title: ACH3K18_shcontrol_DMSO_ChIP-Seq


title: ACH3K27_shaml1-eto_DMSO_ChIP-Seq

status: Public on Feb 14 2020

type: SRA

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

country: USA

institute: Saint Louis University School of Medicine

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: human AML cells

growth_protocol: Kasumi-1 cells were maintained in RPMI 1640 with 10% fetal bovine serum (FBS).

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

treatment_protocol: Kasumi-1 cells were transduced with control or AML1-ETO-specific shRNAs. Transduced cells were selected with Puromycin. If appropriate, the cells were also treated with DMSO or TSA (HDAC-specific inhibitor Trichostatin A).

tag: cell type

value: human t(8;21) AML cells

tag: transduction

value: AML1-ETO-specific shRNA

tag: chip antibody

value: ACH3K27 (Abcam, ab96005)

tag: treatment

value: DMSO


title: ACH3K27_shcontrol_DMSO_ChIP-Seq

value: shcontrol


title: ACH3K9_shaml1-eto_TSA_ChIP-Seq

value: ACH3K9 (Abcam, ab32129)

value: TSA (Trichosanthin)


title: ACH3K9_shcontrol_DMSO_ChIP-Seq


title: ACH3K27_shcontrol_TSA_ChIP-Seq


title: ACH3K9_shaml1-eto_DMSO_ChIP-Seq


title: ACH3K27_shaml1-eto_TSA_ChIP-Seq


title: ACH3K9_shcontrol_TSA_ChIP-Seq


title: AML1-ETO_shaml1-eto_ChIP-Seq

value: AML1-ETO (in-house made)


title: GCN5_shcontrol_ChIP-Seq

value: GCN5 (Santa Cruz, SC-20698)


title: AML1-ETO_shcontrol_ChIP-Seq


title: N20_shaml1-eto_ChIP-Seq

value: N20 (Santa Cruz, sc-899)


title: HDAC1_shaml1-eto_ChIP-Seq

value: HDAC1 (Thermo, Fisher PA1-860)


title: HDAC1_shcontrol_ChIP-Seq


title: GCN5_shaml1-eto_ChIP-Seq


title: P300_shcontrol_ChIP-Seq

value: P300 (Santa Cruz, SC-584)


title: HDAC3_shcontrol_ChIP-Seq

value: HDAC3 (Abcam, ab7030)


title: SMRT_shaml1-eto_ChIP-Seq

value: SMRT(Thermo Fisher,PA1-843)


title: HDAC3_shaml1-eto_ChIP-Seq


title: P300_shaml1-eto_ChIP-Seq


title: SMRT_shcontrol_ChIP-Seq


title: SH95_3

city: Amsterdam

first: Emile

middle: van den

last: Akker

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin

library_source: transcriptomic

data_processing:
Sequence quality was confirmed using Fastqc (Babraham Bioinformatics).  Spliced Transcripts Alignment to a Reference (STAR) was used to align the sequences to the human hg38 genomic reference sequence, using the following parameters: --outFilterMultimapNmax 20, --outFilterMismatchNmax 1, --outSAMmultNmax 1, - outSAMtype BAM SortedByCoordinates, quantMode GeneCounts, -outWigType wiggle, -outWigStrand Stranded, --outWigNorm RPM.  A .gtf file accessed from the UCSC genome browser on August-2018 was passed to STAR.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: vst transformed counts

molecule: total RNA

source_name: Megakaryocyte cells line, MEG-01

growth_protocol: MEG-01 were cultured in RPMI 1640 (Gibco) supplemented with 20% FSC, 50 U/mL penicillin-streptomycin (ThermoFisher Scientific, USA), L-glutamin 2mM (ThermoFisher Scientific).

extract_protocol:
RNeasy Plus Micro kit, (#74034) Qiagen, mRNA was fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation
library preparation was performed using the NEB Next® Ultra™ RNA Library Prep Kit and enriched using oligo(dT) beads
Illumina HiSeq 2500 (mRNA, 2x150bp, paired end, poly-A selected)

treatment_protocol: 24hr after lentiviral transduction, puromycin select was started and maintained over the course of 16 days.

value: short hairpin RNA targeting ATXN2

tag: time point

value: 16 days, puro selected

tag: depletion confirmed

value: Western Blot, ATXN2


title: SH95_2


title: SH93_3


title: SH93_2


title: SH95_1


title: SH002_3

value: Scrambled short hairpin RNA


title: SH93_1


title: SH002_2


title: NT_3

value: Non-tranduced


title: NT_1


title: NT_2


title: Ewing Sarcoma PDX-1058

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Raw data not submitted due to patient privacy concerns.

data_processing:
The programs "cellranger mkfastq" and "cellranger count" from the Cell Ranger software suite (v. 1.3.1) provided by 10X Genomics were used for demultiplexing and counting the reads on the reference genome GRCh38.
Sample-to-sample normalization was performed using the total number of reads in the log scale.  For all data analyses the number of reads was log10(x+1) transformed. More specifically if X is the count matrix the R code to obtain the normalised matrix X.tpm is the following : median.umi <- median(colSums(X)); X.tpm <- log(t(t(X)/colSums(X))*median.umi+1).
For each cell, reads from the k = 5 most similar cells were pooled together to define the new cell measurement, in order to reduce the effect of drop-outs.
Genome_build: GRCh38
Supplementary_files_format_and_content: The matrix.mtx file contains genewise read counts for all cells in Matrix Market format designed to encode information on sparse matrices. In this format, only cell-gene combinations with one or more reads are included in the file. genes.tsv contains the corresponding Ensembl IDs and gene symbols as tab-delimited text and barcode.tsv contains the 10X barcodes used to identify cells.

source_name: Ewing Sarcoma PDX

growth_protocol: Ewing Sarcoma Patient Derived Xenografts (PDX) were established in the laboratory by subcutaneous implantation of tumor samples in SCID mice. Patients consented preoperatively to take part in the study which received agreement by the Institutional Review Board Protocol.

extract_protocol:
Ewing PDX were dissected from mice and mechanically dissociated. The finely minced tissue was transferred to a digestion mix consisting of C02 independent medium (Gibco) containing 1 mg/mL collagenase D (Roche), 2 mg/mL hyaluronidase (Sigma) and 25 µg/mL DNAse (Sigma), incubated for 45 min at 37 °C and gently resuspended every 10 min. Cell suspension was then filtered using 70 µm and 30 µm cell strainers (Miltenyi Biotec).
Single-cell RNA-seq was performed using the Single Cell 3’GEM Code Single-Cell instrument (10x Genomics, Pleasanton, CA, USA), according to the manufacturer’s protocol. Cellular suspension (5,300 cells) was loaded on a 10x Chromium instrument to generate 3,000 single-cell GEMs, using the Chromium™ Single Cell 3' Library & Gel Bead Kit v2. The initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10x cell barcodes, UMI (Unique Molecular Identifiers) and poly(dT) sequences. GEM-RT was performed to generate barcoded full-length cDNA (53°C for 45 min, 85°C for 5 min, held at 4°C). After RT, GEMs were broken using the recovery agent and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific).
Bulk cDNA was amplified (98 °C for 3 min; 12 cycles : 98 °C for 15 s, 67 °C for 20 s, 72 °C for 1 min; 72 °C for 1 min; held at 4 °C) and then cleaned up with the SPRIselect Reagent Kit (Beckman Coulter). A qualitative analysis on the amplified cDNA was performed using Agilent Bioanalyzer high sensitivity chip.
Libraries were then constructed in 4 main steps: 1) fragmentation, end repair and A-tailing, 2) adaptor ligation, 3) post ligation cleanup with SPRIselect and 4) sample index PCR, quantified by Qubit fluorometric assay (Invitrogen) with dsDNA HS (High Sensitivity) Assay Kit and qualified using LabChip (LabChip® GX Touch™ PerkinElmer). Indexed libraries were equimolarly pooled and sequenced on an Illumina HiSeq 2500 in rapid run mode, using paired-end (PE) 26/98 according to 10x recommendations. Using a full rapid flow cell, a coverage around 100M reads per sample were obtained corresponding to 100,000 reads/cell.

treatment_protocol: No treatment

tag: tissue

value: Ewing Sarcoma


title: Ewing Sarcoma PDX-856


title: Ewing Sarcoma PDX-861


title: N20_shcontrol_ChIP-Seq

value: human t(8;21) AML cells


title: Ewing Sarcoma PDX-352


title: Ewing Sarcoma PDX-184


title: Ewing Sarcoma PDX-111: A540U437

data_processing:
Reads obtained from sequencing of cells were aligned on the human genome (v. hg19) using TopHat (version 2.0.6). Reads mapping more than once (parameter -x 1) or having edit distances of more than 3 (-N 3) were discarded.
Counting of reads on annotated genes from the GRCh37 gene build was done using htseq-count (v. HTSeq-0.5.3p9) with the following parameters: reads with a quality score less than 10 (-a 10) were discarded and reads partially overlapping with the annotated gene transcript were included in the counts unless they overlapped with another read. In all experiments analysed the STRANDED=no option was used.
Sample-to-sample normalization was performed by rescaling using DESeq-type size factors. For all data analyses the number of reads was log10(x+1) transformed.
Genome_build: hg19
Supplementary_files_format_and_content: GeneXCell tab-delimited text file with read counts

source_name: Ewing Sarcoma PDX-111

extract_protocol:
Ewing PDX were dissected from mice and mechanically dissociated. The finely minced tissue was transferred to a digestion mix consisting of C02 independent medium (Gibco) containing 1 mg/mL collagenase D (Roche), 2 mg/mL hyaluronidase (Sigma) and 25 µg/mL DNAse (Sigma), incubated for 45 min at 37 °C and gently resuspended every 10 min. Cell suspension was then filtered using 70 µm and 30 µm cell strainers (Miltenyi Biotec).
Single-cell RNA-seq was performed using the Single Cell 3’GEM Code Single-Cell instrument (10x Genomics, Pleasanton, CA, USA), according to the manufacturer’s protocol. Cellular suspension (5,300 cells) was loaded on a 10x Chromium instrument to generate 3,000 single-cell GEMs, using the Chromium™ Single Cell 3' Library & Gel Bead Kit v2. The initial step consisted in performing an emulsion where individual cells were isolated into droplets together with gel beads coated with unique primers bearing 10x cell barcodes, UMI (Unique Molecular Identifiers) and poly(dT) sequences. GEM-RT was performed to generate barcoded full-length cDNA (53°C for 45 min, 85°C for 5 min, held at 4°C). After RT, GEMs were broken using the recovery agent and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific).
Bulk cDNA was amplified (98 °C for 3 min; 12 cycles : 98 °C for 15 s, 67 °C for 20 s, 72 °C for 1 min; 72 °C for 1 min; held at 4 °C) and then cleaned up with the SPRIselect Reagent Kit (Beckman Coulter). A qualitative analysis on the amplified cDNA was performed using Agilent Bioanalyzer high sensitivity chip.
After harvest from the C1 device, each cDNA library was tagmented using the Nextera XT DNA Sample Preparation Kit (Illumina).  Libraries were quantified by Qubit fluorometric assay (Invitrogen) with dsDNA HS (High Sensitivity) Assay Kit and qualified using LabChip (LabChip® GX Touch™ PerkinElmer)


title: Ewing Sarcoma PDX-111: A540U436


title: Ewing Sarcoma PDX-111: A540U434


title: Ewing Sarcoma PDX-111: A540U438


title: Ewing Sarcoma PDX-111: A540U435


title: Ewing Sarcoma PDX-111: A540U432


title: Ewing Sarcoma PDX-111: A540U427


title: SH002_1


title: Ewing Sarcoma PDX-111: A540U428


title: Ewing Sarcoma PDX-111: A540U433


title: Ewing Sarcoma PDX-111: A540U431


title: Ewing Sarcoma PDX-111: A540U423


title: Ewing Sarcoma PDX-111: A540U426


title: Ewing Sarcoma PDX-111: A540U425


title: Ewing Sarcoma PDX-111: A540U424


title: Ewing Sarcoma PDX-111: A540U421


title: Ewing Sarcoma PDX-111: A540U429


title: Ewing Sarcoma PDX-111: A540U420


title: Ewing Sarcoma PDX-111: A540U419


title: Ewing Sarcoma PDX-111: A540U418


title: Ewing Sarcoma PDX-111: A540U416


title: Ewing Sarcoma PDX-111: A540U417


title: Ewing Sarcoma PDX-111: A540U413


title: Ewing Sarcoma PDX-111: A540U414


title: Ewing Sarcoma PDX-111: A540U415


title: Ewing Sarcoma PDX-111: A540U430


title: Ewing Sarcoma PDX-111: A540U412


title: Ewing Sarcoma PDX-111: A540U411


title: Ewing Sarcoma PDX-111: A540U422


title: Ewing Sarcoma PDX-111: A540U410


title: Ewing Sarcoma PDX-111: A540U405


title: Ewing Sarcoma PDX-111: A540U406


title: Ewing Sarcoma PDX-111: A540U407


title: Ewing Sarcoma PDX-111: A540U408


title: Ewing Sarcoma PDX-111: A540U404


title: Ewing Sarcoma PDX-111: A540U401


title: Ewing Sarcoma PDX-111: A540U403


title: Ewing Sarcoma PDX-111: A540U396


title: Ewing Sarcoma PDX-111: A540U400


title: Ewing Sarcoma PDX-111: A540U399


title: Ewing Sarcoma PDX-111: A540U397


title: Ewing Sarcoma PDX-111: A540U391


title: Ewing Sarcoma PDX-111: A540U392


title: Ewing Sarcoma PDX-111: A540U395


title: Ewing Sarcoma PDX-111: A540U393


title: Ewing Sarcoma PDX-111: A540U394


title: Ewing Sarcoma PDX-84: A472U390

source_name: Ewing Sarcoma PDX-84


title: Ewing Sarcoma PDX-84: A472U389


title: Ewing Sarcoma PDX-84: A472U386


title: Ewing Sarcoma PDX-84: A472U387


title: Ewing Sarcoma PDX-84: A472U388


title: Ewing Sarcoma PDX-84: A472U383


title: Ewing Sarcoma PDX-111: A540U409


title: Ewing Sarcoma PDX-84: A472U384


title: Ewing Sarcoma PDX-84: A472U380


title: Ewing Sarcoma PDX-84: A472U381


title: Ewing Sarcoma PDX-111: A540U398


title: Ewing Sarcoma PDX-84: A472U375


title: Ewing Sarcoma PDX-84: A472U377


title: Ewing Sarcoma PDX-84: A472U372


title: Ewing Sarcoma PDX-84: A472U371


title: Ewing Sarcoma PDX-84: A472U378


title: Ewing Sarcoma PDX-84: A472U369


title: Ewing Sarcoma PDX-84: A472U367


title: Ewing Sarcoma PDX-84: A472U370


title: Ewing Sarcoma PDX-84: A472U368


title: Ewing Sarcoma PDX-84: A472U366


title: Ewing Sarcoma PDX-84: A472U363


title: Ewing Sarcoma PDX-84: A472U365


title: Ewing Sarcoma PDX-84: A472U385


title: Ewing Sarcoma PDX-84: A472U364


title: Ewing Sarcoma PDX-84: A472U361


title: Ewing Sarcoma PDX-84: A472U360


title: Ewing Sarcoma PDX-84: A472U357


title: Ewing Sarcoma PDX-84: A472U358


title: Ewing Sarcoma PDX-84: A472U359


title: Ewing Sarcoma PDX-84: A472U382


title: Ewing Sarcoma PDX-111: A540U402


title: Ewing Sarcoma PDX-84: A472U356


title: Ewing Sarcoma PDX-84: A472U355


title: Ewing Sarcoma PDX-84: A472U353


title: Ewing Sarcoma PDX-84: A472U354


title: Ewing Sarcoma PDX-84: A472U379


title: Ewing Sarcoma PDX-84: A472U352


title: Ewing Sarcoma PDX-84: A472U373


title: Ewing Sarcoma PDX-84: A472U351


title: Ewing Sarcoma PDX-84: A472U374


title: Ewing Sarcoma PDX-84: A472U348


title: Ewing Sarcoma PDX-84: A472U345


title: Ewing Sarcoma PDX-84: A472U341


title: Ewing Sarcoma PDX-84: A472U342


title: Ewing Sarcoma PDX-84: A472U346


title: Ewing Sarcoma PDX-84: A472U344


title: Ewing Sarcoma PDX-84: A472U340


title: Ewing Sarcoma PDX-84: A472U338


title: Ewing Sarcoma PDX-84: A472U339


title: Ewing Sarcoma PDX-84: A472U337


title: Ewing Sarcoma PDX-84: A472U343


title: Ewing Sarcoma PDX-84: A472U347


title: Ewing Sarcoma PDX-84: A472U349


title: Ewing Sarcoma PDX-83: A472U330

source_name: Ewing Sarcoma PDX-83


title: Ewing Sarcoma PDX-84: A472U350


title: Ewing Sarcoma PDX-84: A472U334


title: Ewing Sarcoma PDX-83: A472U331


title: Ewing Sarcoma PDX-83: A472U332


title: Ewing Sarcoma PDX-83: A472U333


title: Ewing Sarcoma PDX-84: A472U335


title: Ewing Sarcoma PDX-83: A472U328


title: Ewing Sarcoma PDX-83: A472U329


title: Ewing Sarcoma PDX-83: A472U326


title: Ewing Sarcoma PDX-83: A472U325


title: Ewing Sarcoma PDX-84: A472U336


title: Ewing Sarcoma PDX-83: A472U324


title: Ewing Sarcoma PDX-83: A472U322


title: Ewing Sarcoma PDX-83: A472U323


title: Ewing Sarcoma PDX-83: A472U321


title: Ewing Sarcoma PDX-83: A472U317


title: Ewing Sarcoma PDX-83: A472U316


title: Ewing Sarcoma PDX-83: A472U315


title: Ewing Sarcoma PDX-83: A472U312


title: Ewing Sarcoma PDX-83: A472U313


title: Ewing Sarcoma PDX-83: A472U305


title: Ewing Sarcoma PDX-83: A472U308


title: Ewing Sarcoma PDX-83: A472U306


title: Ewing Sarcoma PDX-83: A472U319


title: Ewing Sarcoma PDX-83: A472U314


title: Ewing Sarcoma PDX-83: A472U327


title: Ewing Sarcoma PDX-83: A472U320


title: Ewing Sarcoma PDX-83: A472U311


title: Ewing Sarcoma PDX-83: A472U307


title: Ewing Sarcoma PDX-83: A472U310


title: Ewing Sarcoma PDX-83: A472U304


title: Ewing Sarcoma PDX-83: A472U303


title: Ewing Sarcoma PDX-83: A472U300


title: Ewing Sarcoma PDX-83: A472U299


title: Ewing Sarcoma PDX-83: A472U298


title: Ewing Sarcoma PDX-83: A472U296


title: Ewing Sarcoma PDX-83: A472U295


title: CLB-BERLUD: A399U96

description: CLB-BERLUD Neuroblastoma cell line

source_name: CLB-BERLUD

growth_protocol: CLB-berlud are cultured in RPMI (Gibco) 10% FBS (Eurobio), 100U/mL

extract_protocol:
Dissociated cells were captured and processed with the C1 Single-Cell Auto Prep System (FluidigmTM) following the manufacturer’s protocol
After harvest from the C1 device, each cDNA library was tagmented using the Nextera XT DNA Sample Preparation Kit (Illumina).
Libraries were quantified by Qubit fluorometric assay (Invitrogen) with dsDNA HS (High Sensitivity) Assay Kit and qualified using LabChip (LabChip® GX Touch™ PerkinElmer)

value: Neuroblastoma

value: Neuroblastoma cell line

tag: cell line

value: CLB-BERLUD


title: Ewing Sarcoma PDX-83: A472U318


title: CLB-BERLUD: A399U94

description: CLB-BERLUD Neuroblastoma cell line


title: Ewing Sarcoma PDX-83: A472U309


title: Ewing Sarcoma PDX-83: A472U302


title: CLB-BERLUD: A399U95

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U93

description: CLB-BERLUD Neuroblastoma cell line


title: Ewing Sarcoma PDX-83: A472U301


title: CLB-BERLUD: A399U89

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U86

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U87

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U83

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U90

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U88

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U81

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U79

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U80

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U78

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U76

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U75

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U74

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U92

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U91

description: CLB-BERLUD Neuroblastoma cell line


title: Ewing Sarcoma PDX-83: A472U297


title: CLB-BERLUD: A399U72

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U71

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U82

description: CLB-BERLUD Neuroblastoma cell line


title: ASP14_day10: A281U150

description: A673TRshEF cells, after 3 days of doxycycline removal in media of cells that were previously subjected to 7 days of doxycycline inducing downregulation of EWS-FLI1 (“d7+3”)

growth_protocol: A673/TR/shEF are cultured in DMEM (Gibco) 10% FBS (Eurobio), with 50 μg/mL Zeocin (Invitrogen), 2 μg/mL Blasticidin (Invitrogen) added ex-tempo.

extract_protocol:
Dissociated cells were captured and processed with the C1 Single-Cell Auto Prep System (FluidigmTM) following the manufacturer’s protocol
After harvest from the C1 device, each cDNA library was tagmented using the Nextera XT DNA Sample Preparation Kit (Illumina).   Libraries were quantified by Qubit fluorometric assay (Invitrogen) with dsDNA HS (High Sensitivity) Assay Kit and qualified using LabChip (LabChip® GX Touch™ PerkinElmer)

treatment_protocol: EWSR1-FLI1 specific small hairpin RNA was induced in A673/TR/shEF cells by adding DOX at 1 ug/mL. After 7 days, DOX was removed and cells were washed three times to allow silencing of the shRNA and induction of EWSR1-FLI1. For ASP14 xenograft, 20 millions cells were resuspended in 200 µL of PBS and subcutaneously injected into severe combined immunodeficiency (SCID) mice. When tumor volume reached 1,000 mm3, DOX was added in the drinking water of a subset of mice (+ DOX group) for 7 days.

tag: passages

value: Ewing sarcoma


title: CLB-BERLUD: A399U85

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U66

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U73

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U68

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U70

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U84

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U69

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U65

description: CLB-BERLUD Neuroblastoma cell line


title: CLB-BERLUD: A399U67

description: CLB-BERLUD Neuroblastoma cell line


title: ASP14_day10: A281U149


title: CLB-BERLUD: A399U77

description: CLB-BERLUD Neuroblastoma cell line


title: ASP14_day10: A267T71


title: ASP14_day10: A267T72


title: ASP14_day10: A281U146


title: ASP14_day10: A281U147


title: ASP14_day10: A281U148


title: ASP14_day10: A267T67


title: ASP14_day10: A267T69


title: ASP14_day10: A267T65


title: ASP14_day10: A267T68


title: ASP14_day10: A267T66


title: ASP14_day10: A267T62


title: ASP14_day10: A267T63


title: ASP14_day10: A267T64


title: ASP14_day10: A281U145


title: ASP14_day10: A267T61


title: ASP14_day10: A267T60


title: ASP14_day10: A267T59


title: ASP14_day10: A267T70


title: ASP14_day10: A267T58


title: ASP14_day10: A267T57


title: ASP14_day10: A267T56


title: ASP14_day10: A267T54


title: Apices, H3_WT_bio2

city: Cologne

first: Alice

last: Pajoro

address: Carl-von-Linné-Weg 10

country: Germany

institute: MPIPZ

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie (Langmead et al., 2009) using the default parameters.
Clonal reads were filtered using a constumized script
Peaks were called using Dpeak function of DANPOS2  (Chen et al., 2013), using the default parameters, excet for -l (read length) that was set to 300.
Differentially enriched regions between WT and chr4-2 were obtained with DANPOS2
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files contained peak calling for each condition
Supplementary_files_format_and_content: excel file contain list of enriched region and differential analysis of DANPOS2

organism: Arabidopsis thaliana

source_name: apical meristem enriched 5 weeks short days

growth_protocol: Plants were grown in shot day conditions (8h light/ 16h dark) at 21C for 5 weeks

extract_protocol:
Nuclei isolation and chromatin immunoprecipitation was performed according to Kaufmann et al 2010 Nature Protocols. After the preclearing step, the sample was split in three aliquots, the first aliquot was incubated with anti-H3K27me3 antibody (Active Motif, Cat. 39155, Lot. 25812014), the second aliquot was incubated with anti-H3K4me3 antibody (Millipore, Cat.17–614, Lot.1973237) and the third aliquot with anti-H3 antibody (ab1791, abcam)
ChIP Libraries were prepared with the Ovation Ultralow V2 DNA-Seq library preparation kit from Tecan Genomics

tag: genotype

value: WT

value: 5w SDs enriched SAM


title: Apices, H3K4me3_WT_bio3

description:
K4_WT_3bio.bgsub.Fnor.smooth.wig
K4_WT_3bio-K4_chr4_3bio.peaks.integrative.txt


title: Apices, H3K4me3_WT_bio1


title: Apices, H3K27me3_chr4_bio2

description:
K27_chr4_3bio.bgsub.Fnor.smooth.wig
K27_WT_3bio-K27_chr4_3bio.peaks.integrative.txt


title: Apices, H3K27me3_WT_bio1

description:
K27_WT_3bio.bgsub.Fnor.smooth.wig
K27_WT_3bio-K27_chr4_3bio.peaks.integrative.txt


title: Apices, H3K4me3_WT_bio2


title: Apices, H3_WT_bio3


title: Apices, H3K27me3_WT_bio3


title: Apices, H3K4me3_chr4_bio1

description:
K4_chr4_3bio.bgsub.Fnor.smooth.wig
K4_WT_3bio-K4_chr4_3bio.peaks.integrative.txt


title: Apices, H3K4me3_chr4_bio2


title: Apices, H3K27me3_chr4_bio3


title: Apices, H3K27me3_WT_bio2


title: Apices, H3_WT_bio1


title: ASP14_day10: A267T51


title: ASP14_day10: A267T52


title: Apices, H3_chr4_bio3


title: ASP14_day10: A267T50


title: ASP14_day9: A281U144

description: A673TRshEF cells, after 2 days of doxycycline removal in media of cells that were previously subjected to 7 days of doxycycline inducing downregulation of EWS-FLI1 (“d7+2”)


title: ASP14_day10: A267T49


title: ASP14_day9: A281U143


title: Apices, H3_chr4_bio2


title: Apices, H3K4me3_chr4_bio3


title: ASP14_day9: A281U142


title: ASP14_day9: A281U141


title: ASP14_day10: A267T53


title: Apices, H3_chr4_bio1


title: ASP14_day10: A267T55


title: Apices, qem2 II 6 weeks SDs

description:
TableS3
Sample 47

data_processing:
RNA-Seq reads were then mapped to A. thaliana TAIR10 using tophat2 under default settings (Kim et al., 2013), except only a single alignment was permitted per read and the coverage based junction search was disabled (settings: -g 1 –no-coverage-search).
Samtools was used to sort and index BAM alignment files and to calculate BAM file statistics (Li et al., 2009).
HTSeq was used to tabulate the number of reads mapping to each genomic feature, with counts tabulated only for genes that completely overlapped a given feature (Anders et al., 2015).
The wald-test implemented in DESeq2 was used to detect differentially expressed genes for pair-wised.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tables containing counts and differentially expressed genes.

source_name: apical meristem enriched

growth_protocol: Plants were grown in shot day conditions (8h light/ 16h dark) at 21C. Samples were collect at 3,4,5, and 6 weeks after sowing.

extract_protocol:
Total RNA was extracted from three independent biological replicates of shoot 15 apices by using the RNeasy Plant Mini Kit (Qiagen) and treated with DNase (Ambion) to remove residual genomic DNA
Library for sequencing was prepared using the Illumina TruSeq library preparation kit according to the manufacturer’s protocol

tag: developmental stage

value: 6w SDs

value: apical meristem enriched

tag: biological replicate


title: ASP14_day9: A281U139


title: ASP14_day9: A281U138


title: ASP14_day9: A281U134


title: ASP14_day9: A281U136


title: ASP14_day9: A281U133


title: ASP14_day9: A281U135


title: Apices, svp flc ft tsf soc1 II 6 weeks SDs

description:
TableS1
TableS3
Sample 44

value: svp flc ft tsf soc1


title: Apices, sail_783c05 II 6 weeks SDs

description:
TableS3
Sample 41


title: Apices, svp flc ft tsf soc1 III 6 weeks SDs

description:
TableS1
TableS3
Sample 45


title: Apices, svp flc ft tsf soc1 I 6 weeks SDs

description:
TableS1
TableS3
Sample 43


title: ASP14_day9: A281U137


title: Apices, qem2 I 6 weeks SDs

description:
TableS3
Sample 46


title: ASP14_day9: A281U132


title: ASP14_day9: A281U131


title: Apices, WT III 6 weeks SDs

description:
TableS1
TableS3
Sample 39

value: col


title: Apices, WT I 6 weeks SDs

description:
TableS1
TableS3
Sample 37


title: Apices, qem2 III 5 weeks SDs

description:
TableS3
Sample 36

value: 5w SDs


title: ASP14_day9: A281U130


title: Apices, qem2 II 5 weeks SDs

description:
TableS3
Sample 35


title: ASP14_day9: A281U128


title: Apices, WT II 6 weeks SDs

description:
TableS1
TableS3
Sample 38


title: ASP14_day9: A281U129


title: Apices, qem2 I 5 weeks SDs

description:
TableS3
Sample 34


title: ASP14_day9: A281U127


title: Apices, sail_783c05 III 6 weeks SDs

description:
TableS3
Sample 42


title: Apices, svp flc ft tsf soc1 III 5 weeks SDs

description:
TableS1
TableS3
Sample 33


title: Apices, svp flc ft tsf soc1 II 5 weeks SDs

description:
TableS1
TableS3
Sample 32


title: ASP14_day9: A281U126


title: ASP14_day9: A281U125


title: ASP14_day9: A281U124


title: ASP14_day9: A281U122


title: Apices, sail_783c05 II 5 weeks SDs

description:
TableS3
Sample 29


title: ASP14_day9: A281U121


title: Apices, svp flc ft tsf soc1 I 5 weeks SDs

description:
TableS1
TableS3
Sample 31


title: Apices, WT III 5 weeks SDs

description:
TableS1
TableS3
Sample 27


title: Apices, sail_783c05 III 5 weeks SDs

description:
TableS3
Sample 30


title: ASP14_day9: A281U123


title: Apices, sail_783c05 I 5 weeks SDs

description:
TableS3
Sample 28


title: ASP14_day9: A267T48


title: ASP14_day9: A267T46


title: Apices, qem2 III 4 weeks SDs

description:
TableS3
Sample 24

value: 4w SDs


title: Apices, WT II 5 weeks SDs

description:
TableS1
TableS3
Sample 26


title: ASP14_day9: A267T45


title: Apices, qem2 II 4 weeks SDs

description:
TableS3
Sample 23


title: ASP14_day9: A267T47


title: Apices, qem2 I 4 weeks SDs

description:
TableS3
Sample 22


title: Apices, WT I 5 weeks SDs

description:
TableS1
TableS3
Sample 25


title: ASP14_day9: A267T44


title: ASP14_day9: A267T42


title: Apices, svp flc ft tsf soc1 III 4 weeks SDs

description:
TableS1
TableS3
Sample 21


title: Apices, qem2 III 6 weeks SDs

description:
TableS3
Sample 48


title: ASP14_day9: A267T43


title: Apices, svp flc ft tsf soc1 II 4 weeks SDs

description:
TableS1
TableS3
Sample 20


title: ASP14_day9: A267T41


title: ASP14_day9: A281U140


title: Apices, svp flc ft tsf soc1 I 4 weeks SDs

description:
TableS1
TableS3
Sample 19


title: ASP14_day9: A267T40


title: Apices, sail_783c05 III 4 weeks SDs

description:
TableS3
Sample 18


title: Apices, WT III 4 weeks SDs

description:
TableS1
TableS3
Sample 15


title: Apices, sail_783c05 II 4 weeks SDs

description:
TableS3
Sample 17


title: ASP14_day9: A267T38


title: Apices, sail_783c05 I 4 weeks SDs

description:
TableS3
Sample 16


title: ASP14_day9: A267T37


title: Apices, WT II 4 weeks SDs

description:
TableS1
TableS3
Sample 14


title: ASP14_day9: A267T35


title: ASP14_day9: A267T34


title: ASP14_day9: A267T36


title: Apices, sail_783c05 I 6 weeks SDs

description:
TableS3
Sample 40


title: Apices, H3K27me3_chr4_bio1


title: Apices, qem2 III 3 weeks SDs

description:
TableS3
Sample 12

value: 3w SDs


title: ASP14_day9: A267T31


title: Apices, WT I 4 weeks SDs

description:
TableS1
TableS3
Sample 13


title: ASP14_day9: A267T33


title: Apices, svp flc ft tsf soc1 III 3 weeks SDs

description:
TableS1
TableS3
Sample 9


title: Apices, qem2 I 3 weeks SDs

description:
TableS3
Sample 10


title: ASP14_day9: A267T39


title: Apices, qem2 II 3 weeks SDs

description:
TableS3
Sample 11


title: ASP14_day9: A267T32


title: ASP14_day9: A267T30


title: Apices, svp flc ft tsf soc1 II 3 weeks SDs

description:
TableS1
TableS3
Sample 8


title: ASP14_day9: A267T28


title: ASP14_day9: A267T27


title: Apices, sail_783c05 III 3 weeks SDs

description:
TableS3
Sample 6


title: ASP14_day9: A267T26


title: Apices, svp flc ft tsf soc1 I 3 weeks SDs

description:
TableS1
TableS3
Sample 7


title: Apices, sail_783c05 II 3 weeks SDs

description:
TableS3
Sample 5


title: Apices, WT II 3 weeks SDs

description:
TableS1
TableS3
Sample 2


title: Apices, WT III 3 weeks SDs

description:
TableS1
TableS3
Sample 3


title: Apices, sail_783c05 I 3 weeks SDs

description:
TableS3
Sample 4


title: HUVEC_Vein_ERG_ChipSeq_2

city: Worcester

first: Nathan

middle: D.

last: Lawson

state: MA

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
basecalls were made with standard Illumina pipeline for indicated instrument
for ChIPSeq and Cut&Run, reads were aligned to hg19 using Bowtie2
peak-calling was performed using MACS or MACS2
for RNA-seq, reads were mapped to ENSEMBL annotated transcripts using Tophat2 and differentially expressed genes were identified using EdgeR
Genome_build: hg19
Supplementary_files_format_and_content: big wig and bed files

source_name: venous endothelial cells

growth_protocol: Umbilical cords were collected from UMass Memorial Medical Center and washed with phosphate-buffered saline (PBS) to remove excessive blood. For HUVEC isolation, the vein was cannulated at one end and perfused with 0.1% type 2 collagenase in PBS (Worthington Biochemical), then clamped at both ends, wrapped in aluminum foil and placed in a humidified incubator for 20 minutes at 37°C. Endothelial cells were collected by flushing collagenase solution through the vein with ECCM (EGM Endothelial Cell Growth Medium with SingleQuots Supplement, Lonza).  Cells were centrifuged and re-suspended in ECCM, seeded in 0.2% gelatin-coated flasks and allowed to attach overnight at in a humidified incubator (37°C, 5% CO2).  Medium was replaced the following day to remove erythrocytes and cells were grown to confluence (2-3 days).  The same cords were used for HUAEC isolation by dissecting out arteries, which were washed twice with PBS and perfused with 0.05% Collagenase using a 20-gauge needle (Fisher) attached to a 20 ml syringe. Arteries were clamped on both ends, placed in a beaker containing PBS and incubated for 20 minutes in a 37°C water bath.  Detached endothelial cells were collected by flushing the collagenase with EC complete medium followed by centrifugation. For passaging, cells were re-suspended in ECCM and grown for 3-4 days, or until ~80% confluence.

extract_protocol:
For ChIP-seq, DNA was extracted using phenol-chloroform followed by ethanol precipitation and quantified using Qubit Fluorometric Quantitation assay
ChIP-Seq libraries were constructed using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs) with 50-100 ng of ChIP DNA according to manufacturer's protocol. In all cases, library quality and concentration were determined using an Agilent bioanalyzer (UMass Medical School Deep Sequencing Core)

treatment_protocol: HUAEC and HUVEC were used prior to passage 3; for knockdown experiments, HUVEC were transduced with lentiviral vectors expressing a control shRNA or an shRNA targeting NR2F2

value: HUVEC

tag: passage

value: wildtype

value: ERG (Abcam, catalog number 92513)


title: ASP14_day7: A281U116

description: A673TRshEF cells after 7days of Dox inducing downregulation of EWS-FLI1


title: HUVEC_Vein_ERG_ChipSeq_1


title: ASP14_day7: A281U120


title: HUVEC_VeinInput_ERG_2

value: none (input)


title: ASP14_day7: A281U115


title: ASP14_day7: A281U118


title: Apices, WT I 3 weeks SDs

description:
TableS1
TableS3
Sample 1


title: ASP14_day7: A281U119


title: ASP14_day7: A281U117


title: ASP14_day7: A281U114


title: ASP14_day7: A281U113


title: HUVEC_Artery_ERG_ChipSeq_2

source_name: arterial endothelial cells

value: HUAEC


title: HUVEC_Artery_ERG_ChipSeq_1


title: ASP14_day9: A267T29


title: HUVEC_VeinInput_ERG_1


title: HUVEC_ArteryInput_ERG_1


title: ASP14_day9: A267T25


title: HUVEC_inputNR2F2_2


title: ASP14_day7: A281U105


title: ASP14_day7: A281U108


title: HUVEC_ArteryInput_ERG_2


title: ASP14_day7: A281U111


title: ASP14_day7: A281U103


title: ASP14_day7: A281U112


title: ASP14_day7: A281U109


title: ASP14_day7: A281U110


title: ASP14_day7: A281U107


title: HUVEC_inputNR2F2_1


title: HUVEC_NR2F2_ChIPSeq_2

value: NR2F2 (Perseus Proteomics, catalog number PP-H7147-00)


title: HUVEC_NR2F2_ChIPSeq_1


title: HUVEC_H3K27me3_ChIPSeq_Rep2

value: H3K27me3 (Active Motif, catalog number 39156)


title: HUVEC_VeinRNAseq_Rep3

description:
HUVECvsHUAEC_DEseq2out.csv
V6
instrument model unknown by submitter. HiSeq 2000 used as placeholder.

molecule: polyA RNA

extract_protocol:
mRNA was isolated using the NEB PolyA mRNA magnetic bead isolation module
RNA-seq libraries were constructed as described in the NEB Poly(A) mRNA magnetic isolation module (#E7490S) and NEB RNA-Seq Library Prep Reagent Set for Illumina (#E6100 L), using mRNA isolated from 5 μg of total RNA with NEB magnetic Oligo d(T)25 beads. In all cases, library quality and concentration were determined using an Agilent bioanalyzer (UMass Medical School Deep Sequencing Core)


title: ASP14_day7: A281U100

value: Ewing sarcoma


title: ASP14_day7: A281U104


title: HUVEC_InputK27meRep2


title: HUAEC_ArteryRNAseq_Rep4

description:
HUVECvsHUAEC_DEseq2out.csv
A26
instrument model unknown by submitter. HiSeq 2000 used as placeholder.


title: HUVEC_VeinRNAseq_Rep1

description:
HUVECvsHUAEC_DEseq2out.csv
V4
instrument model unknown by submitter. HiSeq 2000 used as placeholder.


title: ASP14_day7: A281U102


title: HUAEC_ArteryRNAseq_Rep2

description:
HUVECvsHUAEC_DEseq2out.csv
A6
instrument model unknown by submitter. HiSeq 2000 used as placeholder.


title: HUVEC_H3K27me3_ChIPSeq_Rep1


title: HUVEC_InputK27meRep1


title: ASP14_day7: A281U99


title: ASP14_day7: A281U106


title: ASP14_day7: A281U98


title: ASP14_day7: A281U97


title: HUAEC_ArteryRNAseq_Rep1

description:
HUVECvsHUAEC_DEseq2out.csv
A5
instrument model unknown by submitter. HiSeq 2000 used as placeholder.


title: HUVEC_EP300_ChipSeq_Rep2

description: instrument model unknown by submitter. HiSeq 2000 used as placeholder.

value: EP300 (Cell Signaling, catalog number 4771)


title: ASP14_day7: A267T23


title: ASP14_day7: A281U101


title: ASP14_day7: A267T24


title: ASP14_day7: A267T22


title: ASP14_day7: A267T20


title: HUVEC_InputK27acRep2


title: HUVEC_InputP300Rep2


title: HUVEC_InputK27acRep1


title: HUVEC_InputP300Rep1


title: ASP14_day7: A267T21


title: HUVEC_VeinRNAseq_Rep2

description:
HUVECvsHUAEC_DEseq2out.csv
V5
instrument model unknown by submitter. HiSeq 2000 used as placeholder.


title: ASP14_day7: A267T19


title: ASP14_day7: A267T18


title: HUVEC_H3K27ac_ChipSeq_Rep2

value: H3K27ac (Abcam, catalog number ab4729)


title: HUVEC_EP300_ChipSeq_Rep1


title: ASP14_day7: A267T15


title: ASP14_day7: A267T17


title: HUAEC_InputP300Rep2


title: HUVEC_H3K27ac_ChipSeq_Rep1


title: HUAEC_InputK27acRep2


title: ASP14_day7: A267T13


title: HUAEC_H3K27ac_ChipSeq_Rep2


title: HUAEC_InputK27acRep1


title: ASP14_day7: A267T9


title: HUAEC_H3K27ac_ChipSeq_Rep1


title: HUAEC_EP300_ChipSeq_Rep2


title: ASP14_day7: A267T14


title: HUAEC_InputP300Rep1


title: HUAEC_EP300_ChipSeq_Rep1


title: ASP14_day7: A267T11


title: ASP14_day7: A267T10


title: ASP14_day7: A267T12


title: ASP14_day7: A267T7


title: ASP14_day7: A267T5


title: ASP14_day7: A267T8


title: Oculomotor neuron ALS rep4

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

data_processing:
Base-calling using Illumina Cassava 1.7
Alignment to the human genome (hg38) performed using STAR version 2.4.1 with parameter outSAMstrandField set to intronMotif.
Raw read counts were extracted using the function featureCounts (version 1.4.6) using default parameters
Differential gene expression analysis was performed on the read counts using DESeq version 1.12.4. Only genes with reads in 2 samples or more were considered in the analysis.
Normalized abundance measurements (RPKMs) were generated using the Cufflinks version 2.2.1 with the parameter library-norm-method set to geometric.
Genome_build: hg38
Supplementary_files_format_and_content: One processed data file is added providing normalized abundance measurements (RPKM) organized as a matrix for all samples (tab-delimited txt).

source_name: Oculomotor neurons

extract_protocol:
Lysis buffer is directly added to the cells after laser capture. No RNA extraction is conducted. The cell lysate is direcly used for library preparation.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation.

tag: case number (refer to table in paper)

tag: disease status

value: Amyotrophic lateral sclerosis


title: ASP14_day7: A267T4


title: ASP14_day7: A267T3


title: ASP14_day7: A267T16


title: ASP14_day7: A267T2


title: ASP14_day7: A267T6


title: Oculomotor neuron ALS rep2


title: Oculomotor neuron ALS rep1


title: Oculomotor neuron ALS rep3


title: ASP14_d17_FLI1

data_processing:
Reads mapped with bowtie2 version 2.1.10 against human genome (hg19)
Peaks called with MACS2 version 2.0.10 with option narrow for FLI1 (default option) and broad for H3K27ac (input DNA was used as control)
Genome_build: hg19
Supplementary_files_format_and_content: peaks called by MACS2

source_name: A673/TR/shEF Ewing sarcoma cells

extract_protocol:
DNA-protein cross-linking was performed in the presence of 1% of paraformaldehyde. Cell lysis, chromatin shearing, immunoprecipitation and DNA purification was performed with reagents from iDealChIP-seq kit for Transcription Factors
ChIP-seq - HiSeq2500 (Illumina) using 100 bp single-end sequencing.

treatment_protocol: EWSR1-FLI1 specific small hairpin RNA was induced in A673/TR/shEF cells by adding DOX at 1 ug/mL. After 7 days, DOX was removed and cells were washed three times to allow silencing of the shRNA and induction of EWSR1-FLI1

tag: chip-antibody

value: FLI1 rabbit polyclonal antibody (abcam, ab15289-ChIP grade)


title: Spinal motor neuron ALS rep9

source_name: Spinal motor neurons


title: ASP14_d14_FLI1


title: ASP14_day7: A267T1


title: Spinal motor neuron ALS rep6


title: Spinal motor neuron ALS rep8


title: ASP14_d11_FLI1


title: Spinal motor neuron ALS rep10


title: Spinal motor neuron ALS rep5


title: ASP14_d9_FLI1


title: Spinal motor neuron ALS rep4


title: ASP14_d10_FLI1


title: Spinal motor neuron ALS rep3


title: ASP14_d7_FLI1


title: ASP14_d7_H3K27ac

value: H3K27ac antibody (abcam, ab4729)


title: Spinal motor neuron ALS rep2


title: Spinal motor neuron ALS rep1


title: ASP14_d0_H3K27ac


title: ASP14_d0_input

value: input DNA


title: Spinal motor neuron ALS rep7


title: L80

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

data_processing:
Quality control of raw reads was carried out with FastQC.
PCR primers and Illumina adapter sequences were removed with Trimmomatic. Minimum base quality 15 over a 4-base sliding window was required, then only sequences longer than 36 nucleotides were included in the downstream analysis.
Read mapping with STAR aligner.
BAM file sorting and indexing with Samtools
Read counts per gene extracted with Htseq-count
Genome_build: Bos taurus UMD3.1.68
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

organism: Bos taurus

source_name: whole blood

extract_protocol:
Total RNA was extracted using the PAXgene® Blood miRNA Kit (PreAnalytiX GmbH) according to the manufacturer’s protocol. Total RNA was eluted in a final volume of 80 μL. RNA concentration was measured by NanoDrop™ 1000 spectrophotometer (Thermo Scientific) and RNA integrity was assessed with an Agilent 2200 TapeStation system (Agilent Technologies).
Libraries were prepared with the Illumina Truseq RNA sample prep kit (Illumina Inc., USA) following the manufacture’s protocol and the size and yield evaluated using an Agilent TapeStation 2200. Libraries were then quantified with an ABI9700 qPCR instrument using the KAPA Library Quantification Kit in triplicate, according to the manufacture’s protocol (Kapa Biosystems, Woburn, MA, USA) and then normalized to 10 nM as recommended by Illumina for cluster generation on the Hiseq2000. Fifteen libraries were prepared and equimolar amounts of 5 samples were mixed before NaOH denaturation. Each of the pools was run in a lane of a Hiseq Flowcell.

tag: id sample

value: whole blood

tag: race

value: frisona

tag: age

value: 4 to 5 years old

tag: bcs

tag: dim

value: 170 to 190 days in milk

tag: group

value: Negative to ELISA


title: L82


title: L83


title: L78


title: RNAPII-hypo +UV_-DRB_X4h

city: Vari

first: Maria

last: Fousteri

address: 34 Fleming Street

department: Institute for Fundamental Biomolecular Research

country: Greece

institute: Biomedical Sciences Research Center "Alexander Fleming"

description: RNAPII-hypo  +UV / -DRB / X 4h

data_processing:
Base calling and Quality filtering were done with default parameters within Illumina pipeline.
Short read filtering, alignment and wig profile generation was performed as described in [Lavigne et al., 2017]. Briefly, reads were quality trimmed, Illumina adapter contaminants were removed and filtered reads were aligned uniquely to the GRCh37/hg19 reference genome. For each experiment, read depth normalisation of all samples was performed among considered samples.
Genome_build: hg19
Supplementary_files_format_and_content: Normalised BigWig files were generated using in-house developed shell, perl, and R scripts, compiling functions of software commonly used by most laboratories.

growth_protocol: VH10 cells were maintained in DMEM containing 10% FBS at 37 C and 5% CO2.

extract_protocol:
For ATAC-seq method, nuclei preparation and transposition and amplification of transposed fragments for library preparation was performed as described in Corces et al, 2017 with minor modifications; (i) 70,000 cells were used per experimental condition and (ii) The DNase treatment of cells in culture medium, before the transposition reaction, was skipped. For ChIP-seq, lysates were clarified from sonicated nuclei and chromatin (in the range of 150-400 bp) was isolated and precipitated with  anti-RNAPII-CTD-hypo (8WG16; 05-952, lot: 2262610) from Millipore or anti-H3K27ac (ab4729, Abcam) or anti-H3K27me3 (07-449, Millipore).
For ATAC-seq method, transposition and amplification of transposed fragments for library preparation was performed using Nextera DNA Library Prep Kit (Illumina, Inc) and primers as described in Corces et al., 2017. For ChIP-Seq, DNA libraries were generated by ligation adapters and amplification by LM-PCR (Truseq) or (NEBNext). Briefly, ChiPed or Input dsDNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase as described previously (Lavigne et al., 2017). The blunt, phosphorylated ends were treated with Klenow fragment  and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Alternatively, we used NEBnext and Truseq approaches to multiplex samples for sequencing different samples in a single lane of the flowcell. qPCR with Illumina primers was used to control for overamplification. The purified DNA library was size selected by AMpure beads purification as previously described and was typically in the range of 200 to 500 bp. In all cases, libraries were sequenced on Hiseq2000 or 2500 in Genecore, EMBL following manufacturer's protocols.
double-stranded single-end DNA-seq was performed for ChIP-seq, Input-seq and ATAC-seq.

treatment_protocol: VH10 cells were irradiated with  UV-C as previously described (Lavigne et al., Nature Communications, 2017). Specifically, we monitored changes occuring during reccovery from DNA damage for Chromatin accessibility (ATAC-seq) (NO UV and 2 h after 15 J/m2), chromatin modifications (H3K27ac (NO UV and 2 h after 15 J/m2) and H3K27me3 (NO UV and 2 h after 20J /m2)) and transcriptional changes (RNA polymerase II hypophosphorylated (NO UV or 15 J/m2). When the inhibitor of transcription DRB was used it was during recovery to inhibit release of RNA polymerases from promoter-proximal regions and to monitor the accumulation of RNAPII-hypo at TSSs.

tag: cell type

value: Fibroblast cells immortalized with hTERT

tag: antibody

value: anti-RNAPII-CTD-hypo (8WG16; 05-952, lot:2262610) from Millipore

tag: treatment

value: +UV / +DRB / X 4h


title: L77

tag: tissue


title: H3K27me3_NO_UV

description: H3K27me3 NO UV

tag: cell line

value: anti-H3K27me3 (07-449, Millipore)


title: Input_NO_UV

description: Input NO UV

value: input


title: RNAPII-hypo_+UV_+DRB_X4h

description: RNAPII-hypo +UV / +DRB / X 4h


title: H3K27ac_+UV_1

description: H3K27ac +UV replicate 1

value: anti-H3K27ac (ab4729, Abcam)

value: UV irradiation


title: H3K27ac_NO_UV_2

description: H3K27ac NO UV replicate 2


title: H3K27ac_NO_UV_1

description: H3K27ac NO UV replicate 1


title: quarterGV_1

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

institute: HHMI Janelia

description:
ERCC added
quarterGV_1_S8_L001

data_processing:
Raw sequence reads were trimmed with Cutadapt 2.5 to remove adapters while performing light quality trimming with parameters "-m 10 -q 20, 20".
Sequencing library quality was assessed with FastQC v0.11.8 with default parameters. Trimmed reads were mapped to the Mus musculus mm10 reference genome plus ERCC.fasta using STAR v2.7.2a.
Multi-mapping reads were filtered using samtools 1.9. Uniquely aligned reads were then mapped to gene features using HTseq v0.9.1 as an unstranded library with default parameters.
A gene/ERCC count was considered valid when present in at least 5 reads in at least 2 libraries. Differential expression between groups of samples was tested using R version 3.5.1 (2018-07-02) with DESeq2 v1.24.0. The oocyte libraries were normalized by ERCC counts by defining the ERCC genes as the controlGenes when estimating the sizeFactors in DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab deliminated original counts of each gene

organism: Mus musculus

source_name: quarterGV_single mouse oocyte

growth_protocol: Mouse GV oocytes are cultured ex vivo in M2 medium.

extract_protocol:
polyA RNAs: Each oocyte  was lysed in RLT-plus buffer. The oligo-dT beads were used to isolate the polyA RNA. The oocyte fractions were picked after oocyte lysis
For polyA RNAs: Single oocyte RNA-seq libraries were prepared according to a published single-cell RNA seq pipeline with subtle modifications (Macaulay et al., 2016). Briefly, the oocytes at desired stages were collected individually into 2.5 ml RLT plus and stocked at -80 °C until all samples were collected. In the beginning of RNA purification, ERCC RNA spike-in mix (ThermoFisher 4456740) was diluted 10^5 fold, and 1 ml of the diluted ERCC mix was added to each lysis. Poly(A) RNA were isolated by oligo (dT) beads, reverse transcribed, amplified and purified. The purified cDNAs were analyzed by Bioanalyzer 2100 to confirm successful amplification range and quality. cDNAs passing a quality test were further constructed into sequencing libraries by Nextera DNA Sample Preparation Kit.

tag: Stage

value: germinal vesicle (GV)

value: oocyte

tag: fraction


title: halfGV_1

description:
ERCC added
halfGV_1_S12_L001

source_name: halfGV_single mouse oocyte


title: eighthGV_1

description:
ERCC added
eighthGV_1_S4_L001

source_name: eighthGV_single mouse oocyte


title: halfGV_2

description:
ERCC added
halfGV_2_S3_L001


title: eighthGV_2

description:
ERCC added
eighthGV_2_S9_L001


title: quarterGV_2

description:
ERCC added
quarterGV_2_S13_L001


title: ATAC_+UV_2

description: ATAC-seq +UV replicate 2


title: 1GV_18c_2

description:
ERCC added
1GV_18c_2_S1_L001

source_name: 1GV_18c_single mouse oocyte

tag: amplification cycles


title: M-MDSCs isolated from tumour tissues from HSD treated tumour-bearing mice

type: RNA

city: Hefei

first: Wei

last: He

state: Anhui

address: Meishan road

country: China

institute: Anhui medical university

description: Gene expression after HSD treated tumour-bearing mice for 16 days

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction, and slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. Hand-tighten the clamp onto the chamber. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. Hybridize at 65°C for 17 hours.

scan_protocol: Slides were scanned immediately using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Extract data using Agilent Feature Extraction Software

source_name: M-MDSC-Na

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: M-MDSCs were firstly isolated from the tumour tissues by the Myeloid-Derived Suppressor Cell Isolation Kit according to the manufacturer’s instructions (Miltenyi Biotec, Bergisch Gladbach, Germany), with all steps performed at 4 °C. An equal number of isolated tumour M-MDSCs from each group were mixed, and total RNA was extracted by TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and the RNA extracts were first evaluated by a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and RNA quality was determined by the ratios of A260/A280 (close to 2) and A260/A230 (close to 2).

treatment_protocol: Female BABL/c mice were subcutaneously injected with 1×10^6 4T1 cells after 1 day of starvation. The cells were injected into the left armpit of each mouse. Then, mice were randomly assigned to receive the NSD (0.4% NaCl in chow plus tap water) or HSD (4% NaCl in chow plus 1% NaCl in the water) via random lottery for 16 days. On day 16, M-MDSCs were isolated from tumour tissues from NSD and HSD group, and directly tested using Agilent’s mouse gene chip array after extracted total RNA.

tag: strain background

value: BABL/c

tag: Sex

value: female

tag: injected with

value: 1×10^6 4T1 cells

value: HSD (4% NaCl in chow plus 1% NaCl in the water) for 16 days

value: tumour tissue

value: myeloid-derived suppressor cell (MDSC)


title: M-MDSCs isolated from tumour tissues from NSD treated tumour-bearing mice

description: Gene expression after NSD treated tumour-bearing mice for 16 days

source_name: M-MDSC-Ctrl

value: NSD (0.4% NaCl in chow plus tap water) for 16 days


title: 1GV_18c_1

description:
ERCC added
1GV_18c_1_S10_L001


title: 1GV_14c_2

description:
ERCC added
1GV_14c_2_S11_L001

source_name: 1GV_14c_single mouse oocyte


title: ATAC_NO_UV_1

description: ATAC-seq NO UV replicate 1


title: ATAC_NO_UV_2

description: ATAC-seq NO UV replicate 2


title: RNAPII-hypo_+UV_X2h

description: RNAPII-hypo +UV / X 2h

value: +UV / X 2h


title: H3K27ac_+UV_2

description: H3K27ac +UV replicate 2

value: Fibroblast cells immortalized with hTERT


title: 1GV_14c_1

description:
ERCC added
1GV_14c_1_S6_L001


title: RNAPII-hypo_NO UV_+DRB_X4h

description: RNAPII-hypo NO UV / +DRB / X 4h

value: anti-RNAPII-CTD-hypo (8WG16; 05-952, lot:2262610) from Millipore

value: NO UV / +DRB / X 4h


title: dcl4-2 MS-N whole seedling_rep2 (smRNA)

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

description:
Nitrogen_deficient_smallRNA_processed_data
dcl4_N_smRNA_rep2

data_processing:
Sequence reads were filtered and then mapped to TAIR10 genome using Bowtie-1.2.2 with following parameters: -v 0 -a -M 3 --best --strata
21-nt and 22-nt small RNA read were selected using samtools v1.9
21-nt and 22-nt small RNA read (Tags per Million,TPM) from vairous gene catagories were caculated by personal script
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include TPM of 21- and 22-nt small RNA from various catagories

source_name: dcl4-2 MS-N

growth_protocol: Plants were grown on the MS medium with (MS) or without nitrogen (MS-N) for 10 days.Whole seedlings of 10-day-old plant were collected at 15:00 for total RNA extraction.

extract_protocol:
miRNeasy mini kit(Qiagen)
NEBNext® Small RNA Library Prep Set for Illumina

value: whole seedling

tag: genotype

tag: medium

value: MS-N


title: 1GV_10c_1

description:
ERCC added
1GV_10c_1_S2_L001

source_name: 1GV_10c_single mouse oocyte


title: 1GV_10c_2

description:
ERCC added
1GV_10c_2_S7_L001


title: H3K27me3_+UV

description: H3K27me3 +UV

value: anti-H3K27me3 (07-449, Millipore)


title: dcl4-2 MS-N whole seedling_rep3 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
dcl4_N_smRNA_rep3

treatment_protocol: MS medium with (MS) or without nitrogen (MS-N)

tag: age


title: LSK cells, 14359X7 shCtrl-4

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

description:
RNA isolated from sorted LSK cells
14359R_counts.txt
14359X7

data_processing:
The mouse GRCm38 reference genome and gene feature files were downloaded from Ensembl release 90.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 10% false discovery rate with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

source_name: Bone marrow

extract_protocol:
RNA was isolated from 50,000 to 20,000 sorted LSK cells using DNA/RNA isolation kit (Zymo Research- Quick-DNA/RNA Microprep Plus Kit)
RNA samples were quantified using NanoDrop 8000 and Qubit RNA HS Assay. RNA integrity numbers were calculated on Agilent HS RNA ScreenTape. RNA was subjected to library construction with the Illumina TruSeq Stranded mRNA Sample Preparation Kit (Cat#RS-122-2101, RS-122-2102) according to manufacturer’s protocol. Chemically denatured sequencing libraries (25 pM) are applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (Cat#GD-401-4001). Following the transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50-cycle single-read or 125-cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (Cat#FC-401-4002).

tag: strain

value: BALB/c

value: Bone marrow

value: LSK cells

value: control


title: dcl4-2 MS-N whole seedling_rep1 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
dcl4_N_smRNA_rep1


title: LSK cells, 14359X2 shCtrl-2

description:
RNA isolated from sorted LSK cells
14359R_counts.txt
14359X2


title: LSK cells, 14359X6 shCxxc5-3

description:
RNA isolated from sorted LSK cells
14359R_counts.txt
14359X6

value: Cxxc5 knockdown


title: Col-0 MS-N whole seedling_rep3 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
Col_N_smRNA_rep3

source_name: Col-0 MS-N

value: wild type


title: dcl4-2 MS whole seedling_rep3 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
dcl4_MS_smRNA_rep3

source_name: dcl4-2 MS

value: MS


title: dcl4-2 MS whole seedling_rep2 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
dcl4_MS_smRNA_rep2


title: LSK cells, 14359X5 shCxxc5-2

description:
RNA isolated from sorted LSK cells
14359R_counts.txt
14359X5


title: Col-0 MS-N whole seedling_rep1 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
Col_N_smRNA_rep1


title: ATAC_+UV_1

description: ATAC-seq +UV replicate 1

value: UV irradiation


title: LSK cells, 14359X3 shCtrl-3

description:
RNA isolated from sorted LSK cells
14359R_counts.txt
14359X3


title: LSK cells, 14359X11 shCxxc5-4

description:
RNA isolated from sorted LSK cells
14359R_counts.txt
14359X11


title: Young DN rep2_reanalyzed

city: Washington

first: Brett

middle: Adam

last: Shook

state: DC

address: 2300 I St NW

department: Biochemistry & Molecular Medicine

institute: George Washington University

description:
young_5d3_DN
**reanalysis of GSM2828270 (GSE105790)

data_processing:
Basecalls performed using CASAVA version 1.8.2
For each read, the first 6 and the last nucleotides were trimmed to the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the whole read was discarded.
Mapping with HISAT2 v2.1
Gene counts were produced with StringTie v1.3.3b and the Python script “prepDE.py” provided in the package
DESeq2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Excel file (Gene Counts per each sample, and Deseq2 results)

source_name: Dermis

extract_protocol:
Extraction of RNA was performed using Absolutely RNA Nanoprep Kit from Agilent
SMARTer Ultra Low RNA Kit (Clonetech) was used with 500pg-1ng RNA. RNA sequencing libraries were prepared for sequencing using standard Illumina protocols

value: dermis

value: male

value: 7 week old

tag: days post injury

value: wound bed day 5


title: Young DN rep1_reanalyzed

description:
young_5d2_DN
**reanalysis of GSM2828269 (GSE105790)


title: Col-0 MS whole seedling_rep2 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
Col_MS_smRNA_rep2

source_name: Col-0 MS


title: Col-0 MS whole seedling_rep1 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
Col_MS_smRNA_rep1


title: Col-0 MS whole seedling_rep3 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
Col_MS_smRNA_rep3


title: ski2-2 dcl4-2 ago1-27 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
sda1_27_smRNA_rep3

data_processing:
Sequence reads were filtered and then mapped to TAIR10 genome using Bowtie-1.2.2 with following parameters: -v  0  -a  -M  3  --best  --strata
22-nt small RNA read were selected using samtools v1.9
Tags Per Million (TPM) were calculated and differential 22-nt siRNA production genes were called out using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include TPM values for each sample, the log2(FoldChange) value and the according p-value of pair-comparisons

source_name: ski2-2 dcl4-2 ago1-27 aerial part

growth_protocol: plants were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts of 20-day-old were collected for small RNA extraction.

value: aerial part

value: 20-day-old plant


title: Young CD29 rep2_reanalyzed

description:
young_5d4_CD29
**reanalysis of GSM2828268 (GSE105790)


title: Young CD29 rep1_reanalyzed

description:
young_5d2_CD29
**reanalysis of GSM2828267 (GSE105790)


title: ski2-2 dcl4-2 ago1-27 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
sda1_27_smRNA_rep2


title: dcl4-2 MS whole seedling_rep1 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
dcl4_MS_smRNA_rep1

value: whole seedling


title: Col-0 MS-N whole seedling_rep2 (smRNA)

description:
Nitrogen_deficient_smallRNA_processed_data
Col_N_smRNA_rep2

value: MS-N


title: ski2-2 dcl4-2 ago1-27 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
sda1_27_smRNA_rep1


title: Young AP - CD9Low rep2_reanalyzed

description:
young_5d4_APCD9low
**reanalysis of GSM2828264 (GSE105790)


title: ski2-2 dcl4-2 ago1-45 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
sda1_45_smRNA_rep4

source_name: ski2-2 dcl4-2 ago1-45 aerial part


title: Young AP - CD9Low rep1_reanalyzed

description:
young_5d2_APCD9low
**reanalysis of GSM2828263 (GSE105790)


title: CD26_rep2


title: B10.R1.B: lower leaf - plant 1

city: Hatfield

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Plant Sciences Complex, Entrance 11 - Corner Lunnon Road & Herold Street

department: Dept. Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

data_processing:
Reads were filtered to remove adapters and trimmed for quality using
Trimmomatic (v0.30; (Bolger et al., 2014); settings TruSeq3-PE-2.fa:2:30:10 HEADCROP:15 SLIDINGWINDOW:4:20 MINLEN:50
Filtered reads were de novo assembled using Trinity (v2.5.1; (Haas et al., 2013) with default settings but Kmer=31 to create a "master assembly" of all reads from the six samples (3 lower leaf and 3 upper leaf)
The transcript abundance was estimated using salmon by mapping the filtered reads from each of the six samples to the "master assembly"
Differential expression analysis was done using edgeR
Annotation of the master assembly transcripts was done using PLAZA 4.0 workbench (maize B73 V4; B73-like and plant genes annotated by BLASTX against the plant genome within PLAZA)(C. zeina genes annotated based on the draft genome Genbank accession MVDW01000014.1)
Genome_build: maize B73 v4, Cercospora zeina draft genome (Genbank accession MVDW01000014.1)
Supplementary_files_format_and_content: Tab-delimited text file including log fold change for each gene.

organism: Zea mays

source_name: leaf, moderate C. zeina infection (<4% GLS lesion area on leaves)

growth_protocol: Maize B73 grown in the field in Greytown, Kwazulu-Natal, South Africa with natural infection of Cercospora zeina. Planted in December 2012.

extract_protocol:
Total RNA was extracted using Qiazol, treated with DNase, and purified with RNeasy Plant Mini kit according to manufacturer's instructions (Qiagen, Hilden, Germany). Total RNA was shown to be of good quality using an Agilent Bioanalyser (average RIN number = 7.7).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: maize cultivar

value: lower leaf

tag: c. zeina infection

value: severe

tag: plant id


title: B10.R3.A: upper leaf - plant 3

source_name: leaf, minimal C. zeina infection (<0.02% GLS lesion area on leaves)

value: upper leaf

value: minimal


title: B10.R3.B: lower leaf - plant 3


title: ski2-2 dcl4-2 ago1-45 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
sda1_45_smRNA_rep2


title: CD26_rep1


title: Young AP - CD9High rep2_reanalyzed

description:
young_5d4_APCD9high
**reanalysis of GSM2828266 (GSE105790)


title: B10.R2.A: upper leaf - plant 2


title: AdipoqTraced_rep2


title: ski2-2 dcl4-2 ago1-45 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
sda1_45_smRNA_rep1


title: brain_PL_con_01

city: Xi'an

first: Guohong

last: Cai

address: NO.169 Changle West Road

institute: Fourth Military Medical University

description: Gene expression data from SNI SD rats 14 days after surgery (control group)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Rattus norvegicus

source_name: brain_PL_SNI (control)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: no

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

treatment_protocol: Spared nerve injury(SNI) surgery was performed in SNI group. Briefly, the sural common peroneal and tibial branches of the left sciatic nerve were exposed under isoflurane anesthesia. The tibial and common peroneal nerves were transected. The sural nerve was kept intact. For sham surgery, nerves were exposed but not transected.

value: Sprague Dawley

value: brain

tag: treatment

value: control


title: brain_PL_SNI_03

description: Gene expression data from SNI SD rats 14 days after surgery

tag: tissue

value: SNI


title: ein5-1 dcl4-2 ago1-27 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
eda1_27_smRNA_rep4

source_name: ein5-1 dcl4-2 ago1-27 aerial part


title: AdipoqTraced_rep1


title: Young AP - CD9High rep1_reanalyzed

description:
young_5d2_APCD9high
**reanalysis of GSM2828265 (GSE105790)


title: HUVEC_HDAC1_cut&run_1

data_processing:
Library strategy: Cut&Run
basecalls were made with standard Illumina pipeline for indicated instrument
for ChIPSeq and Cut&Run, reads were aligned to hg19 using Bowtie2
peak-calling was performed using MACS or MACS2
for RNA-seq, reads were mapped to ENSEMBL annotated transcripts using Tophat2 and differentially expressed genes were identified using EdgeR
Genome_build: hg19
Supplementary_files_format_and_content: big wig and bed files

source_name: venous endothelial cells

extract_protocol: Following Cut&Run, DNA was purified using phenol/chloroform/isoamyl alcohol (PCI) extraction followed by ethanol precipitation. DNA was suspended in 60  ul H2O. Libraries were constructed using the NEBNext   Ultra    II DNA Library Prep Kit for Illumina   according to manufacturer's protocols.

tag: cell type

value: HUVEC

tag: passage

value: wildtype

tag: chip antibody

value: HDAC1 (Abcam, catalog number ab7028)


title: brain_PL_con_03

value: male


title: brain_PL_SNI_02


title: brain_PL_con_02


title: B10.R1.A: upper leaf - plant 1


title: ∆rpoN Glucose Replicate 2

city: Newark

first: E Fidelma

last: Boyd

state: DE

address: 118 Wolf Hall

institute: University of Delaware

description: Total RNA depleted for rRNA

data_processing:
Base calling and Q scoring was done using BCL2FASTQ version 1.8.4
Raw 51-base reads were filtered to remove adaptor only sequences and low quality reads using the FASTX Toolkit.
Filtered reads were aligned to the Vibrio parahaemolyticus RIMD2210633 genome (Refseq ID NC_004603.1 Chromosome 1 and NC_004605.1 Chromosome 2) using Burrows-Wheeler Aligner (BWA.aln) version 0.7.7. Gene annotations were obtained from Ensembl bacteria, Rfam, Bacterial Small Regulatory RNA database and RAST.
Number of reads aligning to each genomic position was calculated using Htseq version 0.6.1.
Differential expression analysis was performed on obtained read counts using DESeq2 version 1.4.5.
Genome_build: ASM19609v1

organism: Vibrio parahaemolyticus

source_name: bacterium

growth_protocol: Vibrio parahaemolyticus wild-type and mutant strains were grown for 4 h in LB 3% NaCl and then diluted 1:50 into M9 medium supplemented with glucose or mouse cecal mucus as the sole carbon source. In order to best mimic the limited oxygen in vivo conditions the cells were grown statically without any shaking. To determine expression patterns upon initial exposure to mucus, we examined early-exponential-phase cultures that were grown for 90 mins in the medium.

extract_protocol:
Total RNA was extracted from cells obtained by centrifugation at the end of 90 mins using Trizol (Invitrogen, Carlsbad, CA) according to manufacturer’s protocol. The RNA samples were then quantified using a Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA). The samples were then treated with Turbo DNase (Invitrogen) according to manufacturer’s instructions. For each sample of the wild-type and mutant, RNA samples from two independent cultures were pooled together. Nanodrop quantifications were used to ensure equal representation of RNA from both biological replicates. Then, 3 μg of RNA was used for rRNA depletion using the Ribo-Zero rRNA removal kit for Gram-negative bacteria (Illumina).
Libraries for each sample were prepared from 100ng of rRNA-depleted-RNA using the Illumina TruSeq Stranded mRNA kit (Illumina) following standard manufacturer's protocol.

tag: genotype and description


title: ein5-1 dcl4-2 ago1-27 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
eda1_27_smRNA_rep3


title: B10.R2.B: lower leaf - plant 2


title: ∆rpoN Mucus Replicate 2

description: Total RNA depleted for rRNA


title: ski2-2 dcl4-2 ago1-45 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
sda1_45_smRNA_rep3


title: Adipocyte_rep2

value: dermis

value: 7 week old

value: wound bed day 5


title: ein5-1 dcl4-2 ago1-27 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
eda1_27_smRNA_rep1

value: aerial part

value: 20-day-old plant


title: MSC rep6_ATAC-seq

city: indianapolis

first: siwen

last: xu

state: IN

address: 410 W 10th St

department: School of Medicine

institute: Indiana University

data_processing:
For ATAC-seq footprinting analysis, all of the read start sites were adjusted to represent the center of the transposon binding event; reads aligning to the forward strand were offset by +4 bp and reads aligning to the reverse strand were offset by -5 bp (Buenrostro et al., 2013). MACS2 (Feng et al., 2011) was used with default parameters to identify all ATAC-seq peaks. Since ATAC-seq also detects nucleosome positions in the genome, we exempted such regions (total number of cutting sites in each peak < 200) from downstream analysis.
Heterozygous SNPs were identified using SAMtools-1.6 and bcftools-1.6 with the parameters mpileup -uf and view -Nvcg, respectively (Li et al., 2009). SNPs were further filtered by vcffilter with the parameter DP > 10 & MQ > 20 (Erik, 2016). In each open chromatin region, we used FIMO (Grant et al., 2011) to recognize potential TF binding sites from both reference and alternative alleles. Lastly, we used BEDTools IntersectBed (Quinlan and Hall, 2010) to merge the loci of heterozygous variants and potential TF binding sites. The set of TF binding sites intersecting SNPs were regarded as potential allele-specific TF binding sites.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq peaks, RNA-seq counts

source_name: human mesenchymal stem cells

extract_protocol: ATAC-seq was performed according to the published protocol (Buenrostro et al., 2013). Briefly, cells were collected in cold PBS and cell membranes were disrupted in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). The nuclei were pelleted and resuspended in the transposase reaction mix (25 µL 2× TD buffer, 2.5 µL transposase (Illumina) and 22.5 µL nuclease-free water). Directly following transposition, the sample was purified using DNA clean & concentratorTM-5 (ZYMO research). Following purification, libraries were amplified using 1× NEBnext PCR master mix and 1.25 µM of custom Nextera PCR primers. AMPure XP beads (Beckman Coulter) were used to purify the transposed DNA and the amplified PCR products. All libraries were sequenced on a 100-cycle paired-end run on an Illumina NOVAseq instrument.

value: human mesenchymal stem cells


title: Adipocyte_rep1


title: ein5-1 dcl4-2 ago1-27 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
eda1_27_smRNA_rep2


title: WT Mucus Replicate 2

description: Total RNA depleted for rRNA

value: Wild-type O3:K6 clinical isolate


title: WT Glucose Replicate 1

description: Total RNA depleted for rRNA


title: ∆rpoN Mucus Replicate 3

description: Total RNA depleted for rRNA


title: WT Glucose Replicate 2

description: Total RNA depleted for rRNA


title: HDAC1_cut&run_2

data_processing:
Library strategy: Cut&Run
basecalls were made with standard Illumina pipeline for indicated instrument
for ChIPSeq and Cut&Run, reads were aligned to hg19 using Bowtie2
peak-calling was performed using MACS or MACS2
Genome_build: hg19

growth_protocol: Umbilical cords were collected from UMass Memorial Medical Center and washed with phosphate-buffered saline (PBS) to remove excessive blood. For HUVEC isolation, the vein was cannulated at one end and perfused with 0.1% type 2 collagenase in PBS (Worthington Biochemical), then clamped at both ends, wrapped in aluminum foil and placed in a humidified incubator for 20 minutes at 37°C. Endothelial cells were collected by flushing collagenase solution through the vein with ECCM (EGM Endothelial Cell Growth Medium with SingleQuots Supplement, Lonza). Cells were centrifuged and re-suspended in ECCM, seeded in 0.2% gelatin-coated flasks and allowed to attach overnight at in a humidified incubator (37°C, 5% CO2). Medium was replaced the following day to remove erythrocytes and cells were grown to confluence (2-3 days). The same cords were used for HUAEC isolation by dissecting out arteries, which were washed twice with PBS and perfused with 0.05% Collagenase using a 20-gauge needle (Fisher) attached to a 20 ml syringe. Arteries were clamped on both ends, placed in a beaker containing PBS and incubated for 20 minutes in a 37°C water bath. Detached endothelial cells were collected by flushing the collagenase with EC complete medium followed by centrifugation. For passaging, cells were re-suspended in ECCM and grown for 3-4 days, or until ~80% confluence.

extract_protocol: Following Cut&Run, DNA was purified using phenol/chloroform/isoamyl alcohol (PCI) extraction followed by ethanol precipitation. DNA was suspended in 60 ul H2O. Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's protocols.


title: MSC rep5_ATAC-seq


title: ein5-1 dcl4-2 ago1-45 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
eda1_45_smRNA_rep4

source_name: ein5-1 dcl4-2 ago1-45 aerial part


title: ein5-1 dcl4-2 ago1-45 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
eda1_45_smRNA_rep1


title: ein5-1 dcl4-2 ago1-45 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
eda1_45_smRNA_rep3


title: ski2-2 dcl4-2 dcl2-1 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
sdd_smRNA_rep4

source_name: ski2-2 dcl4-2 dcl2-1 aerial part

value: ski2-2 dcl4-2 dcl2-1


title: MSC rep2_ATAC-seq


title: WT Mucus Replicate 1

description: Total RNA depleted for rRNA


title: MSC rep4_ATAC-seq


title: ein5-1 dcl4-2 ago1-45 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
eda1_45_smRNA_rep2


title: MSC rep3_ATAC-seq


title: ∆rpoN Glucose Replicate 1

description: Total RNA depleted for rRNA


title: MCF-7 rep9_ATAC-seq

source_name: MCF-7 breast cancer cells

value: MCF-7 breast cancer cells


title: ski2-2 dcl4-2 dcl2-1 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
sdd_smRNA_rep2


title: MCF-7 rep8_ATAC-seq


title: MSC rep1_ATAC-seq


title: ski2-2 dcl4-2 dcl2-1 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
sdd_smRNA_rep1


title: CIH 8W+Nor 4W, biological rep4

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from ApoE-/- mouse aorta in CIH for 8 weeks followed by normoxia for 4 weeks

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on  [MTA-1_0] Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

source_name: ApoE-/- mouse in CIH for 8 weeks followed by normoxia for 4 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: All mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: For microarray profiling, the mouse aorta total RNA was harvested using TRIzol reagent (Life Technologies, CA, USA) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The amount and quality of RNA were determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, MA, USA). The mRNA expression profiling was measured using Affymetrix ClariomTM D mouse Array (Affymetrix, Thermo Fisher Scientific), which contains 65956 gene-level probe sets.

treatment_protocol: The ApoE-/- mice were randomly divided into five groups: Nor 8W (mice in normoxia for 8 weeks), CIH 8W (mice in CIH for 8 weeks), Nor 12W (mice in normoxia for 12 weeks), CIH 12W (mice in CIH for 12 weeks), and CIH 8W+Nor 4W groups (mice in CIH for 8 weeks followed by normoxia for 4 weeks). All ApoE-/- mice were fed with high-fat feed. The aorta was harvested and performed to further analysis.

value: ApoE-/-

tag: protocol

value: aorta


title: CIH 8W+Nor 4W, biological rep2

value: CIH for 8 weeks followed by normoxia for 4 weeks


title: CIH 12W, biological rep4

description: Gene expression data from ApoE-/- mouse aorta in CIH for 12 weeks

source_name: ApoE-/- mouse in CIH for 12 weeks

value: CIH for 12 weeks


title: CIH 8W+Nor 4W, biological rep1


title: CIH 12W, biological rep3


title: MCF-7 rep7_ATAC-seq


title: ski2-2 dcl4-2 dcl2-1 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
sdd_smRNA_rep3


title: CIH 8W+Nor 4W, biological rep3


title: CIH 12W, biological rep1


title: MCF-7 rep6_ATAC-seq


title: CIH 12W, biological rep2


title: ski2-2 dcl2-1 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
sd2_smRNA_rep4

source_name: ski2-2 dcl2-1 aerial part

value: ski2-2 dcl2-1


title: Nor 12W, biological rep4

description: Gene expression data from ApoE-/- mouse aorta in normoxia for 12 weeks

source_name: ApoE-/- mouse in normoxia for 12 weeks

value: normoxia for 12 weeks


title: Nor 12W, biological rep2


title: Nor 12W, biological rep5


title: Nor 12W, biological rep3


title: ski2-2 dcl2-1 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
sd2_smRNA_rep2


title: MCF-7 rep5_ATAC-seq


title: CIH 8W, biological rep4

description: Gene expression data from ApoE-/- mouse aorta in CIH for 8 weeks

source_name: ApoE-/- mouse in CIH for 8 weeks

value: CIH for 8 weeks


title: ski2-2 dcl2-1 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
sd2_smRNA_rep1


title: CIH 8W, biological rep3


title: ski2-2 dcl4-2 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
sd4_smRNA_rep4

source_name: ski2-2 dcl4-2 aerial part

value: ski2-2 dcl4-2


title: Nor 12W, biological rep1


title: MCF-7 rep4_ATAC-seq


title: MCF-7 rep3_ATAC-seq


title: MCF-7 rep2_ATAC-seq


title: ski2-2 dcl4-2 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
sd4_smRNA_rep2


title: brain_PL_SNI_01

value: Sprague Dawley

value: brain

tag: Sex

value: male

value: SNI


title: ski2-2 dcl4-2 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
sd4_smRNA_rep3

value: aerial part

value: 20-day-old plant


title: CIH 8W, biological rep2


title: Nor 8W, biological rep3

description: Gene expression data from ApoE-/- mouse aorta in normoxia for 8 weeks

source_name: ApoE-/- mouse in normoxia for 8 weeks

value: normoxia for 8 weeks


title: Deder2, waterlogged 120h, replicate 4

city: Brandon

first: Ana

last: Badea

state: Manitoba

address: 2701 Grand Valley Rd

country: Canada

institute: Agriculture and Agri-Food Canada

description:
fpkm.xls
readcount.xls

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly (publicly available Morex genome assembly (International Barley Genome Sequencing Consortium, 2012) was accessed through Ensembl Plants (release 40)). Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: GCA_901482405.1, Ensembl 40
Supplementary_files_format_and_content: Data is provided in .xls file containing fragments per kilobase of transcript per million mapped reads (FPKM) values for each gene and sample.

organism: Hordeum vulgare

source_name: Roots

growth_protocol: Seeds of Yerong and Deder2 barley genotypes were placed in cone-tainer cells with a dimension of 4 × 14 cm (top diameter × height) in growth chamber conditions (20 ± 2°C, 16 h photoperiod) at Brandon Research and Development Centre (BDRC), Brandon, Manitoba, Canada. Cones were filled with the soil collected from a field where water is prone to accumulate creating excess moisture problems. The experiment consisted of four replications for both the control and treatments for each of the two genotypes tested. Plants were watered on demand from germination.

extract_protocol:
Root tissue was pulverized in liquid nitrogen using a mortar and pestle, and total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen, Canada) following the manufacturer’s protocol. Four biological replicates of Yerong at 0 and 72 h, and of Deder2 at 0, 72, and 120 h time-points, were subjected to RNA-seq analysis. The RNA quality and concentration were verified using a NanoDrop 1000 spectrophotometer (ThermoFisher Scientific, Canada) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Canada) prior to sequencing.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase （RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Two-week-old Yerong and Deder2 seedlings were submitted to waterlogging treatment, which involved keeping the water level above soil level for the duration of the treatment. Root tissue samples were collected at the time-points 0 and 72 h of treatment for Yerong from both treated and control plants, and at the points 0, 72, and 120 h of treatment for Deder2 from both treated and control plants. All samples collected were immediately submerged in liquid nitrogen and stored at -80 °C until further processing.

value: Roots

value: Waterlogging

tag: time point


title: CIH 8W, biological rep5

tag: genotype

value: ApoE-/-


title: CIH 8W, biological rep1

value: aorta


title: Deder2, waterlogged 120h, replicate 3

description:
fpkm.xls
readcount.xls


title: Deder2, waterlogged 120h, replicate 2

description:
fpkm.xls
readcount.xls


title: MCF-7 rep1_ATAC-seq

value: MCF-7 breast cancer cells


title: ein5-1 dcl4-2 dcl2-1 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
edd_smRNA_rep4

source_name: ein5-1 dcl4-2 dcl2-1 aerial part

value: ein5-1 dcl4-2 dcl2-1


title: KO I tumor

city: Buffalo

first: Minhui

last: Chen

state: New York

address: 665 Elm St

department: Immunology

institute: Roswell Park Cancer Institute

description: Gene Expression CodeSet profiling 561 genes; 547 immunology-related mouse genes + 14 internal reference controls.

hyb_protocol: Followed NanoString nCounter XT gene expression assay protocol. Briefly, hybridization buffer was mixed with the nCounter Mouse Immunology Panel reporter codeset to prepare a master mix. Master mix, sample and Rnase-fee water was combined with nCounter Mouse Immunology Panel Capture codeset. Samples with 25ng total RNA were then incubated for 20 h at 65 deg C.

scan_protocol: Raw counts of mRNA hybridized to oligos were counted using the NanoString nCounter SPRINT instrument.

data_processing: Data were quantified, normalized and analyzed using the NanoString Mouse Immunology panel (NanoString Technologies Inc, Seattle, WA). All data was normalized to 14 housekeeping genes (nSolver).

label: Capture probe-3'biotin, Reporter probe-5' barcode signal

source_name: KO I tumor

growth_protocol: 5x10^5 CT26.CL25 cells cells were subcutaneously injected into both hindlimbs of the wildtype or β2-AR KO female mice. Tumors were harvested on day 7 post irradiation.

extract_protocol: Cells were isolated from tumors by enzymatic digestion and CD8+ T cells were purified by sorting. Samples are first lysed and homogenized. The lysate is passed through a gDNA Eliminator spin column, ethanol is added to the flow-through, and the sample is applied to an RNeasy MinElute spin column. RNA binds to the membrane and contaminants are washed away. High quality RNA is eluted in 30 µl, or more, of water.

treatment_protocol: When tumors became palpable (~100 mm^3), one of bilateral tumors per mouse was received 6 Gy of 200kVp x-ray local radiation therapy, using a Philips RT-250

value: BALB/c

tag: gender

value: Female

value: 6-8 weeks

tag: genotypes

value: β2-adrenergic receptor knockout

tag: therapy

value: One of bilateral tumors was locally irradiated

value: CD8+ T cells

value: Irradiated CT26.CL25 tumor


title: Nor 8W, biological rep4

tag: strain


title: WT I tumor

source_name: WT I tumor

label_protocol: Followed NanoString nCounter XT gene expression assay protocol

tag: age

value: β2-adrenergic receptor wildtype


title: Nor 8W, biological rep1


title: Nor 8W, biological rep2


title: 12V_KB23

city: Brisbane

first: Kyle

middle: R

last: Upton

state: Qld

address: Cooper Road

department: SCMB

country: Australia

institute: University of Queensland

data_processing:
To confirm all libraries had high quality reads, all fastq files were first checked using FastQC
Trimmomatic was used to remove adapter sequences from reads.
Sequencing reads were aligned to GRCh38.p12 using HISAT2 with default options.
HTSeq was used to generate tag count files with default options
EdgeR with a standard generalised linear model was used to identify differentially expressed genes from the read count files. Reported results are from virus infected vs mock infected for normoglycemic (7M) and hyperglycemic (12M) samples separately.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tabular files with raw read counts. CSV files with Edge-R output

source_name: HPMEC

growth_protocol: Human epithelial NCl-H441 cells were obtained from the American Type Culture Collection and cultured in Roswell Park Memorial Institute medium (RPMI) with 10% fetal bovine serum and 1% penicillin-streptomycin. NC1-H441 cells were used at passages 3-8. Primary human pulmonary microvascular endothelial cells (HPMEC) were obtained from Sciencell (Carlsbad, CA, USA) and cultured in endothelial cell growth medium (Sciencell) in fibronectin coated tissue culture flasks (2μg/cm2, Sigma). HPMEC cells were used at passages 3-7. In vitro co-culture and mono-culture models of the pulmonary epithelial-endothelial barrier were established as described in Short et al. (European Respiratory Journal 2016; 47(3): 954). Once the NCI-H441 cells reached confluency, the media in both upper and lower compartments was refreshed every 12 hours. The medium of the upper compartment was refreshed with RPMI (5% FBS, 1μM dexamethasone and 7mM of glucose) (Gibco), while the lower compartment was refreshed with RPMI (5% FBS and either 7mM glucose or 12mM glucose) until a trans-barrier electrical resistance (TER) of greater than 800Ω was observed. Influenza virus strain A/Solomon Islands/03/2006 (Solomon Islands/f06; H1N1) was used to model IAV infection. Virus stocks were prepared in embryonated chicken eggs. Titres of IAV were determined by plaque assays on MDCK cells.

extract_protocol:
Qiagen RNeasy plus mini kit (manufacturers recommended protocol was used)
Stranded

treatment_protocol: One hour prior to infection, the medium of the transwell plate was refreshed with RPMI (2% FBS). Cells were infected or mock infected by adding A/Solomon Islands/03/2006 (Solomon Islands/06; H1N1) at multiplicity of infection (MOI) OF 0.5 or PBS respectively to the upper compartment of the transwell system. Virus was not removed after infection and cells were monitored for a duration of 24 hr post-infection.

value: Human epithelial cells and human pulmonary microvascular endothelial cells

value: high glucose

value: Virus Infection


title: ein5-1 dcl4-2 dcl2-1 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
edd_smRNA_rep3

value: aerial part

value: 20-day-old plant


title: 12V_KB15


title: Deder2, control 120h, replicate 4

description:
fpkm.xls
readcount.xls

value: Roots

value: Control


title: 12V_KB7


title: ski2-2 dcl4-2 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
sd4_smRNA_rep1

value: ski2-2 dcl4-2


title: Era- mature-osteoclast progenitors 3

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: The data were normalised using quantile normalisation with IlluminaGUI in R

data_processing: quantile normalized

source_name: Era- mature-osteoclast progenitors

label_protocol: Standard Illumina hybridization protocol

growth_protocol: Cells were plated in α-MEM complete media (10% fetal bovine serum, 100 U ml-1 penicillin, and 100 µg ml-1 streptomycin). Twenty-four hours later, non-adherent cells were re-plated in Petri dishes with 30 ng ml-1 M-CSF for 4 days to obtain macrophages. To generate pre-osteoclasts and mature osteoclasts, macrophages were cultured in α-MEM complete media with 30 ng ml-1 M-CSF and 30 ng ml-1 RANKL (R&D Systems) for 2 and 4 days, respectively

extract_protocol: A RNA extraction kit

treatment_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

tag: strain background

tag: genotype/variation

value: ERalphaf/f;LysM-Cre

value: bone marrow

value: mature-osteoclast progenitors


title: Deder2, control 120h, replicate 3

description:
fpkm.xls
readcount.xls

tag: treatment


title: Nor 8W, biological rep5

value: ApoE-/-

value: normoxia for 8 weeks

tag: tissue

value: aorta


title: ein5-1 dcl4-2 dcl2-1 aerial part_rep1 (smRNA)

description:
SmallRNA_processed_data
edd_smRNA_rep1

value: ein5-1 dcl4-2 dcl2-1


title: Deder2, control 120h, replicate 2

description:
fpkm.xls
readcount.xls


title: ein5-1 dcl4-2 dcl2-1 aerial part_rep2 (smRNA)

description:
SmallRNA_processed_data
edd_smRNA_rep2


title: WT A tumor

source_name: WT A tumor

value: BALB/c

value: Female

value: 6-8 weeks

value: One of bilateral tumors was locally irradiated

tag: cell type

value: CD8+ T cells

value: Non-irradiated CT26.CL25 tumor


title: Era- mature-osteoclast progenitors 2


title: 12M_KB21

value: Human epithelial cells and human pulmonary microvascular endothelial cells

value: high glucose

value: Mock Infection


title: Era- mature-osteoclast progenitors 1


title: KO A tumor

source_name: KO A tumor

value: β2-adrenergic receptor knockout


title: ein5-1 dcl2-1 aerial part_rep4 (smRNA)

description:
SmallRNA_processed_data
ed2_smRNA_rep4

source_name: ein5-1 dcl2-1 aerial part

value: aerial part

value: 20-day-old plant

value: ein5-1 dcl2-1


title: Deder2, control 120h, replicate 1

description:
fpkm.xls
readcount.xls

value: Roots

value: Control


title: 12V_KB24

value: Virus Infection


title: ein5-1 dcl2-1 aerial part_rep3 (smRNA)

description:
SmallRNA_processed_data
ed2_smRNA_rep3


title: 12M_KB14