title: 320d_SCX

city: Herts

first: Deborah

middle: Jane

last: Guest

address: Hawkshead Lane, North Mymms, Hatfield

department: Deptartment of Clinical Sciences and Services

country: United Kingdom

institute: Royal Veterinary College

description: 2x100 paired-end sequence reads

data_processing:
RNA sequencing was performed on a NovaSeq6000 (Illumina) both by an external provider (Edinburgh Genomics, Edinburgh, UK).
17.6 – 26.2 million reads  of 100 base pair paired end data were generated per sample.
Resulting FASTQ files generated were then quality control (QC) checked using FASTQC and FASTQ Screen (Babraham Bioinformatics, Cambridge, UK).
QC checked reads were then aligned to the Ensemble version v96 EquCab 3.0 transcriptome using the pseudoaligner Salmon in Quasi-mapping based mode with GC-bias correction (-gcBias).
The tximport package (Soneson et al 2015) was then used to import the quantified gene-level abundance data into R (v.3.5.2) and differential expression analysis conducted using R/Bioconductor DSeq2 (v.1.22.2) as described in Love et al., 2014
Genes with adjusted pvalue of less than 0.05 and log2 fold change of ± 1 were considered as differentially expressed.
Genome_build: Ensemble version v96 EquCab 3.0
Supplementary_files_format_and_content: Comma Seperated Value (CSV) files include raw counts of sequencing reads for each sample in a matrix table

organism: Equus caballus

source_name: Tenocytes

growth_protocol: Adult and Fetal cells were cultured in Dulbecco’s modified eagle medium (DMEM) high glucose, 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin (all from Invitrogen, Renfrewshire, UK) and passaged using 0.25% trypsin-EDTA (Sigma-Aldrich) every 3-4 days.

extract_protocol:
RNA was extracted using Tri-reagent (Sigma), purified using an RNeasy mini Kit (Qiagen, Manchester, UK) and contaminating genomic DNA removed using Ambion DNA-free (Life Technologies, Paisley, UK). RNA concentration was measured using a Nanodrop (ThermoFisher, Loughborough, UK) and a Qubit (ThermoFisher). RNA integrity was confirmed on a Tapestation (Agilent, Milton Keynes, UK) by an external provider (Cambridge Genomics, Cambridge, UK).
mRNA libraries were prepared using a TruSeq stranded mRNA kit (Illumina, Cambridge, UK)

treatment_protocol: TRC2-pLKO.1-puro vector plasmids containing a shRNA specific for human SCX (clone NM_001008271.1-95s21c1; Sigma) or a non-target, scrambled (NT) shRNA sequence (SHC202; Sigma) were utilised for stable cell line generation.

value: fetal

tag: passages

value: 320 day gestation


title: Fibroblasts AD-HIES1_NT

status: Public on Aug 12 2020

type: SRA

city: Bethesda

first: Manfred

last: Boehm

state: MD

address: 9000 Rockbille Pike

country: USA

institute: NHLBI

library_source: transcriptomic

data_processing:
RNA-seq data quality was assessed using FastQC
Reads obtained for each sample were aligned to the hg19 human reference genome using Tophat2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include total counts values for all samples

molecule: total RNA

organism: Homo sapiens

source_name: skin biopsy

growth_protocol: 3 Control and 3 AD-HIES patient-derived fibroblasts lines were generated from 3-4-mm skin biopsies following informed consent under protocols approved by NHLBI IRB. The skin biopsy was cut into 1mm pieces and digested for 1h at 37C in 10ml of 0.1% Collagenase Type II (No.17101-015, Thermo Fisher Scientific) / 0.25 U/ml Dispase (No. 17105-0411, Thermo Fisher Scientific)/PBS solution. The skin pieces were then transferred to 2 wells of a 6 well culture plate, covered with cover slips to facilitate attachment, and cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 20% fetal bovine serum and antibiotics in 20% O2, 5% CO2 incubator. Fibroblasts outgrown from the explants were subcultured after 3-4 weeks when they occupied most of the well’s surface. The fibroblasts then were cultured in DMEM medium supplemented with 10% fetal bovine serum (No. S10250, Atlanta biological, Flowery Branch, GA) and antibiotics.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (No. 15596026, ThermoFisher Scientific).
One mg of total RNA was used as input for library preparation using the TruSeqRNA Sample Preparation Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: The fibroblasts were routinely grown in DMEM medium supplemented with 10% fetal bovine serum and seeded for experiments on six well plates at a density of 250,000 cells per well and switched to serum free medium after they reached confluence. After 24h in serum free medium, media was replaced with fresh serum free media and treated of not with TNFa 50ng/ml for 8h

tag: isolated cells

value: skin fibroblasts

tag: treatment

value: no treatment

tag: genotype/variation

value: AD-HIES STAT3 mutation


title: 320d_NT

description: 2x100 paired-end sequence reads

tag: cell type

tag: age


title: RR057e_00759_C12_S179

city: San Francisco

first: Charles

last: Langelier

state: CA

address: 499 Illinois St

department: Medicine

institute: University of California San Francisco

data_processing:
Alignment against human genome- Kallisto v 0.46.1
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport
Fitering to retain samples with 400,000 gene counts
Differential expression with R package limma
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv files with genecounts

source_name: NP/OP swab

growth_protocol: Clinical naso/pharyngeal swab specimens

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion

treatment_protocol: DNAse

tag: gender

value: M

tag: sars-cov-2 rpm

value: POS

tag: sars-cov-2 pcr

tag: disease state


title: 319d_SCX

description: 2x100 paired-end sequence reads

value: 319 day gestation


title: RR057e_00431_L21_S332

value: NEG

value: other virus


title: RR057e_00456_G12_S183

value: no virus


title: Fibroblasts CONTROL3_NT

value: control


title: Fibroblasts AD-HIES2_TNF

value: TNFa 50ng/ml for 8h


title: 319d_NT

description: 2x100 paired-end sequence reads


title: RR057e_00724_F06_S86

value: F


title: Fibroblasts CONTROL2_NT


title: RR057e_00534_G08_S119


title: RR057e_00747_D14_S212


title: Fibroblasts CONTROL1_NT


title: RR057e_00761_L14_S220


title: 316d_SCX

description: 2x100 paired-end sequence reads

value: 316 day gestation


title: 316d_NT

description: 2x100 paired-end sequence reads


title: RR057e_00401_G04_S55


title: RR057e_00512_G06_S87


title: Fibroblasts AD-HIES2_NT


title: 271d_SCX

description: 2x100 paired-end sequence reads

value: 271 day gestation


title: RR057e_00173_M18_S285


title: RR057e_00073_L18_S284


title: Ldlr_null_Donor_into_Ager_null_sample_3

city: New York

first: Richard

middle: A

last: Friedman

state: NY

address: 1130 St. Nicholas Av

institute: Columbia University Irving  Medical Center

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Fastq files were trimmed of low quality bases and adapters with Trimmomatic
Reads were mapped to the genome with Bowtie 2.1.0 Tophat 2.0.0 and HTSeq 0.6.1 .
Genome_build: mm10
Supplementary_files_format_and_content: text file with raw counts for each gene

organism: Mus musculus

source_name: Ldlr null donor macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standard chow-fed Ager null CD45.1 diabetic mice.

extract_protocol:
RNA was prepared for sequencing using the NuGEN Ovation RNA-Seq system v2 reagents.
The Ovation Ultralow DR Multiplex system was used for for the adapter ligation step.
Libraries were amplified by 9 cycles, according to the manufacturer’s instructions.

value: macrophage


title: Wilms' tumor cell line Wit49

city: Beaverton

last: Keller

state: Oregon

address: 12655 Sw Beaverdam Rd West

department: Pediatric Cancer Biology

institute: cc-TDI

data_processing:
raw reads aligned to GRCh38 human reference genome using STAR
aligned transcripts were quantified using RSEM
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: result files are In tabular format. These files have quantified TPM data with additional information

source_name: tumor cells

extract_protocol:
Total RNA was extracted at BGI and analyzed on a Agilent 2100.
Library was constructed using the BGISeq-500 Transcriptome library construction protocol: 1. Calculate the DNA input and prepare the library adapters. 2. End-repair step following Carøe et al. 2017 with the addition of 1 μl "Reaction enhancer" consisting of 25% Poly-Ethylene Glycol (PEG4000); 2 μg/μL Bovine Serum Albumin (BSA) and 400 mM NaCl. 3. Ligation step following Carøe et al. 2017 by using 1 μl 10 μM BGISeq-500 adapters. 4. Fill-in step of the adapter to complete library building and purification using 1:5 volume of PB binding buffer (Qiagen) and using Monarch DNA Cleanup Columns (New England Biolabs, Massachusetts, USA). 5. Wash with 750 µl buffer PE (Qiagen). 6. Incubate for 5 minutes at 37 °C. 7. Elute in 40 µl buffer EB (Qiagen). 8. To determine the number of cycles used in index PCR, performe a qPCR in a 20 µl reaction volume using 1:20 dilution of: purified library template, 0.2 mM dNTPs (Invitrogen), 0.04 U/µl AmpliTaq Gold DNA polymerase (Applied Biosystems, Foster City, California, USA), 2.5 mM MgCl2 (Applied Biosystems), 1X GeneAmp, 10X PCR Buffer II (Applied Biosystems), 1 µl SYBR Green (Invitrogen, Carlsbad, California, USA), 0.2 µM forward and reverse primers mixture(CommonprimerBGI forward primer and one of the indexed reverse primers), 13.48 µl AccuGene molecular biology water (Lonza)

value: tumor cells

value: Wilms' tumor cell line Wit49


title: RR057e_00223_I22_S345


title: Ldlr_null_Donor_into_Ager_null_sample_4


title: RR057e_00586_G04_S55


title: Wilms' tumor PDX explant KT18

source_name: PDX explant tissue

value: Wilms' tumor PDX explant KT18


title: 271d_NT

description: 2x100 paired-end sequence reads

value: fetal


title: S_SCX

description: 2x100 paired-end sequence reads

value: adult

value: 2-10 years old


title: Ldlr_null_Donor_into_Ager_null_sample_2


title: Ldlr_null_Donor_into_Ager_null_sample_1


title: S_NT

description: 2x100 paired-end sequence reads


title: Wilms' tumor cell line IM-WT-6

value: Wilms' tumor cell line IM-WT-6


title: RR057i_00180_N21_S334


title: RR057i_00072_M05_S77

value: POS


title: TB130911_SCX

description: 2x100 paired-end sequence reads


title: Ager_null_Recipient_sample_6

source_name: Ager null recipient macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standart chow-fed Ager null CD45.1 diabetic mice.


title: Ager_null_Recipient_sample_5


title: TB130911_NT

description: 2x100 paired-end sequence reads


title: Wilms' tumor cell line IM-WT-1

value: Wilms' tumor cell line IM-WT-1


title: Ager_null_Recipient_sample_4


title: TB180412_SCX

description: 2x100 paired-end sequence reads


title: Wilms' tumor cell line IM-WT-10

value: Wilms' tumor cell line IM-WT-10


title: RR057e_00260_E14_S213

value: NEG

value: no virus


title: Ager_null_Recipient_sample_3


title: RR057e_00259_C14_S211

value: M


title: TB180412_NT

description: 2x100 paired-end sequence reads


title: RR057e_00756_K10_S155

value: F


title: TB171012_SCX

description: 2x100 paired-end sequence reads


title: Wilms' tumor primary culture CF-00136

value: Wilms' tumor primary culture CF-00136


title: Ager_null_Recipient_sample_2


title: Wilms' tumor primary culture CF-00108

value: Wilms' tumor primary culture CF-00108


title: Wilms' tumor primary culture PCB-00007

value: Wilms' tumor primary culture PCB-00007


title: RR057i_00131_L05_S76


title: Ldlr_null_Donor_into_WT_sample_3

source_name: Ldlr null donor macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standard chow-fed WT CD45.1 diabetic mice.

value: macrophage


title: Ldlr_null_Donor_into_WT_sample_4


title: TB171012_NT

description: 2x100 paired-end sequence reads


title: Ager_null_Recipient_sample_1


title: Ldlr_null_Donor_into_WT_sample_2


title: RR057e_00488_J19_S298

value: other virus


title: 223gy

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

country: Hungary

institute: Seqomics Ltd.

data_processing:
Basecalls performed using Abi Solid 5500xl-S
Data was filtered based on read length. Minimum number of nucleotides in reads = 50, Software: CLC Genomics Workbench Tool 7.5.1
CLC "Legacy" RNA-Seq analysis was carried out. Min. length fraction = 0.8, Min. similarity fraction = 0.8, Maximum number of mismatches allowed 2, Unspecific match limit = 10, Use colorspace encoding = Yes, Use strand specific assembly = No, Expression level = Genes, Software: CLC Genomics Workbench Tool 7.5.1
Reads mapping to rRNA genes were removed
TMM scale normalization was used. Function: calcNormFactors(), package: edgeR
common negative binomial dispersion value across all genes was estimated with function estimateCommonDisp(), package: edgeR
tagwise negative binomial dispersion values were estimated with function estimateTagwiseDisp(), package: edgeR
exactTest() function from package edgeR combined with FDR adjustment was applied to find genes with significantly changed gene expression. Log2 fold change of 1 and FDR value of 0.05 were used as thresholds for significance
Genome_build: RNOR-5.0
Supplementary_files_format_and_content: MS Excel, gene expressions

organism: Rattus norvegicus

source_name: Colon

extract_protocol:
Samples from the colon were homogenized in TRIzol reagent by ULTRA-TURRAX T-18 (IKA) instrument. 0,1 ml of chloroform (Sigma-Aldrich) was added to 0.3 ml homogenized sample with vigorous vortexing. Samples were centrifuged at 13000 rpm for 10 minutes. Total RNA was than extracted from the upper aqueous phase with RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA-Seq was performed by SOLiD total RNA-Seq Kit (Life Technologies), according to the manufacturer’s instructions and sequenced on SOLiD 5500xl instrument using the 50-base sequencing chemistry. For this, 5µg of RNA was DNaseI treated and the ribosomal RNA depleted using RiboMinus Eucaryote kit for RNA-Seq and RiboMinus Concentration Module all three from Thermo Fisher Scientific, Waltham, MA USA. The leftover was fragmented using RNaseIII (part of the kit), the 50-200 nt fraction size-selected, sequencing adaptors ligated and the templates reverse transcribed using ArrayScript reverse transcriptase (part of the kit). The cDNA library was purified with Qiagen MinElute PCR Purification Kit (QIAGEN GmbH, Hilden, Germany) and size-selected on a 6% TBE-Urea denaturing polyacrylamide gel (Thermo Fisher Scientific, Waltham, MA USA). The 150-250 nt cDNA fraction was amplified using AmpliTaq polymerase (Thermo Fisher Scientific, Waltham, MA USA) and purified by AmPureXP Beads (Agencourt, Beckman Coulter GmbH Krefeld, Deutschland). Concentration of each library was determined using the SOLiID Library TaqMan Quantitation Kit (Thermo Fisher Scientific, Waltham, MA USA). Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR (ePCR) (Thermo Fisher Scientific, Waltham, MA USA). Emulsions were broken with butanol (Thermo Fisher Scientific, Waltham, MA USA) and ePCR beads enriched for template-positive beads by hybridization with magnetic enrichment beads (Thermo Fisher Scientific, Waltham, MA USA). Template-enriched beads were extended at the 3' end in the presence of terminal transferase and 3' bead linker. Beads with the clonally amplified DNA were deposited onto SOLiD flowchip (Thermo Fisher Scientific, Waltham, MA USA) and sequenced on SOLiD 5500xl System (Thermo Fisher Scientific, Waltham, MA USA).

treatment_protocol: Animals were randomly divided into two groups: first group served as control (n=2; vehicle-treated hence non-colitis induced) and the second group was induced by 2,4,6-trinitrobenzene sulphonic acid (TNBS) (n=6; colitis-induced). TNBS was intracolonically administered in a volume of 0.25 ml, via an 8 cm long plastic catheter under transient ether anaesthesia. 72 hours after the treatment all animals were sacrificed, ~8cm of distal colons were removed, opened longitudinally and gently cleaned of fecal content using ice-cold physiological saline. In the case of the control group, since non-inflamed, samples were taken from random colon sections. In case of colitis-induced animals, samples were taken from inflamed colon region as well as from non-adjacent uninflamed region.

tag: strain

value: Wistar

tag: tissue

value: colon

tag: Sex

value: male

tag: group

value: TNBS treated inflamed


title: RR057e_00752_E10_S149


title: RR057e_00161_N07_S110


title: Wilms' tumor cell line 17.94

value: tumor cells

value: Wilms' tumor cell line 17.94


title: Wilms' tumor cell line COG-W-408

value: Wilms' tumor cell line COG-W-408


title: Ldlr_null_Donor_into_WT_sample_1


title: 221gy


title: 220gy


title: Wilms' tumor PDX explant KT13

value: Wilms' tumor PDX explant KT13


title: MS_HT3h-3

city: WuHan

first: Hongfang

last: Liu

address: Tuanjie Road

country: China

institute: OCRI

data_processing:
sequencing was conducted on Hiseq 2500 platform
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Darmor-bzh whole genome using hisat2
Clean reads of MS samples were de novo togeter by Trinity software with K-mer value of 31. And the unigenes were generated by the TGICL package to exclude redundant data.
FPKM (fragments per kilobase of exon per million) and TPM (transcripts per million) are used to measure gene or transcript expression levels
Genome_build: Darmor-bzh
Supplementary_files_format_and_content: tab-delimited text files include FPKM/TPM values for each Sample

molecule: polyA RNA

organism: Moricandia suffruticosa

source_name: Leaf tissue-heat treated_rep3

growth_protocol: Grown for 35 days in soil in a chamber set with temperature of 25 °C and humidity of 60% in 16 h light

extract_protocol:
The tissues were homogenized in liquid nitrogen. Then RNA was isolated using an RNA extraction kit (Takara, Dalian), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Drought treatment: One replicate was drought (withdrawing water) treated for 3 days. Heat treatment: Treated at the temperature of 40 °C for 3 hours.

value: leaf

value: heat treated


title: RR057e_00168_I18_S281

value: M

value: NEG

value: no virus


title: RR057e_00540_M08_S125

value: F


title: WT_Recipient_sample_4

source_name: WT recipient macrophages, from the transplant: Aortas of Ldlr null CD45.2 diabetic mice fed a Western Diet, and transplanted into standard chow-fed WT CD45.1 diabetic mice.


title: 219gy


title: RR057e_00743_H12_S184

value: POS


title: MS_HT3h-1

source_name: Leaf tissue-heat treated_rep1


title: 222gy


title: RR057e_00093_F22_S342


title: MS_D3d-4

source_name: Leaf tissue-drought treated_rep4

value: drought treated


title: WT_Recipient_sample_1

value: macrophage


title: WT_Recipient_sample_2


title: MS_D3d-3

source_name: Leaf tissue-drought treated_rep3


title: RR057i_00149_L11_S172


title: RR057e_00133_J05_S74

value: other virus


title: RR057e_00102_H22_S344


title: 220

value: Wistar

value: colon

value: TNBS treated uninflamed


title: Ldlr_null_Donor_sample_4

source_name: Macrophages from the aortas of  Ldlr null CD45.2 diabetic mice fed a Western Diet, and not transplanted.


title: MS_D3d-1

source_name: Leaf tissue-drought treated_rep1


title: RR057i_00151_D13_S196


title: MS_D3d-2

source_name: Leaf tissue-drought treated_rep2


title: MS_CK-3

source_name: Leaf tissue-normal_rep3

value: non-treated


title: Ldlr_null_Donor_sample_3


title: RR057e_00748_F14_S214


title: MS_HT3h-2

source_name: Leaf tissue-heat treated_rep2


title: Ldlr_null_Donor_sample_2


title: RR057e_00723_D06_S84

source_name: NP/OP swab


title: 219

value: male


title: MS_CK-2

source_name: Leaf tissue-normal_rep2


title: 218gy

value: TNBS treated inflamed


title: WT_Recipient_sample_3


title: Ldlr_null_Donor_sample_1


title: RR057e_00088_N20_S318


title: 218


title: 223


title: MS_CK-1

source_name: Leaf tissue-normal_rep1


title: 217

value: control


title: 221


title: RR057i_00171_H19_S296


title: MS_Stem

source_name: Stem tissue-normal

value: stem


title: Th17_Ctrl_2

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description: In-vitro generated IL17a reporter-positive CD4+ T cells

data_processing:
The raw reads were trimmed of the adaptors and aberrant reads were removed by TrimGalore (version 0.4.5). The quality controlled reads were mapped onto the mouse genome build GRCm38 using STAR (version2.5.3) (Dobin et al. 2013). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq count values for each sample

growth_protocol: All mouse strains were bred and maintained at UAB in accordance with IACUC guidelines.

extract_protocol:
Total RNA from sorted Foxp3/GFP–, Ifn-γ/Thy1.1–, IL-17a/hCD2+ T cells was isolated with Qiazol and miRNeasy micro kits according to manufacturer’s recommendations (Qiagen 217084 and 79306
TruSeq Stranded mRNA Library Prep Kit (Illumina RS-122-2103)

treatment_protocol: Sorted naïve CD4+ T cells were stimulated for 5 days with 5ug/mL of soluble anti-CD3, irradiated CD4-depleted splenocytes, 20ng/mL of IL6, 2.5ng/mL of TgfB, 30ng/mL of desIgf1, 10ug/mL of anti-Ifng and 10ug/mL of anti-IL4

value: spleen

value: CD4+ T cells

tag: genotype

value: IL17a/hCD2 Ifng/Thy1.1 Foxp3/GFP Reporter


title: Th17_Ctrl_1

source_name: In-vitro generated IL17a reporter-positive CD4+ T cells


title: MS_Silique

source_name: Silique tissue-normal

value: silique


title: Th17_Tx_3

description: In-vitro generated IL17a reporter-positive CD4+ T cells treated with desIgf1


title: MS_Flower

source_name: Flower tissue-normal

value: flower


title: RR057e_00206_M20_S317

value: M

value: NEG

value: no virus


title: RR057e_00231_K12_S187

value: F


title: A549_C2: A549 NTC CONTROL REP 2 [RNA-seq]

city: Omaha

first: Shrabasti

last: Roychoudhury

state: NE

address: S 42nd &, Emile St

institute: University of Nebraska Medical Center

data_processing:
Raw reads were filtered if they contained adapters, had N > 0.1%, or have a Qscore <=20.
FASTA files were aligned to the human genome (GRCh37/hg19) by STAR.
Differential expression analysis was performed using DESeq2 R package.
Genome_build: hg19
Supplementary_files_format_and_content: text of FPKM values for genes

source_name: A549 CELLS

growth_protocol: Cells were plated in a 150 mm cell culture dish with DMEM media supplemented with 10% FBS and 1% PEN-STREP and cultured for 24 hours.

extract_protocol:
total RNA was purified using a Qiagen kit (#74104)
Sequenced using Illumina Hi-seq

treatment_protocol: Doxycycline inducible APE1-shRNA and NTC- shRNA A549 cells were treated with Doxycycline (2 μg/mL) for 3 days

tag: cell line

value: lung adenocarcinoma cells

tag: passage

value: 3 to 5


title: Th17_Tx_2

source_name: In-vitro generated IL17a reporter-positive CD4+ T cells treated with desIgf1


title: MS_Root

source_name: Root tissue-normal

value: root


title: 222

source_name: Colon

value: Wistar

value: colon

value: TNBS treated uninflamed


title: Th17_Tx_1


title: RR057e_00187_D09_S132


title: A549_KD3: A549 APE1 KNOCK DOWN REP 3 [RNA-seq]


title: STM815 rpoN mt free-living conditions, rep3

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Pp STM815 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: STM815 genome sequence (accession no. NC_010622.1, NC_010623.1, NC_010625.1 and NC_010627.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample

organism: Paraburkholderia phymatum STM815

source_name: Pp STM815 planktonic cells

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . The cDNA was produced and nugen libraries obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq DR Multiplex Systems

value: rpoN mt

tag: growth state

value: planktonic cells, OD600 equal 0.6

tag: medium

value: minimal medium shift experiment (15 mM to 0.3 mM NH4)


title: Th17_Ctrl_3

value: spleen

value: CD4+ T cells


title: A549_C1: A549 NTC CONTROL REP 1 [RNA-seq]


title: STM815 rpoN mt free-living conditions, rep2


title: RR057i_00084_M09_S141

value: POS


title: RR057e_00416_C08_S115


title: HuH7 1D142 rep3

city: Derqui

first: Juan

last: Bayo

state: Buenos Aires

address: Av Peron 1500

department: IIMT

country: Argentina

institute: Universidad Austral-Conciet

description: HuH-7 cells treated for 24 h with 1D-142 (10 µM)

data_processing:
Basecalls were performed using CASAVA (v. 1.8.1)
Reads were aligned to hg19 geneome assembly and transcript assembly was performed using tophat (v.2.0.12)
CPM calculation and differential expression analysis was performed using edgeR (v.3.16.5)
Genome_build: hg19
Supplementary_files_format_and_content: Normalized CPM values for each sample

growth_protocol: HuH7 cell line was maintained in DMEM (Life Technologies Inc.) with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 4x10^6 HuH-7  cells were seeded in P150 dishes. Next day cells were treated with the different JumonjiC inhibitors, RAC1 inhibitors or DMSO as control during 24 h.

tag: histology

value: Hepatocellular carcinoma

tag: race

value: Japanese

tag: treatment


title: A549_KD1: A549 APE1 KNOCK DOWN REP 1 [RNA-seq]

tag: cell type


title: HuH7 1D142 rep2

tag: age

tag: gender

value: M


title: 216

value: male

value: control


title: RR057i_00086_E11_S165

value: F

tag: sars-cov-2 rpm

tag: sars-cov-2 pcr


title: RR057e_00750_J14_S218

tag: disease state


title: STM815 rpoN mt free-living conditions, rep1


title: HuH7 1D142 rep1


title: A549_C3: A549 NTC CONTROL REP 3 [RNA-seq]

value: lung adenocarcinoma cells

value: 3 to 5


title: STM815 wt free-living conditions, rep3

value: wt

value: planktonic cells, OD600 equal 0.5


title: STM815 wt free-living conditions, rep2


title: P6

city: Hangzhou

first: Ningning

last: Xie

address: 1 Xueshi Road

institute: Women’s Hospital, School of Medicine, Zhejiang University

description: processed data file: placenta RNA-seq.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim Galore, then FastQC (v0.11.5) was used to check the quality.
Fragments per kilobase of exon per million reads mapped (FPKM) were calculated using cuffnorm.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: Table with different methylation level of CGI and promoter.

extract_protocol:
Isolation of the total RNA was performed using Trizol Reagent (Invitrogen, USA). Total genomic DNA was extracted by TIANamp Genomic DNA Kit (Tiangen Biotech, China).
The libraries for RNA-seq were obtained by TruSeq RNA LT Sample Prep Kit v2 (Illumina, USA). RRBS libraries of genomic DNA were prepared using TruSeq DNA LT Sample Prep Kit v2 (Illumina, USA). The libraries were quantified with Quant-iT PicoGreen dsDNA Assay Kit (Life technologies, USA).

tag: subject status

value: Polycystic ovarian syndrome (PCOS)

tag: tissue

value: placenta


title: RR057e_00762_N14_S222

value: NEG

value: no virus


title: STM815 wt free-living conditions, rep1

value: planktonic cells, OD600 equal 0.6

value: minimal medium shift experiment (15 mM to 0.3 mM NH4)


title: RR057e_00037_M22_S349

value: other virus


title: mESC-scSPRITE-50%-02

city: Pasadena

first: Mary

middle: Villanueva

last: Arrastia

address: 1200 E California Blvd

department: Chemistry and Chemical Engineering

institute: California Institute of Technology

library_source: genomic

data_processing:
Library strategy: single-cell SPRITE
Basecalls performed using STAR 2.6.1 using the following parameters: --outFilterMultimapNmax 50 --outFilterScoreMinOverLread 0.30 --outFilterMatchNminOverLread 0.30 --outFilterIntronMotifs None --alignIntronMax 50000 --alignMatesGapMax 1000 --genomeLoad NoSharedMemory --outReadsUnmapped Fastx --alignIntronMin 80 --alignSJDBoverhangMin 5 --sjdbOverhang 100 --limitOutSJcollapsed 10000000 --limitIObufferSize=300000000
SAMtools 1.9 was applied to filter mapped reads, and only uniquely mapped reads (-q 255) were kept.
Alignments that had overlapped a masked region as denoted by Repeatmasker (UCSC, milliDiv < 140) were removed using bedtools (version 2.25.0)
Finally, reads that were aligned to a non-unique region of the genome were removed by excluding alignments that mapped to regions by the ComputeGenomeMask program (read length = 35 nt)
After these filtration steps, all BAM files that corresponded to the same sample but contained different Illumina primers at sequencing were pooled together before cluster identification
Genome_build: mm9
Supplementary_files_format_and_content: Other (clusters file - all DNA fragments that are tagged with the same 6 barcodes are grouped together by barcode name)

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem (ES) cell lines were cultured in serum-free 2i/LIF medium and maintained at an exponential growth phase as previously described (Engreitz et al., 2014).

extract_protocol:
mESC nuclei were isolated and permeabilized. In-nuclei restriction digest occurred followed by in-nuclei dA-tailing. 3 rounds of in-nuclei barcoding were performed to uniquely label DNA complexes inside individual nuclei with a cell-specific barcode. Sonication was done to lyse nuclei, and 3 round of DNA-complex barcoding was done to preserve spatial DNA information. After barcoding, DNA complexes were reverse crosslinked and DNA was purified for PCR.
Crosslinked (with 1% formaldehyde, 2mM disuccinimidyl glutarate) chromatin was first digested in-nuclei with HpyCH4V restriction enzyme. DNA complexes in-nuclei were then ligated with a cell-specific DNA barcode by split-and-pooling over a 96 well-plate (where each well contains a unique DNA barcode) over 3 rounds. Nuclei are then sonicated to release DNA complexes, which still contain the cell-specific DNA barcodes. Three additional rounds of split-pool barcoding were done to add a spatial barcode, which identifies all DNA molecules in that DNA complex. Here, a total of 6 barcodes are added. DNA complexes are then reverse crosslinked, DNA is purified and amplified using Illumina-standard primers. Library is cleaned up by running on a 1% agarose gel, cutting the library between 300-1000 bp, and purifying the library using Zymo's gel clean-up columns. The library is then sequenced with paired-end sequencing.

treatment_protocol: mESCs were crosslinked in suspension with 1% formaldehyde and 2 mM disuccinimidyl glutarate

tag: strain

value: bsps

value: embryonic stem cells


title: P5


title: RR057i_00119_K21_S331


title: A549_KD2: A549 APE1 KNOCK DOWN REP 2 [RNA-seq]


title: A549 IgG

data_processing:
FASTQ files were generated after adaptor sequences, and low quality (Phred score < 20) ends were trimmed from the ChIP sequences using the Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). FASTQ files were aligned to the human genome (GRCh37/hg19) using the sequence aligner Bowtie2 (version 2.2.3)
The software package Picard routine Mark Duplicates (http://broadinstitute.github.io/picard/) was used to remove sequence duplications.
Biological replicates were then merged using SAMtools.
The merged files were used to call peaks using MACS2 peak caller software (version 2.1.1). A peak from a given antibody was considered significant if it had a fold change ≥2 over IgG, ≥15 reads, and a p-value<0.001.
All bigWig files generated using the deepTools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: Cells were plated in a 150 mm cell culture dish with respective media and cultured for 24 hours.

extract_protocol:
Lysates were clarified from sonicated nuclei. ARP-tagged DNA was isolated with Streptavidin and DNA-protein complexes were isolated with antibody.
The library was made using New England Biolabs NEB Next Ultra II DNA Library Prep Kit. High-throughput sequencing was conducted at the UNMC Sequencing Core, using an Illumina HiSeq 2500 Genome Analyzer.

treatment_protocol: For mapping AP sites, 1 mM biotin-conjugated ARP (Life Technologies, #A10550) was fed to cells for 3 hours.

tag: chip antibody

value: IgG antibody


title: C6


title: 20200329_Double_positive

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz

source_name: 10x run of human PBMC

extract_protocol:
Bone marrow derived cell culture:  Female mice were sacrificed by cervical dislocation. To isolate the bone marrow, femora and tibiae from one leg were removed, cleaned from flesh, and flushed with C10 culture medium (RPMI-1640 supplemented with 15% serum, 1% x100 non-essential amino acids, 10mM HEPES buffer, 1mM sodium pyruvate, 2mM L-glutamine, and 50μM b-mercaptoethanol) using a G21 needle syringe. Flushed bone marrow was filtered through a 70-μm cell strainer and spun down in a cold centrifuge at 300xg for 5 min. Cells were re-suspended in 250 μl RBC lysis solution (Sigma) per leg and incubated for 5 min at room temperature, washed, and resuspended in pre-warmed C10 medium. Cultures were set by plating 2x106 cells in 10mL C10 supplemented with 20 ng/ml GM-CSF in a 100 mm non-tissue culture plate, and incubated under standard culture conditions (37°C, 5% CO2) (Day 0). On day 2 another 10 ml C10 medium supplemented with 20 ng/ml GM-CSF was added. On day 5, three quarter of the medium was replaced with fresh C10 medium supplemented with 20 ng/ml GM-CSF. On day 7, another 5 ml of C10 medium supplemented with 10 ng/ml GM-CSF. On day 8, non-adherent and loosely adherent cells in the culture supernatant were harvested by gentle washing and re-cultured in a fresh C10 medium supplemented with 10 ng/ml GM-CSF in new non-tissue culture plates and used as starting material for all BMDC experiments.  Tumor cell line  MCA-205 fibrosarcoma cell lines were kindly provided by Sergio Quezada group at UCL cancer institute, London, UK. Cells were cultured in DMEM (41965-039) medium supplemented with 10% heat-inactivated FBS, 1mM sodium pyruvate, 2mM l-glutamine, 1% penicillin-streptomycin (Thermo Fisher Scientific). Cells were cultured in 100 mm tissue culture plates in an incubator with humidified air and 5% CO2 at 37°C. Cell lines were validated for lack of mycoplasma infection using primers for mycoplasma-specific 16S rRNA gene region (EZPCR Mycoplasma Kit; Biological Industries).    Tumor growth measurements  Mice were inoculated intradermally (i.d.) with 5x105 MCA-205 cells suspended in 100μl PBS on their right flank. At day 19, tumors volume was measured using a caliper. Tumor volume was assessed by measuring two diameters and calculated using the formula X2 × Y × 0.52 (where X, smaller diameter and Y, larger diameter).  Isolation of tumor infiltrating leukocytes  Tumor bearing mice were sacrificed at 10 and 19 days after tumor cell inoculation. The tumors underwent mechanical (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA) and enzymatic digestion (0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640) for 15 min at 37°C. Cells then filtered through 100µm cell strainer, washed with ice cold sorting buffer, centrifuged (5 min, 4°C, 300g), and stained with fluorophores conjugated antibodies.  Human peripheral blood of healthy donors and Isolation of peripheral blood PBMC  Blood was taken from 3 healthy peripheral blood donors. The peripheral blood collecting samples is part of the (0220-15-TLV) approval. PBMCs were purified from fresh blood samples by sterile density gradient separation by density centrifugation media (Ficoll-Paque (GE Healthcare Life Sciences)) in a 1:1. Centrifugation (460 g, 25 min,) was performed at 10 °C, and the mononuclear cells were carefully aspirated and washed with ice-cold FACS buffer, followed by red blood lysis (Sigma-Aldrich) for 5min at 4°C and washing with ice cold FACS buffer.      Isolation of T-regulatory cells from mouse tumors and cervical lymph nodes  CD45+, TCR-+, CD11b- and Foxp3+ (by endogenous Foxp3-RFP or anti Foxp3-APC conjugated antibody) cells were isolated from cervical lymph nodes or MCA-205 fiborosarcoma tumors from Foxp3RFP mice.
10x - Fresh or INs-seq-fixed cells were FACS sorted into 0.04% PBS-BSA buffer or INs-seq collection buffer respectively. Cells were stained with trypan blue and counted using light microscopy and then loaded onto a 10x Chromium microfluidics system according to the manufacturer’s guidelines. scRNA-seq 5’ gene expression (GEX) libraries were generated using the 10X Genomics Chromium Single Cell 5' Kit v2 and the 10x Chromium Controller (10x Genomics) according to the 10x Single Cell 5’ v2 protocol guidelines. The 5′ mRNA library was sequenced with Illumina’s NextSeq 500 using 75 paired-end reads.
10x genomics according to the manufacturer protocol
single cell RNA-seq 5'

tag: organ

value: PBMC

tag: selection marker

value: CD45+CD8+TCF7+ID2+ FACS gating

value: Treated wit INs-seq fixation method


title: mESC-scSPRITE-50%-01


title: 20200329_Id2

value: CD45+CD8+ID2+ FACS gating


title: RR057e_00076_D20_S308

value: F


title: P4


title: 20191227_Yonatan_PTM

value: CD45+ FACS gating


title: 20191227_Yonatan_Fresh

value: Fresh, control


title: RR057e_00449_F21_S326


title: C5

value: control


title: 20191227_Foxp3


title: DMHFD-Vehicle-2

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

country: Canada

institute: St. Michael's Hospital

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequence quality was examined using FASTQC software (v0.11.7).
Trimmed reads (trimmed 5', 3'-adaptor bases using cutadapt) were aligned to the reference genome (GRCm38) using Hisat2 software (v2.1.0).
Transcript abundances for each sample were estimated using StringTie (v1.3.3) and the FPKM value for gene and transcript level were calculated using R package Ballgown (v2.10.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene features and FPKM values for the samples in Excel (xlsx) format

source_name: Adult cardomyocytes

extract_protocol:
RNA was isolated using Trizol reagent and quantified using NanoDrop ND-1000.
1-2µg of total RNA was used to prepare sequencing libraries using KAPA Stranded RNA-Seq Library Prep kit (Illumina).

value: Primary cultured

value: High fat diet for 26 weeks, streptozotocin injection after 12 weeks of high fat diet

value: Treated with 0.1% DMSO for 24h


title: RR057e_00736_F10_S150

value: POS


title: DMHFD_Vehicle-3

source_name: Adult cardiomyocytes


title: 20191227_Fadi_PTM


title: DMHFD-Vehicle-1


title: C4

value: placenta


title: RR057e_00427_I08_S121

value: NEG

value: other virus


title: 20200329_TCF

value: CD45+CD8+TCF7+ FACS gating


title: 20191227_Fadi_Fresh


title: P3

description: processed data file: placenta RRBS CGI diff.xlsx;placenta RRBS Promoter diff.xlsx

value: Polycystic ovarian syndrome (PCOS)


title: RR057e_00250_L11_S172

value: M


title: DMHFD-Treated-3

value: Treated with 9nmol/L linagliptin for 24h


title: RR057e_00403_K04_S59


title: DMHFD-Treated-2


title: RR057e_00516_E06_S85


title: 20191111_Fixed-Human-Blood

value: PBMC

value: Treated wit INs-seq fixation method


title: P2


title: P1


title: C3


title: RR057e_00066_D05_S68

value: F

value: no virus


title: Stress-B367c

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
STAR for alignment to hg19
featureCount for RPKM counting
voom-limma for differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: An Excel file including RPKM of each gene for all 24 samples

source_name: interneurons

growth_protocol: interneurons were generated from iPSCs according to previously published protocols (Kim, T.G., et al. Efficient specification of interneurons from human pluripotent stem cells by dorsoventral and rostrocaudal modulation. Stem cells 32, 1789-1804, 2014), and were harvested for RNA preparation after 8 weeks of differentiation.

extract_protocol:
Samples were harvested using Trizol reagent (Invitrogen).
TruSeq Stranded HT mRNA kit

value: iPSC-derived interneurons

value: normal

tag: condition

value: stress


title: DMHFD-Treated-1

value: Primary cultured

value: High fat diet for 26 weeks, streptozotocin injection after 12 weeks of high fat diet


title: RR057i_00139_D09_S132

source_name: NP/OP swab

value: POS


title: Stress-B367a


title: Control-Vehicle-3

value: Aged approximately 8 weeks

value: Treated with 0.1% DMSO for 24h


title: Stress-B367b


title: RR057e_00137_I16_S249

value: NEG

value: other virus


title: C1

value: control

value: placenta


title: Control-Vehicle-2


title: Stress-B272c


title: M9-2

first: Harish

last: Vasudevan

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

description:
Primary human meningioma methylation profile
NormalizedCounts_DESeq_Heterogeneity.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with normalized expression values from DESeq2 using variance stabilizing transformation

source_name: Meningioma

extract_protocol:
RNA was extracted and purified from primary tumor samples using Qiagen AllPrep Kit according to standard instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

tag: disease

value: Meningioma

tag: site

value: Intracranial


title: M9-6


title: RR057e_00494_H17_S264

value: M


title: Control-Vehicle-1

tag: treatment


title: Stress-B272b


title: RR057e_00272_K14_S219


title: Stress-B272a


title: C2


title: Control-Treated-5

tag: cell type

value: Treated with 9nmol/L linagliptin for 24h


title: Control-Vehicle-4

tag: age


title: Stress-B226c


title: RR057e_00105_J22_S346

tag: gender

value: F

value: no virus


title: RR057e_00134_L05_S76

tag: sars-cov-2 rpm


title: M8-7


title: Control-Treated-4


title: RR057i_00154_J13_S202

tag: sars-cov-2 pcr


title: Control-Vehicle-5


title: M8-8


title: M8-6


title: RR057i_00179_L21_S332

tag: disease state


title: M8-5


title: Stress-B226b

value: iPSC-derived interneurons

value: normal


title: RR057e_00454_C12_S179


title: Stress-B190c

value: stress


title: M9-1


title: Control-Treated-1

value: Primary cultured


title: M8-4


title: Stress-B190b


title: RR057e_00741_D12_S180

value: POS


title: Control-Treated-2

value: Aged approximately 8 weeks


title: Stress-B190a


title: RR057e_00084_H05_S72


title: Control-Treated-3


title: wt

city: Somerville

first: Daniel

last: Burkhardt

state: MA

address: 101 South Street, 6th Floor

institute: Cellarity

description: Pooled  islets derived from four C57/B6 mice

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using 10X Cellranger v1.2
Genome_build: mm9
Supplementary_files_format_and_content: filtered_counts.library_normalized.csv is the filtered and processed gene counts after library size normalization and square-root transformation.

source_name: Pancreatic islets

growth_protocol: Mice were analyzed at 12 weeks of age

extract_protocol:
10X Genomics 3' Single Cell RNA v3 library preparation system
scRNA-seq libraries were prepared for sequencing with the 10X Genomics 3' Single Cell RNA v3 library preparation system per manufacturer's instructions.
RNA-seq (paired end reads with sample index)

treatment_protocol: All mice were housed in specific-pathogen free cages and given free access to food and water ad libitum.

tag: genotype

value: Wild-type


title: M8-2


title: RR057e_00116_N22_S350

data_processing:
Alignment against human genome- Kallisto v 0.46.1
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport
Fitering to retain samples with 400,000 gene counts
Differential expression with R package limma
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv files with genecounts

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion

value: NEG


title: Stress-A212c

tag: tissue

value: schizophrenia


title: Stress-B226a


title: M8-1


title: RR057e_00086_L20_S316


title: Stress-A212b


title: 4dpa_fin1_scRNA

city: St. Louis

first: Ting

last: Wang

state: MO

address: 4515 McKinley Avenue, Room 5121

department: Genetics

institute: Washington University St Louis

data_processing:
All libraries were sequenced on Illumina HiSeq platforms. Reads were adapter-trimmed with cutadapt.
RNA reads were aligned to Zv10 genome using STAR.
Genome_build: Zv10
Supplementary_files_format_and_content: Digital gene expression matrices were generated by cellranger count. Briefly, sequencing reads were first mapped to Zv10 genome assembly using STAR. Mapped reads were assigned to genes based on genome annotation from Ensembl release 91 then be counted by cell.

organism: Danio rerio

source_name: 4dpa caudal fin

growth_protocol: Tg(sp7:EGFP) strains are maintained under standard husbandry in the Washington University Fish Facility, with system water temperature at 28.5˚C, and a day-night cycle controlled as 14 hr-light/10 hr-dark.

extract_protocol:
We anesthetized one-year old fish with 0.16g/L MS-222 in system water, and then removed the distal half of their caudal fin with sterilized razor blades. Collected fin tissues were digested by Accumax™ (ICT), filtered through 40µm cell strainers, and washed with 1xDPBS-0.04%BSA to generate single cell suspensions.
Libraries were constructed from these cell suspensions following the instruction of the Chromium Single Cell Gene Expression Solution (10xGenomics)

tag: strain

value: 1 year

value: caudal fin

tag: timepoint

value: 4 day post amputation


title: Stress-A212a


title: RR057e_00052_F05_S70

last: Langelier

address: 499 Illinois St


title: M8-3

value: Meningioma

value: Intracranial


title: M7-7


title: ob/ob

value: ob/ob


title: 2dpa_fin2_scRNA

source_name: 2dpa caudal fin

value: 2 day post amputation


title: M7-6

value: F


title: RR057i_00165_H17_S264


title: 2dpa_fin1_scRNA


title: M7-5


title: Stress-A162b

value: iPSC-derived interneurons


title: Stress-A162c


title: 1dpa_fin2_scRNA

source_name: 1dpa caudal fin

value: 1 day post amputation


title: M7-4


title: RR057e_00318_F15_S230

value: no virus


title: RR057e_00744_J12_S186

value: M


title: 4dpa_fin2_scRNA


title: M7-2


title: 20191111_Fresh-Human-Blood

tag: organ

value: PBMC

value: CD45+ FACS gating

value: Fresh, control


title: RR057e_00729_D08_S116

value: POS


title: preinjury_fin2_scRNA

source_name: Preinjury caudal fin

value: preinjury


title: Stress-A128c

value: schizophrenia

value: stress


title: M6-7


title: 1dpa_fin1_scRNA

value: 1 year

value: caudal fin


title: RR057e_00296_D13_S196

value: NEG

value: other virus


title: Stress-A128b


title: preinjury_fin1_scRNA


title: M6-5

value: Meningioma

value: Intracranial


title: RR057e_00131_G16_S247

value: F


title: RR057e_00491_L15_S236


title: Stress-A128a

value: iPSC-derived interneurons


title: Stress-A67c


title: M6-4


title: M6-3


title: Stress-A162a


title: M6-2


title: Stress-A67a


title: RR057e_00237_D11_S164


title: RR057e_00763_D16_S244

value: no virus


title: M6-1


title: RR057e_00107_L22_S348

value: M


title: RR057e_00737_H10_S152


title: M5-6


title: M5-5


title: RR057e_00549_E04_S53


title: M5-4


title: SigH (30 ℃)

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: KAIST

data_processing:
Basecalls performed using CASAVA version 1.4
All sequencing reads were mapped to E. coli MG1655 reference genome (NC_000913) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
To capture target protein binding sites corresponding genomic position of mapped reads start position (MRSP) was counted and stored for visual inspection using in-house scripts.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: gff file is generated by in-house script

organism: Escherichia coli str. K-12 substr. MG1655

source_name: SigH (30 ℃)

growth_protocol: Only in ChIP-assay for σ32, E. coli K12 MG1655 rpoH::8Myc::Kan (MG1655_rpoHmyc) isogenic strain was used, which was constructed as replacing rpoH to 8myc-rpoH encoding eight copies of the c-myc epitope tag and kan at the 3’ end. And two types of cells (50 ml) were inoculated into M9 minimal media of 5 ml supplemented 0.2% glucose, and grown at 30 ℃ with constant agitation overnight.

extract_protocol:
Cultured cells of 50 ml were cross-linked by 1% formaldehyde at room temperature for 30 min. To quench the unused formaldehyde and to stop the reaction, 2 mL of 2.5 M glycine was added to the cell. The cells were washed three times with 50 mL of ice-cold Tris-buffered saline (TBS) and then were incubated with 0.5 mL of lysis buffer (50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 μg/mL RNaseA, protease inhibitor cocktail and 1 kU Ready-Lyse lysozyme (Epicentre, Madison, WI)) at 37 ℃ for 30 min1. The cells were then treated with 0.5 mL of 2×IP buffer (100 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 2%(v/v) Triton X-100, and protease inhibitor cocktail), followed by incubation on ice for 30 min. For the lysis of cell and fragmentation of DNA, the lysate was then sonicated in an ice bath using Sonic Dismembrator Model 500 (four times for 20 s each, output level, 2.5). The size distribution of fragmented DNAs was confirmed using agarose gel electrophoresis (200-400 bp) after removing cell debris by centrifugation.
After stringent sequential washings, the IP-DNAs were reverse-crosslinked from DNA-protein complexes at 65 ℃ overnight. The RNAs and proteins in the supernatant were degraded with 1 µg RNase A and 8 µg protease K, respectively. The IP-DNAs were further purified using Qiagen PCR purification kit. The purified IP-DNAs were then modified and amplified by TruSeq DNA Sample Prep Kit v2 for the Illumina next-generation sequencing according to the manufacturer’s instruction (Illumina). The PCR-amplified DNA products were then loaded onto 2% agarose gel and extracted using QIAquick gel purification columns.

treatment_protocol: Then, cells were diluted to 1:100 into fresh same minimal medium and cultured at 30 ℃ up to mid-exponential phase (OD600 = 0.6). To treat the heat shock, cultured cells were subsequently mixed slowly with pre-warmed 55 ℃ media of equivalent volume to adjust to 42 ℃. For non-heat shocked condition, all experiments were performed in same manner except using 30 ℃ instead of 55 ℃ media. All mixture were further incubated shaking at 30 ℃ and 42 ℃ for 5 min.

tag: chip antibody

value: Anti-myc (9E10) (Santa Cruz, Dallas, TX)

tag: substrain


title: Stress-A67b

tag: condition


title: RNAP beta (42 ℃) mock IgG

source_name: RNAP beta (42 ℃) mock IgG

extract_protocol:
Cultured cells of 50 ml were cross-linked by 1% formaldehyde at room temperature for 30 min. To quench the unused formaldehyde and to stop the reaction, 2 mL of 2.5 M glycine was added to the cell. The cells were washed three times with 50 mL of ice-cold Tris-buffered saline (TBS) and then were incubated with 0.5 mL of lysis buffer (50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 μg/mL RNaseA, protease inhibitor cocktail and 1 kU Ready-Lyse lysozyme (Epicentre, Madison, WI)) at 37 ℃ for 30 min1. The cells were then treated with 0.5 mL of 2×IP buffer (100 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 2%(v/v) Triton X-100, and protease inhibitor cocktail), followed by incubation on ice for 30 min. For the lysis of cell and fragmentation of DNA, the lysate was then sonicated in an ice bath using Sonic Dismembrator Model 500 (four times for 20 s each, output level, 2.5). The size distribution of fragmented DNAs was confirmed using agarose gel electrophoresis (200-400 bp) after removing cell debris by centrifugation.
Prior to the reverse-crosslinking in the ChIP procedure, the IP-DNA in the crosslinked DNA-protein complexes attached on the magnetic beads were end-polished using T4 DNA polymerase (NEB, Ipswich, MA), ligated with the annealed adaptor 1 (5’- Phospho-AACTGCCCCGGGTTGCTCTTCCGATCT and 5’- OH-AGATCGGAAGAGC-OH), nick-repaired using phi29 polymerase (NEB), and digested with λ exonuclease (NEB) as reported previously3. Between the enzymatic treatments, the crosslinked DNA-protein complexes were sequentially washed with 10 mM TE (pH 8.0) and 10 mM Tris-HCl (pH 7.5-8.0). The magnetic beads were then resuspended in 50 µL of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS, and 1 mM EDTA). The exonuclease-treated IP-DNA (IP-exo-DNA) was then reverse-crosslinked from DNA-protein complexes at 65 oC overnight. The RNAs and proteins in the supernatant were degraded with 1 µg of RNase A (Invitrogen) and 8 µg of protease K (Invitrogen), respectively. The IP-exo-DNAs were further purified using Qiagen PCR purification kit according to the manufacturer’s instruction (QIAGEN, Hilden, Germany). The purified IP-exo-DNAs were denatured at 95 ℃ and extended by P1 primer (5’-OH-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT). Subsequently, the extended ends of the IP-exo-DNAs were ligated with the annealed adaptor 2 (5’-OH-ACACTCTTTCCCTACACGACGCTCTTCCGATCT and 5’-OH-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG). The ligated DNA products were purified using Qiagen PCR purification kit and were PCR-amplified by P2 primer (5’-OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and P3 primer (5’-OH-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT). The degenerative sequence (the underlined 6Ns) in the P3 primer indicates the index sequence for the Illumina next-generation sequencing (Illumina, San Diego, CA). The PCR-amplified DNA products were then loaded onto 2% agarose gel and extracted using QIAquick gel purification columns.

value: Normal IgG (Millipore) and Dynabeads Pan mouse IgG (Invitrogen)


title: M5-3

city: San Francisco

institute: University of California San Francisco

tag: individual

tag: disease


title: RR057e_00290_L13_S204

first: Charles


title: RNAP beta (42 ℃) rep2

source_name: RNAP beta (42 ℃) rep2

value: anti-RNAP β subunit (NT63), Neoclone (Madison, WI)


title: M5-7

tag: site


title: RR057e_00508_C04_S51


title: SigH (30 ℃) mock IgG

source_name: SigH (30 ℃) mock IgG


title: SigH (42 ℃)

source_name: SigH (42 ℃)


title: RR057e_00442_G10_S151


title: RNAP beta (42 ℃) rep1

source_name: RNAP beta (42 ℃) rep1


title: RR057e_00324_H15_S232


title: RR057e_00232_J13_S202


title: M5-2


title: SigH (42 ℃) mock IgG rep2

source_name: SigH (42 ℃) mock IgG rep2


title: RR057e_00148_F09_S134


title: genomic  DNA from 165_PT

type: genomic

city: Rio de Janeiro

first: Sheila

middle: Coelho

last: Soares-Lima

state: Rio de Janeiro

address: Rua André Cavalcanti 37

department: Molecular Carcinogenesis Program

country: Brazil

institute: Brazilian National Cancer Institute

description: PT sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: iScan was used to scan the slides

data_processing: Illumina Infinium Human Methylation450k (HM450K) Bead-Chips (Illumina, San Diego, CA) were used for establishing genome-wide DNA methylation profiling. Raw data were subject to quality control, prefiltering, signal normalization across samples, and normalization using the funnorm function (R packages minfi)

label: cy3 and cy5

label_protocol: Standard Illumina Protocol

extract_protocol: genomic and genomic DNA were extracted by PDAC and PT samples using PureLink Genomic DNA Kit according to standard instructions

value: female

tag: Stage


title: genomic  DNA from 171_PT

description: PT sample

tag: age


title: RR057e_00246_H13_S200

tag: gender


title: M4-5


title: M4-7


title: SigH (42 ℃) mock IgG rep1

source_name: SigH (42 ℃) mock IgG rep1


title: genomic  DNA from 158_PT

description: PT sample

value: male


title: M4-6


title: M4-4


title: genomic  DNA from 104_PT

description: PT sample


title: RR057e_00577_N21_S334

tag: sars-cov-2 rpm


title: RR057e_00184_E20_S309

tag: sars-cov-2 pcr


title: K5-3

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Mapping with STAR_2.4.0a versus phytophthora_parasitica_310.3 folowing Encode RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20".
Features counting using featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M -C" options.
Genome_build: phytophthora_parasitica_310.3
Supplementary_files_format_and_content: tab-delimited text file including log2 counts per million for each sample.

organism: Phytophthora nicotianae

source_name: K+-treated zoospores

growth_protocol: Mycelium of P. parasitica (isolate 310, Phytophthora INRA collection, Sophia Antipolis) was cultured and zoospores were produced as described by (Galiana et al., 2019; DOI:      10.1098/rsif.2019.0367), except for droplet volume that was increased to 1 mL.

extract_protocol:
Trizol extraction - miRNeasy ® Mini Kit (Qiagen, Hilden, Germany).
Libraries were generated from 500 ng of total RNA using Truseq Stranded mRNA kit (Illumina). Libraries were then quantified with Qubit ds DNA HS assay kit (Invitrogen) and pooled. 4nM of this pool were loaded on a Nextseq 500 high output flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2 × 75bp paired-end chemistry.

treatment_protocol: 10 µL 1M KCl solution was applied in a local and oriented-manner to the freshly prepared zoospores suspension, to reach a complete diffusion, as described by (Galiana et al., 2019; DOI:      10.1098/rsif.2019.0367). The experiment was performed in triplicates (R1, R2 and R3).

tag: isolate


title: SigH (30 ℃) mock IgG rep2

source_name: SigH (30 ℃) mock IgG rep2


title: genomic  DNA from 27_PT

description: PT sample


title: SigH (30 ℃) mock IgG rep1

source_name: SigH (30 ℃) mock IgG rep1


title: RR057e_00222_G22_S343

source_name: NP/OP swab

tag: disease state


title: SigH (30 ℃) rep2

source_name: SigH (30 ℃) rep2


title: M4-3

source_name: Meningioma


title: SigH (42 ℃) rep2

source_name: SigH (42 ℃) rep2


title: genomic  DNA from 99_PT

description: PT sample


title: M4-2


title: M5-1


title: genomic  DNA from 64_PT

description: PT sample


title: K15-2

value: isolate 310, Phytophthora INRA collection, Sophia Antipolis


title: M3-6


title: SigH (42 ℃) rep1

source_name: SigH (42 ℃) rep1


title: genomic DNA from 167_PDAC

description: PDAC sample

value: III


title: RR057e_00410_J17_S266


title: genomic  DNA from 137_PT

description: PT sample


title: genomic DNA from 18_PT

description: PT sample


title: K15-1


title: genomic DNA from 158_PDAC

description: PDAC sample

value: IIB


title: M3-5


title: genomic DNA from 163_PDAC

description: PDAC sample


title: genomic DNA from 37_PDAC

description: PDAC sample


title: K10-3


title: M4-1


title: RR057e_00742_F12_S182

value: POS


title: RR057e_00200_I20_S313

value: NEG


title: RR057e_00117_N03_S46


title: genomic DNA from 23_PDAC

description: PDAC sample


title: K15-3


title: RR057e_00268_I14_S217


title: M3-7


title: M3-4


title: RR057e_00515_M04_S61


title: M3-3


title: K10-2


title: Human_left ventricle_113 (worsening-LVF)

type: RNA

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with SST-RMA by Transcriptome Analysis Console Ver 4.0

label: biotin

source_name: Human heart tissue

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated from LV appendages with the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and was further purified and concentrated by using the WelPrep tissue RNA array (Welgene, Taipei, Taiwan). The quality and quantity of total RNA were analyzed by using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA)

tag: tissue

value: Heart

value: Male

tag: group

value: worsening-LVF

value: left ventricle


title: K10-1


title: M3-2

value: Meningioma

value: F

value: Intracranial


title: RR057e_00757_M10_S157


title: Human_left ventricle_112 (worsening-LVF)

value: Female


title: M2-7

value: M


title: K5-2


title: C5-2

source_name: zoospores swimming freely


title: C5-1


title: RR057e_00198_G20_S311

value: no virus


title: AIR3

city: Guangzhou

first: Yixun

last: Yu

address: Wushan

department: College of Forestry and Landscape Architecture

institute: South China Agricultural University

data_processing:
Library strategy: MeRIP-seq
Basecalls performed using CASAVA version 1.4
Adaptor and low quality of MeRIP-seq reads were trimmed by cutadapt (v1.9.3)
Clean reads were aligend to reference genome (HG19) by STAR (v2.5.1b)
MACS (v1.4.2) identified methylated regions from aligned reads.
diffReps( v1.55.6) calculated differentially methylated sites from aligned reads.
Genome_build: mm10
Supplementary_files_format_and_content: BED, coordinates of methylated regions along genome.

organism: Petunia x hybrida

source_name: petunia

extract_protocol:
The total RNA of the samples was isolated using the Trizol Kit (Promega, USA) and was treated with RNase-free DNase I (Takara Bio, Japan) for 30 min at 37℃ to remove residual DNA. Briefly, fragmented RNA was incubated with anti-m1A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N1-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m1A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.
library construction protocol

tag: cultivar

value: Mitchell

value: corrola

tag: treatment

value: air

tag: time point

tag: antibody

value: anti-m1A polyclonal antibody


title: RR057e_00140_K16_S251


title: M2-3


title: RR057e_00581_C08_S115

value: other virus


title: M2-6


title: M2-5


title: AIR2


title: M2-2


title: C5-3

value: isolate 310, Phytophthora INRA collection, Sophia Antipolis


title: RR057e_00423_E08_S117

value: NEG


title: AIR1


title: Human_left ventricle_104 (worsening-LVF)

value: Heart


title: Human_left ventricle_119 (worsening-LVF)

value: Male


title: Human_left ventricle_106 (preserved-LVF)

value: preserved-LVF


title: Human_left ventricle_109 (preserved-LVF)

value: left ventricle


title: Human_left ventricle_108 (preserved-LVF)


title: Human_left ventricle_110 (preserved-LVF)


title: K5-1


title: RR057e_00727_L06_S92

value: POS


title: Human_left ventricle_111 (preserved-LVF)


title: M13-5

value: Meningioma


title: RR057e_00042_D03_S36

value: F


title: genomic DNA from 137_PDAC

description: PDAC sample

value: male

value: IB


title: M13-6

value: M

value: Intracranial


title: RR057e_00119_L03_S44

value: no virus


title: Human_left ventricle_102 (preserved-LVF)

value: Female


title: RR057e_00418_J21_S330


title: Human_left ventricle_103 (preserved-LVF)


title: M13-7


title: ETH2

description: 2 µl l–1 ethylene 16 h

value: Mitchell

value: corrola

value: ethylene

value: anti-m1A polyclonal antibody


title: RR057e_00765_H16_S248

value: NEG


title: M13-4


title: ETH1

description: 2 µl l–1 ethylene 16 h


title: RR057e_00291_N11_S174


title: ETH3

description: 2 µl l–1 ethylene 16 h


title: AIR16h2.mRNA.m6A

tag: cv

value: air 16 h


title: AIR16h1.mRNA.m6A


title: M13-3

tag: individual


title: M13-2

tag: disease


title: RR057e_00485_N17_S270


title: ETH16h2.mRNA.m6A

value: 2 ul/l ethylene 16 h


title: M13-1

tag: site


title: M12-LivMet_2

value: Liver


title: RR057i_00176_F21_S326


title: M12-7


title: T3_Ba_Tumor tissue_Basal-like

city: CDMX

first: Alberto

last: Cedro-Tanda

state: CMDX

address: Periferico sur #4809

country: Mexico

institute: INMEGEN

description: SST-RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). GeneChips were scanned using The Genechip Scanner 3000 7G (Affymetrix , Santa Clara, USA).

data_processing: Array signal intensitive were analyzed with the Affymetrix Expression Console using Signal Space Transformation-Robust Multichip Analysis (SST-RMA) for the background correction.

source_name: Fresh frozen breast cancer tumor

label_protocol: WT Plus Reagent Kit were used to generate the biotinylated cRNA starting from 100ng of total RNA according to the manufacturer (Manual Target preparation for GeneChip Whole transcript (WT) expression arrays, Affymetrix).

extract_protocol: We used AllPrep DNA/RNA Mini Kit

tag: population

value: Mexico hispanic

tag: pam50 molecular subtype

value: Basal-like

value: RNA from tumor tissue


title: T169_LB_Tumor tissue_Luminal B

value: Luminal B


title: T55_LB_Tumor tissue_Luminal B


title: M12-6

value: Meningioma

tag: age

tag: gender

value: F


title: Human_left ventricle_101 (preserved-LVF)

value: Heart

value: preserved-LVF

value: left ventricle


title: BPD, Sample 51

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description: bronchopulmonary dysplasia

data_processing:
Data were analyzed in excel using Ct values for each sample,  normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
non-normalized_data.txt are raw Ct values. Data are normalized to the global mean. Fold changes are calculated with the livak method (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])
For fold change calculations, ΔΔCt based fold-change values were obtained using an average of control sample Ct values (2^-ΔΔCt, where -ΔΔCt = -[ΔCtsample -ΔCtavgcontrol])). A fold change of 50 was considered as cutoff.

label: SYBR Green

source_name: tracheal aspirate

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 1066 human miRNAs was assayed with the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z).

extract_protocol: MicroRNAs were purified from 0.5 mL of TAs with the Plasma/Serum RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada).

treatment_protocol: Tracheal aspirates were obtained from control patients (no lung disease, no prematurity), and premature patients with Bronchopulmonary dysplasia. Total RNA was purified from TAs and the expression of 1066 human miRNAs was detected with a PCR array.

tag: bpd

value: yes

tag: control

value: no


title: T82_LB_Tumor tissue_Luminal B


title: RR057e_00273_M14_S221

tag: sars-cov-2 rpm

tag: sars-cov-2 pcr

tag: disease state

value: no virus


title: T201_Ba_Tumor tissue_Basal-like

tag: tissue


title: T97_Ba_Tumor tissue_Basal-like


title: RR057e_00754_E12_S181

value: M

value: POS


title: RR057e_00295_N13_S206

value: NEG


title: Control, Sample 50

description: control - no lung disease


title: M12-5

value: Intracranial


title: RR057e_00079_F20_S310


title: RR057e_00051_J03_S42


title: M12-4


title: RR057e_00735_D10_S148


title: ETH16h1.mRNA.m6A

value: Mitchell

value: corrola

tag: treatment

value: 2 ul/l ethylene 16 h


title: SigH (30 ℃) rep1

source_name: SigH (30 ℃) rep1

tag: chip antibody

value: Anti-myc (9E10) (Santa Cruz, Dallas, TX)

tag: substrain


title: M12-3


title: RR057e_00169_J07_S106


title: T78_He_Tumor tissue_Her2-enriched

value: Mexico hispanic

value: RNA from tumor tissue


title: Human_left ventricle_115 (worsening-LVF)

value: Male

tag: group

value: worsening-LVF


title: Control, Sample 46

description: control - no lung disease


title: BPD, Sample 47

description: bronchopulmonary dysplasia


title: BPD, Sample 48

description: bronchopulmonary dysplasia


title: M12-2

tag: individual

value: Meningioma

value: F


title: T75_He_Tumor tissue_Her2-enriched


title: RR057e_00154_G18_S279


title: Control, Sample 49

description: control - no lung disease

value: yes


title: M11-9

tag: disease


title: RR057e_00145_H07_S104


title: T5_He_Tumor tissue_Her2-enriched


title: T45_Ba_Tumor tissue_Basal-like

value: Basal-like


title: M11-8

tag: site


title: T47_He_Tumor tissue_Her2-enriched

tag: population


title: RR057e_00171_K18_S283

value: no virus


title: M11-7


title: RR057e_00340_J15_S234


title: RR057i_00121_D03_S36


title: M11-6


title: BPD, Sample 45

description: bronchopulmonary dysplasia

value: no


title: Control, Sample 44

description: control - no lung disease


title: RR057e_00590_M06_S93


title: RR057e_00049_D18_S276

value: M


title: Control, Sample 42

description: control - no lung disease


title: Control, Sample 43

description: control - no lung disease


title: Control, Sample 41

description: control - no lung disease


title: M11-5


title: Control, Sample 40

description: control - no lung disease


title: RR057e_00216_E22_S341

value: NEG


title: M11-2

value: Intracranial


title: M11-1


title: RR057e_00138_F07_S102


title: BPD, Sample 39

description: bronchopulmonary dysplasia


title: T15_He_Tumor tissue_Her2-enriched

tag: pam50 molecular subtype


title: Control, Sample 38

description: control - no lung disease


title: T232_LB_Tumor tissue_Luminal B

value: Luminal B


title: T239_LB_Tumor tissue_Luminal B


title: T229_LA_Tumor tissue_Luminal A

value: Luminal A


title: RR057e_00567_I06_S89

tag: age


title: T227_LB_Tumor tissue_Luminal B


title: M10-7

tag: gender


title: T248_LB_Tumor tissue_Luminal B


title: T29_LA_Tumor tissue_Luminal A


title: BPD, Sample 37

description: bronchopulmonary dysplasia

tag: bpd


title: T218_LB_Tumor tissue_Luminal B


title: T213_LB_Tumor tissue_Luminal B


title: M11-4


title: M10-6


title: RR057e_00143_C18_S275


title: T206_LA_Tumor tissue_Luminal A


title: M10-4


title: RR057e_00224_J09_S138

value: other virus


title: RR057i_00076_I07_S105

value: POS


title: M10-3


title: M1-5


title: Control, Sample 36

description: control - no lung disease

tag: control


title: BPD, Sample 35

description: bronchopulmonary dysplasia


title: Control, Sample 34

description: control - no lung disease


title: Control, Sample 33

description: control - no lung disease


title: RR057e_00074_N18_S286

tag: sars-cov-2 rpm


title: RR057i_00173_L19_S300

tag: sars-cov-2 pcr


title: M1-3


title: RR057e_00280_N09_S142

tag: disease state


title: T193_He_Tumor tissue_Her2-enriched

value: Mexico hispanic

tag: tissue


title: M1-2


title: Control, Sample 32

description: control - no lung disease


title: RR057e_00475_D17_S260


title: T165_LA_Tumor tissue_Luminal A

value: RNA from tumor tissue


title: Im1390

city: Miki

first: Kazuya

last: Akimitsu

state: Kagawa

address: Ikenobe 2393

department: Faculty of Agriculture

country: Japan

institute: Kagawa University

data_processing:
Base-calling and data filtering were performed using CASAVA ver.1.8.1 software.
Adapter sequences were removed from the reads using cutadapt program.
RNA-seq reads were aligned using the TopHat (ver.2.0.2) and Cufflinks (ver.2.0.2) softwares with the data of "Arabidopsis_thaliana.TARI10.17.dna.toplevel.fa", "Arabidopsis_thaliana.TARI10.17.gtf", "Hyaloperonospora_arabidopsidis.HyaAraEmoy2_2.0.17.dna.toplevel.fa" and "Hyaloperonospora_arabidopsidis.HyaAraEmoy2_2.0.17.gtf" from Ensembl database.
Normalized FPKM value (Fragment Per Kilobase of exon Model per million mapped reads) was calculated using Cuffdiff program.
Log2 fold change value, p-value and q-value were calculated using Cuffdiff program with FPKM values from D-tagatose- and mock-treated samples.
Genome_build: "Arabidopsis_thaliana.TARI10.17.dna.toplevel.fa" and "Hyaloperonospora_arabidopsidis.HyaAraEmoy2_2.0.17.dna.toplevel.fa" from Ensembl database were used for genome build.
Supplementary_files_format_and_content: Processed data file in Excel format including "gene ID",

organism: Arabidopsis thaliana

source_name: mock-treated Arabidopsis thaliana Col-0 with Hyaloperonospora arabidopsidis Noco-2 inoculation

growth_protocol: Seedlings of A. thaliana ecotype Colombia-0 (Col-0) were grown on soil in plastic pot (7.5 cm diameter) at 22ºC under 16 h light with a light intensity of 100-150 µmol m-2 sec-1/8 h dark condition for 10 days.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plant Mini Kit following the manufacture's instruction.
Libraries for NGS analysis were constructed using TruSeq RNA Sample Prep Kit following the manufacture's instruction.

treatment_protocol: Seedlings were sprayed with or without 10 ml of 1% (w/v) of D-tagatose in water per pot, and kept for a day at 22ºC under 16 h light with a light intensity of 100-150 µmol m-2 sec-1/8 h dark condition. Following the rare sugar treatment, conidiospores of Hyaloperonospora arabidopsidis isolate Noco-2 with a concentration of 1×106 conidiospores ml-1 were spray-inoculated to the Arabidopsis plants, and incubated at 18ºC and 90 to 100% relative humidity under 10 h photoperiod with a light intensity of 150-200 µmol m-2 sec-1/14 h dark condition for 6 days.

value: Arabidopsis leaves

tag: ecotype

value: grown for 10 days in water, for 1 day in mock solution, for 6 days with Hpa inoculation in water.

tag: inoculation

value: Hyaloperonospora arabidopsidis hypha in leaves

tag: agent

value: mock


title: T190_LA_Tumor tissue_Luminal A


title: Control, Sample 30

description: control - no lung disease

value: yes


title: RR057e_00239_H11_S168


title: T150_LB_Tumor tissue_Luminal B


title: T144_Ba_Tumor tissue_Luminal B


title: T140_Ba_Tumor tissue_Luminal B


title: T186_LB_Tumor tissue_Luminal B


title: Im1389

source_name: D-tagatose-treated Arabidopsis thaliana Col-0 with Hyaloperonospora arabidopsidis Noco-2 inoculation

value: grown for 10 days in water, for 1 day in D-tagatose solution, for 6 days with Hpa inoculation in water.

value: D-tagatose


title: RR057e_00440_N15_S238

value: F

value: no virus


title: M1-4

value: Meningioma


title: BPD, Sample 29

description: bronchopulmonary dysplasia

value: no


title: Control, Sample 28

description: control - no lung disease


title: RR057e_00489_L19_S300

value: M

value: NEG


title: BPD, Sample 27

description: bronchopulmonary dysplasia


title: BPD, Sample 31

description: bronchopulmonary dysplasia


title: RR057e_00142_M16_S253


title: T106_LA_Tumor tissue_Luminal A

value: Luminal A


title: T137_LB_Tumor tissue_Luminal B

value: Luminal B


title: RR057e_00302_C16_S243


title: BPD, Sample 25

description: bronchopulmonary dysplasia


title: RR057e_00309_D15_S228


title: RR057e_00460_L17_S268


title: T196_LB_Tumor tissue_Luminal B

value: Mexico hispanic


title: Control, Sample 26

description: control - no lung disease


title: RR057e_00414_K06_S91


title: Control, Sample 23

description: control - no lung disease


title: rAb EP size-matched input

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: eCLIP

data_processing:
Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1). Args: --length 10
Reads were then trimmed with cutadapt (1.9.1). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Trimmed reads were then mapped with STAR (2.4.0i) against a mouse-specific repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir mouse_repbase \  --readFilesIn path/to/read1 path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a mouse genome (mm10). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 /path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.4.1)
Sorted reads were collapsed with barcodecollapsepe.py included in eclip 0.1.5+ pipelines. Args: -o preRmDup.bam -m metrics_file -b rmDup.bam
PCR de-duped reads from each inline barcode were then merged with samtools (1.4.1) merge (merged.bam)
Merged alignments were split to keep just read2 using samtools (1.4.1) view. Args: -h -b -f 128
Read2 BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species mm10 --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using read2 BAM files for IP against read2 BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Reproducible peaks were annotated by overlapping peak regions with Gencode M10 annotations
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include -log10pValues and Log2FoldChange values for each IDR peaks called after cutoff of 3,3 in each parameter

source_name: Colon epithelium

growth_protocol: Epithelial cells were harvested from small intestine of 8wk adult female mice using 5 mM EDTA in PBS containing 1 mM of DTT for 20 min at 37°C. mAb/rAb/mAb samples were harvested from 120 days old Apcfl/+ CDX2Cre mice and treated similarly.

extract_protocol:
Small intestine epithelial cells were extracted using the paired-end eCLIP protocol as described https://www.ncbi.nlm.nih.gov/pubmed/27018577. Colon/tumor cells were extracted using the single-end eCLIP protocol as described: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991800/.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used.
eCLIPseq

treatment_protocol: UV-mediated crosslinking, lysis, and treatment with limiting amounts of RNases, followed by immunoprecipitation (IP) of the DDX5 containing RNA complexes. RNA fragments protected from RNase digestion were subjected to RNA linker ligation, reverse-transcription and DNA linker ligation to generate eCLIP libraries for high-throughput Illumina sequencing.

tag: strain

value: Colon

tag: sample type

value: EDTA fractionation

tag: genotype

value: wild type

tag: rip antibody


title: hiHepPC-4

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

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

department: Medical Institute of Bioregulation

institute: Kyushu University

description: 4 x 180 sample4

hyb_protocol: Hybridization and washing was done according to Agilent protocol method (67ºC 24h, 20rpm）

scan_protocol: Array were scanned using Agilent SureScan G2600D according to the manufacturer's instructions.

data_processing: Agilent Feature Extraction software (version 12.0.3.1) was used for data extraction.

source_name: human induced hepatic progenitor cells

label_protocol: 500 ng genomic DNA were labeled using Agilent CGH enzymatic protocol 7.5 (Agilent Technologies)

growth_protocol: HUVECs were cultured in 1:1 mixture of Medium 200 and FibroLife medium supplemented with LSGS and LS-1038 supplements. human induced hepatic progenitor cells were cultured in DMEM/F12 and Fibrolife mixture medium with 4% FBS, 1 µg/ml insulin, 10-7 M dexamethasone, 10 mM nicotinamide, 2mM L-glutamine, 50 µM 2-mercaptoethanol, and penicillin/streptomycin, containing 20 ng/ml HGF, 1 µM A83-01, 2 µM SB43852, and 5 µM Y27632.

extract_protocol: Genomic DNA were extrated by proteinase K treatment with subsequent phenol-chloroform extraction.

treatment_protocol: We purchased HUVECs on the market. To generate human induced hepatic progenitor cells, HUVECs were infected with retroviruses that contained genes encoding indicated transcription factors.

value: female

tag: transfection

value: infected with FOXA3, HNF1A and HNF6

source_name: HUVEC

value: umbilical vein


title: mAb EP size-matched input

description: eCLIP


title: BPD, Sample 22

description: bronchopulmonary dysplasia

value: yes


title: T120_Ba_Tumor tissue_Basal-like

tag: population

tag: pam50 molecular subtype

value: Basal-like

value: RNA from tumor tissue


title: RR057e_00437_E10_S149

tag: gender

tag: age

value: other virus


title: T116_LB_Tumor tissue_Luminal B


title: hiHepPC-2

description: 4 x 180 sample2

value: male


title: hiHepPC-3

description: 4 x 180 sample3


title: BPD, Sample 21

description: bronchopulmonary dysplasia

tag: bpd

tag: control

value: no


title: RR057e_00436_C10_S147

value: M

tag: sars-cov-2 rpm

tag: sars-cov-2 pcr


title: RR057e_00047_H03_S40

value: NEG

tag: disease state


title: mAb EP CLIP

description: eCLIP

tag: tissue

value: DDX5 (Abcam, catalog# ab53216)


title: BPD, Sample 20

description: bronchopulmonary dysplasia


title: T333_LA_Tumor tissue_Luminal A

value: Luminal A


title: WT G, CLIP rep2

description:
eCLIP
GT_G.IDR_reproducible_peaks.txt

source_name: Small intestine epithelium

growth_protocol: Epithelial cells were harvested from small intestine of 8wk adult female mice using 5 mM EDTA in PBS containing 1 mM of DTT for 20 min at 37°C. Th17 cells were polarized from naïve CD4 T cells obtained from 8wk old female mice and treated with anti-CD3, anti-CD28, IL6, and TGFb for 72hrs in culture.

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used.
eCLIPseq

tag: cell type

value: Small intestine


title: Control, Sample 24

description: control - no lung disease


title: WT G, Input rep2

description:
eCLIP
GT_G.IDR_reproducible_peaks.txt


title: RR057e_00412_G06_S87

source_name: NP/OP swab

value: no virus


title: rAb EP CLIP

description: eCLIP

value: Colon

value: EDTA fractionation


title: T4_LA_Tumor tissue_Luminal A

value: Mexico hispanic


title: BPD, Sample 19

description: bronchopulmonary dysplasia


title: RR057e_00253_M12_S189


title: WT G, Input rep1

description:
eCLIP
GT_G.IDR_reproducible_peaks.txt

value: wild type


title: Control, Sample 18

description: control - no lung disease


title: WT G, CLIP rep1

description:
eCLIP
GT_G.IDR_reproducible_peaks.txt


title: RR057e_00294_F13_S198

value: F


title: Control, Sample 17

description: control - no lung disease

value: yes


title: BPD, Sample 16

description: bronchopulmonary dysplasia


title: BPD, Sample 15

description: bronchopulmonary dysplasia


title: RR057e_00749_H14_S216

value: POS


title: T6_LB_Tumor tissue_Luminal B

value: Luminal B

value: RNA from tumor tissue


title: T331_LA_Tumor tissue_Luminal A


title: T332_He_Tumor tissue_Her2-enriched


title: T325_He_Tumor tissue_Her2-enriched


title: T326_Ba_Tumor tissue_Luminal B


title: Toehold_OFF_state_bin_3

city: Boston

first: Alexander

last: Garruss

address: 77 Avenue Louis Pasteur, Rm 238

institute: Harvard Medical School

description: genomic/plamid DNA

data_processing:
Base-calling by Illumina Analysis Software 2.2.04 - RTA 2.4.11
Paired-end sequencing reads were quality filtered and merged with PEAR 0.9.1.
Only sequences matching intended designs were retained for further analysis, which excluded sequences with synthesis errors, truncation events, etc. The individual fluorescence distribution of the ON and OFF state for each switch was measured by calculating its frequency in each bin and assigning a normalized signal metric in the range of [0,1]. An ON/OFF metric was calculated as the difference between the ON and OFF signal metrics respectively. Frequencies of each variant were tabulated for each cell-sorted bin and normalized to the total reads per bin. Each variant’s functional value was computed as the weighted mean of its normalized frequencies across all bins, scaled between 0 and 1. The ON/OFF ratios were then calculated as the subtracted difference between ON and OFF (since the fluorescence data had been collected on a logarithmic scale), resulting in a range scaled between -1 and 1.
Genome_build: Reference designs (n=244,000) provided in the processed data file. Viral genomes were obtained on November 6th, 2018, from https://www.ncbi.nlm.nih.gov/genome/viruses/ Each retrieved genome was tiled 30bp at a time (the trigger length), with a stride of 5bp, spanning the respective genome. Human transcription factors were obtained using ENSEMBL 94 BioMart (4) utilizing the Gene Ontology term GO:0044212 (transcription regulatory region DNA binding). The coding region of each transcription factor was tiled 30bp at a time with a stride of 10. A remaining portion of the designs (~10,000) was based on random 30bp triggers.
Supplementary_files_format_and_content: Sequence design references; Raw read counts per design; Normalized read counts; processed ON and OFF values; Quality Control values. Comma-delimited values.

organism: synthetic construct

source_name: plasmid

growth_protocol: Cells were grown overnight at 37C in LB media with carbenicillin (carb) selection and then diluted 50x into fresh media. After the cells reached OD600 of 0.3 at 37C (~2 hours of growth), 0.2mM IPTG was added, and the cells were allowed to express for another 3 hours at 37C.

extract_protocol:
Cells in collected bins were diluted 10x into fresh LB media with carb selection and allowed to expand overnight at 30C. The expanded cells were then harvested using a MaxiPrep kit (Qiagen #12162).
Both ON and OFF inserts were ligated separately into the ColE1 backbone in front of the GFPmut3b-ASV gene using golden gate cloning, as follows. The linearized plasmid backbone was diluted to 500ng total mass. The ON or OFF insert was added according to a 1:1 molar ratio of insert to plasmid backbone. The inserts and backbone dilutions were prepared into 50uL ligation reaction volumes, containing 5uL NEB buffer 3.1 (#B7203S), 5uL T4 ligase buffer (NEB #B0202S), 1uL BsmBI (NEB #R0729), 0.5uL Dpn1 (NEB #R0176), 1uL T4 ligase (NEB #M0202T), and any remaining volume with nuclease-free water. The 50uL reaction was placed into a thermocycler for 100 cycles of two steps: 16C for 10 min and 37C for 10 min. A final enzyme inactivation step at 65C for 15min was done. The ligation products were precipitated out of their reaction buffers using ethanol precipitation. The 50uL ligation reactions were added to 1.5mL Eppendorf tubes containing 150uL of pure ethanol, 5uL 0.3M sodium acetate (pH 5.2), and 1uL GlycoBlue (Invitrogen #AM9515). Tubes were left on dry ice for 20 min and then immediately placed in a 4C tabletop centrifuge and spun at max RPM for 30 min. Tubes were decanted, and 175uL of 70% ethanol was added to the tube containing the pellet. Tubes were spun at max speed for 5 min. Tubes were then removed from the centrifuge, decanted, and allowed to dry for 15 min. Ligation products were then eluted in 4uL TE buffer. For initial library transformation, 50uL EclonI Supreme (Lucigen #60080) cells were given the full 4uL ligation product elution and electro-transformed.

treatment_protocol: The cells were then moved to room temperature and sorted on a Sony FACS machine (#SH800) using four bins.

value: BL21 Star DE3

tag: host

value: Escherichia coli


title: Toehold_OFF_state_bin_4

description: genomic/plamid DNA

tag: strain


title: T319_Ba_Tumor tissue_Basal-like

value: Basal-like


title: hiHepPC-1

description: 4 x 180 sample1

value: female

value: infected with FOXA3, HNF1A and HNF6

value: umbilical vein


title: RR057i_00167_L17_S268

growth_protocol: Clinical naso/pharyngeal swab specimens

value: M


title: Toehold_OFF_state_bin_2

description: genomic/plamid DNA


title: Control, Sample 14

description: control - no lung disease

value: no


title: Toehold_OFF_state_bin_1

description: genomic/plamid DNA


title: RR057e_00165_L07_S108

value: NEG

value: no virus


title: Toehold_ON_state_bin_4

description: genomic/plamid DNA


title: RR057i_00157_D15_S228


title: BPD, Sample 12

description: bronchopulmonary dysplasia


title: BPD, Sample 13

description: bronchopulmonary dysplasia


title: Toehold_ON_state_bin_3

description: genomic/plamid DNA


title: RR057e_00755_I10_S153


title: T318_Ba_Tumor tissue_Basal-like

value: Mexico hispanic


title: Control, Sample 11

description: control - no lung disease


title: RR057e_00399_C04_S51


title: Control, Sample 10

description: control - no lung disease


title: RR057e_00560_C06_S83


title: Toehold_ON_state_bin_2

description: genomic/plamid DNA


title: T321_He_Tumor tissue_Her2-enriched


title: 29005_HT3h-3

city: WuHan

first: Hongfang

last: Liu

address: Tuanjie Road

institute: OCRI

data_processing:
sequencing was conducted on Hiseq 2500 platform
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Darmor-bzh whole genome using hisat2
Clean reads of MS samples were de novo togeter by Trinity software with K-mer value of 31. And the unigenes were generated by the TGICL package to exclude redundant data.
FPKM (fragments per kilobase of exon per million) and TPM (transcripts per million) are used to measure gene or transcript expression levels
Genome_build: Darmor-bzh
Supplementary_files_format_and_content: tab-delimited text files include FPKM/TPM values for each Sample

organism: Brassica napus

source_name: Leaf tissue-heat treated_rep3

growth_protocol: Grown for 35 days in soil in a chamber set with temperature of 25 °C and humidity of 60% in 16 h light

extract_protocol:
The tissues were homogenized in liquid nitrogen. Then RNA was isolated using an RNA extraction kit (Takara, Dalian), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

tag: treatment

value: heat treated


title: T313_LA_Tumor tissue_Luminal A

value: Luminal A


title: T311_He_Tumor tissue_Her2-enriched


title: BPD, Sample 9

description: bronchopulmonary dysplasia

value: yes


title: T314_He_Tumor tissue_Her2-enriched


title: RR057e_00285_F11_S166

value: F


title: RR057e_00060_F03_S38

value: other virus


title: 29005_HT3h-1

source_name: Leaf tissue-heat treated_rep1


title: Control, Sample 7

description: control - no lung disease


title: RR057e_00254_J11_S170


title: BPD, Sample 8

description: bronchopulmonary dysplasia


title: 29005_D3d-3

source_name: Leaf tissue-drought treated_rep3

value: drought treated


title: RR057e_00726_J06_S90

value: POS


title: RR057e_00451_I10_S153


title: Control, Sample 6

description: control - no lung disease


title: BPD, Sample 4

description: bronchopulmonary dysplasia


title: BPD, Sample 5

description: bronchopulmonary dysplasia


title: Toehold_ON_state_bin_1

description: genomic/plamid DNA

value: BL21 Star DE3

value: Escherichia coli


title: 29005_HT3h-2

source_name: Leaf tissue-heat treated_rep2


title: BPD, Sample 3

description: bronchopulmonary dysplasia


title: RR057e_00764_F16_S246


title: 29005_D3d-2

source_name: Leaf tissue-drought treated_rep2


title: 29005_D3d-1

source_name: Leaf tissue-drought treated_rep1


title: T94_LB_Tumor tissue_Luminal B

source_name: Fresh frozen breast cancer tumor

value: Luminal B

value: RNA from tumor tissue


title: T307_LA_Tumor tissue_Luminal A


title: RR057i_00083_K09_S139


title: T85_He_Tumor tissue_Her2-enriched


title: T73_LB_Tumor tissue_Luminal B


title: T79_LB_Tumor tissue_Luminal B


title: Control, Sample 2

description: control - no lung disease

source_name: tracheal aspirate


title: T98_LA_Tumor tissue_Luminal A


title: T71_LA_Tumor tissue_Luminal A


title: T59_LA_Tumor tissue_Luminal A


title: RR057e_00505_K04_S59

value: M


title: T41_LA_Tumor tissue_Luminal A


title: 29005_CK-1

source_name: Leaf tissue-normal_rep1

value: non-treated


title: 29005_CK-2

source_name: Leaf tissue-normal_rep2


title: plank_rel-spot_3

city: Burnaby

first: Amy

middle: H.

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

description: planktonic culture

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq2500
fastq file quality control was performed using FastQC v0.11.6 and MultiQC v1.6
fastq files were aligned to the PAO1 genome using STAR v2.6
BAM files were sorted as part of read alignment with STAR
read count tables were generated using htseq-count v0.11.2
Genome_build: PAO1 (pseudomonas.com)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

organism: Pseudomonas aeruginosa PAO1

source_name: bacteria

extract_protocol:
RNA stabilized using RNAprotect Bacteria (Qiagen), extracted using Rneasy Mini Kit (Qiagen), DNAase treated using TURBO DNA-free kit (Thermo Fisher), rRNA depletion conducted with Ribozero Bacteria kit (Illumina - USA)
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)

tag: genotype

value: relA-spoT double mutant


title: plank_rel-spot_2

description: planktonic culture


title: plank_rel-spot_1

description: planktonic culture


title: RR057e_00751_C10_S147

state: CA

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion


title: RR057e_00520_I04_S57

value: NEG


title: BPD, Sample 1

description: bronchopulmonary dysplasia

value: no


title: RR057e_00753_G10_S151


title: 29005_CK-3

source_name: Leaf tissue-normal_rep3

value: leaf


title: plank_WT_3

description: planktonic culture

value: wild type


title: plank_WT_1

description: planktonic culture


title: RR057e_00080_H20_S312

value: no virus


title: RR057e_00287_L09_S140


title: plank_WT_2

description: planktonic culture


title: RR057e_00202_N05_S78