title: T12_PuHSFA4a-OE_Zn

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The RNA-seq reads were aligned to the Populus genome (version 3.0, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa) using TopHat (version 2.1.1) .
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: text file with abundance measurements

organism: Populus ussuriensis

source_name: 7-day-old PuHSFA4a-OE grow two weeks under excess Zn stress

growth_protocol: The in vitro plants of Populus ussuriensis were kept under16-h-light/8-h-dark cycles at 120 μmol m−2 s−1 irradiation at 25°C.

extract_protocol:
Roots were removed, flash frozen on dry ice, and RNA was harvested using CTAB method. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In vitro P. ussuriensis plants were grown on 1/2 MS plates with 0.6% w/v agar and 2% w/v sucrose for 1 week and then cultured in medium supplemented with 1.2 mM ZnSO4 for 2 week

value: Root

value: 21-day old plants


title: T10_PuHSFA4a-OE_Zn

status: Public on Aug 01 2019

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: genotype

tag: tissue

tag: age


title: T09_WT_Zn

source_name: 7-day-old WT grow two weeks under excess Zn stress

value: WT


title: Leaf_P5_Aux_3

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

data_processing:
Expression calling was performed using Salmon 0.8.2, by aligning to the tomato genome ITAG3.2. As the library is 3’ biased, we extended all genes to cover 500 additional base pairs downstream.
Expression data were normalized using Deseq2 and genes induced at False Discovery Rate (FDR )<0.01 were selected
Genome_build: Solanum lycopersicum ITAG3.2
Supplementary_files_format_and_content: Normalized expression reads for all samples

organism: Solanum lycopersicum

source_name: Leaf #5, P5 stage

growth_protocol: For the root response, tomato seedlings were germinated on ½ Murashige and Skoog plates in a growth chamber at 22C of continuous  light. For the shoot response, tomato plants were grown in a greenhouse for three weeks

extract_protocol:
For root tissues,  1cm root tips were cut and flash frozen in liquid nitrogen. For shoot, 15 young leaf primordia (Leaf number 5 at the P5 stage) were collected and flash frozen. RNA-extraction was performed using Qiagen RNAEasy Microkit
sequencing libraries prepared using Lexigen 3’ Quant-Seq kit, according to the manufacturer instructions.

treatment_protocol: For root response assay, 4 days after germination, seedlings were transferred to plates containing 1µM of the auxin analog 2,4-D (Sigma D7299) for 3h. For shoot samples, plants were sprayed with either mock or 1 µM of the auxin analog Picloram (Sigma P5575) for 3 hours

tag: line

value: Leaf #5, P5 stage

tag: treatment

value: Picloram 1 µM


title: Leaf_P5_Aux_2


title: T08_WT_Zn


title: 8c_5

type: RNA

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

country: USA

institute: University of Pennsylvania

description: Gene expression in 8c hepatocytes.

hyb_protocol: For each hybridization, 0.60 μg of Cy3 labeled cRNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Rat GE v2 8x60K Microarray (Design ID: 074036).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing:
Intensity values of each scanned feature were quantified using Agilent Feature Extraction software version 10.7.3.1, which performs background subtractions.
Normalization was performed using Agilent GeneSpring version 12.6.1 (per chip: normalization to 75 percentile shift; per gene: normalization to median of all samples).

organism: Rattus norvegicus

source_name: 8c hepatocytes

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA).

extract_protocol: RNA was extracted from sorted hepatocytes using the miRNeasy mini kit (QIAGEN).

tag: strain/background

value: Wistar

value: 6 weeks

tag: Sex

value: Female

tag: cell type

value: Hepatocytes

tag: ploidy


title: T06_PuHSFA4a-OE_control

source_name: 7-day-old PuHSFA4a-OE grow two weeks under control condition


title: Leaf_P5_Mock_2

value: mock


title: 2c Hepatocytes [Hep_2c_12]

data_processing:
Expression levels were normalized with Actb.
A -deltaCt value normazized to Actb is used as a gene expression level for each gene.

label: FAM

source_name: Percoll-treated and FACS-sorted 2c hepatocytes

label_protocol: Single cell capture, lysis and RT pre-amplification experiments were performed using C1 Auto Prep System (Fluidigm) according to the manufacturer's instructions. After lysis, reverse-transcription (25 °C for 10 min, 42 °C for 60 min, 85 °C for 5 min) and pre-amplification for 18 cycles (each cycle: 95 °C for 15 sec, 60 °C for 4 min), single-cell cDNA was harvested, transferred to a 96-well plate and diluted 6 times with cDNA dilution buffer. After lysis, reverse-transcription (25 °C for 10 min, 42 °C for 60 min, 85 °C for 5 min) and pre-amplification for 18 cycles (each cycle: 95 °C for 15 sec, 60 °C for 4 min), single-cell cDNA was harvested, transferred to a 96-well plate and diluted 6 times with cDNA dilution buffer.

extract_protocol: Adult hepatocytes were isolated from Wistar rats by two-step collagenase perfusion. NPCs were harvested from the undigested remnant tissue by further digestiong with collagenase-hyaluronidase.

tag: strain

value: 6 week old


title: 614489L

city: Indianapolis

first: Kok

middle: Lim

last: Kua

state: IN

address: RR208  PNEO  IN

department: PED-NEONATAL MEDICINE

institute: Indiana University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NextSeq 500.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featurecounts.txt (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.12.1).
Genome_build: UCSC rn6
Supplementary_files_format_and_content: Raw counts.txt and normalized abundance measurement from edgeR

source_name: Islets

growth_protocol: RPMI with 5mM glucose

extract_protocol:
RNA was isolated using Qiagen RNEasy Plus micro kit.
Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Islets were extracted from 2 fetal pancreata after 48 hours of 4mg/min glucose infusion and recovered 24hrs in culture media

value: Fetal (GD22)

value: High glucose infusion

value: Sprague Dawley


title: 8c_3

description: Gene expression in 8c hepatocytes.


title: Leaf_P5_Mock_3


title: 4c_4

description: Gene expression in 4c hepatocytes.

source_name: 4c hepatocytes

value: 5 weeks


title: T11_PuHSFA4a-OE_Zn


title: 2c_5

description: Gene expression in 2c hepatocytes.

source_name: 2c hepatocytes


title: 2c_3

description: Gene expression in 2c hepatocytes.


title: 4c_2

description: Gene expression in 4c hepatocytes.

value: 14 weeks


title: 8c_4

description: Gene expression in 8c hepatocytes.


title: 4c_5

description: Gene expression in 4c hepatocytes.


title: 4c_3

description: Gene expression in 4c hepatocytes.


title: 2c_4

description: Gene expression in 2c hepatocytes.


title: Leaf_P5_Mock_1


title: T04_PuHSFA4a-OE_control


title: RootTip_Aux_2

source_name: 1cm root tip

value: 1cm root tip


title: T05_PuHSFA4a-OE_control

value: Root


title: 8c_2

description: Gene expression in 8c hepatocytes.


title: adenine riboswitch minusDMS

city: Houston

first: Anthony

middle: M

last: Mustoe

state: TX

address: 1 Baylor Plaza

department: Biochemistry and Molecular Biology

institute: Baylor College of Medicine

description: Sequencing was done in a single batch and sequences were aligned to addcassette.fa

data_processing:
ShapeMapper (v2.1.4) was used to align and parse mutations from DMS-MaP sequencing data. The --amplicon option was used for amplicon datasets, which masks out primer regions and filters out spurious reads that do not align at the expected 5' and 3' primer sites. The --random-primer-len 9 option was used to mask RT primer sites in randomly primed datasets (16S and 23S rRNAs). The --output-parsed option was used to generate parsed mutation files.
PairMapper (v1.0) was used compute normalized DMS reactivity profiles and identify correlated nucleotides from ShapeMapper-generated parsed mutation files using default parameters.
Genome_build: Sequences used for alignments are noted in SAMPLE description field and are provided as supplementary files

organism: Vibrio vulnificus

source_name: in vitro transcript

extract_protocol:
Reverse-transcription was performed using specific primers, and DNA libraries were generated using a two-step PCR protocol.
Sample-specific modification and extraction details are provided in the SAMPLES section. All samples were DNase treated and purified using ethanol precipitation prior to reverse transcription.
Mutational profiling (MaP) reverse transcription (RT) was performed using an updated protocol that substantially improves yield and product length. In a 10 μL volume, RNA was mixed with 200 nM specific primer or 20 ng/μL random 9mer and 2 mM dNTPs and incubated at 65 °C for 10 min followed by 4 °C for 2 min. 9 uL 2.22x MaP buffer [1x MaP buffer consists of 6 mM MnCl2, 1 M betaine, 50 mM Tris (pH 8.0), 75 mM KCl, 10 mM DTT] was added and the combined solution incubated at 23 °C for 2 min. Finally, 1 μL SuperScript II Reverse Transcriptase (Invitrogen) was added and the RT reaction was performed according to the following temperature program: 25 °C for 10 min, 42 °C for 90 min, 10x[50 °C for 2 min,  42 °C for 2 min], 72 °C for 10 min. For the adenine riboswitch, ~1 pmol RNA was input into RT. For E. coli and human short RNAs, 0.5-2 μg total RNA was input into RT. For randomly primed E. coli RNA samples (16S and 23S rRNA), 1.5-3 μg total RNA was input into RT. RT products were then purified (Agencourt RNAclean XP beads, Beckman Coulter). Sequencing adaptors were added according to protocols listed in the SAMPLES section.

treatment_protocol: In vitro transcribed adenine riboswitch constructs were refolded for 30 minutes at 30 °C in 300 mM bicine (pH 8.0), 100 mM NaCl, 5 mM MgCl2, with 0 or 100 mM adenine ligand, followed by treatment with 10% ethanol (final vol/vol) for 10 minutes at 30 °C.

tag: probing condition

value: in vitro


title: Leaf_P5_Aux_1


title: T07_WT_Zn

value: WT

value: 21-day old plants


title: adenine riboswitch [100 adenine] plusDMS

treatment_protocol: In vitro transcribed adenine riboswitch constructs were refolded for 30 minutes at 30 °C in 300 mM bicine (pH 8.0), 100 mM NaCl, 5 mM MgCl2, with 0 or 100 mM adenine ligand, followed by modification with 170 mM DMS for 10 minutes at 30 °C.


title: RootTip_Mock_2


title: 2c_2

description: Gene expression in 2c hepatocytes.


title: 8c_1

description: Gene expression in 8c hepatocytes.

value: 12 weeks


title: adenine riboswitch [0 adenine] plusDMS


title: T01_WT_control

source_name: 7-day-old WT grow two weeks under control condition


title: RootTip_Mock_1


title: T03_WT_control


title: 4c_1

description: Gene expression in 4c hepatocytes.

value: Wistar


title: 2c_1

description: Gene expression in 2c hepatocytes.


title: RNA-Seq APOE4_DMSO_rep3

status: Public on Jul 31 2019

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

description: DMSO treatment

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC human reference genome assembly hg19 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). The GTF annotation files for UCSC hg19 was used for gene annotation.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM table format for individual RNA-Seq data

organism: Homo sapiens

source_name: iPSC-derived pericytes

growth_protocol: Pericytes were differentiated according to Patsch et al (2015, Nature Cell Biology).

extract_protocol:
Total RNA was isolated using Trizol and zymogen RNA-direct spin column treated with DNAse on column for 30 minutes prior to washing and elution. Extracted total RNA was subject to QC using an Advanced Analytical fragment Analyzer.
Illumina Neoprep stranded RNA-seq library preparation kit was used to construct library according to manufacture protocol.
Libraries were pooled for sequencing using Illumina HiSeq2000.

treatment_protocol: Pericytes were treated for two weeks with either DMSO (5%) or cyclosporine A (CsA, 2 uM)

tag: human ipsc-derived


title: RNA-Seq APOE4_CsA_rep3

description: Cyclosporin A (CsA) treatment


title: RNA-Seq APOE4_CsA_rep2

description: Cyclosporin A (CsA) treatment


title: RNA-Seq APOE4_rep3


title: RNA-Seq APOE3_DMSO_rep2

description: DMSO treatment


title: RNA-Seq APOE4_DMSO_rep2

description: DMSO treatment


title: RNA-Seq APOE4_CsA_rep1

description: Cyclosporin A (CsA) treatment


title: RNA-Seq APOE3_DMSO_rep3

description: DMSO treatment


title: RNA-Seq APOE4_rep1


title: RNA-Seq APOE3_rep3


title: RNA-Seq APOE4_DMSO_rep1

description: DMSO treatment


title: RNA-Seq APOE3_rep2


title: RNA-Seq APOE4_rep2


title: EAhy926

city: Cartagena

first: Ginés

last: Luengo-Gil

address: C/ Mezquita s/n. 1ª planta

department: Department of Pathology

country: Spain

institute: UCAM

description: Small RNA

data_processing:
FASTX-Toolkit for short-reads FASTA/FASTQ file preprocessing
Next-Generation Sequencing Analysis using HOMER
FASTQ/A Collapser
Genome_build: GenBank, RefSeq
Supplementary_files_format_and_content: Text file with all final processed sequences

source_name: EA.hy926 cells (ATCC)

growth_protocol: Dulbecco's Modified Eagle's Medium. Fetal bovine serum to a final concentration of 10%. 1% sodium Pyruvate, 1% MEM non-essential amino acids solution, 1% penicillin-streptomycin.

extract_protocol:
mirPremier™ microRNA Isolation Kit
RNA libraries were prepared for sequencing using standard Illumina protocols (LC-Sciences)

tag: cell line

value: EA.hy926 cells (ATCC)

value: Somatic cell hybrid

tag: passage

value: Wild type


title: T02_WT_control


title: RNA-Seq APOE3_DMSO_rep1

description: DMSO treatment


title: 2nd ODD

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

library_source: genomic

data_processing:
Library strategy: ChIRP-Seq
base calling were performed using RTA 1.18.61 and CASAVA 1.8.2
ChIRP-Seq reads were trimmed using Trimmomatic and and aligned to the arabidopsis genome using bowtie2.
Peaks were called using MACS2.
Genome_build: TAIR10
Supplementary_files_format_and_content: peaks.xls generated using MACS2 contains the peak information.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 2nd ODD

growth_protocol: long day (16 h light, 90 µE m-2 sec-1/8 h dark) at 23 °C on solid half-strength MS medium

extract_protocol:
ChIRP-Seq is prepared by Chromatin Isolation by APOLO-RNA Purification followed by DNA-Seq (APOLO ChIRP-Seq);
Three independent libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina, for ODD, EVEN and LacZ probes-derived samples

treatment_protocol: APOLO over expressing lines were obtained by transforming Col-0 plants using the full-length APOLO region under the control of the 35S promoter in the vector pB7WG2.

tag: ecotype


title: 1st LACZ

source_name: 1st LACZ


title: 1st EVEN

source_name: 1st EVEN


title: 1st ODD

source_name: 1st ODD


title: Intrahepatic biliary organoids, IDH1-MT, biological rep2

city: Tokyo

first: Hiroaki

last: Fujiwara

address: 2-2-6, Bakurocho

department: Gastroenterology

country: Japan

institute: The Institute of Adult Disease, Asahi Life Foundation

description: Gene expression data from mouse intrahepatic biliary organoids expressing mutant IDH1

hyb_protocol: 3.5 ug of  fragmented and labeled cDNA were hybridized for 16 hr at 45C on Mouse Gene 2.0 ST Array (Affymetrix, Inc., cat.# 902118). GeneChips were washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were normalized using the RMA method.

label: biotin

organism: Mus musculus

source_name: Organoids expressing mutant IDH1

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip WT PLUS Reagent Kit User Manual PN703174, Affymetrix).

extract_protocol: The extraction of total RNA by RNeasy Mini Kit (Qiagen) was performed according to the manufacturer's instructions.

value: intrahepatic bile duct

tag: gender

value: Male

value: 8 weeks

tag: sample type

value: intrahepatic biliary organoids generated from normal liver

value: expressing mutant IDH1


title: Slide 344251

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Avarage ratio of inter slide replicates

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genpix software. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of WT  over mutant strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F635 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown to OD600 of 0.3 in GM17 medium

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006; Shafeeq et al., 2011). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: genotype

value: Wild Type

source_name: F532 Mean

value: plcR Mutant


title: Slide 344250

description: Avarage ratio of inter slide replicates


title: RNA-Seq APOE3_rep1


title: CP58T  tumor unmatched_miRNA

city: Botucatu

first: Rainer Marco

middle: Lopez

last: Lapa

state: SP

address: Av. Prof. Mário Rubens Guimarães Montenegro, s/n, s/n

department: Neogene

country: Brazil

institute: UNESP

description:
CP58T US83203532_253118112984_S01_miRNA_1100_
target sample Cy3-labeled

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were capture in Microarray Scanner System (Agilent), with Scan Control Software 8.1 (Agilent). Images were quantified using Agilent Feature Extraction Software (version v.10.1.1.1).

data_processing: Numeric data was generated and normalized by intensity-dependent global normalization (LOWESS) with Feature Extraction v10.1 software (Agilent)

source_name: laryngeal carcinoma labeled with Cyanine-3 (green)

label_protocol: Tumor and reference samples (300ng) were differentially labeled using Low Input Quick Amp Labeling (Agilent) (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: Total RNA from 32 LSCC and 5 normal pool laryngeal tissue from total laryngectomy was isolated by the standard Rneasy or Trizol-based method.

tag: tissue

value: squamous cell carcinoma

value: male

tag: histological variant

value: transglottic


title: 16406T  tumor unmatched_miRNA

description:
16406T US83203532_253118112984_S01_miRNA_1100_
target sample Cy3-labeled

value: female

tag: age

value: glottic


title: 15983T  tumor unmatched_miRNA

description:
15983T US83203532_253118112988_S01_miRNA_1100_
target sample Cy3-labeled

value: supraglottic


title: CP56T  tumor unmatched_miRNA

description:
CP56T US83203532_253118112989_S01_miRNA_1100_
target sample Cy3-labeled


title: CP55T  tumor unmatched_miRNA

description:
CP55T US83203532_253118112982_S01_miRNA_1100_
target sample Cy3-labeled


title: 15954T  tumor unmatched_miRNA

description:
15954T US83203532_253118112984_S01_miRNA_1100_
target sample Cy3-labeled


title: 15976T  tumor unmatched_miRNA

description:
15976T US83203532_253118112989_S01_miRNA_1100_
target sample Cy3-labeled


title: 15967T  tumor unmatched_miRNA

description:
15967T US83203532_253118112982_S01_miRNA_1100_
target sample Cy3-labeled


title: 4530T  tumor unmatched_miRNA

description:
4530T US83203532_253118112983_S01_miRNA_1100_
target sample Cy3-labeled


title: 4599T  tumor unmatched_miRNA

description:
4599T US83203532_253118112984_S01_miRNA_1100_
target sample Cy3-labeled


title: Intrahepatic biliary organoids, IDH1-MT, biological rep1


title: Intrahepatic biliary organoids, IDH1-WT, biological rep2

description: Gene expression data from mouse intrahepatic biliary organoids expressing wild-type IDH1

source_name: Organoids expressing wild-type IDH1

value: expressing wild-type IDH1


title: 4576T  tumor unmatched_miRNA

description:
4576T US83203532_253118112984_S01_miRNA_1100_
target sample Cy3-labeled


title: 4598T  tumor unmatched_miRNA

description:
4598T US83203532_253118112984_S01_miRNA_1100_
target sample Cy3-labeled


title: 4479T  tumor unmatched_miRNA

description:
4479T US83203532_253118112982_S01_miRNA_1100_
target sample Cy3-labeled


title: Intrahepatic biliary organoids, IDH1-WT, biological rep1


title: 4371T  tumor unmatched_miRNA

description:
4371T US83203532_253118112989_S01_miRNA_1100_
target sample Cy3-labeled


title: 4471T  tumor unmatched_miRNA

description:
4471T US83203532_253118112982_S01_miRNA_1100_
target sample Cy3-labeled


title: 4321T  tumor unmatched_miRNA

description:
4321T US83203532_253118112996_S01_miRNA_1100_
target sample Cy3-labeled


title: 4492T  tumor unmatched_miRNA

description:
4492T US83203532_253118112989_S01_miRNA_1100_
target sample Cy3-labeled


title: 4597T  tumor unmatched_miRNA

description:
4597T US83203532_253118112988_S01_miRNA_1100_
target sample Cy3-labeled


title: 4239T  tumor unmatched_miRNA

description:
4239T US83203532_253118112996_S01_miRNA_1100_
target sample Cy3-labeled


title: 4267T  tumor unmatched_miRNA

description:
4267T US83203532_253118112988_S01_miRNA_1100_
target sample Cy3-labeled


title: 4473T  tumor unmatched_miRNA

description:
4473T US83203532_253118112982_S01_miRNA_1100_
target sample Cy3-labeled


title: 3644T  tumor unmatched_miRNA

description:
3644T US83203532_253118112989_S01_miRNA_1100_
target sample Cy3-labeled


title: 3626T  tumor unmatched _miRNA

description:
3626T US83203532_253118112983_S01_miRNA_1100_
target sample Cy3-labeled


title: 4137T  tumor unmatched_miRNA

description:
4137T US83203532_253118112982_S01_miRNA_1100_
target sample Cy3-labeled


title: 3667T  tumor unmatched_miRNA

description:
3667T US83203532_253118112983_S01_miRNA_1100_
target sample Cy3-labeled


title: 4290T  tumor unmatched_miRNA

description:
4290T US83203532_253118112989_S01_miRNA_1100_
target sample Cy3-labeled


title: 4265T  tumor unmatched_miRNA

description:
4265T US83203532_253118112988_S01_miRNA_1100_
target sample Cy3-labeled


title: 4254T  tumor unmatched_miRNA

description:
4254T US83203532_253118112988_S01_miRNA_1100_
target sample Cy3-labeled


title: 4534T  tumor unmatched_miRNA

description:
4534T US83203532_253118112983_S01_miRNA_1100_
target sample Cy3-labeled


title: 3627T  tumor unmatched _miRNA

description:
3627T US83203532_253118112989_S01_miRNA_1100_
target sample Cy3-labeled


title: 4484T  tumor unmatched_miRNA

description:
4484T US83203532_253118112983_S01_miRNA_1100_
target sample Cy3-labeled


title: 1402N non-tumor unmatched _miRNA

description:
1402N US83203532_253118112996_S01_miRNA_1100_
target sample Cy3-labeled

source_name: Normal laryngeal tissue labeled with Cyanine-3 (green)

value: Normal laryngeal tissue

value: unknown


title: 1400N non-tumor unmatched _miRNA

description:
1400N US83203532_253118112996_S01_miRNA_1100_
target sample Cy3-labeled


title: 1399N non-tumor unmatched _miRNA

description:
1399N US83203532_253118112996_S01_miRNA_1100_
target sample Cy3-labeled


title: 4429T  tumor unmatched_miRNA

description:
4429T US83203532_253118112982_S01_miRNA_1100_
target sample Cy3-labeled


title: 1398N non-tumor unmatched_miRNA

description:
1398N US83203532_253118112982_S01_miRNA_1100_
target sample Cy3-labeled


title: 1401N non-tumor unmatched _miRNA

description:
1401N US83203532_253118112996_S01_miRNA_1100_
target sample Cy3-labeled


title: LRRC31 overexpression  cells Replicate 3

city: New Haven

first: Yong

last: Zhu

state: CT

address: 60 College Street

institute: Yal University

description: Biological replicate 1 of 3. Stable LRRC31-expression 231-Br cells.

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to Affymetrix GeneChip arrays.

scan_protocol: After hybridization, slides were washed and scanned by GeneChip Scanner 3000.

data_processing: The Expression Console software also acquires and converts hybridization intensity data into a presence/absence call for each gene using appropriate algorithms.

source_name: LRRC31 overexpression  cells

label_protocol: 10 µg of total RNA was primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (HyClone, Logan, UT, USA) with 10% fetal bovine serum (Biological Industries, Beit Haemek, Israel ) and 1% penicillin and streptomycin, and were maintained at 37°C and 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Standard cloning techniques were used to insert LRRC31 genes from plasmid pCR4-TOPO (GE DharmaconI,Catalog Number: MHS6278-213244531 ) into the multiple cloning site with EcoR I and BamH1 restriction enzymes of pCDH-CMV-MCS-T2A-Puro lentiviral vector. Artificial lentiviruses were generated in HEK293 cells through transfection with  pCDH-CMV-MCS-T2A-Puro contaning LRRC31  gene together with pMD2.G (Addgene #12259) and psPAX2 (Addgene #12260) according to the standard protocol.  Lentivirus supernatant was concentrated by sediment centrifugation using a SW29 rotor at 50,000 x g for two hours. Concentrated viruses were added to 231-BR cells at a multiplicity of infection (MOI) of 10.Stable cell lines were selected and maintained in puromycin 1mg/l.

value: MDA-MB  231-Br  with LRRC31 overexpression

value: human breast cancer


title: Control  cells Replicate 3

description: Biological replicate 1 of 3. Control  cells.

source_name: Control  cells

treatment_protocol: Control 231-Br  cells with lentiviral vector transduction.  Briefly, pCDH-CMV-MCS-T2A-Puro lentivirus vector plasmid was co-transfected into 293T cells with pMD2.G (Addgene #12259) and psPAX2 (Addgene #12260) according to the standard protocol.  Lentivirus supernatant was concentrated by sediment centrifugation using a SW29 rotor at 50,000 x g for two hours. Concentrated viruses were added ton 231-BR cells at a multiplicity of infection (MOI) of 10.Stable cell lines were selected and maintained in puromycin 1mg/l.

value: MDA-MB  231-Br (human breast cancer)


title: LRRC31 overexpression  cells Replicate 2


title: Control  cells Replicate 1

value: MDA-MB 231-Br  (human breast cancer)


title: Control  cells Replicate 2


title: LRRC31 overexpression cells Replicate 1


title: Output 2 High expression Rep1

city: Barcelona

first: Xianghua

state: Barcelona

address: carrer Dr. Aiguader 88, PRBB building

institute: Centre for Genomic Regulation

description:
PCR amplicon
from plasmid library

data_processing:
Library strategy: Deep mutational scanning
1. Pair end reads were demultiplexed with Sabre  (v 1.000, with parameter -m 2 -pe)
2. Merging reads were performed with PEAR software ( v 0.9.6, with parameters : -m 214 -v 20 -n 214 -j 4 for samples 1-6,10-18; for the sample 7-9,  with the parameter -m  230 -v 4 -n 230 -j 4).
3. fastx_reverse_complement tool from FASTX-Toolkit (v0.0.13) is used to complement the sequences whenever necessary.
4. The primer sequences were trimmed using the seqtk tool (https://github.com/lh3/seqtk,  with parameters -b 19 e-18 for samples 1-6,10-19; and -b 30 e- 30).
5.The number of occurrences of each variant was counted with fastx_collapser from FASTX Toolkit (v 0.0.13) and custom python script.
Supplementary_files_format_and_content: Text file with all merged read count for each variant in each sample

organism: synthetic construct

source_name: Deep mutational scanning

growth_protocol: E.coli BW27783 MK01 strain (Kogenaru and Tans, BMC 2014) bacteria were grown in LB media (containing ampicilin) with arabinose and glucose to induce protein expression at 37ºC for 4 hours in total. Cells before sorting and after sorting were centrifuged and the pellets were stored at -20ºC until DNA extraction

extract_protocol:
All the cell pellets  were first thawed on ice, and plasmid preparation was performed using the QIAGEN miniprep kit on column.
The mutagenized region was amplified using barcoded PCR primers (in order to multiplex, PCR primers carried 8nt barcodes at the 5 prime to identify each sample) for 25 cycles using hot start Phusion polymerase in 50μl reactions, following the manufacturers’ instruction. PCR products were purified using the E-gel 2% size-select system. (Invitrogen) to remove smaller fragments. Samples were mixed equimolarly and and stored at -20 degrees, and sent to EMBL Genecore on dry ice, where PCR-free sequencing library was prepared and sequenced.

tag: mutant protein expression level

value: high


title: Output 1 High expression Rep3

description:
PCR amplicon
from plasmid library


title: Output 2 High expression Rep3

description:
PCR amplicon
from plasmid library


title: Output 2 High expression Rep2

description:
PCR amplicon
from plasmid library


title: Input High expression Rep2

description:
PCR amplicon
from plasmid library


title: OVCAR3 control cells biological replicate 2

city: Mexico City

first: Ernesto

last: Soto-Reyes

state: Mexico City

address: Av. Vasco de Quiroga

department: Departamento de Ciencias Naturales

country: Mexico

institute: Universidad Autónoma Metropolitana

hyb_protocol: Hybridization staining and washing was performed in the GeneChip fluidics station 450 (Affymetrix)

scan_protocol: For scanning, an Affymetrix Scanner Model 3000 G7 and Affymetrix Command Console Software 1.1 were used

data_processing: Data normalization was performed with Robust Multiarray Analysis (RMA) from affy package (Bioconductor). Differentially Expressed Genes (DEG) were selected with “Limma” package (Bioconductor)

source_name: OVCAR3 cell line, total RNA

label_protocol: The cDNA was fragmented and end-labeled with biotinylated dideoxynucleotide according to protocol provided by manufacturer using

growth_protocol: The cancer cell line OVCAR3 was obtained from ATCC (Manassas, Virginia, United States) and subcultured as described by the supplier: RPMI-1640 Medium, 0.01 mg/ml bovine insulin and fetal bovine serum to a final concentration of 20%.

extract_protocol: Total RNA was extracted with TRIzol Reagent (Cat. 15596026, Invitrogen, Carlsbad, California, United States) and Direct-zol RNA Miniprep (Cat. R2050, Zymo Research, Irvine, California, United States), the integrity and quality was analyzed with TapeStation 2200 (Agilent Technologies, Irvine, California, United States).

treatment_protocol: To Knockdown (KD) expression of BORIS, OVCAR3 cells were transfected with a pool of small interfering RNAs (siRNAs) (Cat. A-003819-100-0005, Dharmacon, Lafayette, Colorado, United States) and were incubated for 48 h in Accell Delivery Media (Cat. B-005000, Dharmacon) before total RNA extraction.  The assays were performed by triplicate. Knockout (KO) of BORIS expression was performed by transfection of OVCAR3 cells with 2 µg of BORIS CRISPR/Cas9 (Cat. sc-403313, SCBT, Dallas, Texas, United States) plasmid. Total RNA extraction was performed 24 h post-transfection. The assays were performed by triplicate.

tag: treatment

value: Control


title: OVCAR3 cell line following BORIS Knockout biological replicate 3

source_name: OVCAR3 cell line, total RNA, BORIS knockout, biological replicate 3

value: BORIS knockout


title: OVCAR3 control cells biological replicate 1


title: OVCAR3 cell line following BORIS Knockout biological replicate 2

source_name: OVCAR3 cell line, total RNA, BORIS knockout, biological replicate 2


title: OVCAR3 cell line following BORIS Knockdown biological replicate 3

source_name: OVCAR3 cell line, total RNA, BORIS knockdown, biological replicate 3

value: BORIS knockdown


title: Output 1 High expression Rep2

description:
PCR amplicon
from plasmid library


title: OVCAR3 cell line following BORIS Knockdown biological replicate 1

source_name: OVCAR3 cell line, total RNA, BORIS knockdown, biological replicate 1


title: Output 1 Low expression Rep2

description:
PCR amplicon
from plasmid library

value: low


title: OVCAR3 cell line following BORIS Knockout biological replicate 1

source_name: OVCAR3 cell line, total RNA, BORIS knockout, biological replicate 1


title: RootTip_Aux_1

source_name: 1cm root tip

tag: line

value: 1cm root tip


title: Output 1 High expression Rep1

description:
PCR amplicon
from plasmid library


title: Input High expression Rep3

description:
PCR amplicon
from plasmid library


title: Input High expression Rep1

description:
PCR amplicon
from plasmid library


title: Output 2 Low expression Rep3

description:
PCR amplicon
from plasmid library


title: Output 2 Low expression Rep2

description:
PCR amplicon
from plasmid library


title: Input Low expression Rep2

description:
PCR amplicon
from plasmid library


title: Input Low expression Rep1

description:
PCR amplicon
from plasmid library


title: Output 2 Low expression Rep1

description:
PCR amplicon
from plasmid library


title: Output 1 Low expression Rep1

description:
PCR amplicon
from plasmid library


title: Output 1 Low expression Rep3

description:
PCR amplicon
from plasmid library


title: Input Low expression Rep3

description:
PCR amplicon
from plasmid library


title: H3K27ac ChIPseq 3M WT

city: New York

first: Taiyi

middle: Diana

last: Kuo

state: NY

address: 1150 St Nicholas Ave., Ste. 237

department: Medicine

institute: Columbia University

data_processing:
Reads were aligned to mouse genome mm10 using the Burrows-Wheeler Aligner (BWA) algorithm with default settings
These reads passed Illumina’s purity filter, and aligned with no more than 2 mismatches. Duplicate reads were removed, and only uniquely mapped reads with mapping quality greater or equal to 25 were subjected for further analysis.
Reads were extended to 200bp at their 3’ ends, and bigwig files were created for visualization using Active Motif software (Active Motif Inc., CA).
H3K27ac peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of p value = 1×10-7.
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: FAC-sorted beta cells

growth_protocol: Mice were fed a standard chow diet, and maintained on a 12h light cycle (lights on at 7am).

extract_protocol:
We purified the pancreatic islets (Kuo et al, JBC 2016), applied leptomycin B treatment, and performed FoxO1-Venus ChIPseq using antibody against GFP, purchased from abcam (ab290). For H3K27ac ChIP, we FAC-sorted the beta cells, genetically labeled with RIP-Cre and ROSA26-tomato alleles, from db/db mice and littermate controls. H3K27ac antibody was purchased from Active Motif (39133).
ChIP DNA libraries were prepared from ChIP DNA with the following steps: end-repair, dA-addition, adaptor ligation and PCR amplification.
The resulting ChIPseq DNA libraries were quantified with Bioanalyzer (Agilent), and sequenced on Illumina NextSeq 500 with 75-nt reads and single-end.

treatment_protocol: We generated knock-in FoxO1-Venus mouse, in which the Venus was fused to the C-terminus of endogenous FoxO1. Leptin receptor-deficient db/db mice were purchased from the Jackson Laboratories.

tag: strain background

value: mixed 129J-C57BL/6

tag: genotype/variation

value: wild type

tag: Sex

value: male

tag: cell type

value: FAC-sorted beta cells

tag: chip antibody

value: H3K27ac antibody, Active Motif (39133)


title: OVCAR3 cell line following BORIS Knockdown biological replicate 2

source_name: OVCAR3 cell line, total RNA, BORIS knockdown, biological replicate 2

tag: cell line


title: FoxO1 ChIPseq 3M WT

source_name: pancreatic islets

value: pancreatic islets

value: anti-GFP, abcam (ab290)


title: H3K27ac ChIPseq 3M db/db

value: FoxO1-Venus knock-in


title: eat-2; acs-22-3

city: Nanjing

first: Lina

last: Zou

state: Jiangsu

address: 12 Xue-Fu Road, Pukou District , Nanjing, Jiangsu

department: Model Animal Research Center

institute: Nanjing University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
Reads were aligned to the C.elegans genome (version Wbcel235) using TopHat2 with parameters -r 30 -G  -p 8  --microexon-search --library-type fr-unstranded.
Raw counts of sequencing reads were generated by using the python script HTSeq.
Differential expression and dataset normalization were performed using the Bioconductor package DESeq2.
Genome_build: Wbcel235
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans animals were growing at 20°C until the late L4 stage before collection.

extract_protocol:
Total RNAs were extracted using the RNA MiniPrep (ZYMO RESEARCH#R2052) kit. The concentration and quality of total RNA samples were assessed using a Nanodrop and Agilent’s Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: eat-2; pmk-1; acs-22-3


title: eat-2; acs-22-1


title: eat-2-3


title: eat-2; pmk-1; acs-22-2


title: eat-2; acs-22-2


title: eat-2-1


title: hnRNPC_XLIP_U1AMO

first: Gideon

last: Dreyfuss

address: 415 curie blvd

description: Immunoprecipitated RNAs with hnRNPC antibody from U1 AMO transfected and formaldehye crosslinked cells

data_processing:
Paired-end RNA-seq reads were trimmed of any adaptor sequences with the FASTX- Toolkit (version 0.0.14). The two paired reads were merged into one single fragment using PEAR (version 0.9.8), and then fragments larger than 150nt were filtered out.
The remaining reads were aligned to the GRCh38/hg38 reference genome using STAR (version 2.5.3a) with the following parameters: --twopassMode Basic -- alignSJoverhangMin 5 --alignSJDBoverhangMin 5 --outSAMmapqUnique 255 -- outFilterMultimapNmax 1 --outSJfilterReads Unique.
Reads per exon were grouped, from which RPKM (reads per kilobase per million mapped reads) values were calculated using SAMtools (version 0.1.19).
In order to directly compare samples that have a different number of mapped reads, the read coverage for each sample was normalized to the total number of mapped reads per million (RPM). This normalized value was also used to scale the samples for visualization on the UCSC Genome Browser (http://genome.ucsc.edu/).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format with normalized read counts in RPMs

source_name: Hela cell

growth_protocol: HeLa PV cells were grown in DMEM media supplemented with 10% FBS, L-glutamine, penicillin and streptomycin.

extract_protocol:
RNA-seq: 4SU-labeled RNAs were purified by thiol-affinity selection, and EU-labeled RNAs were purified by click-chemistry and affinity purification.
XLIP-seq: XLIPed RNAs were eluted and reversed by heat, followed by standard RNA purifications.
cDNA synthesis and RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Antisense morpholino oligonucleotide (AMOs) were transfected into HeLa cells by electroporation and grown for 6–8 hr. Transfection of control siRNA or siRNAs targeting CFIm subunits into HeLa cells was performed for 48 hrs. Nascent transcripts were metabolically labeled with 5’-ethynyl uridine (EU) for 5 mins at 8 hr post AMO transfection or with 4-thiouridine (4SU) for 30 mins at 47.5–48 hr post siRNA transfection.

value: Hela cell

tag: molecule type

value: Immunoprecipitated RNAs


title: hnRNPC_XLIP_cAMO

description: Immunoprecipitated RNAs with hnRNPC antibody from cAMO transfected and formaldehye crosslinked cells

value: cAMO


title: Bio-cAMO_XLPD

description: Streptavidin beads captured RNAs from biotinylated cAMO transfected cells


title: Bio-cAMO_Input

description: Total RNAs from biotinylated cAMO tranfected cells

value: Total RNAs from biotinylated cAMO


title: Bio-U1AMO_Input

description: Total RNAs from biotinylated U1 AMO transfected cells

value: Total RNAs from biotinylated U1 AMO


title: Fip1_XLIP_cAMO

description: Immunoprecipitated RNAs with Fip1 antibody from cAMO transfected and formaldehye crosslinked cells


title: CstF64_XLIP_cAMO

description: Immunoprecipitated RNAs with CstF64 antibody from cAMO transfected and formaldehye crosslinked cells


title: Bio-U1AMO_XLPD

description: Streptavidin beads captured RNAs from biotinylated U1 AMO transfected cells


title: CstF64_XLIP_U1AMO

description: Immunoprecipitated RNAs with CstF64 antibody from U1 AMO transfected and formaldehye crosslinked cells


title: CFIm25_XLIP_U1AMO

description: Immunoprecipitated RNAs with CFIm25 antibody from U1 AMO transfected and formaldehye crosslinked cells


title: Fip1_XLIP_U1AMO

description: Immunoprecipitated RNAs with Fip1 antibody from U1 AMO transfected and formaldehye crosslinked cells


title: SF3B1_XLIP_U1AMO

description: Immunoprecipitated RNAs with SF3B1 antibody from U1 AMO transfected and formaldehye crosslinked cells


title: U1C_XLIP_cAMO

description: Immunoprecipitated RNAs with U1C antibody from cAMO transfected and formaldehye crosslinked cells


title: U1A_XLIP_cAMO

description: Immunoprecipitated RNAs with U1A antibody from cAMO transfected and formaldehye crosslinked cells


title: eat-2; pmk-1; acs-22-1


title: SF3B1_XLIP_cAMO

description: Immunoprecipitated RNAs with SF3B1 antibody from cAMO transfected and formaldehye crosslinked cells


title: ctrl_siRNA_U1AMO_labeled

description: 4SU-labeled RNAs from control siRNA and U1 AMO transfected cells

tag: knockdown

value: control siRNA

value: 4SU-labeled nascent RNA


title: siCPSF5_cAMO_labeled

description: 4SU-labeled RNAs from CPSF5 siRNA and cAMO transfected cells

value: siRNA to CPSF5


title: siCPSF6_cAMO_labeled

description: 4SU-labeled RNAs from CPSF6 siRNA and cAMO transfected cells

value: siRNA to CPSF6


title: ctrl_siRNA_cAMO_labeled

description: 4SU-labeled RNAs from control siRNA and cAMO transfected cells


title: EU-labeled_polyA_U1AMO

description: EU-labeled and polyA selected RNAs from U1 AMO transected cells

value: EU labeled nascent RNA


title: EU-labeled_polyA_cAMO

description: EU-labeled and polyA selected RNAs from cAMO transected cells


title: eat-2-2


title: T47D.2

city: Spokane

first: Bin

last: Shan

state: Washington

address: 412 E Spokane Falls Blvd

department: Biomedical Sciences

institute: Washington State University

data_processing:
FASTQ files were trimmed using autoadapt
rsem-calculate-expression --star --star-gzipped-read-file --output-genome-bam -p 12 --paired-end
Genome_build: hg19
Supplementary_files_format_and_content: tab separated value expected_count  TPM     FPKM

source_name: Breast Cancer Cell Line

growth_protocol: A549, H23, MDA-MB-231, MCF-7-TNR, T47D cells were culture in 2D culture in DMEM+10% FBS .

extract_protocol:
Total cell RNA was extracted when cells were ~80% confluent in culture using TRIZOL.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit/Ribo-Zero Gold kit.

treatment_protocol: No treatment.

tag: disease

value: Breast Cancer


title: T47D.1


title: MCF-7-TNR.2


title: MCF-7-TNR.1


title: MCF-7-TNR.3


title: T47D.3


title: CFIm25_XLIP_cAMO

description: Immunoprecipitated RNAs with CFIm25 antibody from cAMO transfected and formaldehye crosslinked cells


title: MB231.2


title: H23.3

source_name: Lung Cancer Cell Line

value: Lung Cancer


title: A549.3


title: A549.1


title: A549.2


title: H23.1


title: H23.2


title: MB231.3


title: HLO 2

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

institute: Tokyo Medical and Dental University

data_processing:
The RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using TopHat (version 2.0.13).
The alignment data from TopHat were fed to an assembler, Cufflinks (version 2.2.1), to assemble aligned RNA-Seq reads into transcripts.
Annotated transcripts were obtained from the UCSC genome browser (http://genome.ucsc.edu) and the Ensemble database.
Transcript abundances were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Fragments Per Kilobase of exon per Million fragments mapped (FPKM)

source_name: Human liver organoids

growth_protocol: iPSCs were differentiated into definitive endoderm. At day1, medium was changed to RPMI 1640 medium containing 100 ng/mL Activin A and 50 ng/mL bone morphogenetic protein 4, 100 ng/mL Activin A and 0.2% fetal calf serum at day 2, and 100 ng/mL Activin A and 2% FCS at day 3. On Day4-6, cells were cultured in Advanced DMEM/F12 with B27 and N2 containing 500 ng/ml fibroblast growth factor and 3 µM CHIR99021. Cells were maintained at 37 °C in 5% CO2 with 95% air and the medium was replaced every day. At day 6, spheroids and attached cells were gently pipetted to be delaminated from dishes. They were centrifuged at 800 rpm for 3 minutes, embedded in a 100% Matrigel drop on the dishes in Advanced DMEM/F12 with B27, N2 and 2 µM retinoic acid, and cultured for 4 days. After RA treatment, the media was switched to Hepatocyte Culture Medium with 10 ng/mL hepatocyte growth factor, 0.1 µM Dexamethasone and 20 ng/mL Oncostatin M. Cultures for HLO induction were maintained at 37 °C in 5% CO2 with 95% air and the medium was replaced every 3 days.

extract_protocol:
RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany).
Total RNA (500 ng) was converted to cDNA using the ABI System according to the manufacturer's protocol (High-Capacity cDNA Reverse Transcrition Kit). The cDNA was then used for Illumina sequencing library preparation by TruSeq Stranded mRNA and Total RNA Library Prep Kit.

value: iPSC derived human liver organoids

tag: cultured day


title: HLO 3


title: HLO 1


title: Human liver organoids

description: single-cell RNA-Seq

data_processing:
Sequenced reads were processed using the Cell Ranger gene expression pipelines mkfastq and count, starting with demultiplexing and conversion of barcode and read data to fastq files.
Raw reads were aligned to the Hg19 genome and filtered, creating gene-barcode matrices.
Analyses were performed in AltAnalyze, where gene and cell clusters were identified unsupervised analysis to identify predominant sample groups via expression clustering. Following removal of outliers, clusters were restricted to having > 5 cells, a minimum Pearson correlation of 0.5, and a between-cluster fold change > 4. Cell cycle effects were removed.
Genome_build: GRCh37/hg19

extract_protocol: 17,500 cells were underwent the single cell RNA-seq library preps and sequenced with 10X Genomics Chromium platform.


title: pFG

source_name: Posterior foregut

value: iPSC derived posterior foregut


title: MB231.1


title: 15983T  tumor unmatched

description:
15983TUS83203532_252800412968_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled

source_name: laryngeal carcinoma labeled with Cyanine-3 (green)

extract_protocol: Total RNA from 35 LSCC and 5 normal pool laryngeal tissue from total laryngectomy was isolated by the standard Rneasy or Trizol-based method.

tag: tissue

value: squamous cell carcinoma

tag: gender

value: male

value: supraglottic

source_name: pool of 5 adjacent normal laryngeal tissue labeled with Cyanine-5 (red)

tag: sample type

value: reference

value: normal laryngeal tissue


title: 4597T  tumor unmatched

description:
4597TUS83203532_252800412968_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: female

tag: age

tag: histological variant

value: transglottic


title: 4599T  tumor unmatched

description:
4599TUS83203532_252800412983_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4598T  tumor unmatched

description:
4598TUS83203532_252800412983_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: CP56T  tumor unmatched

description:
CP56TUS83203532_252800412983_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 15954T  tumor unmatched

description:
15954TUS83203532_252800412983_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 15597T  tumor unmatched

description:
15597TUS83203532_252800412968_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4492T  tumor unmatched

description:
4492TUS83203532_252800412968_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4534T  tumor unmatched

description:
4534TUS83203532_252800412982_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 15976T  tumor unmatched

description:
15976TUS83203532_252800412968_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 16406T  tumor unmatched

description:
16406TUS83203532_252800412968_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: glottic


title: 15967T  tumor unmatched

description:
15967TUS83203532_252800412968_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: CP58T  tumor unmatched

description:
CP58TUS83203532_252800412968_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4576T  tumor unmatched

description:
4576TUS83203532_252800412982_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: CP55T  tumor unmatched

description:
CP55TUS83203532_252800412983_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4371T  tumor unmatched

description:
4371TUS83203532_252800412967_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4290T  tumor unmatched

description:
4290TUS83203532_252800412981_S01_GE2_107
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4321T  tumor unmatched

description:
4321TUS83203532_252800412982_S01_GE2_107
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4471T  tumor unmatched

description:
4471TUS83203532_252800412967_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4239T  tumor unmatched

description:
4239TUS83203532_252800412981_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4479T  tumor unmatched

description:
4479TUS83203532_252800412967_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4484T  tumor unmatched

description:
4484TUS83203532_252800412967_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4473T  tumor unmatched

description:
4473TUS83203532_252800412967_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4265T  tumor unmatched

description:
4265TUS83203532_252800412966_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4530T  tumor unmatched

description:
4530TUS83203532_252800412982_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4137T  tumor unmatched

description:
4137TUS83203532_252800412981_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4373T  tumor unmatched

description:
4373TUS83203532_252800412967_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4429T  tumor unmatched

description:
4429TUS83203532_252800412967_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 32_R7_pptr_1_SX1263

city: Tel Aviv

first: Itai

middle: Antoine

last: Toker

address: Haim levanon St.

department: Neurobiology

institute: Tel Aviv University

description: Small RNA-seq

data_processing:
Adapter trimming - cutadapt
Quality examination - fastQC
Alignment - Shortstack
Filter-20-23 bp
Counting - HTseq_count
Comparisons - DESeq2
Genome_build: WS235/ce11
Supplementary_files_format_and_content: *.count.txt: HTseq_count output files.

growth_protocol: 20C fed on E. coli OP-50 bacteria.

extract_protocol:
TRIZOL (Life Technologies)
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®.

tag: genotype

value: Dissected Gonads

tag: temperature


title: 4254T  tumor unmatched

description:
4254TUS83203532_252800412966_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 31_R5_pptr_1_SX1263

description: Small RNA-seq


title: 29_R5_SX1263

description: Small RNA-seq

source_name: Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)

value: Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)


title: 27_R1_SX1263

description: Small RNA-seq


title: 30_R1_pptr_1_SX1263

description: Small RNA-seq


title: 25_R2-pptr-1_F6_of_gfpRNAi

description: Small RNA-seq

tag: ancestry information

value: F6 progeny of gfp-dsRNA-treated animals


title: 3690T  tumor unmatched

description:
3690TUS83203532_252800412981_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 4267T  tumor unmatched

description:
4267TUS83203532_252800412966_S01_GE2_107
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 24_R3-WT_F6_of_gfpRNAi

description: Small RNA-seq


title: 3644T  tumor unmatched

description:
3644TUS83203532_252800412966_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 21_R4-MEGmut_F2_of_MEGherm_X_WTmale

description: Small RNA-seq

extract_protocol:
miRNeasy Kit (Qiagen)
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®.

value: F2 cross progeny of BFF40 hermaphrodite x SX1263 male


title: 23_R2-WT_F6_of_gfpRNAi

description: Small RNA-seq


title: 22_R1-WT_F6_of_gfpRNAi

description: Small RNA-seq


title: 20_R3-MEGmut_F2_of_MEGherm_X_WTmale

description: Small RNA-seq


title: 16_R1-WT_F2_of_MEGherm_X_WTmale

description: Small RNA-seq


title: 18_R4-WT_F2_of_MEGherm_X_WTmale

description: Small RNA-seq


title: 17_R3-WT_F2_of_MEGherm_X_WTmale

description: Small RNA-seq


title: 19_R1-MEGmut_F2_of_MEGherm_X_WTmale

description: Small RNA-seq


title: 15_R4-MEGmut_F2_of_WTherm_X_MEGmale

description: Small RNA-seq

value: F2 cross progeny of SX1263 hermaphrodite x BFF40 male


title: 14_R3-MEGmut_F2_of_WTherm_X_MEGmale

description: Small RNA-seq


title: 13_R1-MEGmut_F2_of_WTherm_X_MEGmale

description: Small RNA-seq


title: 11_R3-WT_F2_of_WTherm_X_MEGmale

description: Small RNA-seq


title: 28_R4_SX1263

description: Small RNA-seq


title: 26_R3-pptr-1_F6_of_gfpRNAi

description: Small RNA-seq


title: 12_R4-WT_F2_of_WTherm_X_MEGmale

description: Small RNA-seq


title: 3667T  tumor unmatched

description:
3667TUS83203532_252800412981_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 10_R1-WT_F2_of_WTherm_X_MEGmale

description: Small RNA-seq


title: 08_R2-Longterm_MEG_double_mutants

description: Small RNA-seq

value: Longterm meg-3/4 (>80 generations)


title: 05_R2-MEGmut_F15_of_WTherm_X_MEGmale

description: Small RNA-seq

value: F15 cross progeny of SX1263 hermaphrodite x BFF40 male


title: 3627T  tumor unmatched

description:
3627T US83203532_252800412966_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: 06_R3-MEGmut_F15_of_WTherm_X_MEGmale

description: Small RNA-seq


title: 04_R1-MEGmut_F15_of_WTherm_X_MEGmale

description: Small RNA-seq


title: 07_R1-Longterm_MEG_double_mutants

description: Small RNA-seq


title: 02_R2-Wild_Type_SX1263

description: Small RNA-seq


title: 03_R3-Wild_Type_SX1263

description: Small RNA-seq


title: 01_R1-Wild_Type_SX1263

description: Small RNA-seq


title: 09_R3-Longterm_MEG_double_mutants

description: Small RNA-seq


title: PsJN-inoculated Arabidopsis 1 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 3

city: Santiago

first: Andrea

last: Vega

address: Vicuña Mackenna 4860

department: Ciencias Vegetales

country: Chile

institute: Pontificia Universidad Catolica de Chile

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: Array scanning was carried out with the GeneChip® scanner 300 and image analysis was performed using the GeneChip® Operating Software

data_processing: The data were processed and normalized by RMA using the R package known as “affy”.

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (GeneChip® 3’ IVT Express Kit User Manuall, 2008, Affymetrix).

growth_protocol: Col-0 Arabidopsis thaliana seeds were obtained from Arabidopsis Biological Resource Center (ABRC). Seeds were surface sterilized with 50% sodium hypochlorite (100% commercial laundry bleach containing 0.1% Tween 20, rinsed four times with sterile water, and kept at 4°C for 4 days to promote uniform germination. Plants were placed vertically in a growth chamber at 22°C with a photoperiod of 16/8 h (light/dark).

extract_protocol: Total RNA of each sample was extracted using the Trizol® reagent (Invitrogen™, Carlsbad, CA) according to the manufacturer’s recommendations.

treatment_protocol: P. phytofirmans PsJN was routinely grown in minimal saline medium (Dorn et al., 1974), containing 10 mM fructose, in an orbital shaker (120 rpm) at 30°C. Cell suspensions were subsequently collected and adjusted to 1x10e8 colony forming units per milliliter (CFU/ml), as determined by plate counting. To prepare the inoculated square Petri dishes for gnotobiotic assays, the initial inoculum of strain PsJN (1x10e8 CFU/ml) was homogenously diluted in half strength Murashige and Skoog medium (50% MS) 0.8% agar (Murashige and Skoog, 1962) just before gelling, to reach a final inoculum of 1x10e4 CFU/ml of medium, as this concentration was previously reported by Poupin et al. (2013) as the optimum to induce positive effects in A. thaliana plants. Then, 8 sterilized and synchronized seeds were sown per plate, in plates that were inoculated or not with the strain, and that were placed vertically in a growth chamber at 22°C with a photoperiod of 16/8 h (light/dark). Thirteen days after sowing (13 DAS) A. thaliana plants with four visible leaves (LP.04 stage (Boyes et al., 2001)), inoculated or not with P. phytofirmans PsJN, were sampled and stored in 1.5 ml Eppendorf tubes containing RNAlaterTM (Ambion, Austin, TX) according to the manufacturer's instructions. These treatments correspond to 0 hours post-infection (0 hpi). Then, in the remaining plants, rosettes were infected by spraying 100 μl per plate of strain Pst DC3000 at 1x10e5 CFU/ml in 10 mM MgCl2 (Fig. 1A). One and 24 h after strain Pst DC3000 infection (1 and 24 hpi), five pools with four plants each were collected per treatment (non-inoculated plants/Pst and strain PsJN-inoculated plants/Pst) and stored in RNAlaterTM (Ambion, Austin, TX) until RNA extraction (according to the manufacturer's instructions). For RNA extraction, plants were grounded with an electronic pestle in the Eppendorf tube without the RNAlater solution. Pst DC3000 was grown on King’s B medium in an orbital shaker (120 rpm) at 28°C, supplemented with 50 μg/ml of rifampicin and 50 μg/ml of kanamycin, as selection antibiotics.

tag: inoculation with beneficial bacteria p. phytofirmans psjn

value: PsJN-inoculated

tag: infection with pseudomona syringae dc3000

value: P. syringae Pst DC3000

tag: time

value: 1 hr

value: whole plant


title: Patient_14_6m

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Scanned on GeneTitan® Multi-Channel (MC) Instrument, according to the GeneTitan Instrument User Guide for Expression Arrays Plates (PN 702933 Rev 2. Affymetrix Inc., Santa Clara, CA).

data_processing: Data normalization, batch correction, and differential gene expression was performed using Partek Genomics Suite

label_protocol: RNA from each sample was used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT Pico Reagent Kit User Manual (P/N 703262 Rev 1 Affymetrix Inc., Santa Clara, CA).

extract_protocol: CD4+ and CD14+ cells where prepared within an hour after sampling using AutoMACS (Milteny Biotec, Bergisch, Germany) due to the manufactures standard protocol and stored in -70°C. DNA and RNA was extracted simultaneously using Qiagen Allprep DNA/RNA kit (Qiagen, Venlo, Netherlands) due to the manufactures standard protocol and stored in -70°C.

tag: individual

tag: disease state

value: multiple sclerosis

tag: treatment

value: DMF

tag: cell type

value: CD4+ Tcells


title: Patient_14_BL

source_name: BL

value: control

value: BL


title: PsJN-inoculated Arabidopsis 24 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 2

value: 24 hr


title: PsJN-inoculated Arabidopsis Time 0 biological replicate 2

source_name: PsJN-inoculated Arabidopsis Time 0

value: Control time 0

value: 0 hr


title: Patient_13_6m


title: Patient_12_6m


title: PsJN-inoculated Arabidopsis 1 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 1


title: Patient_12_BL


title: Patient_13_BL


title: PsJN-inoculated Arabidopsis 24 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 1


title: PsJN-inoculated Arabidopsis 24 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 3


title: Arabidopsis non-inoculated 1 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 2

source_name: Arabidopsis non-inoculated or control  1 hour after a challenge with Pseudomona syringae Pst DC3000

value: non-inoculated


title: Arabidopsis non-inoculated 24 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 1

source_name: Arabidopsis non-inoculated or control 24 hour after a challenge with Pseudomona syringae Pst DC3000


title: PsJN-inoculated Arabidopsis Time 0 biological replicate 1


title: Patient_8_BL


title: Arabidopsis non-inoculated 1 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 1


title: PsJN-inoculated Arabidopsis Time 0 biological replicate 3


title: Patient_9_BL


title: Patient_11_6m


title: Patient_11_BL


title: Patient_10_6m


title: Arabidopsis non-inoculated 1 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 3


title: Arabidopsis non-inoculated 24 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 3


title: Patient_10_BL


title: Arabidopsis non-inoculated Time 0 biological replicate 3

source_name: Arabidopsis non-inoculated or control time 0


title: Arabidopsis non-inoculated 24 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 2


title: PsJN-inoculated Arabidopsis 1 hour after a challenge with Pseudomona syringae Pst DC3000  biological replicate 2


title: Patient_9_6m


title: Patient_8_6m


title: Patient_6_BL


title: Patient_7_BL


title: Patient_7_6m


title: Patient_6_6m


title: Patient_5_BL


title: Arabidopsis non-inoculated Time 0 biological replicate 2


title: Patient_4_6m


title: Patient_4_BL


title: Patient_3_6m


title: Patient_3_BL


title: RHA1_LB_repA

city: Vicksburg

first: Karl

last: Indest

address: 3909 Halls Ferry Road

institute: US Army Engineer Research and Development Center

description: This sample is of Rhodococcus jostii RHA1 grown under aerobic batch conditions in LB media. It is the first of three biological replicates used in this experiment, each from separate cultures

hyb_protocol: Three hundred and twenty-five micrograms of the labeled DNA was used for subsequent hybridization to custom Agilent 8 x 15K microarrays using the Agilent hybridization kit and following the manufacturer's protocol . The hybridized arrays were washed using the Agilent Wash Buffer Kit.

scan_protocol: Washed arrays were scanned using the Agilent Technologies, High-Resolution Microarray Scanner (Model G2505C, Agilent Technologies, Santa Clara, CA, USA)

data_processing: Microarray images were analyzed using Agilent Feature Extraction software and ArrayStar v4.0.0 (DNAstar, Madison, WI) software. Expression data were log2 transformed and statistical significance was determined using a student t-test for binary transcriptome comparisons (i.e. control vs. experimental). The P-value was set at 0.05 and only those genes induced or repressed at least two-fold were considered in this paper.  Differentially expressed transcripts were assigned to their functional classifications based on pathway enrichment analysis from the Biocyc Database Collection (https://biocyc.org/)

organism: Rhodococcus jostii RHA1

source_name: RHA1 in LB rich conditions rep1

label_protocol: The RNA was used to generate cRNA using the Low Input Quick Amp Labeling Kit (Agilent, Santa Clara, California) and ethanol precipitated following the manufacturer’s directions. At each step the quality of the RNA and cRNA was analyzed using the Agilent 2100 Bioanalyzer and Total RNA Kit (Agilent) and the concentration verified using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA).

growth_protocol: Triplicate cultures of Rhodococcus jostii RHA1 and the Rhodococcus jostii RHA1/pGKT2 transconjugant were grown in LB media at 30°C with continuous shaking at 180 rpm until late log/early stationary phase.

extract_protocol: After ~48 h, cultures were centrifuged at 8,000 x g for 10 min at 4°C and total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and according to the manufacturer’s instructions for RNA cleanup with an added enzymatic lysis step and mechanical disruption step added before cleanup. Enzymatic lysis and mechanical disruption was performed by resuspending the cell pellet in 100 uL TE buffer and 200 uL lysozyme (20 mg/mL), transferring the resuspended pellet to a MP Biomedicals (Solon, OH) Lysing Matrix B tube and bead beating for 30s. The optional on column DNA digestion using the Qiagen RNase-Free DNase Kit was performed to remove DNA. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: genotype/variation

value: wild-type


title: Patient_2_6m


title: RHA1 pGKT2_LB_rep C

description: This sample is of Rhodococcus jostii RHA1/pGKT2 transconjugant strain grown under aerobic batch conditions in LB media. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: RHA1_pGKT2 in LB rich conditions rep3

value: pGKT2 transconjugant


title: RHA1_LB_repC

description: This sample is of Rhodococcus jostii RHA1 grown under aerobic batch conditions in LB media. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: RHA1 in LB rich conditions rep3


title: Patient_1_6m


title: Arabidopsis non-inoculated Time 0 biological replicate 1


title: Patient_1_BL


title: RHA1 pGKT2_LB_rep B

description: This sample is of Rhodococcus jostii RHA1/pGKT2 transconjugant strain grown under aerobic batch conditions in LB media. It is the second of three biological replicates used in this experiment, each from separate cultures

source_name: RHA1_pGKT2 in LB rich conditions rep2


title: RHA1_LB_repB

description: This sample is of Rhodococcus jostii RHA1 grown under aerobic batch conditions in LB media. It is the second of three biological replicates used in this experiment, each from separate cultures

source_name: RHA1 in LB rich conditions rep2


title: RHA1 pGKT2_LB_rep A

description: This sample is of Rhodococcus jostii RHA1/pGKT2 transconjugant strain grown under aerobic batch conditions in LB media. It is the first of three biological replicates used in this experiment, each from separate cultures

source_name: RHA1_pGKT2 in LB rich conditions rep1


title: Patient_2_BL


title: 3626T  tumor unmatched

description:
3626T US83203532_252800412981_S01_GE2_107_
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: squamous cell carcinoma

value: female

value: supraglottic

value: reference

value: normal laryngeal tissue


title: Patient_5_6m


title: genomic DNA from NSCLC 1883

type: genomic

city: Seoul

first: Sung-Yeon

last: Hwang

address: School of Biological Sciences, Seoul National University

country: South Korea

description: tumor NSCLC sample

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: R package minfi

label: Cy5 and Cy3

source_name: NSCLC 1883

label_protocol: Standard Illumina Protocol

growth_protocol: Patient tissue samples

extract_protocol: genomic DNA

treatment_protocol: Tumour samples were obtained before anti-PD1/PD-L1 treatment

value: tumor


title: genomic DNA from NSCLC 2317

institute: School of Biological Sciences, Seoul National University

description: tumor NSCLC sample

source_name: NSCLC 2317


title: genomic DNA from NSCLC 2132

description: tumor NSCLC sample

source_name: NSCLC 2132


title: genomic DNA from NSCLC 2107

description: tumor NSCLC sample

source_name: NSCLC 2107


title: genomic DNA from NSCLC 1778

description: tumor NSCLC sample

source_name: NSCLC 1778


title: genomic DNA from NSCLC 1809

description: tumor NSCLC sample

source_name: NSCLC 1809


title: genomic DNA from NSCLC 1508

description: tumor NSCLC sample

source_name: NSCLC 1508


title: genomic DNA from NSCLC 1960

description: tumor NSCLC sample

source_name: NSCLC 1960


title: genomic DNA from NSCLC 1708

description: tumor NSCLC sample

source_name: NSCLC 1708


title: genomic DNA from NSCLC 2133

description: tumor NSCLC sample

source_name: NSCLC 2133


title: genomic DNA from NSCLC 1412

description: tumor NSCLC sample

source_name: NSCLC 1412


title: genomic DNA from NSCLC 1589

description: tumor NSCLC sample

source_name: NSCLC 1589


title: genomic DNA from NSCLC 2126

description: tumor NSCLC sample

source_name: NSCLC 2126


title: genomic DNA from NSCLC 1637

description: tumor NSCLC sample

source_name: NSCLC 1637


title: genomic DNA from NSCLC 1873

description: tumor NSCLC sample

source_name: NSCLC 1873


title: genomic DNA from NSCLC 1554

description: tumor NSCLC sample

source_name: NSCLC 1554


title: genomic DNA from NSCLC 1619

description: tumor NSCLC sample

source_name: NSCLC 1619


title: genomic DNA from NSCLC 1490

description: tumor NSCLC sample

source_name: NSCLC 1490


title: genomic DNA from NSCLC 1425

description: tumor NSCLC sample

source_name: NSCLC 1425


title: genomic DNA from NSCLC 1352

description: tumor NSCLC sample

source_name: NSCLC 1352


title: genomic DNA from NSCLC 1456

description: tumor NSCLC sample

source_name: NSCLC 1456


title: genomic DNA from NSCLC 1401

description: tumor NSCLC sample

source_name: NSCLC 1401


title: genomic DNA from NSCLC 1510

description: tumor NSCLC sample

source_name: NSCLC 1510


title: genomic DNA from NSCLC 1711

description: tumor NSCLC sample

source_name: NSCLC 1711


title: genomic DNA from NSCLC 1443

description: tumor NSCLC sample

source_name: NSCLC 1443


title: genomic DNA from NSCLC 1751

description: tumor NSCLC sample

source_name: NSCLC 1751


title: genomic DNA from NSCLC 1528

description: tumor NSCLC sample

source_name: NSCLC 1528


title: genomic DNA from NSCLC 1358

description: tumor NSCLC sample

source_name: NSCLC 1358


title: genomic DNA from NSCLC 1337

description: tumor NSCLC sample

source_name: NSCLC 1337


title: genomic DNA from NSCLC 1327

description: tumor NSCLC sample

source_name: NSCLC 1327


title: genomic DNA from NSCLC 1164

description: tumor NSCLC sample

source_name: NSCLC 1164


title: genomic DNA from NSCLC 1322

description: tumor NSCLC sample

source_name: NSCLC 1322


title: genomic DNA from NSCLC 1145

description: tumor NSCLC sample

source_name: NSCLC 1145


title: genomic DNA from NSCLC 1297

description: tumor NSCLC sample

source_name: NSCLC 1297


title: genomic DNA from NSCLC 1250

description: tumor NSCLC sample

source_name: NSCLC 1250


title: genomic DNA from NSCLC 1155

description: tumor NSCLC sample

source_name: NSCLC 1155


title: genomic DNA from NSCLC 990

description: tumor NSCLC sample

source_name: NSCLC 990


title: genomic DNA from NSCLC 658

description: tumor NSCLC sample

source_name: NSCLC 658


title: genomic DNA from NSCLC 1208

description: tumor NSCLC sample

source_name: NSCLC 1208


title: genomic DNA from NSCLC 618

description: tumor NSCLC sample

source_name: NSCLC 618


title: genomic DNA from NSCLC 720

description: tumor NSCLC sample

source_name: NSCLC 720


title: genomic DNA from NSCLC 1017

description: tumor NSCLC sample

source_name: NSCLC 1017


title: genomic DNA from NSCLC 1066

description: tumor NSCLC sample

source_name: NSCLC 1066


title: genomic DNA from NSCLC 1079

description: tumor NSCLC sample

source_name: NSCLC 1079


title: genomic DNA from NSCLC 1104

description: tumor NSCLC sample

source_name: NSCLC 1104


title: genomic DNA from NSCLC 830

description: tumor NSCLC sample

source_name: NSCLC 830


title: genomic DNA from NSCLC 947

description: tumor NSCLC sample

source_name: NSCLC 947


title: genomic DNA from NSCLC 678

description: tumor NSCLC sample

source_name: NSCLC 678


title: genomic DNA from NSCLC 573

description: tumor NSCLC sample

source_name: NSCLC 573


title: genomic DNA from NSCLC 3

description: tumor NSCLC sample

source_name: NSCLC 3


title: genomic DNA from NSCLC 825

description: tumor NSCLC sample

source_name: NSCLC 825


title: genomic DNA from NSCLC 258

description: tumor NSCLC sample

source_name: NSCLC 258


title: genomic DNA from NSCLC 378

description: tumor NSCLC sample

source_name: NSCLC 378


title: genomic DNA from NSCLC 20

description: tumor NSCLC sample

source_name: NSCLC 20


title: genomic DNA from NSCLC 325

description: tumor NSCLC sample

source_name: NSCLC 325


title: genomic DNA from NSCLC 488

description: tumor NSCLC sample

source_name: NSCLC 488


title: genomic DNA from NSCLC 1203

description: tumor NSCLC sample

source_name: NSCLC 1203


title: genomic DNA from NSCLC 541

description: tumor NSCLC sample

source_name: NSCLC 541


title: Patient_17_3m_CD14

hyb_protocol: Bisulfite conversion using EZ DNA MethylationTM Kit from Zymo Research. Product No: D5004 with 250 ng of DNA per sample followed by llumina MethylationEPIC Beadarray hybridization via Standard Illumina Protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina HiScan.

data_processing: BMIQ normalization

label_protocol: Standard Illumina Protocol.

extract_protocol: Sorting strategies listed above. DNA was prepared using QIAamp DNA Micro Kit (Qiagen)

value: multiple sclerosis

value: CD14+ Monocytes


title: Patient_6_BL_CD4

source_name: BL

value: CD4+ Tcells


title: Patient_19_3m_CD14

value: DMF


title: genomic DNA from NSCLC 700

description: tumor NSCLC sample

source_name: NSCLC 700


title: Patient_14_6m_CD14


title: Donor4_Rep2_MSC.EM1_MediumStandard

city: Hanover

first: Anton

last: Selich

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: Gene Expression of the 1 induced MSC-EM from Donor 4 in the medium Standard

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 700 ng of each fluorescently labelled cRNA population was used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.

source_name: Donor 4, Rep 2, MSC.EM 1, Medium Standard

label_protocol: 100 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one-round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. Prior to the reverse transcription reaction, 1 µl of a 1:5000 dilution of Agilent’s One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to 100 ng of total RNA of each analyzed sample. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Thermo Fisher Scientific) as recommended in the manual of the Amino Allyl MessageAmp™ II Kit (twofold downscaled reaction volumes).

extract_protocol: Cells were harvested by 400xg, resuspended in 700 µl of RNAzol B reagent (WAK-Chemie Medical) and frozen at -80°C. Total RNA was isolated with the Direct-Zol RNA MiniPrep Kit (Zymo Research) and on-column DNAse treatment.

tag: donor

tag: replicate

tag: medium

value: Standard


title: Donor4_Rep1_MSC.EM7_MediumStandard

description: Gene Expression of the 7 induced MSC-EM from Donor 4 in the medium Standard

source_name: Donor 4, Rep 1, MSC.EM 7, Medium Standard


title: Donor4_Rep2_MSC.EM7_MediumStandard

source_name: Donor 4, Rep 2, MSC.EM 7, Medium Standard


title: genomic DNA from NSCLC 756

description: tumor NSCLC sample

source_name: NSCLC 756


title: Patient_17_BL_CD4

value: control

value: BL


title: Donor4_Rep1_MSC.EM1_MediumStandard

source_name: Donor 4, Rep 1, MSC.EM 1, Medium Standard


title: Patient_13_BL_CD4


title: Patient_18_BL_CD4


title: Donor5_Rep2_MSC.EM7_MediumActivated

description: Gene Expression of the 7 induced MSC-EM from Donor 5 in the medium Activated

source_name: Donor 5, Rep 2, MSC.EM 7, Medium Activated

value: Activated


title: Donor5_Rep1_MSC.EM6_MediumStandard

description: Gene Expression of the 6 induced MSC-EM from Donor 5 in the medium Standard

source_name: Donor 5, Rep 1, MSC.EM 6, Medium Standard


title: Donor5_Rep1_MSC.EM6_MediumActivated

description: Gene Expression of the 6 induced MSC-EM from Donor 5 in the medium Activated

source_name: Donor 5, Rep 1, MSC.EM 6, Medium Activated


title: Donor2_Rep2_MSC.EM1_MediumStandard

description: Gene Expression of the 1 induced MSC-EM from Donor 2 in the medium Standard

source_name: Donor 2, Rep 2, MSC.EM 1, Medium Standard


title: Donor2_Rep1_MSC.EM7_MediumStandard

description: Gene Expression of the 7 induced MSC-EM from Donor 2 in the medium Standard

source_name: Donor 2, Rep 1, MSC.EM 7, Medium Standard


title: Patient_14_BL_CD4


title: Donor5_Rep2_MSC.EM7_MediumStandard

description: Gene Expression of the 7 induced MSC-EM from Donor 5 in the medium Standard

source_name: Donor 5, Rep 2, MSC.EM 7, Medium Standard


title: Donor2_Rep3_MSC.EM7_MediumStandard

source_name: Donor 2, Rep 3, MSC.EM 7, Medium Standard


title: Patient_15_BL_CD14


title: Patient_9_3m_CD4


title: Patient_10_3m_CD4


title: Patient_12_3m_CD14


title: Patient_4_6m_CD4


title: Patient_5_BL_CD4


title: Patient_1_BL_CD4


title: Patient_16_6m_CD4


title: Patient_3_BL_CD14


title: Patient_19_BL_CD14


title: chicken-3

first: Fan

last: Zhao

address: Weigang 1#

department: Department of Food Science

institute: Nanjing Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two groups was performed using the DESeq2, R package (1.24.0).
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: cecum tissue

extract_protocol:
Total RNA was extracted from cecal tissue by using Takara MiniBEST universal RNA extraction kit (Takara, Kusatsu, Japan). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: large intestine

value: 7 days intervention

tag: diet

value: chicken protein group


title: Donor3_Rep1_MSC.EM7_MediumStandard

description: Gene Expression of the 7 induced MSC-EM from Donor 3 in the medium Standard

source_name: Donor 3, Rep 1, MSC.EM 7, Medium Standard


title: Patient_8_3m_CD4


title: Patient_17_BL_CD14


title: Donor1_Rep2_MSC.EM7_MediumStandard

description: Gene Expression of the 7 induced MSC-EM from Donor 1 in the medium Standard

source_name: Donor 1, Rep 2, MSC.EM 7, Medium Standard


title: Donor1_Rep1_MSC.EM7_MediumStandard

source_name: Donor 1, Rep 1, MSC.EM 7, Medium Standard


title: Donor1_Rep3_MSC.EM7_MediumStandard

source_name: Donor 1, Rep 3, MSC.EM 7, Medium Standard


title: Patient_9_BL_CD14

source_name: BL


title: chicken-2


title: Patient_14_3m_CD4


title: Patient_14_3m_CD14


title: Donor3_Rep3_MSC.EM1_MediumStandard

description: Gene Expression of the 1 induced MSC-EM from Donor 3 in the medium Standard

source_name: Donor 3, Rep 3, MSC.EM 1, Medium Standard


title: casein-1

value: casein group


title: Patient_15_6m_CD14


title: Patient_3_BL_CD4


title: Patient_1_6m_CD4


title: Donor1_Rep3_MSC.EM1_MediumStandard

description: Gene Expression of the 1 induced MSC-EM from Donor 1 in the medium Standard

source_name: Donor 1, Rep 3, MSC.EM 1, Medium Standard


title: Donor3_Rep1_MSC.EM1_MediumStandard

source_name: Donor 3, Rep 1, MSC.EM 1, Medium Standard


title: Donor3_Rep2_MSC.EM1_MediumStandard

source_name: Donor 3, Rep 2, MSC.EM 1, Medium Standard


title: Patient_13_3m_CD14


title: casein-2


title: Patient_2_BL_CD4


title: chicken-1


title: Patient_3_3m_CD14


title: Donor1_Rep2_MSC.EM1_MediumStandard

source_name: Donor 1, Rep 2, MSC.EM 1, Medium Standard


title: Patient_17_6m_CD4


title: H1975, Control

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

department: Institute for Transfusion Medicine and Transplant Engineering

data_processing:
The obtained RNASeq data was analyzed by the Bioinformatics Facility (ISCIII).
quality control analysis involving fastQC v0.11.3 was carried out and any adapter sequences and low quality 3' ends were removed using Trimmomatic v0.36.  v2.0.14 and mapping quality control was performed using RseQC v2.6.4.
High-quality reads were then mapped against Hg38 human genome using STAR v2.4.0.1 and mapping quality control was performed using RseQC v2.6.4.
Transcriptome prediction and gene/isoform quantification was calculated using HT-seq v0.11.1 based on Hg38 RefSeq reference genes.
Differential expression analysis was carried out using GFOLD v1.1.4 (25) in generalized fold change (GFOLD) form.
Genome_build: Hg38
Supplementary_files_format_and_content: DE table generated by GFOLD (in GFOLD form) and raw counts

source_name: NSCLC cell line

growth_protocol: The H1975 and H661 cells were grown in serum free medium without or with addition of 2 mg/ml AAT for 24 hours.

extract_protocol:
The total RNA was isolated and quality was assessed using 1 % agarose gels as well as by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano Kit.
Libraries were prepared in duplicates by using 200 ng of each cell line. The products were then purified with Ampure XP Beads (Beckman Coulter) and enriched with 15 cycles of PCR to create the cDNA library

tag: cell line

value: NSCLC


title: Patient_7_BL_CD4


title: H1975, AAT exposed


title: Patient_16_BL_CD14


title: H661, AAT exposed


title: Patient_15_6m_CD4


title: Patient_14_6m_CD4


title: HMEC-1 SOFT rep6

city: Seattle

first: Effie

middle: Efthimia

last: Bastounis

state: WA

address: UW Biology Life Sciences Bldg, Room 565, 4000 15th Ave NE

department: Biology

institute: University of Washington

data_processing:
Sequencing reads were obtained in Fastq format and evaluated using FastQC v0.11.5 according to the directions on the following website: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. For sequence alignment we used HISAT2 (https://ccb.jhu.edu/software/hisat2/index.shtml) and reads were mapped to reference genome grch38 to generate .bam files.
Python script HTSEQ was then used to generate counts per read (https://htseq.readthedocs.io/en/release_0.11.1/count.html). Both HISAT2 and HTSEQ were run from the command line.
For differential gene expression analysis, we used Deseq2 R package (Bioconductor version: Release 3.8, https://bioconductor.org/packages/release/bioc/html/DESeq2.html). The thresholds that we used for identifying DEGS were: (1) DESeq2 mean normalized counts > 10; (2) padj-value < 0.05; and (3) lof2foldchange >0
Genome_build: grch38
Supplementary_files_format_and_content: text files containing number of sorted counts per gene

source_name: human dermal microvascular endothelial cells

growth_protocol:
2x10^5 cells grown on 12 mm soft 3 kPa plan polyacrylamide hydrogels for 24 h
HMEC-1 were cultured in MCDB 131 medium (Fisher Scientific; 10372-019) supplemented with 10% FBS (GemBio; 900-108), 10 ng/mL epidermal growth factor (Sigma; E9644), 1 μg/mL hydrocortisone (Sigma; H0888), and 2 mM l-glutamine (Sigma; 56-85-9).

extract_protocol:
Cells residing for 24 h on these gels were then harvested and lyzed using the QIAshredder Kit (Qiagen; 79656). mRNA was harvested using the RNeasy Plus Micro Kit (Qiagen; 74004) and eluted in 30 μL RNAase free water. RNA concentrations were measured using the nanodrop machine and were comparable between conditions. RNA quality and quantity were confirmed via bioanalyzer analysis performed by the Stanford Protein and Nucleic Acid (PAN) Facility.
RNA libraries were prepared by the Stanford Functional Genomics Facility using the KAPA stranded RNA-seq kit with RiboErase (Kit code KK8483, Roche Cat. # 07962282001), for a fragment length of 200-300 bp. Sequencing was run on the Illumina NextSeq 500 System using the High-Output Kit with 2x75 read length. We had an average of 30 million reads per sample. We used 2 lanes with 12 samples each ensuring that from each condition 3 replicates go to lane A and the other 3 to lane B (total number of replicates N = 6).

treatment_protocol: To construct polyacrylamide hydrogels the following protocol was used. Glass-bottom plates with 24 wells (MatTek; P24G-1.5-13-F) were incubated for 1 h with 500 μL of 1 M NaOH, then rinsed with distilled water, and incubated with 500 μL of 2% 3-aminopropyltriethoxysilane (Sigma; 919-30-2) in 95% ethanol for 5 min. Following rinsing with water 500 μL of 0.5% glutaraldehyde were added to each well for 30 min. Wells were rinsed with water again and dried at 60°C. To prepare polyacrylamide hydrogels of varying stiffness, mixtures containing 3–10% acrylamide (Sigma; A4058) and 0.06–0.6% bis-acrylamide (Fisher; BP1404-250) were prepared. Specifically, 3 kPa hydrogels contained 5% acrylamide and 0.1% bis-acrylamide and 70-kPa hydrogels contained 10% acrylamide and 0.6% bis-acrylamide68. For each stiffness, two mixtures were prepared, the second of which contained 0.03% 0.1 μm–diameter fluorescent beads (Invitrogen, F8803) for TFM experiments. 0.06% APS and 0.43% TEMED were added to the solutions to initiate polymerization. First, 3.6 µL of the first mixture without the beads was added at the center of each well, capped with 12-mm untreated circular glass coverslips, and allowed to polymerize for 20 min. Then 2.4 µL of the mixture containing tracer beads was added, sandwiched again with a 12-mm untreated circular glass coverslip and allowed to polymerize for 20 min. Next, 50 mM HEPES at pH 7.5 was added to the wells, and coverslips were removed. Hydrogels were UV-sterilized for 1 h and then activated by adding 200 µL of 0.5% weight/volume heterobifunctional cross-linker Sulfo-SANPAH (ProteoChem; c1111) in 1% dimethyl sulfoxide (DMSO) and 50 mM HEPES, pH 7.5, on the upper surface of the hydrogels and exposing them to UV light for 10 min. Hydrogels were washed with 50 mM HEPES at pH 7.5 and were coated with 200 µL of 0.25 mg/ml rat tail collagen I (Sigma-Aldrich; C3867) in 50 mM HEPES at pH 7.5 overnight at room temperature. After hydrogel equilibration with cell media for 30 min at 37°C, cells were seeded to a concentration of 2x10^5 cells per well directly onto the hydrogels 24 h.

value: dermal microvasculature

value: dermal microvascular endothelial cells

tag: nature

value: immortalized

tag: matrix

value: SOFT


title: casein-3


title: Patient_18_BL_CD14

value: multiple sclerosis


title: Patient_9_6m_CD14

value: CD14+ Monocytes


title: HMEC-1 SOFT rep4


title: Patient_13_3m_CD4

value: CD4+ Tcells


title: Patient_9_BL_CD4


title: Patient_19_6m_CD4

value: DMF


title: Patient_2_3m_CD4


title: Donor1_Rep1_MSC.EM1_MediumStandard

source_name: Donor 1, Rep 1, MSC.EM 1, Medium Standard

value: Standard


title: Patient_11_3m_CD4


title: Patient_11_3m_CD14


title: HMEC-1 SOFT rep5


title: Patient_19_3m_CD4


title: Patient_13_BL_CD14

value: control


title: Patient_14_BL_CD14

value: BL


title: HMEC-1 SOFT rep2


title: Lung_fibroblast_IPF_TGFb_5d_rep2 [Affy]

city: Ciudad de Mexico

first: Yalbi

middle: Itzel

last: Balderas-Martinez

state: Distrito Federal

address: Calzada de Tlalpan 4502, Sección XVI, Belisario Domínguez

institute: INER

description: Gene expression data from IPF fibroblast

hyb_protocol: Following fragmentation, 5 ug of fragmented and labeled aRNA were hybridized for 16 hr at 45ºC (GeneChip(R) Hybridization, Wash and Stain Ki, catalog 900720, Affymetrix) to GeneChip(TM) PrimeView Human Gene Expression Array ( catalog 901837, Affymetrix). GeneChips were washed and stained in the Affymetrix GeneChips(R) Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip(TM) Scanner 3000 7G.

data_processing: The array was processed using R 3.4.2 (http://www.r-project.org/), using Bioconductor 3.6 (http://www.bioconductor.org/) with affy package. Background correction and normalization were performed using RMA.

source_name: IPF, TGFb5d

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip(R) 3'IVT Express Kit, technical manual, catalog 901228, Affymetrix).

growth_protocol: All primary cultures were grown in Ham’s F-12 medium with 10% FBS at 37 °C in an atmosphere of 95% air and 5% CO2 until early confluence

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

treatment_protocol: Cells were treated with TGF-β1 (10 ng/ml), using two different time periods (24 hours or 5 days) all of them cultured in HAM´s F-12 with low serum (0.1%).

value: Lung

value: IPF


title: Patient_15_3m_CD14

institute: Karolinska Institutet


title: HMEC-1 SOFT rep1


title: Patient_16_6m_CD14


title: HMEC-1 SOFT rep3


title: Patient_16_3m_CD4


title: HUVEC SOFT rep6

source_name: human umbilical vein endothelial cells

growth_protocol:
2x10^5 cells grown on 12 mm soft 3 kPa plan polyacrylamide hydrogels for 24 h
HUVEC (Lonza C2517A) were cultured according to the manufacturer’s instructions (EGM Bullet Kit-2, Lonza CC-3162).

value: umbilical vein

value: umbilical vein endothelial cells

value: primary


title: Lung_fibroblast_IPF_TGFb_5d_rep1 [Affy]


title: Lung_fibroblast_IPF_TGFb_5d_rep3 [Affy]


title: Patient_10_6m_CD4


title: HUVEC SOFT rep5


title: HUVEC SOFT rep4


title: KTR9_LB_rep C

description: This sample is of Gordonia sp. KTR9 grown under aerobic batch conditions in LB media. It is the third of three biological replicates used in this experiment, each from separate cultures.

organism: Gordonia sp. KTR9

source_name: KTR9 in LB rich conditions rep3

growth_protocol: Triplicate cultures of Gordonia sp. KTR9 and the KTR9DpGKT2 mutant were grown in LB media at 30°C with continuous shaking at 180 rpm until late log/early stationary phase.

value: wild-type


title: Patient_12_3m_CD4


title: Patient_11_BL_CD4


title: Lung_fibroblast_IPF_TGFb_24h_rep2 [Affy]

source_name: IPF, TGFb24h


title: Lung_fibroblast_IPF_TGFb_24h_rep3 [Affy]


title: Lung_fibroblast_IPF_TGFb_24h_rep1 [Affy]


title: Patient_15_BL_CD4


title: HUVEC SOFT rep3


title: H661, Control

value: NSCLC


title: Lung_fibroblast_IPF_control_rep3 [Affy]

source_name: IPF, control


title: Patient_18_3m_CD14


title: Patient_10_BL_CD4


title: KTR9_LB_rep B

description: This sample is of Gordonia sp. KTR9 grown under aerobic batch conditions in LB media. It is the second of three biological replicates used in this experiment, each from separate cultures

source_name: KTR9 in LB rich conditions rep2


title: KTR9_LB_rep A

description: This sample is of Gordonia sp. KTR9 grown under aerobic batch conditions in LB media. It is the first of three biological replicates used in this experiment, each from separate cultures

source_name: KTR9 in LB rich conditions rep1


title: HUVEC SOFT rep1


title: Lung_fibroblast_IPF_control_rep2 [Affy]


title: Patient_11_BL_CD14


title: Patient_17_6m_CD14


title: HMEC-1 STIFF rep5

growth_protocol:
2x10^5 cells grown on 12 mm stiff 70 kPa plan polyacrylamide hydrogels for 24 h
HMEC-1 were cultured in MCDB 131 medium (Fisher Scientific; 10372-019) supplemented with 10% FBS (GemBio; 900-108), 10 ng/mL epidermal growth factor (Sigma; E9644), 1 μg/mL hydrocortisone (Sigma; H0888), and 2 mM l-glutamine (Sigma; 56-85-9).

value: dermal microvasculature

value: dermal microvascular endothelial cells

value: STIFF


title: Lung_fibroblast_IPF_control_rep1 [Affy]


title: HUVEC SOFT rep2

value: SOFT


title: HMEC-1 STIFF rep6

value: immortalized


title: KTR9DpGKT2_LB_rep C

description: This sample is of Gordonia sp. KTR9DpGKT2 mutant grown under aerobic batch conditions in LB media. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: KTR9DpGKT2 in LB rich conditions rep3

value: KTR9 mutant cured of pGKT2 plasmid