eluted by elution buffer with protease K at 65℃.

value: FLAG (Sigma-Aldrich, F3165)


title: PSPC1-0h-trun-Ser2P-1


title: sRNA-RSV-Rep2


title: Gadd45g_2

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from GENERGY BIO company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of GENERGY BIO.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: 46c mESCs_Gadd45g

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. MGI2000 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: cell line

value: mouse embryonic stem cells (mESCs)

tag: genotype/variation

value: flag-tagged gadd45g overexpression


title: A2: sham

city: guizhou

first: Hua

last: Fang

address: 83 Zhongshan East Road, Nanming District

institute: Guizhou university

data_processing:
Reads were counted using htseq-count (version 0.9.1 ) with Ensembl release 75 genome annotation reference .
Reads were mapped to the mm9 genome using bwa mem (version 0.7.5a-r405) with the following options: -t 20 -k 14 -T 1 -L 3,3 -O 6,6 -E 3,3. bwa mem output was processed using find_circ2 (https://github.com/rajewsky-lab/find_circ2) to detect backspliced reads. circRNA candidates flagged by find_circ2 as SHORT or HUGE were discarded
Genome_build: mm9

source_name: normal

extract_protocol:
RNA was harvested using Trizol reagent. VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: treatment

value: sham


title: PSPC1-3h-WT-Ser2P-1

tag: cell type

value: transfected with FLAG-tagged PSPC1-WT 48 hrs prior to ChIP procedure; IAA, 3 hours

tag: affinity purification


title: sRNA-RSV-Rep1

value: 7 days infection


title: Gadd45g_1


title: PSPC1-RRMmut-ChIP-1

source_name: CJ9 mES cells transiently express FLAG-tagged PSPC1-RRMmut

value: embryonic stem cells

value: transfected with FLAG-tagged PSPC1-RRMmut 48 hrs prior to ChIP procedure


title: PSPC1-trun-ChIP-1


title: PID304_HSC

value: patient

value: Blood


title: PSPC1-0h-WT-Ser2P-2

treatment_protocol: Cells were transfected with wildtype PSPC1.

value: transfected with FLAG-tagged PSPC1-WT 48 hrs prior to ChIP procedure


title: PID730_HSC

value: hematopoietic stem/multipotent progenitor cells

value: control


title: PSPC1-0h-WT-Ser2P-1

value: Pol II Ser2P (CST, 13499)


title: PID730_MEP

value: megakaryocyte-erythrocyte progenitors

value: no cytoreductive treatment

value: not progressed


title: Control, liver, fish 2

value: Liver

tag: time point

value: Before infection

tag: sample type

value: Reference


title: PSPC1-WT-ChIP-2

source_name: CJ9 mES cells transiently express FLAG-tagged PSPC1-WT

value: FLAG (Sigma-Aldrich, F3165)


title: PSPC1-RRMmut-ChIP-2


title: PID304_GMP

value: granulocyte-macrophage progenitors

tag: donor id

tag: patient vs control


title: Embryoids_d8

city: Charlottesville

first: Bernard

last: Thisse

state: VA

address: 1340 Jefferson Park Avenue

institute: University of Virginia

data_processing:
Raw base call files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 3.1.0, default parameters)
FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Singel-Cell Gene Expression Software Cell Ranger ("count pipeline", version 3.1.0, default parameters).Genomic reference: "refdata-cellranger-mm10-3.0.0".
Cell Ranger "count" outputs were aggregated and normalized to the same sequencing depth and then the feature-barcode matrices were recomputed on the combined data. Matrix file for the samples were then processed and analyzed with Seurat R software 3.2.1
Genome_build: mm10
Supplementary_files_format_and_content: normalized tpm counts. Csv file

source_name: pool of 90 embryoids

growth_protocol: E14TG2a ESCs were seeded at 4.6x10^4 cells per cm2 in 0.1% gelatinized Petri dishes and cultivated in Knock-Out DMEM supplemented with 15% Serum Replacement, 3 uM CHIR99021, 1 uM PD03259021, ESGRO LIF (1000 U/mL), L-glutamine, non-essential amino acids, beta-mercaptoethanol and antibiotic-antimycotic for 2 days at 37°C and 5% CO2. 50 cells and 100 cells aggregates were generated in hanging drops. Aggregates were transferred into  DMEM/F12 and Neurobasal Medium, supplemented with N2, B27, beta-mercaptoethanol and antibiotic-antimycotic, in hanging drops for 48 hours at 37°C and 5% CO2

extract_protocol:
90 d8 embryoids were pooled and dissociated in accutase (Gibco: #A11105-01) for 30min at 37c with pipetting every 5 minute intervals. Cells were filtered using 40um flowmi cell strainers (Belart cat 136800040).Cells were then fixed in prechilled methanol for 30 min on ice  and stored at -20c.
Cells were rehydrated in 1xDPBS -1.0%BSA -0.5U/ul RNASE inhibitors and filtered again to eliminate debris and cell agglomerates. Cell were immediately counted using the Countess 3 automated cell counter (Thermofisher scientific) and processed for 10X Genomics scRNA-seq
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium‚single cell 3'V3) RNA-seq

treatment_protocol: on Day 3, 50 cell embryoid bodies were incubated in 10ng/ml of BMP4 for 8 hours at 37c, 5%CO2. They were then fused to 100 cell untreated embryoids bodies and let to develop until day 8 in N2B27.

value: E14TG2a ESCs

value: Day 8


title: PID730_CMP_MEP

source_name: Blood

tag: cytoreductive treatment

tag: disease progression status


title: A3: ischemia/reperfusion (I/R)

source_name: myocardial ischemia-reperfusion injury model mice

tag: strain

value: heart


title: PID304_MEP

value: patient


title: PID304_CMP

value: common myeloid progenitors

value: Blood


title: A4: ischemia/reperfusion (I/R)

value: myocardial ischemia-reperfusion injury model mice


title: Flag_2

source_name: 46c mESCs_flag

value: mouse embryonic stem cells (mESCs)

value: Flag overexpression


title: A1: sham

value: sham


title: 8596_IgM

status: Public on Apr 21 2021

type: protein

city: Irvine

first: Li

last: Liang

state: CA

address: MedSurge II

institute: University of California Irvine

description: Total IgM

hyb_protocol: The microarray slides were probed with human sera diluted 1:100 in protein array blocking buffer (GVS Life Sciences, Sanford, ME) overnight at 4°C and washed with TTBS buffer (20mM Tris-HCl, 150mM NaCl, 0.05% Tween 20 in double-distilled water (ddH2O) adjusted to pH 7.5 and filtered) three times for 5 min each. A mixture of human IgG and IgM secondary antibodies conjugated to quantum dot fluorophores Q800 and Q585, respectively, was applied to each of the microarray pads and incubated for 2 h at room temperature, and pads were then washed with TTBS three times for 5 min each and dried.

scan_protocol: The slides were imaged using an ArrayCam imager (Grace Bio-Labs). The output RGB TIFF files generated by the imager were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: Nonspecific binding of secondary antibodies and signals from saline controls were subtracted. Data was then normalized using quantum normalization. The mean fluorescence of the 4 replicate spots for each antigen was used for analysis.

molecule: protein

source_name: Plasma

value: Plasma

tag: sample collection site

value: UCI hospital

tag: days post onset of symptoms

tag: pcr screening for sars-cov-2

value: Positive


title: 8599_IgM

description: Total IgM

tag: tissue


title: 8805_IgM

description: Total IgM


title: PID304_CMP_MEP

value: no cytoreductive treatment

value: not progressed


title: 8512_IgM

description: Total IgM


title: Flag_1


title: PSPC1-WT-ChIP-1

value: embryonic stem cells

value: transfected with FLAG-tagged PSPC1-WT 48 hrs prior to ChIP procedure

tag: chip antibody

value: FLAG (Sigma-Aldrich, F3165)


title: 8281_IgM

description: Total IgM


title: 8524_IgM

description: Total IgM


title: 8808_IgM

description: Total IgM


title: 8810_IgM

description: Total IgM


title: 8761_IgM

description: Total IgM


title: 8736_IgM

description: Total IgM


title: 8205_IgM

description: Total IgM


title: 8397_IgM

description: Total IgM


title: 8045_IgM

description: Total IgM


title: 8090_IgM

description: Total IgM


title: 8273_IgM

description: Total IgM


title: 8347_IgM

description: Total IgM


title: 8801_IgM

description: Total IgM


title: 7965_IgM

description: Total IgM


title: 7972_IgM

description: Total IgM


title: 8006_IgM

description: Total IgM


title: 7811_IgM

description: Total IgM


title: 8003_IgM

description: Total IgM


title: 7740_IgM

description: Total IgM


title: 7999_IgM

description: Total IgM


title: 7702_IgM

description: Total IgM


title: 7594_IgM

description: Total IgM


title: 7970_IgM

description: Total IgM


title: 7769_IgM

description: Total IgM


title: 7940_IgM

description: Total IgM


title: 8078_IgM

description: Total IgM


title: 7896_IgM

description: Total IgM


title: 7736_IgM

description: Total IgM


title: 7697_IgM

description: Total IgM


title: 7516_IgM

description: Total IgM


title: 7442_IgM

description: Total IgM


title: 7457_IgM

description: Total IgM


title: 7688_IgM

description: Total IgM


title: 7470_IgM

description: Total IgM


title: 7549_IgM

description: Total IgM


title: 7488_IgM

description: Total IgM


title: 8761_IgG

description: Total IgG


title: 8805_IgG

description: Total IgG


title: 7460_IgM

description: Total IgM


title: 8736_IgG

description: Total IgG


title: 8808_IgG

description: Total IgG


title: 7422_IgM

description: Total IgM


title: 8801_IgG

description: Total IgG


title: 8599_IgG

description: Total IgG


title: 7424_IgM

description: Total IgM


title: 8810_IgG

description: Total IgG


title: 8512_IgG

description: Total IgG


title: 8524_IgG

description: Total IgG


title: 7502_IgM

description: Total IgM


title: 8596_IgG

description: Total IgG


title: 8281_IgG

description: Total IgG


title: 8397_IgG

description: Total IgG


title: 8205_IgG

description: Total IgG


title: 8273_IgG

description: Total IgG


title: 8006_IgG

description: Total IgG


title: 8347_IgG

description: Total IgG


title: 8078_IgG

description: Total IgG


title: 8003_IgG

description: Total IgG


title: 8090_IgG

description: Total IgG


title: 7999_IgG

description: Total IgG


title: 7970_IgG

description: Total IgG


title: 7965_IgG

description: Total IgG


title: 7896_IgG

description: Total IgG


title: 7811_IgG

description: Total IgG


title: 7769_IgG

description: Total IgG


title: 7736_IgG

description: Total IgG


title: 7697_IgG

description: Total IgG


title: 7702_IgG

description: Total IgG


title: 7940_IgG

description: Total IgG


title: 7516_IgG

description: Total IgG


title: 7594_IgG

description: Total IgG


title: 8045_IgG

description: Total IgG


title: 7972_IgG

description: Total IgG


title: 7502_IgG

description: Total IgG


title: SB-967 adjacent nontumor sample

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

data_processing:
Salmon (version 0.10.2) was used to process RNA-seq data. Human genome assembly GRCh37 was used as reference. After alignment, DEseq2 was used to concatenate all individual samples and run comparative analysis. For 16S rRNA data, llumina Miseq paired-end reads were aligned to human reference genome hg19 with Bowtie2. SINA/SILVA classifier was used for classification. Operational taxonomic units (OTUs) were produced by binning sequences with identical taxonomic assignments.
Genome_build: hg19
Supplementary_files_format_and_content: concatenated results from Salmon for each sample, OTUs

source_name: colorectal

extract_protocol:
DNA and RNA was extracted from the archived frozen tissues using the Qiagen Allprep DNA/RNA/miRNA kits (Qiagen,  Hilden, Germany) according to the manufacturer’s protocol.  DNA and RNA was extracted from sections of FFPE tumor and non tumor samples using the Qiagen Allprep DNA/RNA FFPE (Qiagen, Hilden, Germany) kits according to the manufacturer’ protocol except that xylene was used to de-paraffinize the FFPE samples.
RNA sequence libraries were prepared with the Kapa RNA kit with RiboErase (Roche Sequencing and Life Science Kapa Biosystems, Wilmington, MA) according to the manufacturer’s protocol. 16S rRNA libraries were constructed by generating broad-range PCR amplicons using barcoded primers that target the V3V4 variable region of the 16S rRNA gene: primers 338F (5’ ACTCCTACGGGAGGCAGCAG) and 806R (5’ GGACTACHVGGGTWTCTAAT), Illumina paired-end sequencing was performed on the Miseq platform with versions v2.4 of the Miseq Control Software and of MiSeq Reporter, using a 600 cycle version 3 reagent kit.

value: Non tumor


title: SB-738 tumor sample

value: Tumor


title: SB-1197 tumor sample


title: SB-738 adjacent nontumor sample


title: SB-967 tumor sample


title: 7549_IgG

description: Total IgG


title: 7470_IgG

description: Total IgG


title: 7457_IgG

description: Total IgG


title: 7488_IgG

description: Total IgG


title: 7460_IgG

description: Total IgG


title: 7422_IgG

description: Total IgG


title: 7424_IgG

description: Total IgG


title: SB-950 adjacent nontumor sample


title: SB-920 tumor sample


title: 7688_IgG

description: Total IgG


title: SB-920 adjacent nontumor sample


title: 7368_IgG

description: Total IgG


title: 7442_IgG

description: Total IgG


title: SB-906 tumor sample


title: SB-912 adjacent nontumor sample


title: SB-950 tumor sample


title: Exosome-treated hMSCs 2

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

description: RNA sequencing of Exosome-treated hMSCs

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human or mm10 mouse reference genome using hisat2 software.
Genome_build: hg19 for Homo sapiens and mm10 for Mus musculus
Supplementary_files_format_and_content: Txt file of read count for RNA-seq.

source_name: Mesenchymal stem cell

extract_protocol: For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: cell type/tissue

value: Mesenchymal stem cell

value: Exosome-treated

tag: passage


title: Exosome-treated pMSCs 2

description: RNA sequencing of Exosome-treated pMSCs

source_name: Primary mesenchymal stem cell

value: Primary mesenchymal stem cell

tag: treatment


title: Exosome-treated pMSCs 1

description: RNA sequencing of Exosome-treated pMSCs


title: PBS-treated pMSCs 1

description: RNA sequencing of PBS-treated pMSCs

value: PBS-treated


title: PBS-treated pMSCs 2

description: RNA sequencing of PBS-treated pMSCs


title: PBS-treated hMSCs 2

description: RNA sequencing of PBS-treated hMSCs


title: PBS-treated hMSCs 1

description: RNA sequencing of PBS-treated hMSCs


title: SB-647 tumor sample


title: SB-597 adjacent nontumor sample


title: SB-906 adjacent nontumor sample


title: SB-647 adjacent nontumor sample


title: Exosome-treated hMSCs 1

description: RNA sequencing of Exosome-treated hMSCs


title: SB-597 tumor sample


title: V-WT.ctrl-2

city: GuangZhou

first: Yongfei

last: Hu

state: GUangDong

address: Road LuJing

institute: Dermatology Hospital of Southern Medical University

description:
which figure to present this data: y axis of fig.3G, subfigure 3.
samples.FPKM.Matrix.tar.gz

data_processing:
Deep-seq was used to determine the indel frequency. Briefly, On-target sites were amplified by PCR with indexed forward and indexed reverse primers. After purification and concentration normalization, PCR products were pooled into different libraries. Completed libraries were generated by a second round of PCR using the pooled libraries as templates and sequenced with 150-bp paired-end reads on Illumina HiSeq instrument. Pooled samples were demultiplexed according to the indexes within forward and reverse primers for the first round PCR. The primers were trimmed from the raw reads, and clean reads were mapped to the gene sequences with software BWA v0.7.17. SAMtools v0.1.18 was used to obtain sorted bam files. Finally, R package Genomic Alignments were used to count Indels in alignment results, and all figures were ploted using R package ggplot2.
Hisat2 v2.0.52 was used to build the index of the reference genome and align the RNA-Seq paired-end clean reads with the reference genome. Then, StringTie v2.23 was used to count the read numbers mapped to each gene. Fragments Per Kilobase per Million (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression was defined by a Benjamini-Hochberg adjusted p value (q value | FDR) of <0.05 and fold change of >2 or <0.5. All figures were plotted using R package ggplot2.
Genome_build: hg38
Supplementary_files_format_and_content: samples.FPKM.Matrix.tar.gz: tab-delimited excel files include FPKM values for each sample. samples.indel.counts.tar.gz: the results of insertion and deletion frequency in particular gene locs with gene editing.[three genes were edited in 6F data files(FANCF, MYOD, Site6), three genes were edited in Deep-1/Deep-2 data files(FGF21, HBG, IL1RN)], more detailed information is annotated in the figure legends.

source_name: HEK293T (embryonic kidney cell)

extract_protocol:
The RNA-seq analysis has been described in our previous work. Briefly, total RNA was isolate with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and mRNA was enriched and fragmented. Deep-seq was used to determine the indel frequency. Briefly, total DNA was extracted using sarkosyl lysis buffer and on-target sites were amplified by PCR.
RNA libraries were constructed by the following steps: the first strand synthesis, the second strand synthesis, adaptor adding, and PCR amplification. After verification and quantification, libraries were sequenced by HiSeq instrument with 150bp paired-end module. DNA libraries were constructed by the following steps: on-target sites were amplified by PCR with indexed forward and indexed reverse primers. After purification and concentration normalization, PCR products were pooled into different libraries. Completed libraries were generated by a second round of PCR using the pooled libraries as templates and sequenced with 150-bp paired-end reads on Illumina HiSeq instrument.

tag: cell type

value: embryonic kidney cell

tag: cell line

value: transfected with plasmid V-WT only


title: V-WT.gIL1RN.15nt-2

description:
which figure to present this data: y axis of fig.3G, subfigure 3. And y axis of fig S4K, subfigure 3. And x axis of fig S4K, subfigure 1.
samples.FPKM.Matrix.tar.gz

value: transfected with plasmids V-WT with sgRNA targeting gene IL1RN 15nt


title: V-WT.gIL1RN.15nt-1


title: V-WT.ctrl-1


title: SB-463 tumor sample


title: SB-470 tumor sample

description: SB-470-T-450-S_ATTCAGAA-GTACTGAC_AC8L2CANXX_L001


title: SB-526 tumor sample

description: SB-526-T-498-S_TCTCGCGC-CAGGACGT_AC8L2CANXX_L002


title: V-D.gIL1RN.22nt-2

description:
which figure to present this data: y axis of fig.3G, subfigure 1. And y axis of fig S4K, subfigure 2. And x axis of fig S4K, subfigure 3. And x axis of fig.4H, right panel.
samples.FPKM.Matrix.tar.gz

value: transfected with plasmids V-D with sgRNA targeting gene IL1RN 22nt


title: SB-912 tumor sample


title: 7740_IgG

description: Total IgG

value: Plasma

value: UCI hospital


title: V-D.gIL1RN.22nt-1


title: SB-452 tumor sample


title: SB-463 adjacent nontumor sample


title: SB-452 adjacent nontumor sample


title: SB-396 tumor sample


title: V-D.gIL1RN.15nt-1

description:
which figure to present this data: y axis of fig.3G, subfigure 2. And y axis of fig S4K, subfigure 1. And x axis of fig S4K, subfigure 2.
samples.FPKM.Matrix.tar.gz

value: transfected with plasmids V-D with sgRNA targeting gene IL1RN 15nt


title: V-D.Ctrl-2

description:
which figure to present this data: x axis of fig.3G, subfigure 1/2.
samples.FPKM.Matrix.tar.gz

value: transfected with plasmid V-D only


title: V-D.Ctrl-1


title: SB-396 adjacent nontumor sample


title: SB-300 tumor sample


title: miniCAFE.gIL1RN.22nt-1

description:
which figure to present this data: fig.4H
samples.FPKM.Matrix.tar.gz

value: transfected with plasmids miniCAFE with sgRNAs targeting gene IL1RN


title: SB-298 tumor sample


title: miniCAFE.gIL1RN.22nt-2


title: SB-298 adjacent nontumor sample


title: miniCAFE.Ctrl-1

description:
which figure to present this data: x axis of fig.4H, subfigure 1.
samples.FPKM.Matrix.tar.gz

value: transfected with plasmid miniCAFE only


title: miniCAFE.Ctrl-2


title: SB-296 tumor sample


title: Fruiting stage replicate 2 (RNA-Seq)

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
Real-Time Analysis (RTA) software
sequencing reads were aligned to the AX4 genome by Bowtie2(2.2.9)
The analysis pipeline started with pseudo-alignment of the reads using kallisto, followed by building an index and quantification process, which generated h5 files containing the raw binary files for preliminary differential analysis in sleuth.
Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05.
Genome_build: AX4
Supplementary_files_format_and_content: Data matrix was generated by sleuth

organism: Dictyostelium discoideum

source_name: Fruiting stage cells

growth_protocol: We cultured te strain at 22 °C shaken in the incubator at 180 rpm in HL5 medium with 300 μg/ml streptomycin

extract_protocol:
mRNA was extracted from D. Discoedium cells using Dynabeads mRNA direct micro purification kit (Invitrogen)
8 groups were prepared for RNA-seq libraries using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific)

tag: developmental stage

value: Fruiting


title: Mound stage replicate 2 (RNA-Seq)

source_name: Mound cells

value: Mound


title: SB-157 tumor sample

description: SB-157-T-145_CGGCTATG-CAGGACGT_AC8L2CANXX_L001

tag: sample type

value: Tumor


title: SB-296 adjacent nontumor sample

value: Non tumor


title: V-D.gIL1RN.15nt-2


title: Streaming stage replicate 2 (RNA-Seq)

source_name: Streaming cells

value: Streaming


title: Fruiting stage replicate 1 (RNA-Seq)


title: SB-1230 tumor sample


title: Vegetative stage replicate 2 (RNA-Seq)

source_name: Vegetative cells

value: Vegetative


title: Mound stage replicate 1 (RNA-Seq)


title: SB-1230 adjacent nontumor sample


title: SB-1260 adjacent nontumor sample


title: Vegetative stage replicate 1 (RNA-Seq)


title: SB-141 tumor sample rep2

description: SB-141-T-130_TAATGCGC-CAGGACGT_AC8L2CANXX_L001


title: SB-1260 tumor sample


title: SB-300 adjacent nontumor sample


title: SB-1217 tumor sample


title: SB-1217 adjacent nontumor sample


title: F2_H3K9me3

data_processing:
The raw fastq files were trimmed for the first and last 8 nucleotides, the multiqc was use to summarize the fastQC results, and the trimmed files were mapped to the Dictyostelium discoideum genome using bowtie2
The duplicated reads were removed by picard and sorted bam files were subject to peak calling with MACS2.
Differential binding analyses were performed by R package Diffbind using log2 normalized ChIP read counts with FDR < 0.05
Genome_build: AX4
Supplementary_files_format_and_content: Peak files generated by macs2

source_name: Fruiting cells (AX4) replicate 2

extract_protocol:
10 million D. discoideum cells were cross-linked with 1x linking buffer (11 mM HEPES-NaOH, 110 mM NaCl, 1.1 mM EDTA and 1.1 mM EGTA) with 1% formaldehyde for 10 minutes at RT and quenched by 2M glycine. The samples were fragmented by applying a biorupter for 25 cycles in the cold room with 30 seconds on and 30 seconds off per cycle. The precleared chromatin was incubated with antibody-coupled bead slurries and rotated at 4°C overnight. DNA was eluted from the beads by 200 µl TE with 1% SDS.
Histone ChIP-Seq libraries were generated using the Ovation Ultralow V2 kit (Nugen, 0344-32) according to the manufacturer’s instructions.  Libraries were PCR amplified for 13-16 cycles depending on the antibody, and library quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Seventy-five bp reads were generated on the Illumina Nextseq 500 (Illumina). ChIP-seq were sequenced to a depth of at least 8 million total reads/sample.


title: F2_H3K27ac


title: F2_H3K36me3


title: SB-1173 tumor sample


title: F2_H3K27me3


title: F2_H3K4me3


title: SB-1172 tumor sample


title: F2_H3K4me1


title: SB-1172 adjacent nontumor sample


title: SB-1173 adjacent nontumor sample


title: SB-1150 tumor sample


title: F2_input


title: F1_H3K36me3

source_name: Fruiting cells (AX4) replicate 1


title: F2_H3


title: SB-1140 tumor sample


title: F1_H3K27me3


title: SB-1140 adjacent nontumor sample


title: F1_H3K27ac


title: SB-110 tumor sample

description: SB-110-T-100_GAATTCGT-CAGGACGT_AC8L2CANXX_L001


title: SB-118 tumor sample

description: SB-118-T-108_CTGAAGCT-CAGGACGT_AC8L2CANXX_L002


title: F1_H3K9me3


title: SB-1092 tumor sample


title: SB-1092 adjacent nontumor sample


title: F1_H3K4me3


title: F1_H3K4me1


title: SB-108 tumor sample

description: SB-108-T-098_GAGATTCC-GTACTGAC_AC8L2CANXX_L001


title: SB-1035 adjacent nontumor sample


title: F1_input


title: 7368_IgM

description: Total IgM

value: Positive


title: F1_H3


title: SB-1026 adjacent nontumor sample


title: M2_H3K36me3

source_name: Mound cells (AX4) replicate 2


title: M2_H3K27me3


title: SB-1150 adjacent nontumor sample


title: M2_H3K27ac


title: SB-1026 tumor sample


title: M2_H3K9me3


title: SB-014 tumor sample

description: SB-014-T14_ATTCAGAA-CAGGACGT_AC8L2CANXX_L002


title: SB-010 tumor sample

description: SB-010-T10_GAGATTCC-CAGGACGT_AC8L2CANXX_L001


title: M2_H3K4me3


title: M2_H3K4me1


title: M2_input


title: M2_H3


title: SB-002 tumor sample

description: SB-002-T2_TCCGGAGA-CAGGACGT_AC8L2CANXX_L001


title: SB-867 adjacent nontumor sample


title: SB-1035 tumor sample


title: SB-008 tumor sample

description: SB-008-T8_CGCTCATT-CAGGACGT_AC8L2CANXX_L001


title: M1_H3K27me3

source_name: Mound cells (AX4) replicate 1


title: SB-867 tumor sample


title: SB-521 adjacent nontumor sample


title: SB-521 tumor sample


title: M1_H3K9me3


title: SB-074 tumor sample

description: SB-074-T-067_CGCTCATT-GTACTGAC_AC8L2CANXX_L001


title: SB-501 tumor sample


title: Streaming stage replicate 1 (RNA-Seq)


title: M1_H3K27ac


title: SB-460 adjacent nontumor sample


title: M1_input


title: SB-457 adjacent nontumor sample


title: M1_H3K4me1


title: M1_H3K4me3


title: SB-460 tumor sample


title: S2_H3K36me3

source_name: Streaming cells (AX4) replicate 2


title: M1_H3


title: SB-262 adjacent nontumor sample


title: S2_H3K27me3


title: S2_H3K27ac


title: SB-262 tumor sample


title: M1_H3K36me3


title: SB-226 adjacent nontumor sample


title: SB-1197 adjacent nontumor sample


title: S2_H3K9me3


title: S2_H3K4me3


title: SB-086 tumor sample


title: S2_H3K4me1


title: SB-068 adjacent nontumor sample


title: SB-141 tumor sample rep1


title: S2_H3


title: SB-068 tumor sample


title: S1_H3K36me3

source_name: Streaming cells (AX4) replicate 1


title: SB-064 tumor sample


title: SB-064 adjacent nontumor sample


title: S1_H3K27ac


title: S1_H3K27me3


title: S1_H3K9me3


title: SB-052 tumor sample


title: SB-036 tumor sample


title: S1_H3K4me3


title: S1_H3K4me1


title: S1_input


title: SW1990_LINC00842-KD

city: Guangzhou

first: Xudong

last: Huang

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file contains  expression values of all samples

source_name: pancreatic cancer

growth_protocol: LINC00842-KD and KD-Ctrl PANC-1 or SW1990 cells were cultured in DMEM medium supplemented with 10% FBS at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated from LINC00842-KD and KD-Ctrl PANC-1 or SW1990 cells using the TRIzol reagent according to the manufacturer's protocol, The quantity and integrity of RNA yield was assessed by using the K5500 and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
Briefly,RNAs were ligated with 3' RNA adapter, and followed by 5' adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA). The purified library products were evaluated using the Agilent 2200 TapeStation, The libraries were sequenced by HiSeq 2500 (Illumina, USA) with single-end 50bp at Ribobio Co. Ltd (Ribobio, China)

treatment_protocol: Five μg pLenti-U6-spgRNA v2.0-CMV-sfGFP-P2A-3Flag-spCas9 vector contain control sgRNA or sgRNA targeting the TSS of LINC00842 were co-transfected with 15 μg CMV promoter-puro-3 × polyA stop cassette donor vector, respectively. After electroporation, 0.5 μg/ml puromycin was added and individual colonies were picked and expanded in 96-well plates. When the cell population in each colony was large enough, genomic DNA was extracted and the genomic integration was validated by PCR. After testing the expression of LINC00842 in CRISPR edited PANC-1 and SW190 cells, we chose positive colony named as “LINC00842-KD”, and these cells together with KD-Ctrl cells were then used for RNA-seq

value: pancreatic cancer

value: LINC00842 knockdown by CRISPR/Cas9 system


title: SB-457 tumor sample


title: SB-052 adjacent nontumor sample


title: PANC-1_LINC00842-KD


title: PANC-1_KD-Ctrl

value: Control


title: V2_H3K36me3

source_name: Vegetative cells (AX4) replicate 2


title: V2_H3K27me3


title: ddcc_LL 36 h_Bio1

first: Lei

last: Wang

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

description: ddcc_vs_Col-0 FPKM.txt

data_processing:
150-nucleotide paired-end high-throughput sequencing was performed on an Illumina Hiseq platform
Then low quality sequencing reads were removed. The obtained clean data were aligned against the Arabidopsis thaliana reference genome sequence (TAIR10 Genome Release) with HISAT2. DESeq2 was used for differential gene expression analysis. Genes with q≤0.05 and |log2_ratio|≥1 were identified as differentially expressed genes (DEGs).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: ten day-old whole seedlings

growth_protocol: For Aza vs Mock samples, plants were grown under 12 h light/12 h dark conditions at 22ºC for 10 days. For ddcc vs Col-0 samples, plants were transferred to continous white light condition after grown 8 day in 12 h light/12 dark condition.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion) and treated with DNase I (Thermo Fisher).
sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following manufacturer’s instructions.

treatment_protocol: 40 mg/L was used for Aza treatment at ZT 1 h. And the seedlings were collected at the next day at ZT 1h and ZT 13 h.The seedlings of the experiment group about  ddcc vs Col-0  were collected at constant light at LL 24 h and LL 36 h after 8 days incubation.

tag: time point

value: LL 36 h

tag: medium

value: MS+3% sucrose

tag: genotype

value: drm1-2 drm2-2 cmt3-11t cmt2-3

tag: age


title: V2_H3K27ac

tag: strain


title: S2_input


title: V2_H3K4me3


title: Col-0_LL 36 h_Bio1

description: ddcc_vs_Col-0 FPKM.txt

value: Wild type


title: ddcc_LL 24 h_Bio2

description: ddcc_vs_Col-0 FPKM.txt

value: LL 24 h


title: V2_H3K4me1


title: ddcc_LL 24 h_Bio1

description: ddcc_vs_Col-0 FPKM.txt


title: Col-0_LL36 h_Bio2

description: ddcc_vs_Col-0 FPKM.txt


title: V2_input


title: V2_H3K9me3


title: Col-0_LL 24 h_Bio1

description: ddcc_vs_Col-0 FPKM.txt


title: V1_H3K36me3

source_name: Vegetative cells (AX4) replicate 1


title: Aza_ZT13 h_Bio1

value: ZT 13h


title: V1_H3K27ac


title: S1_H3


title: SW1990_KD-Ctrl


title: Mock_ZT13 h_Bio1


title: Col-0_LL 24 h_Bio2

description: ddcc_vs_Col-0 FPKM.txt


title: Aza_ZT1 h_Bio2

value: ZT 1h


title: ddcc_LL 36 h_Bio2

description: ddcc_vs_Col-0 FPKM.txt


title: Mock_ZT13 h_Bio2


title: V1_H3K4me1


title: Aza_ZT1 h_Bio1


title: V1_input


title: Mock_ZT1 h_Bio2


title: V1_H3


title: Mock_ZT1 h_Bio1


title: Fruiting stage replicate 2

data_processing:
Real-Time Analysis (RTA) software
The raw fastq files were trimmed for the first and last 8 nucleotides, the multiqc was use to summarize the fastQC results, and the trimmed files were mapped to the Dictyostelium discoideum genome using bowtie2
The mitochondria genome was removed in the alignment process
The duplicated reads were removed by picard and sorted bam files were subject to peak calling with MACS2
Open chromatin regions and peak annotation were deducted with Diffbind and ChIPSeeker, respectively
Genome_build: AX4
Supplementary_files_format_and_content: Peak files for open chromatin regions

source_name: Fruiting stage cell nuclei

extract_protocol:
Frozen pellets of D discoideum cells from the various stages were washed twice with cold PBS and lysed with 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal-630
Nuclei were transposed using the Nextera DNA Library Prep Kit.  Transposed libraries were amplified for 11 cycles and size selected for fragments ranging 200-1000 bp. ATAC-seq experiments were sequenced to a minimum depth of 10 million reads/sample.

value: Fruiting


title: Fruiting stage replicate 1


title: Alkbh3-/-_2

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description:
All small RNA from 15 to 50 nt
217KO

data_processing:
The adapters were removed by using cutadapt
the reads were aligned to the mouse(mm10) genome
The tRNA annotations is download from GtRNAdb2.0(ref here)
Reads mapped to tRNA and were counted.
Genome_build: mm10
Supplementary_files_format_and_content: RNA reads count

source_name: Epididymis

growth_protocol: All animal studies were conducted in accordance with institutional guidelines for the care and use of experimental animals

extract_protocol:
Total RNA (100 μg) were denatured at 70 °C for 5 min and separated by a 15% TBE-Urea gel with 20/100 or 10/60 oligo length standard ladder (Integrated DNA Technologies, Coralville, IA). After visualized by SYBR Gold (Ref. S11494 from Life Technologies), tRFs (15~50nt) in gels were cut according to sizes and recovered by small RNA PAGE recovery kit (Zymo Research, Irvine, CA, USA).
The recovered tRFs was used to establish the library by NEB small RNA library preparation kit (E7330S).

value: epididymis


title: V2_H3


title: Alkbh3-/-_1

description:
All small RNA from 15 to 50 nt
215KO


title: V1_H3K9me3


title: ecd1_3

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

country: Germany

institute: CECAD Research Center  Cologne

data_processing:
Base calling were done with the Illumina RTA software at run time
Reads were aligned to the Drosophila reference genome BDGP Release 6 (dm6) using Tophat2 v2.0.10
Mapped reads summarization was performed on the gene meta-feature level using featureCounts v1.6.4
Differential gene expression was assessed using DESeq2
Differential splicing events were determined using LeafCutter algorithm.
Genome_build: BDGP Release 6 (dm6)
Supplementary_files_format_and_content: .xlsx file containing sheet summary, QCR report, Lists of differentially regulated genes and their DESeq2 normalized counts, Enriched GO terms for up- and downregulated genes in ecd1 condition, and List of differentially spliced genes in ecd1 condition

organism: Drosophila melanogaster

source_name: Whole larvae

growth_protocol: w1118 and ecd1 larvae were grown at 18 °C for 10 days.

extract_protocol:
Total RNA was isolated from eight third instar larvae using the standard protocol with TRI Reagent and DNase I treatment.
RNA libraries were generated according to the Illumina protocol and pair-end sequenced on an Illumina HiSeq 2000 instrument at 100 bp read length. Image analysis and base calling were done with the Illumina RTA software at run time.

treatment_protocol: w1118 and ecd1 larvae grown at 18 °C for 10 days were upshifted to 29 °C for 2 days.

tag: condition

value: 18 °C for 10 days, upshifted to 29°C for 2 days

value: Whole larvae


title: V1_H3K4me3


title: Mound stage replicate 1

source_name: Mound cell nuclei

value: Mound


title: Aza_ZT13 h_Bio2


title: V1_H3K27me3

value: Vegetative


title: Streaming stage replicate 1

source_name: Streaming cell nuclei

value: Streaming


title: Wild type

description:
All small RNA from 15 to 50 nt
B6WT


title: Mound stage replicate 2


title: Vegetative stage replicate 1

source_name: Vegetative cell nuclei


title: ecd1_2


title: w1118_1


title: Streaming stage replicate 2


title: Vegetative stage replicate 2


title: w1118_3


title: w1118_2


title: Total_Brain_dilp235T_2

first: Linda

last: Partridge

address: Joseph-Stelzmann-Straße 9B

department: Partridge

institute: Max Planck Institute for Biology of Ageing

description:
Sample Name: AU
tophat2_counts_bdgp6.csv

data_processing:
Adapter trimming using flexbar (version 2.5),  flexbar -n 10 -f i1.8 -q 20 -m 30 -j -z G
Mapping of reads to BDGP6.28 genome using tophat2 (version 2.1.0), tophat2 --library-type fr-firststrand
Read counts determined using summarizeOverlaps function (R package GenomicAlignments, version 1.10.1), mode “intersectionNotEmpty”
Genome_build: BDGP6.26
Supplementary_files_format_and_content: tophat2_counts_bdgp6.csv: comma-separated text file containing raw counts of flybase gene transcripts in all samples

source_name: Brain

growth_protocol: Fly stocks were kept at 25°C on a 12-h light and 12-h dark cycle and fed a standard sugar/yeast/agar diet (SYA). In all experiments, once-mated females were reared at controlled larval densities. Adult flies were aged (10 days) in SYA food vials (10–25 flies per vial) prior to analysis. Dissections were carried out in cold phosphate- buffered saline (PBS) and tissues either directly analysed or frozen on dry ice.

extract_protocol:
Isolation of RNA from frozen tissue samples of all genotypes (wDah control and  dilp2-3,5 flies, both in the presences and absence of Wolbachia) was performed on three independent biological replicates using Trizol Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions, followed by DNase treatment (Qiagen). RNA quality was determined using the BioRad Experion (BioRad). RNA-seq library preparation and sequencing was performed by the Max Planck-Genome-centre Cologne, Germany (http://mpgc.mpipz.mpg.de/home/). Stranded TruSeq RNA-seq library preparation was performed on 2 μg of total RNA after rRNA depletion (Ribo-zero). Brain samples were treated as above, however total RNA input was reduced (500ng).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

value: adult

value: 10 days


title: Total_Brain_dilp235T_3

description:
Sample Name: AV
tophat2_counts_bdgp6.csv


title: Total_Brain_dilp235_3

description:
Sample Name: AS
tophat2_counts_bdgp6.csv


title: Total_Brain_dilp235_2

description:
Sample Name: AR
tophat2_counts_bdgp6.csv


title: Total_Brain_wDahT_3

description:
Sample Name: AP
tophat2_counts_bdgp6.csv

value: wDahT


title: Total_Brain_dilp235_1

description:
Sample Name: AQ
tophat2_counts_bdgp6.csv


title: Total_Brain_wDahT_2

description:
Sample Name: AO
tophat2_counts_bdgp6.csv


title: Total_Brain_wDah_3

description:
Sample Name: AM
tophat2_counts_bdgp6.csv

value: wDah


title: Total_Brain_wDah_2

description:
Sample Name: AL
tophat2_counts_bdgp6.csv


title: Total_Brain_wDah_1

description:
Sample Name: AK
tophat2_counts_bdgp6.csv


title: ecd1_1


title: 3m_2_scRNA

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to Cell Ranger pre-built mm10 genome, and counted following the Cell Ranger v.2.2.0 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R.
Genome_build: Cell Ranger pre-built mm10 reference
Supplementary_files_format_and_content: two csv files containing raw count values for each cell in the two samples, respectively

source_name: cardiac

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
Adult murine hearts were perfused with Langendorff apparatus as described with minor modifications. Hearts were then removed from the Langendorf apparatus while intact (with tissues loosely connected) and saved 10cm culture dish containing ice-cold 4% FBS/PBS solution supplemented with 0.25 mM EDTA. Subsequently, atria were removed, and the ventricle were further mechanically dissociated by pipetting. The resulting cell suspension were collected, passed through 100 um filter. Non-cardiomyocytes suspension was obtained after 2-3 rounds of centrifuging at 50g for 3min to remove CM pellet, followed by last centrifuge at 2,000 rpm for 5 min. The pelleted non-myocytes were treated with 1ml red blood cell lysis buffer (Gibco) at room temperature, and washed twice with wash buffer (4%FBS/PBS).To prepare single live cell suspension for scRNA-seq, the isolated non-myocytes were probed with 7-Amino Actinomycin D (7-AAD, R&D Systems), and Pacific Blue-conjugated Annexin V and SYTOX (Thermo) at 4 °C in the dark for 15min.  The cells were pelleted, and then resuspended with 0.04%BSA/PBS buffer. Flow cytometry sorting was performed on Becton Dickinson FACS Aria II, and the single live cells (7-AAD negative) were captured and collected in buffer containing 0.04%BSA/PBS. Following sorting, cell number concentration and viability of each sample were manually counted, counted using automated cell counter (LUNA system, Logos biosytems) plus Acridine orange (AO)/propidium iodide (PI) dual nuclear staining. andCell concentration was adjusted to 1e6 cells/ml for subsequent scRNA scRNA-seq  via 10x Gemonics platform.
Libraries were prepared using Chromium Single Cell 3’ Library and Gel Bead Kit v.2 and Chromium i7 Multiplex kit.

value: heart

value: 10-12 weeks

value: wild type


title: Total_Gut_dilp235T_3

description:
Sample Name: AJ
tophat2_counts_bdgp6.csv

source_name: Gut

value: Gut


title: Total_Gut_dilp235T_2

description:
Sample Name: AI
tophat2_counts_bdgp6.csv


title: Total_Gut_dilp235_3

description:
Sample Name: AG
tophat2_counts_bdgp6.csv


title: 3m_1_scRNA


title: Total_Gut_wDahT_2

description:
Sample Name: AC
tophat2_counts_bdgp6.csv


title: Total_Brain_dilp235T_1

description:
Sample Name: AT
tophat2_counts_bdgp6.csv


title: Total_Gut_wDahT_1

description:
Sample Name: AB
tophat2_counts_bdgp6.csv


title: Total_Gut_dilp235_2

description:
Sample Name: AF
tophat2_counts_bdgp6.csv


title: Total_Gut_wDah_3

description:
Sample Name: AA
tophat2_counts_bdgp6.csv


title: Total_Gut_wDahT_3

description:
Sample Name: AD
tophat2_counts_bdgp6.csv


title: Total_Gut_wDah_1

description:
Sample Name: Y
tophat2_counts_bdgp6.csv


title: Total_Gut_wDah_2

description:
Sample Name: Z
tophat2_counts_bdgp6.csv


title: Total_Fatbody_dilp235T_2

description:
Sample Name: W
tophat2_counts_bdgp6.csv

source_name: Fat

value: Fat


title: Total_Fatbody_dilp235T_3

description:
Sample Name: X
tophat2_counts_bdgp6.csv


title: Total_Fatbody_dilp235_3

description:
Sample Name: U
tophat2_counts_bdgp6.csv


title: Total_Brain_wDahT_1

description:
Sample Name: AN
tophat2_counts_bdgp6.csv


title: Total_Fatbody_wDahT_2

description:
Sample Name: Q
tophat2_counts_bdgp6.csv


title: Total_Fatbody_dilp235_2

description:
Sample Name: T
tophat2_counts_bdgp6.csv


title: Total_Fatbody_dilp235_1

description:
Sample Name: S
tophat2_counts_bdgp6.csv


title: Total_Fatbody_wDahT_1

description:
Sample Name: P
tophat2_counts_bdgp6.csv


title: Total_Fatbody_wDah_3

description:
Sample Name: O
tophat2_counts_bdgp6.csv


title: Total_Gut_dilp235T_1

description:
Sample Name: AH
tophat2_counts_bdgp6.csv


title: Total_Gut_dilp235_1

description:
Sample Name: AE
tophat2_counts_bdgp6.csv


title: Total_Thorax_dilp235T_1

description:
Sample Name: J
tophat2_counts_bdgp6.csv

source_name: Thorax

value: Thorax


title: Total_Fatbody_wDah_1

description:
Sample Name: M
tophat2_counts_bdgp6.csv


title: Total_Thorax_dilp235T_3

description:
Sample Name: L
tophat2_counts_bdgp6.csv


title: Total_Fatbody_wDah_2

description:
Sample Name: N
tophat2_counts_bdgp6.csv


title: Total_Thorax_dilp235_3

description:
Sample Name: I
tophat2_counts_bdgp6.csv


title: Total_Thorax_dilp235T_2

description:
Sample Name: K
tophat2_counts_bdgp6.csv


title: Total_Thorax_wDahT_2

description:
Sample Name: E
tophat2_counts_bdgp6.csv


title: Total_Thorax_dilp235_2

description:
Sample Name: H
tophat2_counts_bdgp6.csv


title: Total_Thorax_wDahT_1

description:
Sample Name: D
tophat2_counts_bdgp6.csv


title: Total_Thorax_dilp235_1

description:
Sample Name: G
tophat2_counts_bdgp6.csv


title: Total_Thorax_wDahT_3

description:
Sample Name: F
tophat2_counts_bdgp6.csv


title: Total_Thorax_wDah_3

description:
Sample Name: C
tophat2_counts_bdgp6.csv


title: Total_Thorax_wDah_1

description:
Sample Name: A
tophat2_counts_bdgp6.csv


title: Total_Thorax_wDah_2

description:
Sample Name: B
tophat2_counts_bdgp6.csv


title: Total_Fatbody_dilp235T_1

description:
Sample Name: V
tophat2_counts_bdgp6.csv


title: Total_Fatbody_wDahT_3

description:
Sample Name: R
tophat2_counts_bdgp6.csv


title: hert2_batch1

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: single cell RNA-seq from PDX

data_processing:
Single-cell RNA-seq data generated by 10x genomics are preprocessed using the Cell Ranger (https://www.10xgenomics.com/) to obtain the UMI (unique molecular identifier) counts for each gene in each indexed cell type.
To get a reliable single cell transcriptome dataset, we exclude the cells with less than 200 genes expressed (UMI > 0) or the cells with more than 80% UMIs from mitochondrial genes. The filtered data is then normalized and scaled by using Seurat to remove unwanted source of variations {Lun, 2016 #8526}.
Read 1 (R1) has a length of 26 bases corresponding to the 10x cell barcode's 16 bases, followed by the UMI's 10 bases. Read 2 (R2) has a length of 98 bases corresponding to biological RNA. Index 1 (I1) contains the sample index sequence information that is incorporated into the i7 index read (8-bp).
The reads were aligned to both human (hg19) and mouse (mm10) reference genomes and  then assigned to one as part of the Cell Ranger processing pipeline
Each sample consists of six multiplexed libraries that were demultiplexed using Cell Ranger. The sample name and index corresponding to each library are listed in scRNAseq_merged_sample_description.csv
Genome_build: GRCh37
Supplementary_files_format_and_content: csv files contain the raw UMI counts in gene level
Supplementary_files_format_and_content: csv file scRNAseq_merged_sample_description.csv describes the components of each merged sample

organism:
Homo sapiens
Mus musculus

source_name: PDX tumor and stroma cells

growth_protocol: PDX1 and PDX2 cells were injected into mammary fat pads of NOG mice

extract_protocol:
Tumors were dissociated to single cell and processed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v2 Reagent Kit, 10xGenomics).
Libraries were constructed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v2 Reagent Kit, 10xGenomics).

treatment_protocol: mice were randomized when tumors reached 5mm diameter and treated for 3 weeks; paclitaxel weekly 6.5mg/kg, lapatinib 6x/week 30mg/kg, T-DM1 weekly 3.6mg/kg, trastuzumab weekly 6mg/kg, pertuzumab weekly 20mg/kg

tag: animal id

value: mouse 1


title: hert2_batch2

description: single cell RNA-seq from PDX

value: mouse 2


title: hert1_batch1

description: single cell RNA-seq from PDX


title: Experiment 2 - hCD33M

city: Edmonton

first: Jason

middle: R.

last: Plemel

state: Alberta

address: 5-64 Heritage Medical Research Centre

department: Department of Medicine

country: Canada

institute: University of Alberta

data_processing:
10x cell range count
Seurat
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited Count matrix text file

source_name: brain

extract_protocol:
Fluorescence activated cell sorting
10x Chromium 3' platform

value: brain

value: 8 weeks

tag: Sex

value: Male


title: Experiment 2 - Control

tag: tissue

value: Wild type


title: hert1_batch2

description: single cell RNA-seq from PDX


title: Experiment 1 - hCD33m

value: Female


title: Experiment 1 - hCD33M


title: Experiment 1 - Control


title: Experiment 2 - hCD33m