title: Tumor 2366 [SAM24329369]

city: South San Francisco

first: Steffen

last: Durinck

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina Casava 1.8
Illumina bcl2fastq 2.17
Reads were demultiplexed based on perfect matches to expected barcodes
Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (2013-10-10) only considering uniquely mapped reads
Per-gene transcript counts were determined based on the number of unique UMIs for mapped reads overlapping exons in sense orientation, allowing for one mismatch when collapsing UMI sequences
Barcodes were filtered by requiring a minimum number of detected transcripts, where a sample-specific cutoff was set to 0.1 times the total transcript count for cells at rank 30 (the 99th percentile for 3,000 cells)
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene x barcode matrix with UMI counts

source_name: mammary gland

extract_protocol:
10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2
10x Genomics Chromium Single Cell 3' Kits

tag: celltype

value: bulk dissociated tumor cells


title: YPS1009 Dis12 ssd1Δ Rep1

status: Public on Jan 08 2020

type: SRA

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

country: USA

institute: University of Wisconsin

description:
Gasch 872
08302017_HTSeq_results.txt

library_source: transcriptomic

data_processing:
Reads trimmed w/ Trimmomatic-0.30
Read alignment done w/ BWA mem Version: 0.7.12-r1039
Reas sorting and indexing w/ Samtools 1.2 (htslib 1.2.1)
Gene counts generated w/ HTSeq version 0.6.0
RPKM Calculated w/ Gasch Laboratory python script
Genome_build: SGD S288C R58-1-1 w/ YPS1009 snps subsitution
Supplementary_files_format_and_content: HTSeq count tables w/ gene counts for each sample

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: All strains were grown 7+ generations in YPD to OD600 0.3-0.6 except noted samples grown 3 generations in YPD to OD600 0.3-0.6 to minimize loss of aneuploidy

extract_protocol:
RNA was extracted with hot phenol protocol; RNA was rRNA-depleted with Illumina's Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat)
cDNA library was prepared with Illumina's TruSeq Total RNA Stranded Kit

tag: hapoid or diploid

value: Haploid

tag: euploid or aneuploid

value: Aneuploid


title: PDAC6_VEH_1

city: Boston

first: David

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw and normalized read counts in Text format

molecule: polyA RNA

organism: Homo sapiens

source_name: primary pancreatic ductal adenocarcinoma cell line

growth_protocol: PDAC cell lines were plated in 6-well ultra low attachment plates in RPMI base media with 20 ul/ml B27, 20 ng/ml EGF, 20 ng/ml bFGF and 100 U/mL Penicillin and 100 mg/mL Streptomycin. Tumor spheres were grown for 5 days in the presence of 1,25-dihydroxyvitaminD3 or vehicle control prior to harvesting for RNA isolation.

extract_protocol:
After 5 days of culture, cells were harvested for RNA isolation using miRNEasy Mini Kit (Qiagen) including the optional on column DNAse treatment (Qiagen) per manufacturer's protocol.
To generate libraries for total RNA sequencing the Illumina Smarter Stranded Total RNA-Seq kit v2 (Cat No#634413) was used according to the manufacturer's instructions. Pooled libraries were sequenced on an Illumina NextSeq 500 sequencer.

treatment_protocol: Cells were treated with 10nM 1a,25-dihydroxyvitaminD3 or DMSO for vehicle control on D1 and D3 of culture

tag: treatment

value: DMSO

tag: culture condition

value: 3D tumorsphere


title: PDAC8_VITD_1

value: Calcitriol


title: Tumor 307 [SAM24329367]

organism: Mus musculus


title: Tumor 2366 [SAM24329368]


title: PDAC5_VITD_3


title: PDAC5_VEH_3


title: PDAC6_VEH_2


title: IMJCWT4: Wild-type replicate 4 ncRNA-seq

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 E 57th St

department: Pediatrics, Pathology, and Human Genetics

institute: University of Chicago

description: Poly A depleted RNA

data_processing:
Fastq files were aligned to UCSC genome build mm9 using TopHat (version 2.0.10). 168 million and 174 million reads were successfully mapped. RABT assembly was performed by Cufflinks (version 2.2.1, with parameters –g --frag-bias-correct --multi-read-correct --upper-quartile-norm). Analysis of differential expression was performed using Cuffdiff from the Cufflinks package
Genome_build: mm10
Supplementary_files_format_and_content: Significant results in Excel file (mm10)
Supplementary_files_format_and_content: bigWig pooled by genotype and seperated by strand

source_name: Retina

extract_protocol: Libraries were quantitated using the Agilent Bio‐analyzer (model 2100) and pooled in equimolar amounts. The pooled libraries were sequenced with 50-bp stranded single-end reads on the HiSEQ4000 in Rapid Run Mode following the manufacturer's protocols (2013).

tag: tissue

value: retina

tag: age

value: post natal day 21

tag: genotype/variation

value: wild-type


title: wt_sphere_atac_rep2

city: Bergen

first: Gunnar

last: Schulze

state: Hordaland

address: Thormøhlensgt. 55

department: Institute for informatics

country: Norway

institute: University of Bergen

description:
sphere, wild-type
wt_sphere_atac.pooled_samples.bw
consensus_peaks.NFR.bed

library_source: genomic

data_processing:
reads were trimmed for low-quality sequences and adapters using cutadapt v1.9.1 and subsequently aligned to the zebrafish Zv10 genome assembly using bowtie2 (v2.2.4) with parameters:  -X 2000 --no-mixed --no-discordant
Alignments were deduplicated using samtools rmdup and filtered to include only properly paired, high-quality (MAPQ>=q30), non-mitochondrial alignment pairs.
Valid alignments were pooled by stage/condition and converted to BED-files covering the full range of the insert  using R/GenomicAlignments. To center on transposase cut sites, start positions of plus strand alignments  were adjusted by +4bp and end positions of minus strand  alignments were adjusted -5bp.
Open chromatin peaks were called based on  BED-files filtered to include only sub-nucleosomal fragments (130bp cut-off), pooling samples for each stage/condition. MACS2 v2.1.1 was used with (non-default) parameters: --no-model –no-lambda -q 0.05--format BED --keep-dup all -g 1371719383 and providing the gDNA sample as an input control  ( -c switch).
bigwig files were generated using deeptools version 3.1.3 at 20bp (-bs 20) resolution,  normalizing to the library total (--normalizeUsingRPKM), extending paired alignments to full fragments (-e).
Genome_build: Zv10
Supplementary_files_format_and_content: bw files: bigwig files for samples pooled by stage/condition. Scores represent RPKM-normalized ATAC-seq fragment abundance (including nucleosome-free and nucleosomal fragments) per 20bp bins. narrowPeak files: Peak files in narrowPeak format as output from MACS2, representing regions enriched for sub-nucleosomal ATAC-seq fragments, pooled by stage/condition.

molecule: genomic DNA

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish were maintained and raised under standard conditions. Embryos were dechorionated immediately upon fertilization, synchronized and allowed to develop until the desired stage at 28°C in Danieau’s solution

extract_protocol:
The ATAC-seq protocol (Buenrostro et al., 2014) was performed on approximately 70,000 cells. Zebrafish embryos were first deyolked using buffers as described in (Link et al. 2006); briefly, embryos were dissociated in deyolking buffer by brief vortexing and shaking at 1100 rpm at 4°C. Cells were collected by centrifugation at 400 rcf and the supernatant was removed. Cells were washed two more times with deyolking wash buffer. For the 256-cell stage samples, 300 embryos were manually deyolked. Following dissociation, cells were lysed in cell lysis buffer (Buenrostro et al. 2014). Nuclei were spun down at 500 rcf for 10 minutes at 4°C, resuspended in tagmentation mix and incubated at 37°C for 30 minutes with gentle shaking at 800 rpm. Tagmented DNA was cleaned up using the Qiagen Minelute Reaction Cleanup kit.
to make DNA libraries, the number of PCR cycles were determined by qPCR as described in (Buenrostro et al. 2014). Following 11-13 cycles of PCR, the libraries were purified using the Minelute Reaction cleanup kit (Qiagen) and measured with a fragment analyzer. Samples were sequenced following adaptor cleanup

treatment_protocol: for samples where transcription was inhibited, α amanitin (A2263; Sigma) was injected at the 1-cell stage at a concentration of 0.2 ng per embryo.

tag: Stage

value: sphere

value: whole embryo


title: HUVEC DM control, rep 1

type: RNA

city: Frankfurt

last: John

state: Hessen

address: Theodor-Stern-Kai 7

country: Germany

institute: Institute for Cardiovascular Regeneration

description:
N1_day3_DM_SCR
Scrambled condition DM medium

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Gene-expression analysis was performed using the GeneChip Human Exon 1.0 ST array (#900651 Affymetrix) following the supplier’s instructions. Data was analyzed by using the Exon Array Analyzer (EAA) Web interface (http://eaa.mpi-bn.mpg.de/).
probe group file: HuEx-1_0-st-v2.pgf
meta-probeset file: HuEx-1_0-st-v2.mps

label: biotin

label_protocol: standard Affymetrix protocol

growth_protocol: Experiments were performed using human umbilical vein endothelial cells (HUVEC) purchased from Lonza. Cells were cultured in endothelial basal medium without phenol red (#C-22215, PromoCell), supplemented with hydrocortisone (#CC-4035C, Lonza), ascorbic acid (#CC-4116C, Lonza), bovine brain extract (BBE) (#CC-4092C, Lonza), epidermal growth factor (EGF) (#CC-4017, Lonza), 10% fetal bovine serum (FBS) (#CC-4101, Lonza) and GA-1000 (Gentamicin+Amphotericin-B, CC-4081C, Lonza) or for EndMT without EGF and BBE.

extract_protocol: Total RNA was isolated using Qiazol Lysis Reagent (#79306; Qiagen) and miRNeasy-kit (#217004; Qiagen) with additional DNase I (#79254; Qiagen) digestion according to the manufacturer’s protocol. 1 μg of RNA from each sample was reverse-transcribed using random hexamer primed single-strand cDNA (10 min at 25 °C, 15 min at 42 °C, 5 min at 99 °C) by MMLV Reverse Transcriptase (#N8080018; Life technologies) as previously described. (Boeckel et al., 2011) For qPCR, cDNA was amplified using Fast SYBR Green Mastermix (#4385612 Life Technologies) on a ViiA7- Realtime qPCR System (Life Technologies). Expression level of mRNAs were normalized to RPLP0 which served as a housekeeping gene using the 2‑ΔCt method.

treatment_protocol: 4 x 10^5 HUVEC were seeded in a 60 mm cell culture dish, cells were cultivated either full medium (FM) or in differentiation media (DM).  After 24 h of cultivation, cells were treated with 10 ng/ml TGF-β2 (#302-B2, R&D System). After additional 48 h of incubation, the treatment was repeated. 96h later, RNA was isolated.

tag: cell line

value: Wild-type

value: differentiation media (DM)

value: 3 days


title: PDAC5_VEH_2


title: Tumor 2383 [HITS276721]

extract_protocol:
10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v1
10x Genomics Chromium Single Cell 3' Kits


title: Tumor 307 [SAM24329366]


title: wt_shield_atac_rep2

description:
shield, wild-type
wt_shield_atac.pooled_samples.bw
consensus_peaks.NFR.bed

value: shield


title: wt_oblong_atac_rep3

description:
oblong, wild-type
wt_oblong_atac.pooled_samples.bw
consensus_peaks.NFR.bed

value: oblong


title: wt_sphere_atac_rep1


title: wt_shield_atac_rep1


title: Tumor 2375 [HITS276719]


title: YPS1009 Euploid Wild-type Rep1

description:
Gasch 869
08302017_HTSeq_results.txt

value: Euploid


title: PDAC5_VITD_1


title: wt_oblong_atac_rep2


title: PDAC6_VITD_1


title: Tumor 2375 [HITS276718]

value: bulk dissociated tumor cells


title: PDAC3_VITD_3


title: PDAC5_VEH_1


title: Tumor 2050 [HITS178882]


title: wt_oblong_atac_rep1


title: 103148_R6.2_2_IP

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description:
IP R6/2 2 m
2017-9249

data_processing:
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (logCPM) and differential expression analysis using edgeR and limma voom.  Low expressed genes were removed.
Genome_build: mm10
Supplementary_files_format_and_content: logCPM values

source_name: Striatum

extract_protocol:
Input and IP samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using Illumina TruSeq RNA sample prep kit following manufacturer's protocol.  After library preparation, amplified double-stranded cDNA was fragmented into 125 bp (Covaris-S2, Woburn, MA) DNA fragments, which were (200 ng) end-repaired to generate blunt ends with 5’- phosphates and 3’- hydroxyls and adapters ligated.

treatment_protocol: Adeno-associated virus (AAV) was injected in the striatum: the coordinates were 1 mm anterior to bregma, 2 mm lateral to midline, and 2.4 mm deep from the pial surface.

value: striatum

tag: rna-sample type

value: IP

tag: genotype

value: 2 m

tag: strain

value: CBA x C57BL/6


title: PDAC3_VEH_3

value: DMSO

value: 3D tumorsphere


title: wt_high_atac_rep2

description:
high, wild-type
wt_high_atac.pooled_samples.bw
consensus_peaks.NFR.bed

value: high


title: PDAC5_VITD_2

value: Calcitriol


title: wt_high_atac_rep1

value: wild-type


title: 103146_R6.2_3_IN

description:
INPUT R6/2 3 m
2017-9249

value: INPUT

value: 3 m


title: wt_dome_atac_rep3

description:
dome, wild-type
wt_dome_atac.pooled_samples.bw
consensus_peaks.NFR.bed

value: dome

value: whole embryo


title: 103147_NCAR_2_IN

description:
INPUT NCAR 2 m
2017-9249

value: NCAR


title: PDAC3_VITD_2


title: 103145_NCAR_2_IP

description:
IP NCAR 2 m
2017-9249


title: PDAC3_VITD_1


title: PDAC3_VEH_1


title: wt_dome_atac_rep2


title: PDAC2_VITD_3


title: wt_80epi_atac_rep2

description:
80% epiboly, wild-type
wt_80epi_atac.pooled_samples.bw
consensus_peaks.NFR.bed


title: 103144_R6.2_3_IN

description:
INPUT R6/2 3 m
2017-9249


title: 103143_R6.2_3_IP

description:
IP R6/2 3 m
2017-9249


title: PDAC2_VEH_3


title: 103142_NCAR_3_IP

description:
IP NCAR 3 m
2017-9249


title: PDAC2_VITD_2


title: wt_256_atac_rep2

description:
256-cell, wild-type
wt_256_atac.pooled_samples.bw
consensus_peaks.NFR.bed


title: wt_256_atac_rep1


title: 103139_R6.2_2_IP

description:
IP R6/2 2 m
2017-9249


title: PDAC2_VEH_2


title: 103140_R6.2_2_IN

description:
INPUT R6/2 2 m
2017-9249


title: PDAC2_VITD_1


title: sox19b-KO_oblong_atac_rep2

description:
oblong, MZsox19b mutants were generated by CRISPR deletion
sox19b-KO_oblong_atac.pooled_samples.bw

value: oblong


title: 103138_NCAR_3_IP

description:
IP NCAR 3 m
2017-9249


title: PDAC3_VEH_2


title: 103137_R6.2_3_IP

description:
IP R6/2 3 m
2017-9249


title: sox19b-KO_oblong_atac_rep1


title: pou5f3-KO_oblong_atac_rep2

description:
oblong, MZpou5f3 mutants were generated by CRISPR deletion
pou5f3-KO_oblong_atac.pooled_samples.bw


title: PDAC9_FFX_D4

value: FFX


title: PDAC9_FFX_D14


title: wt_dome_atac_rep1


title: 103136_NCAR_2_IN

description:
INPUT NCAR 2 m
2017-9249


title: pou5f3-KO_oblong_atac_rep1


title: 103135_NCAR_3_IN

description:
INPUT NCAR 3 m
2017-9249


title: nanog-KO_oblong_atac_rep2

description:
oblong, MZnanog mutants were from (Veil et al. 2018)
nanog-KO_oblong_atac.pooled_samples.bw

value: nanog-KO


title: PDAC9_FFX_D1


title: 103134_NCAR_2_IP

description:
IP NCAR 2 m
2017-9249

value: striatum


title: nanog-KO_oblong_atac_rep1


title: 103133_NCAR_3_IN

description:
INPUT NCAR 3 m
2017-9249


title: PDAC9_VEH_D0


title: wt_high_atac_rep3


title: gDNA_oblong_tagm_rep1

description:
tagmented, nucleosome-free genomic DNA
gDNA_oblong_atac.pooled_samples.bw


title: 103132_R6.2_3_IP

description:
IP R6/2 3 m
2017-9249

value: IP


title: PDAC8_FFX_D14


title: am_oblong_atac_rep2

description:
oblong, alpha-amanitin treated at 1-cell stage
am_oblong_atac.pooled_samples.bw

value: alpha-amanitin


title: 103131_NCAR_2_IP

description:
IP NCAR 2 m
2017-9249

value: 2 m

value: CBA x C57BL/6


title: PDAC8_FFX_D4

value: 3D tumorsphere


title: am_oblong_atac_rep1


title: 103130_NCAR_2_IN

description:
INPUT NCAR 2 m
2017-9249


title: PDAC8_FFX_D1


title: 103129_NCAR_2_IN

description:
INPUT NCAR 2 m
2017-9249


title: PDAC8_FFX_D0


title: PDAC6_FFX_D14


title: 103127_R6.2_3_IN

description:
INPUT R6/2 3 m
2017-9249


title: 103128_NCAR_3_IP

description:
IP NCAR 3 m
2017-9249


title: PDAC8_VEH_D0

value: DMSO


title: PDAC9_FFX_D0


title: 103126_R6.2_2_IN

description:
INPUT R6/2 2 m
2017-9249


title: 103125_NCAR_2_IP

description:
IP NCAR 2 m
2017-9249


title: PDAC6_FFX_D4


title: 103124_R6.2_3_IP

description:
IP R6/2 3 m
2017-9249


title: Patient 52

city: Seoul

first: Gyeong Back

last: Lim

address: 79, Sangdo-ro 37-gil, Dongjak-gu, Seoul, Republic of Korea

country: South Korea

institute: Asan Medical Center

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Calculate gene length using NCBI GFF file, and obtain value by dividing raw count value for each sample by gene length.

source_name: Triple Negative Breast cancer

label_protocol: One ug of total RNA was assayed on a nCounter Digital Analyzer (NanoString).

extract_protocol: On average, 10 5 um-thick FFPE sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist (HJL) using section stained by H & E.

value: Triple Negative Breast cancer

tag: status after 5 years

value: Dead

tag: relapse

value: non reccurence

tag: pcr

value: non complete remission

tag: pre/post

value: Pre


title: Patient 55

value: reccurence


title: PDAC6_VEH_D0


title: Patient 53


title: Patient 54

value: Alive


title: 103123_R6.2_2_IN

description:
INPUT R6/2 2 m
2017-9249

value: INPUT


title: Patient 51

value: complete remission

value: Post


title: PDAC5_FFX_D14

value: FFX


title: Patient 50


title: 855 CFUMK

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

data_processing:
Illumina's bcl2fastq2 to generate fastq files
Custom script to trim reads to 30nts
Map reads with Bowtie 0.12.8 with parameters -y -v 2 -p 7 --best --strata -k 1 --sam-nohead --sam
Samtools v1.6 to filter chrM and unmapped reads
Fseq v1.85 to generate wiggles.  Use parameters -v -of wig -f 0
Homer v36 to call peaks.  Use parameter -style dnase.
Custom script to format peaks in bed format and bedtools to remove blacklist regions
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Fseq
Supplementary_files_format_and_content: bed, peaks from Homer

source_name: bone marrow

extract_protocol:
Approximately 50,000 cells were collected by centrifugation at 600 xg for 10 min at 4 °C. Cells were washed once with cold 1x PBS and centrifuged as above. Cells were lysed by gently pipetting to resuspend cell pellet in cold lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged as above.
Cells were suspended in the following mix: 25 μl 2X Tagment DNA buffer (Illumina cat# FC-121-1030), 3 μl Tn5 Transposase (Illumina cat#FC-121-1030), 22 μl nuclease-free H2O and incubated for 30 min at 37 °C. Reactions were terminated by adding 5 μl of 1% SDS solution and purified using SPRIselect beads. Following purification, library fragments were amplified using NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min.  Libraries were amplified for a total of 17–19 cycles and then purified using AMPure XP beads (Beckman Coulter cat #A63881).

tag: developmental stage

value: adult

tag: cell type

value: colony forming unit megakaryocyte


title: Patient 49


title: 847 CFUMK


title: 103122_R6.2_2_IP

description:
IP R6/2 2 m
2017-9249

value: striatum

value: IP

value: 2 m


title: PDAC5_FFX_D4

value: 3D tumorsphere


title: Patient 48

value: Triple Negative Breast cancer


title: 846 ERY

value: erythroblast


title: 103121_NCAR_3_IP

description:
IP NCAR 3 m
2017-9249

value: NCAR

value: 3 m

value: CBA x C57BL/6


title: PDAC6_FFX_D0


title: 103120_NCAR_3_IN

description:
INPUT NCAR 3 m
2017-9249


title: 848 iMK

value: megakaryocyte


title: 856 iMK


title: 854 ERY


title: PDAC5_VEH_D0

value: DMSO


title: PDAC5_FFX_D0


title: 103141_NCAR_3_IN

description:
INPUT NCAR 3 m
2017-9249

value: INPUT


title: Patient 46

value: Dead

value: reccurence

value: non complete remission


title: PDAC3_FFX_D4

value: FFX


title: PDAC3_FFX_D14


title: 103119_R6.2_2_IP

description:
IP R6/2 2 m
2017-9249


title: 853 CFUE

value: adult

value: colony forming unit erythroblast


title: 845 CFUE


title: 103118_R6.2_3_IN

description:
INPUT R6/2 3 m
2017-9249

value: striatum


title: PDAC3_FFX_D1


title: 852 MEP

value: megakaryocyte erythroid progenitor


title: 103117_R6.2_2_IN

description:
INPUT R6/2 2 m
2017-9249

value: 2 m


title: Patient 45

value: Triple Negative Breast cancer

value: Alive

value: non reccurence

value: Pre


title: Patient 44

value: Post


title: PDAC2_VEH_1

value: 3D tumorsphere


title: 844 MEP


title: Patient 47


title: Patient 43


title: PDAC3_FFX_D0


title: Patient 42


title: 851 GMP

value: granulocyte macrophage progenitor


title: PDAC3_VEH_D0

value: DMSO


title: Patient 41

value: Dead


title: B14_R6.2_IN

description:
INPUT R6/2 1 m
2017-9269

value: INPUT

value: 1 m

value: CBA x C57BL/6


title: B13_NCAR_IN

description:
INPUT NCAR 1 m
2017-9269

value: NCAR


title: 843 GMP

value: adult


title: PDAC2_FFX_D14

value: FFX


title: 850 CMP

value: common myeloid progenitor


title: PDAC2_FFX_D4


title: Patient 40

value: non complete remission


title: PDAC2_FFX_D0


title: B12_NCAR_IN

description:
INPUT NCAR 1 m
2017-9269

value: striatum


title: B11_NCAR_IP

description:
IP NCAR 1 m
2017-9269

value: IP


title: Patient 38

value: Triple Negative Breast cancer

value: reccurence


title: PDAC2_VEH_D0


title: B10_NCAR_IP

description:
IP NCAR 1 m
2017-9269


title: MGH1312


title: 987 LSK

value: Lin-, Sca1+, cKit+


title: Patient 37

value: Alive

value: non reccurence

value: Pre


title: B15_R6.2_IP

description:
IP R6/2 1 m
2017-9269


title: B16_R6.2_IP

description:
IP R6/2 1 m
2017-9269


title: 183 MEP input

data_processing:
Illumina's bcl2fastq2 to generate fastq files
Mapping to reference genome with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Macs
Supplementary_files_format_and_content: broadpeak, peaks from Macs

extract_protocol:
Lysates were clarified from sonicated nuclei and CTCF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying TruSeq ChIP-seq Sample Preparation Kit. (Part#  IP-202-1012). In brief, ChIP-enriched, fragmented DNA was subjected to end repair to generate blunt-end double stranded DNA, adenylation of 3’ ends, and adaptor ligation. Following ligation, SPRIselect (Beckman Coulter) beads were used at 0.9X and 0.6X for left and right side selection, respectively, to obtain an average library target size of ~300 bp. After size selection, fragments were amplified for 16 cycles, and PCR products were purified using Agencourt AMPureXP beads (Beckman Coulter).

tag: chip ab

tag: cell isolation markers

value: megakaryocyte erythroid progenitor


title: Patient 36

value: Dead


title: MGH1473

tag: treatment

tag: culture condition

value: 3D tumorsphere


title: B9_R6.2_IP

description:
IP R6/2 1 m
2017-9269

tag: tissue

tag: age

value: 1 m

value: CBA x C57BL/6


title: Patient 35

value: complete remission


title: wt_80epi_atac_rep1

tag: Stage

tag: genotype/variation

value: wild-type

value: whole embryo


title: MGH937


title: MGH1222


title: Patient 34

value: non complete remission


title: S96: CTCFKD2_singleCell

city: Shenzhen

first: Wenfei

last: Jin

state: Guangdong

address: 1088 Xueyuan Rd #faculty research building 1

department: Department of Biology

country: China

institute: Southern University of Science and Technology

description: RNA-seq

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
Reads were aligned to the mouse genome (Ensemble version GRCm38.89) utilizing STAR
We calculated the TPM of each gene in single cell RNA-seq
Genome_build: GRCm38.89
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

growth_protocol: EL4 cells were cultured in DMEM (GIBCO Invitrogen) supplemented with 50 IU/mL penicillin, 50 mg/mL streptomycin (GIBCO Invitrogen) and 10% heat inactivated calf serum (Sigma, USA). Cultures were maintained by replacement of fresh medium every 3 days, and cell density was kept between 1 X 105 and 1 X 106 cells/mL.

extract_protocol:
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System

treatment_protocol: 293T cells were co-transfected with an envelope plasmid (pLP/VSVG) to generate lentiviral particles. The medium containing lentiviral particles was harvested after 48h transfection. EL4 cells were infected with the harvested shLuc and shCTCF retroviral particles packaged in GP2-293.

tag: cell number

value: Single cell

value: CTCF knockdown

value: EL4 cells


title: S95: CTCFKD2_singleCell

description: RNA-seq

tag: genotype


title: B8_NCAR_IP

description:
IP NCAR 1 m
2017-9269

value: striatum

tag: rna-sample type

value: IP

value: NCAR

tag: strain


title: Patient 33

value: Triple Negative Breast cancer

tag: status after 5 years

value: Alive

tag: relapse

value: non reccurence


title: S93: CTCFKD2_singleCell

description: RNA-seq


title: Patient 32

value: Dead

value: reccurence

tag: pcr

tag: pre/post

value: Pre


title: MGH1505

value: 3D tumorsphere


title: B6_R6.2_IN

description:
INPUT R6/2 1 m
2017-9269

value: INPUT

value: 1 m

value: CBA x C57BL/6


title: S92: CTCFKD2_singleCell

description: RNA-seq


title: YB-1 RIP-Seq wt Total (Bethyl1_YB1), run 2

city: Pushchino

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

data_processing:
Trimming was performed with cutadapt v1.18 with the following parameters: "-a AGATCGGAAGAGCACACGTCT -j 32 --minimum-length 20 --discard-untrimmed --maximum-length 60 --trim-n" for the Ribo-Seq and the size-matched RNA-Seq samples, "-a AGATCGGAAGAGCACACGTCT -j 32 --minimum-length 20 --trim-n -o" for the RIP-Seq and the respective control RNA-Seq samples. Quality parameter was set as "-q 20" for HiSeq-sequences samples and "--nextseq-trim=20" for NextSeq-sequenced samples.
Mapping to the hg38 genome assembly with GENCODE v29 genome annotation and read counting was performed with STAR v2.6.1d (default parameters).
Genome_build: GRCh38 - hg38
Supplementary_files_format_and_content: Tab-separated plain text files with read counts per gene.

source_name: Human embryonic kidney

growth_protocol: HEK293T cells were routinely cultured in DMEM supplemented with 10% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin, and 100 µg streptomycin.

extract_protocol:
Cells were lysed in two pellet volumes of lysis buffer and centrifuged at 16,000 g for 10 min. YB-1-RNA complex was isolated by antibody-coated Protein-G sepharose. RNA was isolated using TRIzol LS Reagent.
Library was prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina. rRNA depletion was performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat).

tag: cell line

tag: experiment type

value: RIP-Seq

value: wild type

tag: rip antibody


title: B4_NCAR_IN

description:
INPUT NCAR 1 m
2017-9269


title: S91: CTCFKD2_singleCell

description: RNA-seq

value: Single cell

value: CTCF knockdown


title: B3_R6.2_IN

description:
INPUT R6/2 1 m
2017-9269

value: striatum


title: Patient 30

value: non complete remission


title: S90: CTCFKD2_singleCell

description: RNA-seq

value: EL4 cells


title: B2_NCAR_IN

description:
INPUT NCAR 1 m
2017-9269

value: NCAR


title: B7_R6.2_IP

description:
IP R6/2 1 m
2017-9269

value: IP


title: Patient 28

value: Triple Negative Breast cancer


title: Patient 29

value: Dead


title: B1_NCAR_IP

description:
IP NCAR 1 m
2017-9269


title: RNA-Seq deltaYB-1 polyA rep2 (total_polyA_del_2)

description: Control for RIP-Seq

extract_protocol:
Cells were lysed in two pellet volumes of lysis buffer and centrifuged at 16,000 g for 10 min. RNA was isolated using TRIzol LS Reagent.
Library was prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina. PolyA RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module.

value: RNA-Seq


title: MGH1494

tag: treatment


title: S94: CTCFKD2_singleCell

description: RNA-seq


title: 842 CMP

tag: developmental stage

value: adult

tag: cell type

value: common myeloid progenitor


title: YB-3 RIP-Seq deltaYB-1 PolyA (IP_YB3_polyA_del)

extract_protocol:
Cells were lysed in two pellet volumes of lysis buffer and centrifuged at 16,000 g for 10 min. YB-3-RNA complex was isolated by antibody-coated Protein-G sepharose. RNA was isolated using TRIzol LS Reagent.
Library was prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina. PolyA RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module.


title: B5_R6.2_IN

description:
INPUT R6/2 1 m
2017-9269

tag: tissue

value: INPUT

tag: age


title: Patient 27

value: reccurence

value: Pre


title: 48_wt_input

description:
Input WT 6 m
2017-9193

value: Input

value: WT

value: 6 m


title: RNA-Seq wt Total rep2 (total_H_2)

description: Control for RIP-Seq

extract_protocol:
Cells were lysed in two pellet volumes of lysis buffer and centrifuged at 16,000 g for 10 min. RNA was isolated using TRIzol LS Reagent.
Library was prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina. rRNA depletion was performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat).

value: wild type


title: 47_q175_ip

description:
IP Q175 6 m
2017-9193

value: striatum


title: 46_wt_ip

description:
IP WT 2 m
2017-9193

value: 2 m


title: S86: CTCFKD2_singleCell

description: RNA-seq

value: Single cell

value: CTCF knockdown

value: EL4 cells


title: RNA-Seq wt Total rep1 (total_H_1), run 1

description: Control for RIP-Seq


title: RNA-Seq wt Total rep1 (total_H_1), run 2

description: Control for RIP-Seq


title: Patient 25

value: Triple Negative Breast cancer

value: Alive

value: non reccurence

value: non complete remission


title: YB-1 RIP-Seq wt Total (Bethyl1_YB1), run 1

value: RIP-Seq


title: S89: CTCFKD2_singleCell

description: RNA-seq


title: 45_wt_ip

description:
IP WT 6 m
2017-9193

value: IP


title: S84: CTCFKD2_singleCell

description: RNA-seq


title: S85: CTCFKD2_singleCell

description: RNA-seq


title: S88: CTCFKD2_singleCell

description: RNA-seq


title: Patient 31

value: Dead

value: reccurence

value: Post


title: Patient 24

value: Pre


title: Patient 26


title: S87: CTCFKD2_singleCell

description: RNA-seq


title: YB-3 RIP-Seq wt Total (IP_YB3_H), run 2

extract_protocol:
Cells were lysed in two pellet volumes of lysis buffer and centrifuged at 16,000 g for 10 min. YB-3-RNA complex was isolated by antibody-coated Protein-G sepharose. RNA was isolated using TRIzol LS Reagent.
Library was prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina. rRNA depletion was performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat).


title: 44_wt_ip

description:
IP WT 12 m
2017-9193

value: WT


title: Patient 22


title: S83: CTCFKD2_singleCell

description: RNA-seq


title: 43_q175_ip

description:
IP Q175 12 m
2017-9193


title: Patient 21


title: YB-3 RIP-Seq wt Total (IP_YB3_H), run 1

value: wild type


title: Patient 20


title: 42_wt_ip

description:
IP WT 6 m
2017-9193

value: striatum

value: 6 m


title: YB-1 RIP-Seq wt Total (IP_YB1_H), run 2


title: 40_q175_ip

description:
IP Q175 12 m
2017-9193


title: 41_q175_input

description:
Input Q175 12 m
2017-9193

value: Input


title: RNA-Seq wt polyA rep2 (total_polyA_2)

description: Control for RIP-Seq

value: RNA-Seq


title: YB-3 RIP-Seq wt PolyA (IP_YB3_polyA)


title: S78: CTCFKD2_singleCell

description: RNA-seq

value: Single cell

value: CTCF knockdown

value: EL4 cells


title: Patient 18

value: Triple Negative Breast cancer


title: Patient 23

value: non complete remission


title: S79: CTCFKD2_singleCell

description: RNA-seq


title: S82: CTCFKD2_singleCell

description: RNA-seq


title: 39_wt_ip

description:
IP WT 6 m
2017-9193


title: Size-matched RNA-Seq deltaYB-1+HA (RP_tot_del_HA), run 1

description: Control for Ribo-Seq

extract_protocol:
Cells washed with PBS supplemented with cycloheximide 100 µg/ml, lysed in polysome lysis buffer and cleared by centrifugation at 20,000 g for 10 min.
Library was prepared with TruSeq Ribo Profile Kit. rRNA depletion was performed using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat).

value: Size-matched RNA-Seq


title: YB-1 RIP-Seq wt Total (IP_YB1_H), run 1

value: RIP-Seq


title: Patient 16

value: Alive

value: non reccurence

value: complete remission


title: Patient 17

value: Post


title: 38_q175_input

description:
Input Q175 6 m
2017-9193


title: 37_wt_input

description:
Input WT 6 m
2017-9193

value: WT


title: S77: CTCFKD2_singleCell

description: RNA-seq


title: Ribo-Seq deltaYB-1+HA (RP_del_HA), run 1

value: Ribo-Seq


title: S81: CTCFKD2_singleCell

description: RNA-seq


title: S76: CTCFKD2_singleCell

description: RNA-seq


title: Size-matched RNA-Seq wt+HA-YB-1 (RP_tot_wt_YB1), run 1

description: Control for Ribo-Seq

value: wild type+HA-YB-1


title: Patient 15

value: Pre


title: S80: CTCFKD2_singleCell

description: RNA-seq


title: 36_q175_ip

description:
IP Q175 6 m
2017-9193

value: striatum

value: IP

value: 6 m


title: S75: CTCFKD2_singleCell

description: RNA-seq

value: Single cell

value: CTCF knockdown


title: Patient 19

value: Triple Negative Breast cancer


title: 35_wt_ip

description:
IP WT 2 m
2017-9193

value: 2 m


title: Size-matched RNA-Seq wt+HA (RP_tot_wt_HA), run 1

description: Control for Ribo-Seq

value: Size-matched RNA-Seq

value: wild type+HA


title: Patient 14

value: Alive


title: Patient 12

value: non reccurence


title: Patient 13

value: complete remission


title: 34_wt_input

description:
Input WT 12 m
2017-9193

value: Input


title: S73: CTCFKD2_singleCell

description: RNA-seq

value: EL4 cells


title: S48: CTCFKD1_singleCell

description: RNA-seq


title: Ribo-Seq wt+HA (RP_wt_HA), run 1

value: Ribo-Seq


title: 33_wt_input

description:
Input WT 12 m
2017-9193

value: WT


title: S74: CTCFKD2_singleCell

description: RNA-seq


title: DMBP5 96h rep2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: A375 cells treated with DMBP5 during 96h

data_processing:
Mapping with STAR_2.4.0a versus hg19 with default parameters
Gene counting with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1" options.
Genome_build: hg19
Supplementary_files_format_and_content: tablecount.txt: tab-delimited text files include counts values of each gene in each sample

source_name: Human skin malignant melanoma

growth_protocol: A375 cells grown in 10 cm dishes in RMPI medium supplemented with 2% FBS for 24 hrs and them treated for 96 hrs

extract_protocol:
Total RNAs were extracted from A375 cells using the RNAeasy minikit (Qiagen)
500ng of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (15 cycles) with the reagents from the Truseq Stranded Total RNA kit (illumina). Libraries were quantified with the Bioanalyzer 2100 Kit (Agilent). 4nM of libraries were then diluted and denatured according to the Illumina recommendations.  Paired-end 2x75bp reads were sequenced on an Illumina Nextseq 500 sequencer.

treatment_protocol: 75000 cells plated in RPMI medium and 7% FBS. After 24 hrs cells were incubated with RPMI supplemented with 2% FBS and one of the following conditions: DMSO 30uL, DMBP5 10uM final concentration, 20nM si-RNA against NIK complexed with lipofectamine RNAimax (lifetechnologies) or 20nM si-RNA control complexed with lipofectamine RNAimax (lifetechnologies)

value: Human melanoma cells (A375 cells)

tag: concentration sample (ng/ul)

tag: rin number


title: S47: CTCFKD1_singleCell

description: RNA-seq

tag: cell number

tag: genotype


title: Patient 11

value: Pre


title: DMSO 96h rep2

description: A375 cells treated with DMSO during 96h


title: Patient 10


title: Patient 39

value: Dead

value: reccurence

value: non complete remission


title: S46: CTCFKD1_singleCell

description: RNA-seq

tag: strain

value: Single cell

value: CTCF knockdown


title: siRNA NIK 96h rep2

description: A375 cells treated with a siRNA against NIK during 96h


title: 32_q175_input

description:
Input Q175 2 m
2017-9193

value: striatum

tag: rna-sample type

value: 2 m


title: S45: CTCFKD1_singleCell

description: RNA-seq


title: 30_wt_ip

description:
IP WT 2 m
2017-9193

value: IP


title: siRNA Control 96h rep2

description: A375 cells treated with a control siRNA during 96h


title: 31_wt_ip

description:
IP WT 2 m
2017-9193


title: Ribo-Seq wt+HA-YB-1 (RP_wt_YB1), run 1

value: wild type+HA-YB-1


title: 29_wt_ip

description:
IP WT 12 m
2017-9193


title: S44: CTCFKD1_singleCell

description: RNA-seq


title: Patient 8

value: Triple Negative Breast cancer

tag: status after 5 years

value: Alive

tag: relapse

value: non reccurence


title: Patient 9

tag: pcr

tag: pre/post

value: Post


title: Patient 7

value: complete remission


title: 28_q175_input

description:
Input Q175 6 m
2017-9193

value: Input

value: 6 m


title: S43: CTCFKD1_singleCell

description: RNA-seq

value: EL4 cells


title: S42: CTCFKD1_singleCell

description: RNA-seq


title: siRNA NIK 48h rep2

description: A375 cells treated with a siRNA against NIK during 48h

value: Human melanoma cells (A375 cells)


title: DMSO 48h rep2

description: A375 cells treated with DMSO during 48h


title: Patient 6

value: Pre


title: 26_q175_input

description:
Input Q175 2 m
2017-9193


title: S41: CTCFKD1_singleCell

description: RNA-seq


title: DMBP5 48h rep2

description: A375 cells treated with DMBP5 during 48h


title: 25_wt_input

description:
Input WT 2 m
2017-9193

value: WT


title: siRNA Control 48h rep2

description: A375 cells treated with a control siRNA during 48h


title: S40: CTCFKD1_singleCell

description: RNA-seq

value: Single cell


title: Patient 5


title: 27_q175_ip

description:
IP Q175 12 m
2017-9193


title: 24_q175_ip

description:
IP Q175 6 m
2017-9193


title: Patient 3


title: S38: CTCFKD1_singleCell

description: RNA-seq

value: CTCF knockdown


title: N.R13

data_processing:
Mapping with STAR_2.4.0a using Encode RNA-seq options versus hg19 build.
FeatureCounts (subread-1.4.6-p1-Linux-x86_64) genes counting using "--primary -g gene_name -p -s 1 -M " options versusu Ensembl .gtf file Homo_sapiens.GRCh37.75 release.
Genes which did not have at least 50 counts in at least 6 samples were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix count file with genes as rows and sample as columns,  generated using voomWithqualityWeight normalization function from R package limma.

source_name: Nose

extract_protocol:
Cells were isolated from brushings and put in Trizol LS (Invitrogen). Then total RNA was extracted and purified with miRneasy mini kit (Agilent)
Libraries were generated from 500ng of total RNA using Truseq Stranded Total RNA with Ribozero gold kit (Illumina).
Libraries were pooled at 4nM, loaded on Nextseq 500 High Output Flowcells and sequenced on a NextSeq 500 platform (Illumina) with 2 × 75bp paired-end chemistry.

tag: Sex

value: M

tag: clinical condition

value: Rhinitis


title: N.R12

value: F


title: 23_q175_input

description:
Input Q175 12 m
2017-9193

value: striatum


title: Patient 2

value: Triple Negative Breast cancer


title: N.C28

value: Control (Healthy)


title: 22_wt_input

description:
Input WT 2 m
2017-9193

value: 2 m


title: Patient 1

value: Alive

value: non reccurence

value: Post


title: N.R10


title: S37: CTCFKD1_singleCell

description: RNA-seq


title: Patient 4

value: complete remission


title: 21_wt_input

description:
Input WT 12 m
2017-9193

value: Input


title: N.C18


title: S36: CTCFKD1_singleCell

description: RNA-seq

value: EL4 cells


title: 20_q175_input

description:
Input Q175 12 m
2017-9193


title: S35: CTCFKD1_singleCell

description: RNA-seq


title: 19_wt_ip

description:
IP WT 12 m
2017-9193

value: IP


title: N.AR30

value: Asthma + Rhinitis


title: S39: CTCFKD1_singleCell

description: RNA-seq

value: Single cell


title: N.C16


title: S34: CTCFKD1_singleCell

description: RNA-seq

value: CTCF knockdown


title: S33: CTCFKD1_singleCell

description: RNA-seq


title: 18_wt_input

description:
Input WT 6 m
2017-9193

value: WT

value: 6 m


title: 17_wt_input

description:
Input WT 2 m
2017-9193


title: N.C21

value: M


title: N.R38

value: Rhinitis


title: 16_q175_ip

description:
IP Q175 2 m
2017-9193

value: striatum


title: S32: CTCFKD1_singleCell

description: RNA-seq


title: N.AR37

value: F


title: S31: CTCFKD1_singleCell

description: RNA-seq


title: S30: CTCFKD1_singleCell

description: RNA-seq


title: N.AR31


title: S29: CTCFKD1_singleCell

description: RNA-seq


title: 14_wt_ip

description:
IP WT 12 m
2017-9193


title: S28: CTCFKD1_singleCell

description: RNA-seq


title: 13_q175_ip

description:
IP Q175 2 m
2017-9193

value: 2 m


title: N.R22


title: 12_wt_input

description:
Input WT 12 m
2017-9193


title: S27: CTCFKD1_singleCell

description: RNA-seq


title: HEKn_diff_siUc.291_rep1

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier, 1

department: Dept. of Exp. Medicine and Surgery

country: Italy

institute: University of Rome "Tor Vergata"

description:
HEKn_diff_siT-UC291rep1
Gene expression after silencing with Uc.291 siRNA in differentiated keratinocytes

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human 8x60k Microarrays (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.3.7.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Low Input Quick Amp LabellingKit One colour (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Normal human epidermal keratinocytes were purchased from Invitrogen. Cells were cultured in EpiLife medium with Human Keratinocyte Growth Supplements added (Life Technologies) at 37°C in 5% CO2.  Experiments were carried out at passage 2.

extract_protocol: Total RNA was extracted with mirVana miRNA isolation kit (Ambion, AM1561) including DNA digestion with DNA-free kit DNase Treatment & Removal (Ambion, AM1906). RNA was quantified using a NanoDrop-1000 spectrophotometer. The quality of RNA was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 1 million of HEKn were transfected with 180 pmol of either siCTRL siRNA (Qiagen, cat. no. SI03650318) or siUc.291 siRNA (Qiagen, cat. no. 1027423) using Lipofectamine RNAiMAX transfection reagent (Invitrogen). After 48 h cells were induced for differentiation by adding of 1.2 mM CaCl2 in culture medium. Cell were collected at 0 (HEKn proliferative) and 3 (HEKn differentiated) days of differentiation for further RNA extraction.

value: normal human epidermal keratinocytes (HEKn)

tag: transfected with

value: siUc.291 siRNA

tag: cell status

value: differentiated


title: HEKn_diff_siUc.291_rep2

description:
HEKn_diff_siT-UC291rep2
Gene expression after silencing with Uc.291 siRNA in differentiated keratinocytes

tag: cell type


title: N.AR1


title: N.C34

value: Control (Healthy)


title: HEKn_diff_siCTRL_rep3

description:
HEKn_diff_siCTRLrep3
Gene expression after silencing with control siRNA in differentiated keratinocytes

value: siCTRL siRNA


title: HEKn_diff_siCTRL_rep2

description:
HEKn_diff_siCTRLrep2
Gene expression after silencing with control siRNA in differentiated keratinocytes


title: HEKn_diff_siUc.291_rep3

description:
HEKn_diff_siT-UC291rep3
Gene expression after silencing with Uc.291 siRNA in differentiated keratinocytes


title: HEKn_diff_siCTRL_rep1

description:
HEKn_diff_siCTRLrep1
Gene expression after silencing with control siRNA in differentiated keratinocytes


title: 15_q175_input

description:
Input Q175 2 m
2017-9193

tag: tissue

value: Input


title: 11_q175_ip

description:
IP Q175 12 m
2017-9193

value: IP

tag: age


title: HEKn_prolif_siUc.291_rep3

description:
HEKn_prolif_siT-UC291rep3
Gene expression after silencing with Uc.291 siRNA in proliferative keratinocytes

value: proliferative


title: HEKn_diff_siCTRL_rep4

description:
HEKn_diff_siCTRLrep4
Gene expression after silencing with control siRNA in differentiated keratinocytes


title: HEKn_prolif_siUc.291_rep4

description:
HEKn_prolif_siT-UC291rep4
Gene expression after silencing with Uc.291 siRNA in proliferative keratinocytes


title: HEKn_diff_siUc.291_rep4

description:
HEKn_diff_siT-UC291rep4
Gene expression after silencing with Uc.291 siRNA in differentiated keratinocytes


title: S26: CTCFKD1_singleCell

description: RNA-seq

value: Single cell

value: EL4 cells


title: N.AR33

value: Asthma + Rhinitis


title: HEKn_prolif_siUc.291_rep2

description:
HEKn_prolif_siT-UC291rep2
Gene expression after silencing with Uc.291 siRNA in proliferative keratinocytes


title: N.R23


title: 10_wt_ip

description:
IP WT 6 m
2017-9193

value: WT

value: 6 m


title: S25: CTCFKD1_singleCell

description: RNA-seq

value: CTCF knockdown


title: S72: WT2_singleCell

description: RNA-seq

value: wild type


title: HEKn_prolif_siUc.291_rep1

description:
HEKn_prolif_siT-UC291rep1
Gene expression after silencing with Uc.291 siRNA in proliferative keratinocytes


title: 9_q175_ip

description:
IP Q175 2 m
2017-9193

value: striatum


title: 8_q175_ip

description:
IP Q175 2 m
2017-9193

value: 2 m


title: S71: WT2_singleCell

description: RNA-seq


title: HEKn_prolif_siCTRL_rep4

description:
HEKn_prolif_siCTRLrep4
Gene expression after silencing with control siRNA in proliferative keratinocytes

value: normal human epidermal keratinocytes (HEKn)


title: HEKn_prolif_siCTRL_rep3

description:
HEKn_prolif_siCTRLrep3
Gene expression after silencing with control siRNA in proliferative keratinocytes


title: S70: WT2_singleCell

description: RNA-seq


title: 7_q175_input

description:
Input Q175 6 m
2017-9193


title: HEKn_prolif_siCTRL_rep2

description:
HEKn_prolif_siCTRLrep2
Gene expression after silencing with control siRNA in proliferative keratinocytes


title: S69: WT2_singleCell

description: RNA-seq


title: 6_q175_ip

description:
IP Q175 6 m
2017-9193


title: N.R35

value: M

value: Rhinitis


title: Atg5−/−AT2 -BLM-3

city: Tianjin

first: Xue

last: Li

address: 890, Jingu Road

institute: Tianjin University Haihe Hospital

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (0.36) with parameters (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50). Then mapped to  genome using Hisat2 ( 2.2.1.0 ) with parameters (--rna-strandness rf --fr ).
Fragments Per kb Per Million Reads (FPKM) value of each gene was calculated using cufflinks ( 2.2.1 ),and the read counts of each gene were obtained by htseq-count ( 0.9.1 ).
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_anno.txt

source_name: Lung

extract_protocol:
Lung alveolar type 2 cells were sorted by FACS, and RNA was harvested using mirVanaTM miRNA ISOlation Kit (Ambion-1561). Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: AT2 cells

tag: treatment

value: bleomycin (BLM)


title: 5_wt_input

description:
Input WT 6 m
2017-9193

value: Input


title: Atg5−/−AT2 -BLM-2


title: S68: WT2_singleCell

description: RNA-seq


title: N.AR6


title: N.C17

value: Control (Healthy)


title: 4_q175_input

description:
Input Q175 6 m
2017-9193


title: S67: WT2_singleCell

description: RNA-seq

value: Single cell


title: N.C2

value: F


title: AT2-BLM-3


title: N.C15


title: Atg5−/−AT2 -BLM-1


title: N.R14


title: HEKn_prolif_siCTRL_rep1

description:
HEKn_prolif_siCTRLrep1
Gene expression after silencing with control siRNA in proliferative keratinocytes

value: siCTRL siRNA

value: proliferative


title: S66: WT2_singleCell

description: RNA-seq

value: EL4 cells


title: S65: WT2_singleCell

description: RNA-seq


title: N.AR43

value: Asthma + Rhinitis


title: AT2-BLM-1

value: wild type


title: 2_q175_input

description:
Input Q175 2 m
2017-9193

value: striatum


title: N.R3


title: 1_wt_input

description:
Input WT 2 m
2017-9193

value: WT

value: 2 m


title: S64: WT2_singleCell

description: RNA-seq


title: Atg5−/−AT2 -PBS-3

value: PBS


title: N.R42

value: M

value: Rhinitis


title: Atg5−/−AT2 -PBS-2

value: lung

value: AT2 cells


title: S63: WT2_singleCell

description: RNA-seq


title: 3_q175_input

description:
Input Q175 12 m
2017-9193

value: Input


title: S61: WT2_singleCell

description: RNA-seq


title: B.R12

source_name: Bronchi


title: N.C40

value: Control (Healthy)


title: MIR7695-Ac (Infected) - Rep1

city: Bellaterra

first: Blanca

last: San Segundo

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Plant Responses to Stress

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

data_processing:
Raw reads were checked for quality by using FastQC v0.11.3
Trimming and removal of adapters involved using Trimmomatic v0.33 (minimum quality score 35, minimum length 25).
The obtained reads were mapped against the Oryza sativa reference genome (MSU 7.0) by using STAR (v2.4.0j)
Alignment files were filtered to remove reads with mapping quality (MAPQ) <30. FeatureCounts (v1.4.5-p1)
Statistical analysis of read counts was performed with R, with the HTSFilter package to remove low-expressed genes and the edge R package
Genome_build: MSU 7.0

organism: Oryza sativa

source_name: Activation MIR7695 Rice infected with Magnaporthe oryzae

growth_protocol: Rice plants were grown at 28ºC with a 14 h/10 h light/dark cycle. The fungus M. oryzae was grown in Complete Media Agar (CMA, 9 cm plates, containing 30 mg/L chloramfenicol) for 15 days at 28ºC under a 16 h/8 h light/dark photoperiod condition.

extract_protocol:
Total RNA was extracted with the Maxwell 16 LEV Plant RNA Kit (Promega) following manufacturer's instructions.
Indexed libraries prepared from 1ug purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina). Samples pooled; each index-tagged sample present in equimolar amounts (final concentration of pooled samples at 2nm). Pooled samples subjected to cluster generation and sequencing using Illumina Hseq 2500. 2x100 paired-ennd at final concentration of 8pmol.

treatment_protocol: Soil-grown plants (3-4 leaf stage) were mock-inoculated or inoculated with M. oryzae spores for 48 hours . Inoculation was done by spraying whole rice plants with a M. oryzae spore suspension (10E5 spores/ml; 0.2 ml/plant) by using an aerograph at 2 atmospheres of pressure

tag: infection

value: Magnaporthe oryzae strain Guy11

value: leaf

tag: cultivar

value: Tainung67 (japonica)


title: WT-Az (Infected) - Rep2

source_name: Wild-type azygous Rice infected with Magnaporthe oryzae

tag: genotype


title: MIR7695-Ac (Infected) - Rep2


title: Atg5−/−AT2 -PBS-1

tag: strain


title: S62: WT2_singleCell

description: RNA-seq

tag: cell number

value: Single cell


title: WT-Az (Infected) - Rep1


title: AT2-BLM-2

value: bleomycin (BLM)


title: S60: WT2_singleCell

description: RNA-seq

value: EL4 cells


title: AT2-PBS-3

value: wild type


title: AT2-PBS-2


title: B.C28

value: F


title: S59: WT2_singleCell

description: RNA-seq


title: B.R13


title: B.R10


title: MIR7695-Ac (Control) - Rep2

source_name: Activation MIR7695 Rice

value: mock


title: MIR7695-Ac (Control) - Rep1


title: S58: WT2_singleCell

description: RNA-seq


title: B.C18


title: scRNA-seq of Mouse Heart JMJD2B KO [103624-001-002_S3]

description:
ScRNA-SEQ of Mouse Heart JMJD2B Knockout
processed data file: inVivo_Expressionmatrix.csv

data_processing:
Chip-Seq: The samples were sequenced on  Illumina NextSeq hardware and assessed for quality using FastQC (Andrews S. 2010,  FastQC: a quality control tool for high throughput sequence data. Available online at:  http://www.bioinformatics.babraham.ac.uk/projects/fastqc) or used for qRT-PCR analysis  with the primers described before. Reads were trimmed using fastx-trimmer  (http://hannonlab.cshl.edu/fastx_toolkit/). Trimmed sequences were mapped to the  GRCH38 version of the human genome with STAR 2.4.2a 4 using only unique alignments  to exclude reads with unclear placing. PCR duplicates were removed using Picard 1.136  (Picard: A set of tools (in Java) for working with next generation sequencing data in the  BAM format; http://broadinstitute.github.io/picard/) to avoid PCR artefacts leading to  multiple copies of the same original fragment. Peaks were called using homer findPeaks  version 4.0311 with parameter –region to combine close peaks. The minimum distance and size of peaks for H3K9me3 were set to -size 2000 and –minDist 10000
Data were filtered using the following specifications:
RNA:SEQ: Base calling and FASTQ were done with  Illumina's HiSeq Control Software version 1.5.15.1 (RTA v1.13.18 and bclfastq v1.8.3).  Sequenced reads were mapped to the mouse reference genome with TopHat version  2.0.5, and differentially expressed genes were assessed by use of Cuffdiff, a part of the  Cufflinks version 2.1.1 package.
Cellular suspensions were loaded on a 10X Chromium Controller (10X Genomics) according to manufacturer’s protocol based on the 10X Genomics proprietary technology13. HUVEC study and murine scRNA-seq libraries were prepared using Chromium Single Cell 3′ v2 Reagent Kit and Chromium Single Cell 3′ v3 Reagent Kit, respectively (10X Genomics), according to manufacturer’s protocols. Briefly, 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. Reverse transcription reactions were engaged to generate barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). Bulk cDNA was amplified using a Biometra Thermocycler Professional Basic Gradient with 96-Well Sample Block (98°C for 3 minutes; cycled 14×: 98°C for 15 s, 67°C for 20 s, and 72°C for 1 minute; 72°C for 1 minute; held at 4°C). Amplified cDNA product was cleaned with the SPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3′ v2 and Chromium Single Cell 3′ v3 Reagent Kits as follows: fragmentation, end repair and A-tailing; size selection with SPRIselect; adaptor ligation; post-ligation cleanup with SPRIselect; sample index PCR and cleanup with SPRI select beads. Library quantification and quality assessment was performed using Bioanalyzer Agilent 2100 using a High Sensitivity DNA chip (Agilent Genomics). Indexed libraries were equimolarly pooled and sequenced using paired-end 26x98bp as sequencing mode by GenomeScan (Leiden, Netherlands). Single-cell RNA-seq outputs were processed using the Cell Ranger (10X Genomics) suite versions 2.1.1 (in vitro HUVEC samples) or 3.0.1 (in vivo 3d AMI samples). HUVEC in vitro data has been mapped to the GRCh38 (version 1.2.0) reference genome by using the “count” function. Subsequently, individual processed datasets have been merged with “aggregate”. Secondary analysis was conducted using the Seurat 2.3.4 package in R.14 We filtered the data for cells expressing at least 200 genes. Moreover, we aimed to avoid doublets by removing cells with high unique molecular identifier (UMI) counts (> 90000) and high number of genes (> 8000). We also accounted for possible dead cells and removed cells with high mitochondrial content (> 10 % of total UMI). The remaining matrix was log-normalized and scaled. After detecting variable genes, a principal component analysis (PCA) using 10 dimensions was applied. Clustering of the cells was then performed by Seurat’s FindCluster function with 0.6 resolution. We used t-distributed stochastic neighbor embedding (t-SNE) to visualize cell clusters.15 We applied a generic threshold of 2.5 to the scaled value of all candidate genes to separate high and low or no expressing cells. Accordingly, in vivo 3d AMI data we mapped against the mm10 (version 3.0.0) reference genome using Cell Ranger “count”. In Seurat 2.3.4 we applied similar filters for removing cells with high and low UMI counts but removed the upper 5 % and lower 1 % of all cells per individual sample. High mitochondrial content cells (>10 %) were removed similarly. We only kept genes that showed at least in 2 cells an UMI count of more than 1. We merged the data and counted cells expressing at least 1 UMI for Cdh5 and Pecam1 (ECs) as well as Cdh5, Pecam1 and two mesenchymal markers (EndMT cells) between the libraries.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene_expression.tsv was generatedby cuffdiff and assembled by cummerbund; ChIP-seq bed files

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (#79306; Qiagen) and miRNeasy-kit (#217004; Qiagen) with additional DNase I (#79254; Qiagen) digestion according to the manufacturer’s protocol. 1 μg of RNA from each sample was reverse-transcribed using random hexamer primed single-strand cDNA (10 min at 25 °C, 15 min at 42 °C, 5 min at 99 °C) by MMLV Reverse Transcriptase (#N8080018; Life technologies) as previously described. (Boeckel et al., 2011). For qPCR, cDNA was amplified using Fast SYBR Green Mastermix (#4385612 Life Technologies) on a ViiA7- Realtime qPCR System (Life Technologies). Expression level of mRNAs were normalized to RPLP0 which served as a housekeeping gene using the 2‑ΔCt method.
900ng of total RNA was used as input for whole transcriptome RNA-seq library preparation (TruSeq® Stranded Total RNA, Illumina) following low throughput protocol. Sequencing was performed on Illumina Nextseq 500 (Illumina) using V2 chemistry and 75bp single-end setup.

tag: strain background

tag: genotype/variation

value: JMJD2B -/-

value: Whole Heart


title: S57: WT2_singleCell

description: RNA-seq


title: B.AR30

value: M

value: Asthma + Rhinitis


title: S56: WT2_singleCell

description: RNA-seq


title: B.C16


title: scRNA-seq of Mouse Heart WT [103624-001-001_S2]

description:
ScRNA-SEQ of Mouse Heart Wildtype (WT)
processed data file: inVivo_Expressionmatrix.csv

source_name: ScRNA-SEQ of Mouse Heart Wildtype (WT)

value: Wild-type


title: KO3

city: Bronx

first: Ales

last: Cvekl

state: NY

address: 1300 Morris Park Avenue, Ullman 123

department: The Departments Ophthalmology and Visual Sciences, Genetics

institute: Albert Einstein College of Medicine

data_processing:
The reads were trimmed with trim-galore and then aligned to mm10 using TopHat2 (v 2.0.13)
Read counts of each gene were then calculated using HTSeq (v 0.6.1) and FPKMs were calculated using Cuffdiff (v 2.2.1)
Differential expressed genes were identified using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: txt file for raw counts of expressed genes detected in all samples

source_name: E14.5 embryonic lens

extract_protocol:
Embryonic lenses were dissected in ice-cold PBS. The tissues were stabillized for RNA degradation by overnight incubation ay 4°C in RNAlater solution (Qiagen). Next day the solution was removed and the tissues were stored at -80°C. mRNA was extracted using RNeasy Micro Kit (Qiagen) and the quality and quantity of the RNA were analyzed by Bioanalyzer and Qubit. NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina was used for sequencing library preparation of 500ng of mRNA.
RNA libraries were prepared using standard Illumina protocols for polyA selected and stranded libraries

value: Mixed:C57BL/6 + FVB

value: Lens

value: Embryonic day E14.5

value: Gata3 -/-


title: WT-Az (Control) - Rep1

source_name: Wild-type azygous Rice

value: leaf


title: S54: WT2_singleCell

description: RNA-seq


title: control 3

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Reads were aligned to the Drosophila melanogaster.BDGP6.92 genome using STAR (v. 2.5.3a).
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1)
Genome_build: Drosophila melanogaster Ensembl release 92, BDGP6
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package.

organism: Drosophila melanogaster

source_name: antenna

growth_protocol: The flies (both control and PCD-blocked) were maintained at 25ºC in 12 h light:12 h dark conditions, and maintained on a standard cornmeal diet.

extract_protocol:
The antennae from approximately 350 flies were harvested via snap-freezing in a mini-sieve. Total RNA was extracted using a standard TRIzol/chloroform protocol.
From 100 ng total RNA, mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module. RNA-seq libraries were then prepared from the mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: The PCD-blocked flies expressed the baculoviral caspase inhibitor p35 (UAS-p35) in the antennae, whereas the control flies lacked the transgene in an otherwise identical genetic background (peb-Gal4/+;Or49a-GFP/+).

value: female

tag: sample pair

value: sample pair 3


title: B.C21

value: Control (Healthy)


title: PCD-blocked 3


title: control 2

value: sample pair 2


title: S55: WT2_singleCell

description: RNA-seq

value: Single cell

value: wild type

value: EL4 cells


title: B.R38

value: Rhinitis


title: WT3


title: KO1


title: S53: WT2_singleCell

description: RNA-seq


title: PCD-blocked 2


title: AT2-PBS-1

value: lung

value: AT2 cells

value: PBS


title: B.AR31

value: F

value: Asthma + Rhinitis


title: S52: WT2_singleCell

description: RNA-seq


title: control 1

value: sample pair 1


title: WT-Az (Control) - Rep2

value: mock

value: Tainung67 (japonica)


title: B.R22

value: M


title: WT1

value: Mixed:C57BL/6 + FVB

value: Lens

value: Embryonic day E14.5


title: WT2


title: S50: WT2_singleCell

description: RNA-seq


title: PCD-blocked 1

value: female


title: B.C34

value: Control (Healthy)


title: KO2

value: Gata3 -/-


title: HCW4_3

city: Beijing

first: Yunxing

last: Zhang

address: Dongxiaofu 1

institute: Chinese Academy of Forestry

data_processing:
All samples were pooled together and assembled using Trinity method (Grabherr et al. 2011) to construct unique sequences as the reference sequences.
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference sequences using RSEM v1.2.15 wtih bowtie2 parameters mismatch 0.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., Nature biotechnology, 2010.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Salix matsudana

source_name: root

growth_protocol: Stem cuttings (approximately 15 cm long) from annual branches of the same S. matsudana (LCW) and S. matsudana var. matsudana f. umbraculifera (HCW) plants were cultured in 12-L plastic pots. The cuttings were supplied with 10-L water containing 1/2 strength Hoagland solution on every three days in a greenhouse

extract_protocol:
Total RNAs from the root tissues of LCW and HCW treated with 100 μM CdCl2 for 0, 1, and 4 d were extracted using Norgen RNA Purification Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: root of LCW and HCW were treated using 100 μM CdCl2 for 0, 1, and 4 days.

value: HCW; Salix matsudana var. matsudana f. umbraculifera

value: root

value: 100 μM CdCl2 for 4 days


title: S49: WT2_singleCell

description: RNA-seq

value: Single cell

value: wild type

value: EL4 cells


title: B.AR1

value: Asthma + Rhinitis


title: B.AR37

value: F


title: Control_adult_2

first: Jean-Yves

last: Roignant

address: genopode building

description: Lola O control replicate 2

data_processing:
The libraries were sequenced in two different sequencing runs in an HiSeq2500. Lola F and Lola F control samples were sequenced paired end 72 and Lola Null, Lola O and the corresponding control were sequenced single read 68
After sequencing reads were mapped using STAR (v. 2.5.0c) against ensembl release 79 (BDGP6).   For Lola F and the corresponding control the first read was used for mapping to ensure comparability with the other samples.
Mapped reads were filtered for rRNA and mitochondrial RNA reads before further processing.
Counts per gene were calculated using htseq-count (v. 0.6.1p1) with ensembl release 79 as a reference.
Genome_build: BDGP6
Supplementary_files_format_and_content: counts per gene as tab separated file (htseq output)

source_name: Adult fly

growth_protocol: For Lola-F, flies were maintained on apple juice plates supplemented with fresh yeast. Embryos were collected for two hours at 25°C and subsequently developed for 13 hours, collected and flash frozen in liquid nitrogen. Lola-O mutants were collected within 10 hours of eclosion and flash frozen in liquid nitrogen.

extract_protocol:
100 lola-F mutant / control embryos, and 10 Lola-O mutant / control adult flies were collected, flash frozen in liquid nitrogen, and RNA was isolated using Trizol reagent. 1 µg of Dnase I treated RNA was subjected to library preparation using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.
Libraries for sequencing were prepared according to the NEBNext® Ultra™ Directional RNA Library Prep Kit protocol.

tag: developmental stage

value: Adult flies within 10 hours after eclosion

value: Wild type / Df(2R)ED2076


title: HCW4_1


title: B.AR33

tag: Sex

value: M


title: S23: WT1_singleCell

description: RNA-seq

extract_protocol:
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System


title: Lola_O_2

description: Lola O knockout replicate 2

value: lola-O / Df(2R)ED2076


title: HCW4_2


title: Control_adult_1

description: Lola O control replicate 1


title: HCW1_3

value: 100 μM CdCl2 for 1 day


title: S24: WT1_singleCell

description: RNA-seq


title: B.R23

tag: clinical condition

value: Rhinitis


title: B.C15


title: S22: WT1_singleCell

description: RNA-seq


title: Lola_O_1

description: Lola O knockout replicate 1


title: S51: WT2_singleCell

description: RNA-seq


title: HCW1_2


title: S21: WT1_singleCell

description: RNA-seq


title: HCW1_1


title: Embryonic_control_1

description: Lola Null control replicate 1

source_name: Embryo

value: embryo (15 hours after fertilization)


title: B.R3


title: B.R35


title: HCW0_3

value: 100 μM CdCl2 for 0 day


title: Lola-Null_2

description: Lola Null knockout replicate 2

value: lola E76  / Df(2R)ED2076


title: S20: WT1_singleCell

description: RNA-seq


title: S19: WT1_singleCell

description: RNA-seq


title: B.AR6


title: Lola-Null_1

description: Lola Null knockout replicate 1


title: HCW0_2

value: HCW; Salix matsudana var. matsudana f. umbraculifera


title: S18: WT1_singleCell

description: RNA-seq


title: B.C17

value: Control (Healthy)


title: HCW0_1

value: root


title: S17: WT1_singleCell

description: RNA-seq

value: Single cell


title: B.C2


title: control_replicate2

description: Lola F control replicate 2


title: control_replicate3

description: Lola F control replicate 3


title: Embryonic_control_2

description: Lola Null control replicate 2


title: control_replicate1

description: Lola F control replicate 1


title: LCW4_3

value: LCW

value: 100 μM CdCl2 for 4 days


title: S16: WT1_singleCell

description: RNA-seq

value: wild type

value: EL4 cells


title: LCW4_2


title: B.R42


title: S15: WT1_singleCell

description: RNA-seq


title: S14: WT1_singleCell

description: RNA-seq


title: lola-F_replicate3

description: Lola F knockout replicate 3

value: lola-F stop / Df(2R)ED2076


title: B.R14

value: F


title: LCW1_3


title: S13: WT1_singleCell

description: RNA-seq


title: LCW1_2


title: B.C40


title: lola-F_replicate1

description: Lola F knockout replicate 1


title: S12: WT1_singleCell

description: RNA-seq


title: DMBP5 96h

description:
Human skin malignant melanoma
DMBP5_96h

source_name: A375 cells treated with DMBP5 during 96h

extract_protocol:
Total RNAs were extracted from A375 cells using the RNAeasy minikit (Qiagen)
300ng of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (15 cycles) with the reagents from the Truseq Stranded Total RNA kit (illumina). Libraries were quantified with the Bioanalyzer 2100 Kit (Agilent). 4nM of libraries were then diluted and denatured according to the Illumina recommendations.  Paired-end 2x75bp reads were sequenced on an Illumina Nextseq 500 sequencer.

tag: cell line

value: Human melanoma cells

tag: time point (hours)

tag: sample rna concentration (ng/µl)

tag: rin number


title: LCW1_1

tag: tissue


title: S11: WT1_singleCell

description: RNA-seq


title: DMSO 96h

description:
Human skin malignant melanoma
DMSO_96h

source_name: A375 cells treated with DMSO during 96h

tag: cell type


title: LCW0_3

tag: treatment


title: S10: WT1_singleCell

description: RNA-seq


title: LCW4_1


title: S9: WT1_singleCell

description: RNA-seq


title: LCW0_2


title: Patient 6-Gs-knockdown [4R117-P23-ACTGAT]

city: Irvine

first: Moom

middle: R

last: Roosan

address: 9401 Jeronimo Rd

department: Pharmacy Practice

institute: Chapman University School of Pharmacy

description:
4R117-P23-ACTGAT
N012414_Gs_KD

data_processing:
We used the Rsubread package (version v1.30.6; Liao et al., 2014) to align the reads and to produce gene-level summarized values. We used the built-in hg38 annotation from the Rsubread package. This is the NCBI RefSeq annotation with a simplification that overlapping exons from the same gene are merged.
Within this pipeline, we obtained integer-based gene counts using the featureCounts function in the Rsubread package (Liao et al., 2014).
We used the limma (version 3.36.3) and edgeR (version v3.22.3) packages to calculate FPKM values and a custom script to convert FPKM to TPM values . We used R version 3.5.1 and Bioconductor version 3.7 (Gentleman et al., 2004; R Core Team, 2014; http://www.R-project.org/).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt files containing feature counts, FPKM-normalized, and TPM-normalized gene expression data for all 24 samples

source_name: HASM cells_GNAS-knockdown

growth_protocol: Human airway smooth muscle (HASM) cells were isolated from deceased, de-identified lung donors by enzymatic dissociation in accordance with Institutional Review Board approval.  HASM cells were cultured with Ham's F12 medium supplemented with 10% FBS, CaCl2, buffered with HEPES, penicillin/streptomycin, primocin, and additional L-glutamine.  Cells were kept at 5% CO2 and 37° C.  Experiments were performed on cells from passage 3-7 using over 12 different primary cell isolates in total, and at least 3  different isolates for each experiment.

extract_protocol:
Total RNA was extracted from passage 6 HASM cells from 6 different donors using the RNeasy mini kit (Qiagen Sciences, Inc., Germantown, MD).
Approximately 1 µg of RNA from each sample was used to generate RNA-Seq cDNA libraries for sequencing using the TruSeq mRNA Stranded Sample Prep Kit (Illumina, Inc., San Diego, CA). Sequencing of 100 bp single-end reads was performed with an Illumina HiSeq 4000 instrument at the University of California, Irvine Genomics High-Throughput Facility (Irvine, CA).

treatment_protocol: siRNA was transfected into HASM by incubating cells with 1µM siRNA (target or scrambled) with HiPerFect transfection reagent per tube containing approximately 250,000 cells for 30 minutes at room temperature. Cells were then plated on to 6-well plates and incubated for 5 hours at 37C with 5% CO2. After incubation, HASM growth media containing 5% fetal bovine serum was added and the cells were incubated for 48 hours.  Media was replaced with serum-free media for 24 hr prior to budesonide treatment or  siRNA assay

tag: subject id

value: Patient 6

value: Human airway smooth muscle (HASM) cells

tag: treatment condition

value: GNAS-knockdown


title: B.AR43

tag: age

value: M

value: Asthma + Rhinitis


title: S8: WT1_singleCell

description: RNA-seq

tag: strain

tag: cell number

tag: genotype


title: Patient 6-control [4R117-P21-CGTACG]

description:
4R117-P21-CGTACG
N012414_cont

source_name: HASM cells_Control

value: Control


title: lola-F_replicate2

description: Lola F knockout replicate 2

value: embryo (15 hours after fertilization)


title: LCW0_1

value: 100 μM CdCl2 for 0 day


title: siRNA Control 96h

description:
Human skin malignant melanoma
siControl_96h

source_name: A375 cells treated with a control siRNA during 96h


title: siRNA NIK 96h

description:
Human skin malignant melanoma
siNIK_96h

source_name: A375 cells treated with a siRNA against NIK during 96h


title: Patient 5-Gs-knockdown budesonide treated [4R117-P20-GTTTCG]

description:
4R117-P20-GTTTCG
N012317_Gs_KD_+_budesonide

source_name: HASM cells_GNAS-knockdown budesonide treated

value: Patient 5

value: GNAS-knockdown budesonide treated


title: DMBP5 48h

description:
Human skin malignant melanoma
DMBP5_48h

source_name: A375 cells treated with DMBP5 during 48h


title: S7: WT1_singleCell

description: RNA-seq

value: Single cell


title: Zn resupply root-rep3 mRNA-seq

city: Hangzhou

first: Houqing

last: Zeng

address: NO.2318, Yuhangtang Rd, Yuhang District

institute: Hangzhou Normal University

description:
sample name in processed data file:
ZRR_3

data_processing:
The initial base calling and quality filtering of the reads generated with the Illumina analysis pipeline (Fastq format) were conducted using a custom Perl script and the default parameters of the Illumina pipeline (http://www.illumina.com). Additional filtering for poor-quality bases was performed using the FASTX-toolkit available in the FastQC software package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The rice reference genome (https://rapdb.dna.affrc.go.jp/) was indexed by Bowtie2 to facilitate the read mapping. The read mapping was performed using the Tophat software package (Trapnell et al. 2009). Tophat allows multiple alignments per read (up to 40) and a maximum of two mismatches when mapping the reads to the reference genome.
Reads were first mapped directly to the genome using indexing and the unmapped reads were used to identify novel splicing events. The aligned read files were processed by Cufflinks to measure the relative abundances of the transcripts by using the normalized RNA-seq fragment counts.
The estimated gene abundance was measured in terms of the fragments per kilobase of transcript per million mapped reads (FPKM). The differentially expressed genes (DEGs) between the two treatments were identified using Cuffdiff. Only the genes with a log2 fold change ≥1 or ≤−1, and an adjusted P-value (FDR≤0.05) were considered as significantly DEGs.
Genome_build: The rice reference genome (https://rapdb.dna.affrc.go.jp/)
Supplementary_files_format_and_content: one excel file includes FPKM values for each sample

source_name: Root

growth_protocol: Seeds of the rice (Oryza sativa L. japonica) were surface sterilized in 10% (v/v) H2O2 for 20 min and rinsed with sterile water. Seeds were then transferred to seedling trays floating on sterile water for germination. After growing in the sterile water for 10 days, seedlings were transferred to a plastic container with 2.5 L Yoshida solution (Yoshida et al. 1976). The fresh nutrient solution was replenished every 2 day, and the pH was adjusted to 5.6. Plants were grown in a growth chamber under controlled conditions. The light intensity was approximately 180 μmol m-2 s-1 at shoot height with a day/night cycle of 16 h/8 h at 26°C/24°C. The relative humidity was 50%.

extract_protocol:
Rice shoots and roots were collected after Zn-deficiency and Zn-resupply treatments.  Eighteen samples (Zn-plus shoot, Zn-minus shoot, Zn-resupply shoot, Zn-plus root, Zn-minus root, Zn-resupply root, each with three biological replicates) were harvested for small RNA library construction and sequencing. Roots and shoots from three rice seedlings were collected and mixed together as one sample. Total RNAs were extracted from samples using Trizol reagent (Invitrogen, Carlsbad, CA).
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA), and the quantity and the purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA). The RIN value (RNA integrity number) of all RNA samples were more than 8.0. Ten µg of total RNA of each sample was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen, Carlsbad, CA). After purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were then reverse-transcribed to create cDNA libraries according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA). The average insert size for the paired-end libraries was 300 bp (±50 bp). The paired-end sequencing was performed on an Illumina Hiseq4000 at the LC-BIO (Hangzhou, China).

treatment_protocol: After growing in the nutrient solution (with 1.5 µM ZnSO4) for one week, uniform seedlings were used for Zn deficiency treatment. For Zn deficiency, no ZnSO4 was added to the nutrient solution, while normal 1.5 µM ZnSO4 was used for the control treatment. Roots and shoots of rice seedlings were collected after Zn-deficient treatment for two weeks. For Zn-resupply treatment, Zn-deficient seedlings were transferred to nomal nutrient solution containing 1.5 µM ZnSO4 for three days. After Zn-resupply treatment, roots and shoots were collected for analyses at the same time point as collecting the Zn-deficient samples (four hours after illumination).

tag: cultivar

value: L. japonica cv. Nipponbare

value: the whole root system

value: 4 week old seedling

value: Zn resupply


title: Patient 5-Gs-knockdown [4R117-P19-GTGGCC]

description:
4R117-P19-GTGGCC
N012317_Gs_KD


title: S6: WT1_singleCell

description: RNA-seq

value: wild type

value: EL4 cells


title: siRNA NIK 48h

description:
Human skin malignant melanoma
siNIK_48h

source_name: A375 cells treated with a siRNA against NIK during 48h

value: Human melanoma cells


title: Zn resupply root-rep2 mRNA-seq

description:
sample name in processed data file:
ZRR_2

tag: developmental stage


title: Zn resupply root-rep1 mRNA-seq

description:
sample name in processed data file:
ZRR_1


title: Patient 6-Gs-knockdown budesonide treated [4R117-P24-ATTCCT]

description:
4R117-P24-ATTCCT
N012414_Gs_KD_+_budesonide

value: Patient 6

value: Human airway smooth muscle (HASM) cells


title: S5: WT1_singleCell

description: RNA-seq


title: siRNA Control 48h

description:
Human skin malignant melanoma
siControl_48h

source_name: A375 cells treated with a control siRNA during 48h


title: Patient 6-budesonide treated [4R117-P22-GAGTGG]

description:
4R117-P22-GAGTGG
N012414_cont_+_budesonide

source_name: HASM cells_Control budesonide treated

value: Control budesonide treated


title: Patient 5-control [4R117-P17-GTCCGC]

description:
4R117-P17-GTCCGC
N012317_cont


title: S3: WT1_singleCell

description: RNA-seq


title: S4: WT1_singleCell

description: RNA-seq


title: Zn resupply shoot-rep2 mRNA-seq

description:
sample name in processed data file:
ZRL_2

source_name: Shoot

value: the leaf and stem


title: Patient 4-Gs-knockdown budesonide treated [4R117-P16-CCGTCC]

description:
4R117-P16-CCGTCC
N101317K_Gs_KD_+_budesonide

value: Patient 4


title: DMSO 48h

description:
Human skin malignant melanoma
DMSO_48h

source_name: A375 cells treated with DMSO during 48h


title: Zn resupply shoot-rep1 mRNA-seq

description:
sample name in processed data file:
ZRL_1


title: Patient 4-Gs-knockdown [4R117-P15-ATGTCA]

description:
4R117-P15-ATGTCA
N101317K_Gs_KD

value: GNAS-knockdown


title: Zn plus root-rep3 mRNA-seq

description:
sample name in processed data file:
ZPR_3

value: normal Zn level


title: Patient 5-budesonide treated [4R117-P18-GTGAAA]

description:
4R117-P18-GTGAAA
N012317_cont_+_budesonide

value: Patient 5


title: S1: WT1_singleCell

description: RNA-seq


title: Patient 4-control [4R117-P13-AGTCAA]

description:
4R117-P13-AGTCAA
N101317K_cont

value: Control


title: Zn resupply shoot-rep3 mRNA-seq

description:
sample name in processed data file:
ZRL_3


title: Zn plus shoot-rep3 mRNA-seq

description:
sample name in processed data file:
ZPL_3


title: Zn plus shoot-rep2 mRNA-seq

description:
sample name in processed data file:
ZPL_2


title: S2: WT1_singleCell

description: RNA-seq

value: Single cell


title: Patient 3-control [4R117-P09-GATCAG]

description:
4R117-P09-GATCAG
N021014_cont

value: Patient 3


title: Patient 3-budesonide treated [4R117-P10-TAGCTT]

description:
4R117-P10-TAGCTT
N021014_cont_+_budesonide


title: Zn plus shoot-rep1 mRNA-seq

description:
sample name in processed data file:
ZPL_1

value: L. japonica cv. Nipponbare


title: Patient 4-budesonide treated [4R117-P14-AGTTCC]

description:
4R117-P14-AGTTCC
N101317K_cont_+_budesonide


title: Zn plus root-rep1 mRNA-seq

description:
sample name in processed data file:
ZPR_1

value: the whole root system

value: 4 week old seedling


title: Patient 2-Gs-knockdown budesonide treated [4R117-P08-ACTTGA]

description:
4R117-P08-ACTTGA
N041717_Gs_KD_+_budesonide

value: Patient 2

value: GNAS-knockdown budesonide treated


title: Patient 3-Gs-knockdown budesonide treated [4R117-P12-CTTGTA]

description:
4R117-P12-CTTGTA
N021014_Gs_KD_+_budesonide


title: Zn minus root-rep3 mRNA-seq

description:
sample name in processed data file:
ZMR_3

value: Zn-deficient


title: Zn plus root-rep2 mRNA-seq

description:
sample name in processed data file:
ZPR_2


title: Patient 3-Gs-knockdown [4R117-P11-GGCTAC]

description:
4R117-P11-GGCTAC
N021014_Gs_KD


title: 10003_cl_2_2_T13

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

hyb_protocol: Equal quantities (325 ng) of Cy3- and Cy5-labeled cRNA targets were mixed and incubated on microarray slides at 65°C for 17 hours.

scan_protocol: After washing, slides were scanned using the Microarray Scanner (G2565CA, Agilent Technologies) at 5-µm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

data_processing:
The data were extracted from these images using the Agilent Feature Extraction 10.7.3.1. software.
Data were computed using the Genespring GX version 12.6 ( Agilent Technologies), a web-based tool suite that allows integrated analysis of two-color microarrays. Arrays were background corrected using minimum method (any intensity which is zero or negative after background subtraction is set equal to half the minimum of the positive corrected intensities for that array), and a within-array loess normalization were performed. Finally, array data were normalized using quantile normalization. Log intensity ratios for each spot were obtained with background subtraction.

organism: Aspergillus nidulans

source_name: Total Mycelium

label_protocol: Target preparation and hybridization were done according to the manufacturer’s instructions. Briefly, 200 ng of total RNA was labeled using the Low Input Quick Amp Labeling Kit, 2 colors (Agilent Technologies), Cy5-CTP for the reference RNA made of a mix of all samples, and Cy3-CTP for individual samples. Internal standards were derived from the Two-Color RNA Spike-in Kit (Agilent Technologies). The labeled targets were purified using the RNeasy® Mini Kit (Qiagen) and their quality and quantity were confirmed by spectrophotometry and the Bioanalyzer 2100 technology (Agilent Technologies).

growth_protocol: Two independent series of quadruplicate cultures from A. nidulans CV125 strain were grown in liquid culture medium with 0,007% Roundup for 15 h at 30°C with agitation at 150 rpm. Total Mycelium was harvested from each culture,  immediately frozen in  liquid nitrogen and stored at -80°C.

extract_protocol: Extraction of total RNA started by protein denaturation in guanidine 6 M, sodium acetate 20 mM pH 5 and dithiotreitol 1 mM. After a 15-min centrifugation at 10000 rpm, +4°C, supernatant was filtered to remove cell debris, and  RNA was precipited by 2-hours incubation in 2,5 volumes of ethanol 95% at -20°C. These steps were repeated and RNA extract was stored in 1.5 ml of ethanol 70% with sodium acetate 100 mM at -80°C until use. Further purification was performed from 25% volume of each alcoholic RNA extract, by high-speed centrifugation followed by three washes of the pellet with 75% ethanol before solubilization in 250 µL RNase-free water, then extraction of impurities with 900 µL TRIzol® (Life Technologies) according to the manufacturer's instructions. After precipitation in 500 µL isopropanol at room temperature, RNA was pelleted by high-speed centrifugation and the pellet washed twice with 75% ethanol, then solubilized in 100 µL RNase-free water and stored at -80°C until molecular analyses.

tag: biological replicate

tag: array slide

tag: reference

value: Reference RNA (mixed samples)


title: 10003_cl_2_1_R16

treatment_protocol: A. nidulans CV125 strain were grown in liquid culture medium with 0,007% Roundup for 15 h at 30°C with agitation at 150 rpm

value: Roundup


title: Normal3

city: Guangzhou

first: Bi

last: Xuan

address: No. 600 Tianhe Road, Tianhe District

department: Department of Internal Medicine,

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: lncRNA data

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: Fibroblast-like synoviocytes of healthy control

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The fibroblast-like synoviocytes were plated in culture flasks contained an appropriate amount of DMEM (Gibco, USA) culture medium supplemented with 10% fetal bovine serum (FBS, Gibco, USA) in a 37°C, 5% CO2 thermostatic incubator.  Fresh culture medium was changed every 2–3 days with 10% FBS.

extract_protocol: Total RNA was isolated using TRIzol® reagent according to the manufacturer’s instructions. RNA quantity and integrity were examined using a NanoDrop® ND-1000 (Thermo scientific, Scotts Valley, CA, USA) and standard denaturing agarose gel electrophoresis, respectively

treatment_protocol: FLSs which come from different people are cultured in the same condition without extra treatment.

tag: subject status

value: healthy control

value: human healthy control synoviocytes cell line


title: Patient 2-Gs-knockdown [4R117-P07-CAGATC]

description:
4R117-P07-CAGATC
N041717_Gs_KD

value: Human airway smooth muscle (HASM) cells


title: 10003_cl_1_4_R7


title: Normal1

description: lncRNA data


title: 10003_cl_2_3_R17


title: 10003_cl_2_4_T18


title: Zn minus root-rep2 mRNA-seq

description:
sample name in processed data file:
ZMR_2


title: RA4

description: lncRNA data

source_name: Fibroblast-like synoviocytes of rheumatoid arthritis

value: rheumatoid arthritis patient

value: human rheumatoid arthritis synoviocytes cell line


title: 10003_cl_1_3_T8


title: Normal2

description: lncRNA data


title: 10003_cl_1_2_R6


title: 10003_cl_1_1_T7


title: scRNA-seq of HUVEC in DM KDM4B Knockdown [103838-001-003_S7]

city: Frankfurt

first: David

last: John

address: Theodor-Stern-Kai 7

institute: Institute for Cardiovascular Regeneration

description:
ScRNA-SEQ of HUVEC in differentiation medium KDM4B Knockdown
processed data file: inVitro_siScr_vs_siJMJD2B_EndMt_FM_Expressionmatrix.csv

tag: genotype/variation

value: JMJD2B Knockdown

value: human umbilical vein endothelial cells (HUVEC)

tag: passages

value: differentiation media (DM)


title: RA3

description: lncRNA data


title: 10002_cl_2_3_R15


title: Zn minus shoot-rep3 mRNA-seq

description:
sample name in processed data file:
ZML_3

tag: tissue

value: the leaf and stem


title: 10002_cl_2_4_T12

value: Control


title: Zn minus root-rep1 mRNA-seq

description:
sample name in processed data file:
ZMR_1

value: L. japonica cv. Nipponbare

value: the whole root system


title: scRNA-seq of HUVEC in DM Control [103838-001-002_S6]

description:
ScRNA-SEQ of HUVEC in differentiation medium Control
processed data file: inVitro_siScr_vs_siJMJD2B_EndMt_FM_Expressionmatrix.csv

value: Wild-type

tag: cell type


title: Patient 2-control [4R117-P05-ACAGTG]

description:
4R117-P05-ACAGTG
N041717_cont

value: Patient 2


title: Patient 2-budesonide treated [4R117-P06-GCCAAT]

description:
4R117-P06-GCCAAT
N041717_cont_+_budesonide

value: Control budesonide treated


title: scRNA-seq of HUVEC in FM Control [103838-001-001_S5]

description:
ScRNA-SEQ of HUVEC in full medium Control
processed data file: inVitro_siScr_vs_siJMJD2B_EndMt_FM_Expressionmatrix.csv

tag: treatment

value: full medium (FM)


title: Patient 1-Gs-knockdown budesonide treated [4R117-P04-TGACCA]

description:
4R117-P04-TGACCA
N100217Gs_KD_+_budesonide

tag: subject id

value: Patient 1

value: GNAS-knockdown budesonide treated


title: scRNA-seq of HUVEC in DM [103350-001-002_S1]

description:
ScRNA-SEQ of HUVEC in differentiation medium
processed data file: inVitro_FM-vs_EndMT_Expressionmatrix.csv


title: Zn minus shoot-rep1 mRNA-seq

description:
sample name in processed data file:
ZML_1

value: 4 week old seedling

value: Zn-deficient


title: Patient 1-Gs-knockdown [4R117-P03-TTAGGC]

description:
4R117-P03-TTAGGC
N100217_Gs_KD

value: Human airway smooth muscle (HASM) cells

tag: treatment condition

value: GNAS-knockdown


title: Zn minus shoot-rep2 mRNA-seq

description:
sample name in processed data file:
ZML_2


title: RnPDA3

city: Malaga

first: Maria

middle: Clara

last: Pliego

state: Malaga

address: Cortijo de la Cruz s/n

institute: IFAPA Centro de Malaga

data_processing:
Basecalls performed using Illumina CASAVA
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Genomics Workbench ver.10.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Genomics Workbench ver.10.0
Genome_build: Rnecatrix_2.0
Supplementary_files_format_and_content: Normalized expression values

organism: Rosellinia necatrix

source_name: mycelium

growth_protocol: In RnPDA samples Rosellinia necatrix were grown 5 days at 25ºC on potato dextrose agar (PDA; Difco Laboratories, Detroit). In RnRC samples Rosellinia necatrix mycelium were grown 5 days at room temperature on avocado roots.

extract_protocol:
Mycelium was collected and frozen in liquid nitrogen and was macerated in a mortar with a small amount of sand and liquid nitrogen. After macerating, the powder was collected in a 2 ml eppendorf up to half and resuspended in 1 ml of denaturation solution for the isolation of RNA (Fluka; Switzerland) and saturated phenol pH 4.3 (1:1) plus 7 µl of β-Mercaptoethanol. 100 µl of chloroform was added and mixed well by vortexing, samples were incubated 3 min at room temperature, and centrifuged at 12000 g for 10 min at 4 ºC. The aqueous phase was collected for downstream steps. Total RNA was extracted  using NucleoSpin RNA plant kit (Macherey-Nagel, Germany), following the instructions provided by the manufacturer.
Libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina Inc) according to the protocols recommended by the manufacturer.

value: wild type

value: grown on potato dextrose agar (PDA)

value: mycelium


title: Patient 1-budesonide treated [4R117-P02-CGATGT]

description:
4R117-P02-CGATGT
N100217_cont_+_budesonide


title: 10002_cl_2_2_T11

value: Reference RNA (mixed samples)


title: 10002_cl_2_1_R12

value: Roundup


title: LJR

description: lncRNA data

value: rheumatoid arthritis patient

value: human rheumatoid arthritis synoviocytes cell line


title: 10002_cl_1_4_R5


title: rpn5-ts rep3 [Rpn5_TS_RNA_P3_DNAse_S87]

city: Indianapolis

first: Sarah

last: Peck Justice

state: IN

address: 635 Barnhill Dr

department: Biochemistry and Molecular Biology

institute: Indiana University

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC sacCer3
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

growth_protocol: YPD; OD ~0.5

extract_protocol:
hot acid phenol; DNAse treated
KAPA mRNA HyperPrep kit

treatment_protocol: no treatment

tag: strain information

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0   lys2Δ0 can1Δ::LEU2-MFA1pr::His3 rpn5-ts::URA3

tag: molecule subtype

value: polyA-enriched RNA


title: Patient 1-control [4R117-P01-ATCACG]

description:
4R117-P01-ATCACG
N100217_cont

value: Control


title: RnPDA2

tag: strain


title: rpn5-ts rep4 [Rpn5_TS_RNA_P4_DNAse_S88]


title: rpn5-ts rep2 [Rpn5_TS_P2_S86]


title: RnPDA1

tag: genotype


title: RnRC3

value: grown on avocado roots