title: SH26-1095-Vehicle

tag: genotype

value: Treated with vehicle


title: SH26-1196-TDM1

status: Public on Nov 11 2021

type: SRA

city: New York

first: Han

last: Han

address: 550 First Avenue

country: USA

institute: NYU Langone Medical Health

library_source: transcriptomic

data_processing:
STAR analysis for alignment
RSEM analysis for the level of expression
Genome_build: mm10
Supplementary_files_format_and_content: Count and TPM

molecule: total RNA

organism: Mus musculus

source_name: Lung Tumor Nodules

extract_protocol:
Lung tumor nodules were snap frozen and RNAs were extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Long term treatment with vehicle, monocertinib (TAK-788), T-DM1 and the combination.

tag: strain

tag: tissue

value: Lung Tumor Nodules

value: HER2 Exon20YVMA

tag: treatment

value: Treated with T-DM1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c9

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

description: umi0.csv, umi1.csv, counts.csv

data_processing:
After demultiplexing, UMIs from the barcode read (8nt) were concatenated onto the 5’ part of corresponding mappable reads using a custom Python script.
The concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --quantMode TranscriptomeSAM so that output alignments are translated into transcript coordinates for downstream analysis, and --clip5pNbases 8 so that the UMI sequences are not mapped. All other options for STAR are set as default.
Specifically, for mix-species experiments, the concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --outFilterMultimapNmax 1 so that only reads that uniquely mapped are considered.
The mapped transcripts per gene and mapped reads per gene were quantified using a custom Python script. When measuring mapped transcripts per gene, we use hamming distance threshold 1, which means only if the hamming distance between two UMIs is greater than 1, then they are considered from different transcripts.
Genome_build: UCSC hg38 for HEK293 RNA-Seq and scRNA-Seq, and U87 scRNA-Seq.
Genome_build: Concatenated UCSC hg38 and mm10 for U87-3T3 cell mixture scRNA-Seq profiles.
Supplementary_files_format_and_content: comma separated file including umi matrix, counts matrix and cross-species matrix.

molecule: polyA RNA

organism: Homo sapiens

source_name: Single cell from cultured HEK293 cells

extract_protocol:
published scPLATE-Seq protocol
published scPLATE-Seq protocol

tag: cell line


title: leaf, R1

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

country: China

institute: Northwest A&F University

data_processing:
Bcl2fastq Conversion software (v2.20) was used for basecalling.
The raw data was trimmed with strict standards as followsd:(1) Trimmed Reads with adapter seq;(2) Trimmed low quality bases(Reads would be discarded if percent of N base is greater than 10% or percent of low quality bases is greater than 50%).
We mapped the clean data against the reference genome of Darmor-bzh (http://www.genoscope.cns.fr/brassicanapus/data/). HISAT2 (https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-source/download) is used as an alignment software for RNA-seq. Based on mapped data, we carried out library insert size check, sequencing randomness check, gene expression quantification analysis, alternative splicing analysis, novel genes detection and genes structure optimization.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).
Differential expression analysis of two sample groups was performed using the DEseq2. Fold Change(FC)≥2 and FDR<0.01 were used as the screening criteria to identify differentially expressed genes.
Genome_build: Darmor-bzh (http://www.genoscope.cns.fr/brassicanapus/data/)
Supplementary_files_format_and_content: Tab-delimited text files include count number and fragments per kilobase of transcript per million fragments mapped (FPKM) values for each sample.

organism: Brassica napus

source_name: leaf

growth_protocol: The plants of different lines of  the BC1F3 generation of 'White Flower' x 'Zhongshuang11' were cultivated in a greenhouse.

extract_protocol:
The leaf samples were collected and put into liquid nitrogen. Total RNAs were extracted using the Trizol® Reagent (Invitrogen, USA). The total RNA quantity and purity were analyed by using of Bioanalyzer 2100 (Agilent, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, the cDNA libraries were sequenced on Illumina Novaseq6000 platform with flow cell type PE150, generating high-quality raw data in FASTQ format. Raw data for each sequencing sample included two FASTQ files contain all cDNA fragments were measured at both ends of reads.
RNA-seq. Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, the cDNA libraries were sequenced on Illumina Novaseq6000 platform with flow cell type PE150. Raw Data for each sequencing sample included two FASTQ files contain all cDNA fragments were measured at both ends of reads.

treatment_protocol: The seedlings growing in the greenhouse were inoculated with powdery mildew. The symptom on each individual seedling were observed to determine the resistant and susceptible plants in the segregating population.

value: leaf

tag: inoculation

value: powdery mildew

tag: development stage

value: ten-days after inoculation

tag: phenotype

value: resistant

tag: replicate


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c8

description: umi0.csv, umi1.csv, counts.csv


title: SH26-1125-TDM1


title: leaf, S2

value: susceptible


title: SH26-1274-TAK

value: Treated with mobocertinib (TAK-788)


title: Human jejunum – control 2

type: RNA

city: Maastricht

first: Marco

last: Manca

state: Limburg

address: P. Debyelaan 25

department: CARIM

country: Netherlands

institute: University of Maastricht

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised robust spline normalization in lumi (BioConductor, R)

label: biotin

source_name: Human jejunum – control

label_protocol: Per sample, 200 ng RNA was used for anti-sense RNA synthesis, amplification, purification, and labelling with the Illumina TotalPrep 96 RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) according to the manufacturer's protocol

extract_protocol: RNA was isolated from snap-frozen tissue samples using AllPrep DNA/RNA/Protein kit (Qiagen, Hilden, Germany). Disruption and homogenization of the tissue was performed using an Ultra Turrax Homogenizer (IKA Labortechnik, Staufen, Germany) in lysis buffer containing β-mercaptoethanol (Promega, Madison, WI). RNeasy spin columns were used to bind RNA. Columns were washed and RNA was eluted in RNase-free water. RNA samples were treated with DNAse (Promega) to ensure removal of contaminating genomic DNA.

value: Control

tag: patient

value: jejunum


title: leaf, R2


title: leaf, S1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c12

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c11

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c5

description: umi0.csv, umi1.csv, counts.csv


title: SH26-1261-TAK


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c4

description: umi0.csv, umi1.csv, counts.csv


title: leaf, R3


title: BC5-scRNA

city: Shanghai

first: Jia

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26). Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: bladder cancer tissue

extract_protocol:
Tumor tissues were ressected by surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

tag: subject status

value: patient with bladder cancer

tag: gender

value: male

tag: age

tag: tumor stage


title: TGFβ-treated Smad7KO Cardiac fibroblasts, sample 1-TS71

first: CLAUDIO

middle: DIEGO

last: HUMERES

state: New York

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

description: Fibroblasts Smad7 KO is achieved by inducing Cre expression in fibroblasts isolated from the hearts of Smad7 floxed animals

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
The library preparations were sequenced on Illumina NovaSeq 6000 devices, generating 100 bp paired end reads. Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis
Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (December 2011 release of the mouse musculus reference genome (mm10; GRCm38.p6) from Ensembl) using TopHat2 algorithm alignment program v.2.0.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm
HTSeq software v.0.6.1 was used to count the number of reads mapped to each gene. Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM), was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length
Genome_build: mm10
Supplementary_files_format_and_content: excel files including raw gene counts for every gene and every sample
Supplementary_files_format_and_content: excel files including FPKM values counts for every gene and every sample

source_name: Cardiac fibroblasts

growth_protocol: Cardiac fibroblasts were isolated from 12-week old mouse (C57BL/6) hearts. Cells were plated on a T75 tissue-culture flask in DMEM-F12 +10% FBS and incubated overnight at 37°C, 5% CO2. After overnight incubation, nonadherent cells were removed, and adherent cells were cultivated. On reaching confluence, cells were detached with trypsin/EDTA, split in a 1:2 or 1:4 ratio, and recultured (passage 1). This was repeated once until passage 2, at which cells were used for adenovirus infection and TGFβ1 treatments.

extract_protocol:
RNA was extracted with Trizol reagent.
RNA sequencing was performed by Novogene. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq. Library preparation was performed by Novogene, Inc., using at least 1 ug high-quality total RNA input per sample. mRNA enrichment was performed with poly-T oligo-attached magnetic beads. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: Fibroblasts were infected with GFP (control) or Cre-expressing adenovirus for 48 hours (100 MOI). After media replacement, cells were stimulated with TGFβ1 (10ng/ml) for 4 hours.

tag: cell type

value: cardiac fibroblasts isolated from Smad7 floxed mice

tag: adenovirus infection

value: Cre-expressing adenovirus infection

value: treated with TGFβ1 for 2 hours


title: BC1-scRNA

value: Ta


title: Control Smad7KO  Cardiac fibroblasts, sample 3-CS73

value: No treatment


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c10

description: umi0.csv, umi1.csv, counts.csv


title: SH26-1313-Vehicle

value: Lung Tumor Nodules

value: HER2 Exon20YVMA

value: Treated with vehicle


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b9

description: umi0.csv, umi1.csv, counts.csv


title: ALUBIA YEM #3

city: LAUSANNE

first: JOAQUIN

last: CLUA

address: BIOPHORE

department: DBMV

country: Switzerland

institute: UNIL

data_processing:
Illumina reads were aligned to the P. vulgaris genome v2.1. using Tophat 2 (Kim et al., 2013)
Differential gene expression analysis of RNA-seq data was performed using Cufflinks pakage (Trapnell et al., 2012)
Genome_build: Phaseolus vulgaris genome v2.1 available at Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Pvulgaris)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each P. vularis gene

organism: Phaseolus vulgaris

source_name: Roots

growth_protocol: P. vulgaris seedlings were grown on acrylic boxes (17 cm x 22 cm x 4.5 cm) containing slanted agar-Fahraeus media and incubated for 7 days in a Persival Intellus Control System growth chamber at 25°C and 75% humidity with a long-day period (16-h-day/8-h-night cycle) and a photosynthetically active radiation of 200 μmol. s-1.cm-2 using mixed lighting containing four OSRAM cool daylight L36W/765 tubesand one OSRAM FLUORA L36W/77 tube.

extract_protocol:
RNA was extracted with Trizol following manufacture´s recommendations (Thermo Fisher). RNA quality was evaluated by capillary gel electrophoresis on an Agilent 2100 Bioanalyzer using the AgilentRNA6000 Pico kit.
Libraries were prepared using 3 µg of RNA and the Illumina TruSeq RNA Sample Preparation kit v2 following provider’s instructions. Superscript II (Invitrogen) reverse transcriptase was used for cDNA synthesis. PCR fragments were purified using AMPure XP beads (Beckman Coulter Genomics). Size of the synthesized fragments was verified in an Agilent 2100 Bioanalyzer using the DNA-1000 kit (Agilent). Libraries were multiplexed following Illumina recommendations for barcode compatibility.

treatment_protocol: After 7 days post germination roots were inoculated with 5 ml of Yeast Extract-Manitol (YEM) media as a control or with 5 ml of a suspension of strain SC15, CE3, 55N1 or 124N1 grown in YEM media until they reached an OD600=0.8

value: YEM


title: ALUBIA SC15 #3


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c2

description: umi0.csv, umi1.csv, counts.csv


title: BC4-scRNA


title: Control Smad7KO  Cardiac fibroblasts sample, 1-CS71


title: TGFβ-treated Smad7KO Cardiac fibroblasts, sample 3-TS73


title: TGFβ-treated Wild Type Cardiac fibroblasts, sample 1-TWT3

value: Control GFP adenovirus infection


title: BC3-scRNA


title: TGFβ-treated Smad7KO Cardiac fibroblasts, sample 2-TS72


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c1

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b6

description: umi0.csv, umi1.csv, counts.csv


title: BC2-scRNA


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b8

description: umi0.csv, umi1.csv, counts.csv


title: ALUBIA 124N1 #1


title: TGFβ-treated Wild Type Cardiac fibroblasts, sample 1-TWT1


title: sample treated for 24 h, biological replicate 3

city: Izola

first: Sasa

last: Kenig

address: Polje 42

department: Faculty of Health Sciences

country: Slovenia

institute: University of Primorska

description: Gene expression data from colon fibroblasts

hyb_protocol: Following fragmentation, 2.3 ug of ss-cDNA were hybridized at 60 rpm for 16 hr at 45°C on Human Clariom S GeneChip Cartridge Array in Affymetrix GeneChip Hybridization oven 645. Cartridge arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Cartridge arrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with R (Version 4.1) / Bioconductor (Version 3.13)

source_name: colon fibroblasts treated with H. italicum infusion for 24 h

label_protocol: Biotinylated sense-strand DNA targets were prepared according to the standard Applied Biosystems protocol from 500 ng total RNA (GeneChip™ WT PLUS Reagent Kit Manual for GeneChip™ Whole Transcript (WT) Expression Arrays, Thermo Fisher Scientific).

growth_protocol: Colon fibroblasts (P4) were seeded in density 16.600 cells/cm2 and grown in DMEM high glucose supplemented with 10 % FBS for 24 h, maintained at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Thermo Fisher Scientific).

treatment_protocol: Cell media was replaced with media containing 0.1 v/v% of freshly prepared and sterile filtered HI infusion or sterile water in the same concentration. Treatment duration was 6 h or 24 h.

value: normal colon fibroblasts

value: 22 weeks gestation

value: female

tag: passage


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b4

description: umi0.csv, umi1.csv, counts.csv


title: sample treated for 24 h, biological replicate 1


title: Control Smad7KO  Cardiac fibroblasts, sample 2-CS72


title: sample treated for 6 h, biological replicate 1

source_name: colon fibroblasts treated with H. italicum infusion for 6 h


title: sample treated for 24 h, biological replicate 2


title: sample treated for 6 h, biological replicate 2


title: ALUBIA CE3 #2


title: Human jejunum – Reperfusion 30 min 1

source_name: Human jejunum – Reperfusion 30min

value: 45-60 min ischaemia 30 min reperfusion


title: ALUBIA 55N1 #2


title: TGFβ-treated Wild Type Cardiac fibroblasts, sample 1-TWT2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b3

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b2

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b5

description: umi0.csv, umi1.csv, counts.csv


title: ALUBIA 55N1 #1


title: tolerogenic_dendritic_cell_repC

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: Tolerogenic Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4+Dexamethasone (replicate C)

hyb_protocol: Hybridization was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

scan_protocol: Scanning was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

data_processing: Raw data were process using the R language. First, background normalisation was performed using Robust Microarray Analysis (RMA) normalisation provided by oligo package. Each probe was then annotated using clariomshumantranscriptcluster.db package, and the average expression level was calculated if more than one probe was mapped to the same gene.

source_name: Tolerogenic dendritic cells derived from monocytes (replicate C)

label_protocol: Labelling was performed using GeneChip® High Throughput Pico Kit (Affymatrix) according to manufacturers' instructions

growth_protocol: Monocytes were isolated from buffy coats by CD14 positive selection (MACS) and cultured 6 days in Roswell Park Memorial Institute (RPMI) Medium 1640 + GlutaMAX™ containing 10% fetal bovine serum, 100 units/mL penicillin, 100 mg/mL streptomycin

extract_protocol: Total RNA was isolated utilizing Maxwell® RSC simplyRNA Cells Kit (Promega)

treatment_protocol: At the beginning of the differentiation process, 10ng/mL human Granulocyte Macrophage Colony-Stimulating Factor, 10ng/mL human Interleukin 4 and 100nM Dexamethasone were added to the cell medium.

value: tolDC

tag: individual

value: donor C


title: control sample, biological replicate 3

source_name: non-treated (control) colon fibroblasts


title: sample treated for 6 h, biological replicate 3


title: control sample, biological replicate 2


title: LKMEA4: LKR10_3D_shAnkrd35_Rep4

city: San Francisco

first: David

last: Simpson

state: California

address: 1550 4th Street

institute: UCSF

data_processing:
Samples were trimmed for adaptor sequence and remove for low-quality sequence using Trimmomatic 0.38,  then mapped to mm10 whole genome using  STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf provided from genecode ( vM13)
Sequences were imported into R , scaled, filter for low counts ( < 1 cpm) and  TMM normalized using the edgeR package.
cpm data adjusted with prior.count = 2 follow by log2 transform
Genome_build: mm10
Supplementary_files_format_and_content: single tab delimited file containing normalize log2 (cpm) adjusted with prior.count=2

source_name: murine cell line LKR10

growth_protocol: 2D growth of LKR10 cells was in DMEM media with 10% FBS and  pen/strep/glutamine. 3D growth in 0.5% methylcellulose in complete DMEM media.

extract_protocol:
TRIzol extraction according to manufacturers protocol, followed by cleanup and Dnase treatment using the RNeasy kit columns with DNase treatment, also according to manufacturers protocol.
RNA was enriched using oligo(dT) beads. The mRNA was then fragmented randomly by adding fragmentation buffer, then the cDNA synthesized by using the mRNA template and random hexamers as primers, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of terminal repair, ligation and sequencing adaptor ligation, the double-stranded cDNA library was size selected and PCR enriched.

treatment_protocol: LKR10 cell lines were transduced with pLKO lentiviral vectos expressing either shRNAs targeting GFP (control) or Ankrd35 (experimental) and selected with 4ug/ml puromycin for 48 hours. Cells were grown for another 96 hours until harvesting RNA

value: murine cell line LKR10

tag: growth type

value: 3D methylcellulose ultra low attachment

tag: shRNA


title: Control Wild Type Cardiac fibroblasts, sample 3-CWT3

value: cardiac fibroblasts isolated from Smad7 floxed mice

tag: strain

tag: treatment


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b12

description: umi0.csv, umi1.csv, counts.csv

tag: cell line


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b10

description: umi0.csv, umi1.csv, counts.csv


title: S. Typhimurium WT_SPI-2 Inducing Conditions 2

city: Boston

first: Jeffrey

last: Bourgeois

address: 136 Harrison Ave

institute: Tufts University

description: Ribosomal RNA depleted RNA

data_processing:
RNA-seq data was processed using the TrimGalore toolkit (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer after trimming were kept for further analysis. Reads were mapped to the ASM2216v1 version of the Salmonella enterica strain 14028S genome and transcriptome using the STAR RNA-seq alignment tool . Reads were kept for subsequent analysis if they mapped to a single genomic location. Gene counts were compiled using the HTSeq tool (http://www-huber.embl.de/users/anders/HTSeq/).  Only genes that had at least 10 reads in any given library were used in subsequent analysis. Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment (https://www.R-project.org/).The false discovery rate was calculated to control for multiple hypothesis testing.
Genome_build: ASM2216v1
Supplementary_files_format_and_content: Processed_yhdJ_RNAseq.xlsx

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium WT

growth_protocol: For SPI-1 inducing conditions, bacteria were grown overnight at 37C in LB broth and subcultured 1:33 into LB broth before growth for 2 hours and 40 minutes. For SPI-2 inducing conditons, bacteria were grown overnight at 37C in LB broth and subcultured 1:50 in LPM media (see Coombes et al. 2004) for 4 hours.

extract_protocol:
RNAprotect Bacteria Reagent (Qiagen) in order to stabilize transcripts. After 5 minutes, bacteria were re-pelleted, and resuspended in 200mL of TE Buffer containing lysozyme (15mg/mL) and 20mL of Proteinase K. After addition of 700uL of buffer RLT+ bME, RNA was extracted using an RNeasy extraction kit (Qiagen). DNase was degraded with two Turbo DNase (Thermo-Fisher) per manufacturer instructions. To remove DNase after treatment, the solution was mixed with 350 L of -mercaptoethanol-containing RLT buffer, and then 700L of 96% ethanol was added. The mixture was then added to a RNeasy MinElute column (Qiagen) and RNA was reisolated according to manufacturer instructions.
Illumina TruSeq Stranded total RNA-Seq Kit combined with Ribo-Zero rRNA removal kit (bacteria) was used to prepare total RNA-seq libraries.
The rRNA depleted RNA was then reverse transcribed.  During the 2nd strand synthesis, the cDNA:RNA hybrid is converted into to double-stranded cDNA (dscDNA) and dUTP incorporated into the 2nd cDNA strand, effectively marking the second strand.  Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. The strand marked with dUTP is not amplified, allowing strand-specificity sequencing.
Libraries were indexed using a dual indexing approach allowing for multiple libraries to be pooled and sequenced on the same sequencing flow cell

tag: growth conditions

value: SPI-2 Inducing Conditions

tag: genotype

value: S. Typhimurium WT


title: monocyte_repC

description: Non-cultured CD14⁺ monocytes (replicate C)

source_name: Non-cultured monocytes (replicate C)

value: MO


title: control sample, biological replicate 1


title: S. Typhimurium ∆yhdJ_SPI-2 Inducing Conditions 3

description: Ribosomal RNA depleted RNA

source_name: S. Typhimurium {delta}yhdJ

value: S. Typhimurium {delta}yhdJ


title: tolerogenic_dendritic_cell_repB

description: Tolerogenic Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4+Dexamethasone (replicate B)

source_name: Tolerogenic dendritic cells derived from monocytes (replicate B)

value: donor B


title: dendritic_cell_repB

description: Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4 (replicate B)

source_name: Dendritic cells derived from monocytes (replicate B)

value: DC


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b1

description: umi0.csv, umi1.csv, counts.csv

source_name: Single cell from cultured HEK293 cells


title: tolerogenic_dendritic_cell_repA

description: Tolerogenic Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4+Dexamethasone (replicate A)

source_name: Tolerogenic dendritic cells derived from monocytes (replicate A)

value: donor A


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b7

description: umi0.csv, umi1.csv, counts.csv


title: S. Typhimurium WT_SPI-1 Inducing Conditions 2

description: Ribosomal RNA depleted RNA

value: SPI-1 Inducing Conditions


title: Control Wild Type Cardiac fibroblasts, sample 2-CWT2

value: Control GFP adenovirus infection

value: No treatment


title: S. Typhimurium ∆yhdJ_SPI-2 Inducing Conditions 1

description: Ribosomal RNA depleted RNA


title: S. Typhimurium WT_SPI-2 Inducing Conditions 3

description: Ribosomal RNA depleted RNA


title: S. Typhimurium ∆yhdJ_SPI-1 Inducing Conditions 3

description: Ribosomal RNA depleted RNA


title: Control Wild Type Cardiac fibroblasts, sample 1-CWT1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a7

description: umi0.csv, umi1.csv, counts.csv


title: dendritic_cell_repC

description: Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4 (replicate C)

source_name: Dendritic cells derived from monocytes (replicate C)


title: LKMEG2: LKR10_3D_shGFP_Rep2

tag: tissue

value: GFP


title: oxic incubation, replicate 6

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

description: whole symbiotic marine nematodes  rRNA-depleted RNA containing both nematode and symbiont RNA

data_processing:
Based on quality assessment of raw sequencing reads using FastQC (Andrews, 2010) and prinseq-lite (Schmieder and Edwards, 2011), reads were trimmed and filtered using Trimmomatic (Bolger et al., 2014) and prinseq-lite as follows: 18 nucleotides were removed from the 5-prime end (HEADCROP), Illumina adapters were removed (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10), reads were trimmed when the average quality of a five-base sliding window dropped below a phred score of 20 (SLIDINGWINDOW:5:20), 3-prime poly-A tails were trimmed (-trim_tail_right 1), and only reads longer than 24 nucleotides were kept (MINLEN:25).
Trimmed reads were mapped to the de novo transcriptome assembly (GenBank: GJNO00000000.1) and transcript abundance was estimated using RSEM v1.3.1 (Li and Dewey 2011) in combination with bowtie2 with default settings except for the application of strandedness (--strandedness forward).
Supplementary_files_format_and_content: counts file

organism: Laxus oneistus

source_name: Laxus oneistus associated with Ca. Thiosymbion oneisti

growth_protocol: Laxus oneistus individual worms were collected on multiple field trips (2016-2019) at approximately 1 m depth from sand bars off the Smithsonian Field Station, Carrie Bow Cay in Belize (16°48′11.01″N, 88°4′54.42″W). The nematodes were extracted from the sediment by gently stirring the sand and pouring the supernatant seawater through a 212 μm mesh sieve. The retained meiofauna was collected in a petri dish, and single worms of similar size (1-2 mm length, representing adult L. oneistus) were handpicked by forceps (Dumont 3, Fine Science Tools, Canada), under a dissecting microscope. Right after collection, the nematodes were incubated under four different conditions.

extract_protocol:
RNA was extracted using the NucleoSpin RNA XS Kit (Macherey-Nagel). Briefly, sets of 50 worms in RNA storage solution were thawed and the worms were transferred into 90 µl lysis buffer RA1 containing Tris (2-carboxyethyl) phosphine (TCEP) according to the manufacturer. The remaining RNA storage solution was centrifuged to collect any detached bacterial cells (10 min, 4°C, 16,100 x g), pellets were resuspended in 10 µl lysis buffer RA1 (plus TCEP) and then added to the worms in lysis buffer. To further disrupt cells, suspensions were vortexed for two minutes followed by three cycles of freeze (-80°C) and thaw (37°C), and homogenization using a pellet pestle (Sigma-Aldrich) for 60 s with a 15 s break after 30 s. Any remaining biological material on the pestle tips was collected by rinsing the tip with 100 µl lysis buffer RA1 (plus TCEP). Lysates were applied to NucleoSpin Filters and samples were processed as suggested by the manufacturer, including an on-filter DNA digest. RNA was eluted in 20 µl RNase-free water. To remove any residual DNA, a second DNase treatment was performed using the Turbo DNA-free Kit (Thermo Fisher Scientific), RNA was then dissolved in 17 µl RNase-free water, and the RNA quality was assessed using a Bioanalyzer (Agilent). To check whether all DNA was digested, real-time quantitative PCR using the GoTaq qPCR Master Mix (Promega) was performed targeting a 158 bp stretch of the sodB gene using primers specific for the symbiont (sodB-F: GTGAAGGGTAAGGACGGTTC, sodB-R: AATCCCAGTTGACGATCTCC, 10 µM per primer). Different concentrations of genomic Ca. T. oneisti DNA were used as positive controls. The program was as follows: 1x 95°C for 2 min, 40x 95°C for 15 s and 60°C for 1 min, 1x 95°C for 15 s, 55°C to 95°C over 20 min. Next, bacterial and eukaryotic rRNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Epidemiology) (Illumina) following the manufacturer’s instructions, but volumes were adjusted for low input RNA (Alberti et al., 2014). In short, 125 µl of Magnetic Beads Solution, 32.5 µl Magnetic Bead Resuspension Solution, 2 µl Ribo-Zero Reaction Buffer and 4 µl Ribo-Zero Removal Solution were used per sample. RNA was cleaned up via ethanol precipitation, dissolved in 9 µl RNase-free water, and rRNA removal was evaluated using the Bioanalyzer RNA Pico Kit (Agilent).
Strand-specific, indexed cDNA libraries were prepared using the SMARTer Stranded RNA-Seq Kit (Takara Bio USA). Library preparation was performed according to the instructions, with 8 µl of RNA per sample as input, 3 min fragmentation time, two rounds of AMPure XP Beads (Beckman Coulter) clean-up before amplification, and 18 PCR cycles for library amplification. The quality of the libraries was assessed via the Bioanalyzer DNA High Sensitivity Kit (Agilent). Libraries were sequenced on an Illumina HiSeq 200 instrument (single-read, 100 nt) at the next generation sequencing facility of the Vienna BioCenter Core Facilities (VBCF, https://www.viennabiocenter.org/facilities/). Demultiplexing was provided by the VBCF.

treatment_protocol: Batches of 50 freshly collected L. oneistus individuals per condition were incubated for 24 h in the dark in 13 ml-exetainers (Labco, Lampeter, Wales, UK) fully filled with 0.2 µm-filtered seawater. Moreover, different oxygen concentrations were applied: (1) high oxygen (exetainers were kept open and submerged in an aquarium constantly bubbled with air), (2) hypoxic (exetainers were kept open and were exposed to air), (3) anoxic (exetainers were kept inside polyethylene glove bags (AtmosBag; Sigma-Aldrich) that were flushed with N2 gas, together with incubation media and all vials, for at least 1 h before closing), and (4) anoxic with 11 µM sulfide (Na2S*9H2O) added ((exetainers were kept inside polyethylene glove bags (AtmosBag; Sigma-Aldrich) that were flushed with N2 gas, together with incubation media and all vials, for at least 1 h before closing). After the 24 h incubations, each set of 50 worms was quickly transferred into 2 ml RNA storage solution (13.3 mM EDTA disodium dihydrate pH 8.0, 16.6 mM sodium citrate dihydrate, 3.5 M ammonium sulfate, pH 5.2), kept at 4°C overnight, and finally stored in liquid nitrogen until RNA extraction.

value: oxic incubation

value: whole worm


title: S. Typhimurium WT_SPI-1 Inducing Conditions 3

description: Ribosomal RNA depleted RNA


title: LKMEA3: LKR10_3D_shAnkrd35_Rep3


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1b11

description: umi0.csv, umi1.csv, counts.csv


title: S. Typhimurium ∆yhdJ_SPI-2 Inducing Conditions 2

description: Ribosomal RNA depleted RNA


title: LKMEA2: LKR10_3D_shAnkrd35_Rep2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a6

description: umi0.csv, umi1.csv, counts.csv


title: LK2DA4: LKR10_2D_shAnkrd35_Rep4

value: 2D monolayer


title: LKMEA1: LKR10_3D_shAnkrd35_Rep1

value: murine cell line LKR10


title: S. Typhimurium ∆yhdJ_SPI-1 Inducing Conditions 2

description: Ribosomal RNA depleted RNA


title: LKMEG4: LKR10_3D_shGFP_Rep4

value: 3D methylcellulose ultra low attachment


title: oxic incubation, replicate 4


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a9

description: umi0.csv, umi1.csv, counts.csv


title: dendritic_cell_repA

description: Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4 (replicate A)

source_name: Dendritic cells derived from monocytes (replicate A)


title: monocyte_repB

description: Non-cultured CD14⁺ monocytes (replicate B)

source_name: Non-cultured monocytes (replicate B)


title: S. Typhimurium ∆metJ_SPI-2 Inducing Conditions_3

description: Ribosomal RNA depleted RNA

data_processing:
RNA-seq data was processed using the TrimGalore toolkit (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer after trimming were kept for further analysis. Reads were mapped to the ASM2216v1 version of the Salmonella enterica strain 14028S genome and transcriptome using the STAR RNA-seq alignment tool . Reads were kept for subsequent analysis if they mapped to a single genomic location. Gene counts were compiled using the HTSeq tool (http://www-huber.embl.de/users/anders/HTSeq/).  Only genes that had at least 10 reads in any given library were used in subsequent analysis. Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment (https://www.R-project.org/).The false discovery rate was calculated to control for multiple hypothesis testing.
Genome_build: ASM2216v1
Supplementary_files_format_and_content: Processed_metJ_RNAseq.xlsx

source_name: S. Typhimurium {delta}metJ

value: S. Typhimurium {delta}metJ


title: oxic incubation, replicate 3


title: LKMEG3: LKR10_3D_shGFP_Rep3


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a8

description: umi0.csv, umi1.csv, counts.csv


title: oxic incubation, replicate 2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a2

description: umi0.csv, umi1.csv, counts.csv


title: LK2DG4: LKR10_2D_shGFP_Rep4


title: monocyte_repA

description: Non-cultured CD14⁺ monocytes (replicate A)

source_name: Non-cultured monocytes (replicate A)


title: S. Typhimurium WT_SPI-1 Inducing Conditions_3

description: Ribosomal RNA depleted RNA


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a12

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a4

description: umi0.csv, umi1.csv, counts.csv


title: hypoxic incubation, replicate 3

value: hypoxic incubation


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a11

description: umi0.csv, umi1.csv, counts.csv


title: S. Typhimurium ∆metJ_SPI-2 Inducing Conditions_2

description: Ribosomal RNA depleted RNA

value: SPI-2 Inducing Conditions


title: S. Typhimurium WT_SPI-2 Inducing Conditions_2

description: Ribosomal RNA depleted RNA

value: S. Typhimurium WT


title: S. Typhimurium WT_SPI-2 Inducing Conditions 1

description: Ribosomal RNA depleted RNA


title: S. Typhimurium ∆metJ_SPI-1 Inducing Conditions_2

description: Ribosomal RNA depleted RNA


title: LKMEG1: LKR10_3D_shGFP_Rep1


title: S. Typhimurium ∆yhdJ_SPI-1 Inducing Conditions 1

description: Ribosomal RNA depleted RNA

value: S. Typhimurium {delta}yhdJ


title: LK2DA3: LKR10_2D_shAnkrd35_Rep3


title: S. Typhimurium WT_SPI-1 Inducing Conditions 1

description: Ribosomal RNA depleted RNA


title: LK2DA2: LKR10_2D_shAnkrd35_Rep2


title: S. Typhimurium WT_SPI-2 Inducing Conditions_3

description: Ribosomal RNA depleted RNA


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a3

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a5

description: umi0.csv, umi1.csv, counts.csv


title: oxic incubation, replicate 5


title: LK2DG2: LKR10_2D_shGFP_Rep2


title: S. Typhimurium ∆metJ_SPI-2 Inducing Conditions_1

description: Ribosomal RNA depleted RNA


title: LK2DA1: LKR10_2D_shAnkrd35_Rep1


title: oxic incubation, replicate 1


title: S. Typhimurium ∆metJ_SPI-1 Inducing Conditions_3

description: Ribosomal RNA depleted RNA


title: anoxic incubation, replicate 5

value: anoxic incubation


title: LK2DG3: LKR10_2D_shGFP_Rep3


title: hypoxic incubation, replicate 2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a10

description: umi0.csv, umi1.csv, counts.csv


title: S. Typhimurium WT_SPI-2 Inducing Conditions_1

description: Ribosomal RNA depleted RNA


title: anoxic + H2S incubation, replicate 3

value: anoxic + H2S incubation


title: LK2DG1: LKR10_2D_shGFP_Rep1


title: hypoxic incubation, replicate 1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1a1

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 RNA-Seq HEK293_BK

description: counts.csv

source_name: Cultured HEK293 cells


title: anoxic + H2S incubation, replicate 2


title: S. Typhimurium WT_SPI-1 Inducing Conditions_2

description: Ribosomal RNA depleted RNA


title: hAECs + placental basal medium _day7_3

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from untreated control hAECs on 7th day

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing: The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the DEGs between day 7 treated hAECs and D0 hAECs and for DEGs between day 7 treated hAECs and D7 hAECs to test whether a priori-defined groups of genes associated with neural differentiation were significantly related to the DEGs between EEA-treated and control cells on day 0 and day 7

source_name: amnion epithelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: AECs were isolated from delivered term placenta and were maintained in Placenta Epithelial Cell Basal Medium (PromoCell, Cat. # C-26140) in 2D culture plate. Finally, 3D spheroids were formed by seeding 1×106 AECs in Placenta Basal Epithelial Cell Medium into each well of the 24-well plate.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour culture, the medium was changed with EEA (at the concentration of 20 µg/ml ) every 48 hours for three times (7days) for the treatment samples. Control samples were maintained in Placental medium that was also changed every 48 hours. Finally, we collected the treatment and control samples from one-week culture.

value: Untreated control hAECs on day9


title: anoxic incubation, replicate 3


title: CD103+CD11b+ dendritic cells from lamina propria

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: CD103+CD11b+ DCs from lamina propria

data_processing:
sample de-multiplexing, cellranger mkfastq, Cell Ranger Single Cell Software Suite (v2.0.1)
single-cell 3′ cellranger count, Cell Ranger Single Cell Software Suite (v2.0.1)
quality control, Cell Ranger Single Cell Software Suite (v2.0.1)
barcode processing, Cell Ranger Single Cell Software Suite (v2.0.1)
alignment, Cell Ranger Single Cell Software Suite (v2.0.1)
gene counting, Cell Ranger Single Cell Software Suite (v2.0.1)
aggregate, cellranger aggr, Cell Ranger Single Cell Software Suite (v2.0.1)
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 Gene_Barcode Matrix files were generated using Cell Ranger Single Cell Software Suite (v2.0.1). For more information on the format and to read the matrix see : https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices.

source_name: small intestines

growth_protocol: Single-cell RNAseq library preparation and sequencing: CD103+CD11b+ dendritic cells were sorted from the lamina propria and epithelium of 2 pooled small intestines of C57BL/6J mice.

extract_protocol:
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol
Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3’ v2 Reagent Kit, following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select; (3) adaptor ligation; (4) post ligation cleanup with SPRI select; (5) sample index PCR and cleanup with SPRI select beads.

value: wild-type

value: lamina propria


title: anoxic incubation, replicate 2


title: anoxic + H2S incubation, replicate 1


title: S. Typhimurium WT_SPI-1 Inducing Conditions_1

description: Ribosomal RNA depleted RNA

value: SPI-1 Inducing Conditions


title: hAECs + placental basal medium _day7_1

value: Untreated control hAECs on day7


title: PLL_miRNA-seq

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and GRCh38. genome.
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Exosomes

growth_protocol: 10%FBS high-glucose DMEM were used as culture medium for primary ligament cell culture. When cells reach 80% confluent, the cell were lysed with trypsin for passage. After 2 passages, the primary cells were ready to perform exosome collection. For exosome collection, we use 1% exosome free FBS/DMEM for culture, the medium were collected at a 3-days interval for exosome collection.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
Proton Sequencing Protocol

treatment_protocol: no treatment

value: normal posterior longitudinal ligament (PLL)tissue

tag: molecule subtype

value: Exosomes


title: anoxic incubation, replicate 1

value: whole worm


title: S. Typhimurium ∆metJ_SPI-1 Inducing Conditions_1

description: Ribosomal RNA depleted RNA


title: CD103+CD11b+ dendritic cells from epithelium

description: CD103+CD11b+ DCs from epithelium

value: epithelium


title: OPLL_miRNA-seq

value: Ossification of Posterior Longitudinal Ligament (OPLL)


title: Treated mouse MPPs, rep 2

status: Public on Nov 10 2021

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

library_source: genomic

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina and Nextera adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against MM10 whole genome using bowtie2.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
Peaks were called with MACS3, using parameters "--nomodel --shift -100 --extsize 200", and "-q 0.05" as the false discovery rate cut-off.
Genome_build: MM10
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ATAC-seq peaks, using MACS3.

molecule: genomic DNA

source_name: Mouse MPPs

growth_protocol: Mice were treated for 2 weeks with 50 µL of MV130 (300 Formazin Turbidity Units [FTU]/mL ~ 1.0E+9 bacteria/mL)  or excipient intranasal (4 mice for condition). After one week of resting mice were sacrified in a CO2 chamber to collect femurs and tibia that were subsequently flushed with cold PBS to harvest bone marrow. Red blood cells lysis was performed once for 3 minutes.

extract_protocol:
Flow sorted mouse MPPs were collected in ice-cold Flow cytometry buffer and 30.000 cells were obtained pooling two biological replicates for every condition. Samples were immediately processed following previously published protocol (Buenrostro et al, 2013). The transposition reaction was started by adding Nextera’s Tn5 Transposase in reaction buffer and maintained by incubation for 30 minutes at 37°C. DNA was purified using a Quiagen MinElute PCR purification kit.
ATAC-seq libraries were generated following Buenrostro et al (2013), purified using a PCR purification MinElute kit (Quiagen) and quantified using a 2100 Bioanalyzer instrument (Agilent). Finally, libraries were sequenced 2x50 in a paired end flowcell (PE) run on Illuminaa NextSeq 2000 System.

treatment_protocol: Bone marrow cells were incubated in cold flow cytometry buffer with a panel of antibodies against lineage committed cells (CD3, CD45R, CD11b, Ter-119, Gr-1) all biotinylated and from BD Pharmigen. After washing, cells were incubated with streptavidin magnetic beads (Miltenyi) and passed through LS columns (Miltenyi) . Thus, collected cells were stained with Sca-1, c-kit (CD117), CD48, CD150 antibodies and with the viability marker Hoechst 33258 prior to be sorted by FACS Aria II. MPPs were identified as Lin-c-kit+ sca-1+ CD48+ CD150- cells.

value: Mouse MPPs


title: Treated mouse MPPs, rep 1


title: Control mouse MPPs, rep 2

value: Control (excipient)


title: hAECs+ EEA 2

description: Gene expression data from EEA treated hAECs on 7th day

value: EEA for 7 days


title: hAECs + placental basal medium _day7_2

value: Untreated control hAECs on day8


title: hAECs+ EEA 3


title: Control human monocytes, rep 3

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina and Nextera adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against HG38 whole genome using bowtie2.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
Peaks were called with MACS3, using parameters "--nomodel --shift -100 --extsize 200", and "-q 0.05" as the false discovery rate cut-off.
Genome_build: HG38
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ATAC-seq peaks, using MACS3.

source_name: Human monocytes

growth_protocol: Buffy coats from healthy volunteers were obtained from Andalusian Biobank. Human peripheral blood mononuclear cells (hPBMCs) were isolated by differential centrifugation using Biocoll Separating Solution and human monocytes were selected by adhesion.

extract_protocol:
At day 5, human monocytes were detached and 50.000 cells were colleceted in ice-cold Flow cytometry buffer and immediately processed following a previously published protocol (Buenrostro et al, 2013). The transposition reaction was started by adding Nextera’s Tn5 Transposase in reaction buffer and mantained by incubation for 30 minutes at 37°C. DNA was purified using a Quiagen MinElute PCR purification kit.
ATAC-seq libraries were generated following Buenrostro et al (2013), purified using a PCR purification MinElute kit (Quiagen) and quantified using a 2100 Bioanalyzer instrument (Agilent). Finally, libraries were sequenced 2x50 in a paired end flowcell (PE) run on Illuminaa NextSeq 2000 System.

treatment_protocol: 1.5E+6 human monocytes were plated in in 10 cm Petri dishes and stimulated at day 0 with MV130 (3.0E+6 bacteria/plate) or excipient. After 24 hours cells were washed and left resting for 5 days.

value: Human monocytes


title: Control mouse MPPs, rep 1


title: hAECs+ EEA 1


title: Treated human monocytes, rep 2


title: shRACK1 J1

city: La Jolla

first: George

last: Sen

address: 9452 Medical Center Dr

department: Dermatology

institute: University of Californai San diego

data_processing:
Illumina Nextseq2000 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using STAR.
Aligned reads were mapped to RefSeq and normalized using Partek Flow. Genes with reads less than 10 were excluded in every sample.
Statistics were calculated by ANOVA and differential genes was selected based on p-values <0.05 and with a >2 fold change (+/-).
Genome_build: hg19
Supplementary_files_format_and_content: txt file with normalized gene read counts

source_name: epidermal progenitor cells

growth_protocol: Epidermal progenitor cells were grown on culture dishes and maintained in keratinocyte Epilife medium plus HKGS (Life technologies)

extract_protocol:
Total RNA was isolated using GeneJET RNA purification kit (Thermo Scientific)
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: shCTR (non-targeting), shRACK1-A, shRACK1-J knockdown

value: neonatal foreskin

value: primary keratinocytes

value: shRACK1-J knockdown


title: Control human monocytes, rep 2


title: shRACK1 J2


title: Control human monocytes, rep 1


title: shRACK1 A2

value: shRACK1-A knockdown


title: Treated human monocytes, rep 1


title: ago1-57 AGO1 IP TuYVs81 R2

city: Strasbourg cedex

first: Pascal

last: Genschik

address: 12, rue du général Zimmer

institute: Institut de biologie moléculaire des plantes

data_processing:
Library preparation and sRNA sequencing (single-read, 50bp, V4 chemistry) on Illumina HiSeq were performed by Fasteris (http://www.fasteris.com), with each sample split and sequenced in two independent lanes. FASTQ file generation, demultiplexing, and adapter removal were done by Fasteris
Basecalling pipeline - HiSeq Control Software 2.2.58 RTA 1.18.64.0_CASAVA-1.8.2
Reads (18 to 26 nucleotides long) were aligned and quantified using using Shortstack v3.8.5 with the ‘fractional’ option, allowing for no mismatches, with the Arabidopsis genome (TAIR10) and TuYVs81 genome as reference
Genome_build: TAIR10 and TuYVs81 genome

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: seeds were directly sown on soil (Hawita Fruhstorfer) in trays and kept under a 12-h-light/12-h-dark regime for about 4 weeks before inoculation

extract_protocol:
Total RNA samples and AGO1 IP samples were both obtained from Col-0 and ago1-57 rosette leaves from TuYVs81 infected of mock -inoculated plants 16 days after inoculation. For both genotypes, only plants with vein yellowing were included in the analysis. Plants were separated into pools of 7-8 plants per biological replicate, and the resulting mixed and ground tissue was used as the input material for the AGO1 IP and the total RNA. About 100 mg of material was used to extract total RNA using tri-reagent as described, and IPs were performed from 1 g starting material. AGO1-loaded sRNAs were then extracted by adding Tri-Reagent directly on the magnetic beads
size fractionation

treatment_protocol: recombinant viruses were grown overnight at 28°C in antibiotic-supplemented LB media, pelleted 15 minutes at 4000g and resuspended in 10.5 g/L K2HPO4/4.5 g/L KH2PO4/1 g/L (NH4)2SO4/0.5 g/L sodium citrate/0.1 g/L MgSO4/0.4% (v/v) glycerol/0.1 g/L MES/200 μM Acetosyringone and incubated 5-6 hours in the dark. Cells were pelleted again and resuspended in infiltration medium (10mM MgCl2/10mM MES/200µM Acetosyringone)The cells were then adjusted to an OD600nm of 0.5 and agroinfiltrated into three leaves per plants with a needleless syringe. Plants post-inoculation were then grown in either 12-h-light/12-h-dark period with fluorescent light

value: rosette leaves

value: Columbia-0 wild type

value: TuYVs81 infected


title: shRACK1 A1


title: shCTR2

value: control


title: BV2-LPS-NT-rep1

city: Hefei

first: Jiagen

last: Wen

state: Anhui

address: NO.81, Meishan Road, Anhui Medical University

institute: Anhui Medical University

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: BV-2 microglial cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using Low Input Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed purification by QIAGEN RNeasy Mini kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: BV-2 microglial was cultured in Dulbecco’s modified Eagle’s medium (DMEM) high glucose medium supplemented with 10% fetal bovine serum (FBS), 1 mM pyruvate, 100 U/ml penicillin/100 µg/ml streptomycin in a 5% CO2 humidifified atmosphere at 37◦C.

extract_protocol: Takara RNAiso Plus (Dalian, Liaoning, China) was used to extract total RNAs following the manufacturer’s protocol. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The culture medium of cells seeded in the 6-well plate was changed to the medium supplemented with lipopolysaccharide or not. Then, the plates were kept in carbon dioxide incubator with the temperature setting at 33◦C or 37◦C for 4 hours.

value: mouse microglial cell line

value: after 4 hour treatment of lipopolysaccharide


title: BV2-LPS-NT-rep2


title: BV2-vehicle-NT-rep3

value: for normal culture


title: Rut-C30-delta-vps13 V13_1

city: 无锡

first: 肃

last: 闫

state: 江苏

address: 江苏省无锡市滨湖区江南大学生物工程学院

institute: Jiangnan 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 Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels.
Genome_build: ensemblfungi_trichoderma_reesei_qm6a_gca_000167675_2_gca_000167675_2
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

organism: Trichoderma reesei

source_name: mycelia

extract_protocol:
Total RNA was extracted using Trizol reagent. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: time

value: Avicel induction for 96 h


title: Rut-C30-delta-vps21 V21_1

address: 江苏省无锡市滨湖区江南大学生物工程学院


title: wild type strain Rut-C30 C30_3

address: 江苏省无锡市滨湖区江南大学生物工程学院

description: wild type strain Rut-C30


title: BV2-LPS-YT-rep3

value: after 4 hour treatment of lipopolysaccharide in 33C incubator


title: shCTR1


title: wild type strain Rut-C30 C30_2

address: 江苏省无锡市滨湖区江南大学生物工程学院

description: wild type strain Rut-C30


title: BV2-vehicle-YT-rep2

value: after 4 hour culture in 33C incubator


title: Rut-C30-delta-vps21 V21_2

address: 江苏省无锡市滨湖区江南大学生物工程学院


title: BV2-LPS-NT-rep3


title: BV2-vehicle-NT-rep1


title: BV2-LPS-YT-rep1


title: BV2-vehicle-NT-rep2


title: Rut-C30-delta-vps13 V13_3

address: 江苏省无锡市滨湖区江南大学生物工程学院


title: Col-0 AGO1 IP TuYVs81 R2


title: Treated human monocytes, rep 3


title: Rut-C30-delta-vps13 V13_2

address: 江苏省无锡市滨湖区江南大学生物工程学院


title: ago1-57 AGO1 IP mock R2

value: Mock inoculated


title: wild type strain Rut-C30 C30_1

address: 江苏省无锡市滨湖区江南大学生物工程学院

description: wild type strain Rut-C30


title: ago1-57 AGO1 IP mock R1


title: BV2-vehicle-YT-rep3


title: BV2-LPS-YT-rep2


title: BV2-vehicle-YT-rep1


title: Col-0 AGO1 IP mock R1


title: ago1-57 total RNA TuYVs81 R2


title: ago1-57 total RNA TuYVs81 R1


title: ago1-57 AGO1 IP TuYVs81 R1


title: Col-0 AGO1 IP TuYVs81 R1


title: Col-0 total RNA TuYVs81 R1


title: ago1-57 total RNA mock R2


title: ago1-57 total RNA mock R1


title: Col-0 total RNA TuYVs81 R2


title: Col-0 AGO1 IP mock R2


title: Col-0 total RNA mock R2


title: Col-0 total RNA mock R1


title: Time4_HEK_120mins

city: Lausanne

first: Marjan

last: Biočanin

state: Vaud

address: Station 19, SV 3820

department: SV-IBI

institute: EPFL

data_processing:
Drop-seq tools package on the EPFL SCITAS HPC platform. After trimming and sequence tagging, reads were aligned to the mouse  reference genome (mm10) using STAR (version 2.7.0.e). https://github.com/mccrowjp/Dropseq
Following the alignment, the gene annotation was added, bead synthesis errors were corrected and cell barcodes extracted. Subsequently, the BAM files containing the processed data were used to obtain digital gene expression matrices.
Downstream data analysis was carried out using R (version 3.5.0)
Genome_build: hs.g38r91
Supplementary_files_format_and_content: tab-delimited text files include read-count matrices for each experiment and digital gene expression files

source_name: HEK 293T

growth_protocol: The human embryonic kidney 293T cell line was cultured in suspension in a DMEM medium supplemented 10% fetal bovine serum and 1% antibiotics (L-Glutamine-penicillin-streptomycin).

extract_protocol:
Recovered cells were centrifuged at 600g for 5 min and supernatant was replaced with 25 µl of PBS containing 0.01 % bovine serum albumin (Sigma). Subsequently 25 ml of lysis buffer were added, containing 0.1 % Sarkosyl (Sigma), 5 mM EDTA (Life Technologies), 0.1 M Tris (pH 7.5, Sigma) and 25 mM 1,4-Dithioreitol (DTT, Sigma), 800 units/ml RNase inhibitor (NEB) and 500 Drop-Seq beads (Beads, Lot 120817, ChemGenes). All beads pelleting steps were carried out at 1000 g for 1 min in 1.5 ml microtubes (Axygen). Reverse transcription (RT), exonuclease I (ExoI) treatment and PCR were performed as described Macosko et al. with minor adaptations30. Lysed cells were incubated at 1400 rpm for 5 min at room temperature and subsequently washed twice with 1 ml of 6x SSC buffer (Sigma).
Reverse transcription was performed for 90 min at 42°C in 50 µl of 1 mM dNTPs (Clontech), 2.5 µM template switch oligo (see Table 1), 1250 units/ml RNase inhibitor, 1x Maxima RT buffer and 10,000 units/ml Maxima H minus reverse transcriptase (Thermo Fisher Scientific). Drop-seq beads were washed twice with 0.5 % SDS (Applichem) in 10 mM Tris (TE‑SDS), twice with 0.01 % Tween‑20 (Sigma) in 10 mM Tris (TE‑TW) and once with 10 mM Tris pH 7.5. The Drop-seq beads pellet was then incubated with 50 µl of exonuclease mix containing 1x Exonuclease I Buffer and 1000 units/ml Exonuclease I (NEB), and incubated at 37°C for 45 min at 1,400 rpm). Drop-seq beads were washed twice with TE‑SDS, twice with TE‑TW and once with double-distilled H2O. Beads were amplified by PCR in 25 µL of 1x Hifi HotStart Readymix (Kapa Biosystems) and 0.8 µM TSO-PCR primer (Table 1) at 95 C 3 min; 4 cycles of: 98 C for 20 sec, 65 C for 45 sec, 72 C for 3 min; then 16 cycles of: 98°C for 20 sec, 67°C for 20 sec, 72°C for 3 min and an extension step of 5 min. Libraries were purified using Ampure XP beads (0.6x ratio to remove small fragments), cDNA was quantified using a Qubit HS kit (Thermo Fisher Scientific) and integrity analyzed on a Fragment Analyzer (Agilent). Libraries were prepared using in-house produced Tn5 loaded with adapters, as described31. Size selected and purified libraries were sequenced paired-end on a NextSeq 500 system (Illumina) in High-Output mode following recommendations from the original protocol (read 1 20 bp and read 2 50 bp)

value: HEK 293T

tag: sample type

value: In vitro cell culture

value: 25-30 passage

tag: condition


title: C1_HEK_148_H8_S74

data_processing:
Libraries were then sequenced on a NextSeq500 sequencer (Illumina) using paired-end run (read 1 - 16 bp, read 2 - 59 bp) with an average of 3 x 10^6 reads per library.
Read quality of sequenced libraries was evaluated with FastQC.
Sequencing reads were aligned to the reference human genome assembly GRCh38.90 using STAR (Dobin et al., 2013). Reads aligned to annotated genes were quantified with htseq-count (Anders et al., 2015).
Genome_build: GRCh38.90
Supplementary_files_format_and_content: tab-delimited text file include read-count matrices

source_name: cell culture

extract_protocol:
Recovered cells were centrifuged at 600g for 5 min and subsequently processed according the Fluidigm C1 Quick Reference User Guide (ID: PN 100-5003 C1). cDNAs were generated per cell using the" SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System" (Cat. Nos. 635025 & 635026) according to the manufacturers recommended procedure. cDNA libraries were quantified using Qbit and size distribution assessed via Fragmentanalyzer.
cDNAs obtained from each C1 Fluidigm chip were normalized for DNA concentration 0.3ng/ul. cDNA libraries were processed to obtain sequencing libraries using Nextera XT library prep kit (FC-131-1096) together with Nextera XT inxed kit 96 indexes set A (FC-131-2001) for each cell's cDNA. Sequencing libraries originated from one C1 Fluidigm chip were pooled and subsequently sequenced utilizing the NextSeq500.
Dual-indexed paired-end Illumina Nextera XT libraries (read1 = 16bp, read2 = 59bp)

value: In vitro

value: single cell


title: Time5_HEK_180mins


title: C1_HEK_148_H7_S66


title: Time3_HEK_60mins


title: C1_HEK_148_H1_S24


title: C1_HEK_148_H2_S32


title: C1_HEK_148_G7_S65


title: Time2_HEK_40mins


title: Time1_HEK_20mins

description: Drop-seq library


title: C1_HEK_148_H9_S82


title: C1_HEK_148_G3_S38


title: C1_HEK_148_H5_S52


title: C1_HEK_148_G11_S96


title: C1_HEK_148_H3_S39


title: C1_HEK_148_F7_S64


title: C1_HEK_148_F8_S72


title: C1_HEK_148_F5_S50


title: C1_HEK_148_F9_S80


title: C1_HEK_148_G9_S81


title: C1_HEK_148_H12_S104


title: C1_HEK_148_F12_S102


title: C1_HEK_148_F1_S22


title: C1_HEK_148_G5_S51


title: C1_HEK_148_G8_S73


title: C1_HEK_148_G6_S58


title: C1_HEK_148_E8_S71


title: C1_HEK_148_G4_S44


title: C1_HEK_148_E9_S79


title: C1_HEK_148_E6_S56


title: C1_HEK_148_E5_S49


title: C1_HEK_148_E3_S36


title: C1_HEK_148_F4_S43


title: C1_HEK_148_G1_S23


title: C1_HEK_148_G10_S89


title: C1_HEK_148_G12_S103


title: C1_HEK_148_G2_S31


title: C1_HEK_148_E11_S94


title: C1_HEK_148_F6_S57


title: C1_HEK_148_F3_S37


title: C1_HEK_148_D8_S70


title: C1_HEK_148_F2_S30


title: C1_HEK_148_D5_S48


title: C1_HEK_148_D1_S20


title: C1_HEK_148_D3_S35


title: C1_HEK_148_D2_S28


title: C1_HEK_148_D12_S100


title: C1_HEK_148_E1_S21


title: C1_HEK_148_E4_S42


title: C1_HEK_148_E2_S29


title: C1_HEK_148_F10_S88


title: C1_HEK_148_E12_S101


title: Rut-C30-delta-vps21 V21_3

address: 江苏省无锡市滨湖区江南大学生物工程学院


title: C1_HEK_148_F11_S95


title: C1_HEK_148_E10_S87


title: C1_HEK_148_D6_S55


title: C1_HEK_148_D7_S62


title: C1_HEK_148_C9_S77


title: C1_HEK_148_D9_S78


title: C1_HEK_148_C8_S69


title: C1_HEK_148_C6_S54


title: C1_HEK_148_C11_S92


title: C1_HEK_148_C10_S85


title: C1_HEK_148_B9_S76


title: C1_HEK_148_B3_S33


title: C1_HEK_148_C7_S61


title: C1_HEK_148_C5_S47


title: C1_HEK_148_B1_S18


title: C1_HEK_148_C2_S27


title: C1_HEK_148_D10_S86


title: C1_HEK_148_C3_S34


title: C1_HEK_148_C4_S40


title: C1_HEK_148_D11_S93


title: C1_HEK_148_C1_S19


title: C1_HEK_148_C12_S99


title: C1_HEK_148_D4_S41


title: C1_HEK_148_B6_S53


title: C1_HEK_148_A7_S59


title: C1_HEK_148_A8_S67


title: C1_HEK_148_A2_S25


title: C1_HEK_148_B2_S26


title: C1_HEK_148_B10_S84


title: C1_HEK_148_B11_S91


title: C1_HEK_148_E7_S63


title: C1_HEK_148_B5_S46


title: C1_HEK_148_A5_S45


title: C1_HEK_148_B7_S60


title: C1_HEK_148_A1_S17


title: C1_HEK_148_B8_S68


title: C1_HEK_148_A12_S97


title: C1_HEK_148_B12_S98


title: C1_HEK_150_H9_S74


title: C1_HEK_148_A11_S90


title: C1_HEK_150_H1_S59


title: C1_HEK_150_H7_S68


title: C1_HEK_150_H3_S65


title: C1_HEK_150_G8_S71


title: C1_HEK_148_A9_S75


title: C1_HEK_150_H2_S62


title: C1_HEK_150_H8_S72


title: C1_HEK_150_G3_S64


title: C1_HEK_150_F8_S70


title: C1_HEK_150_C8_S69


title: C1_HEK_150_G2_S61


title: C1_HEK_150_G7_S67


title: C1_HEK_150_E7_S66


title: C1_HEK_150_G1_S58


title: C1_HEK_150_F9_S73


title: C1_HEK_147_H9_S57


title: C1_HEK_150_F2_S60


title: C1_HEK_147_H8_S53


title: C1_HEK_147_G7_S46


title: C1_HEK_147_G8_S52


title: C1_HEK_150_F3_S63


title: C1_HEK_147_H2_S35


title: C1_HEK_147_H3_S41


title: C1_HEK_147_H7_S47


title: C1_HEK_147_G2_S34


title: C1_HEK_147_G9_S56


title: C1_HEK_147_G3_S40


title: C1_HEK_148_A10_S83


title: C1_HEK_147_E8_S50


title: C1_HEK_147_F2_S33


title: C1_HEK_147_E9_S55


title: C1_HEK_147_F3_S39


title: C1_HEK_147_E7_S45


title: C1_HEK_147_D8_S49


title: C1_HEK_147_E1_S25


title: C1_HEK_147_E2_S32


title: C1_HEK_147_G1_S27


title: C1_HEK_147_F1_S26


title: C1_HEK_147_F8_S51


title: C1_HEK_147_H1_S28


title: C1_HEK_147_E3_S38


title: C1_HEK_147_C2_S30


title: C1_HEK_147_C1_S23


title: C1_HEK_147_C5_S42


title: C1_HEK_147_B8_S48


title: C1_HEK_147_D7_S44


title: C1_HEK_147_C3_S36


title: RNAseq_GRSF1_WT2

city: Cambridge

first: Sergio

last: Martínez Cuesta

address: 1 Francis Crick Avenue

department: Data Sciences and Quantitative Biology, Discovery Sciences

country: United Kingdom

institute: AstraZeneca

data_processing:
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/sblab-bioinformatics/rna-g4-proteins
Genome_build: hg38
Supplementary_files_format_and_content: bigwig and normalized genomic signal as calculated in https://github.com/sblab-bioinformatics/rna-g4-proteins

growth_protocol: HEK293FT stable cells expressing DHX36 and GRSF1 were generated using pcDNA5.1 FRT vector (Life Technologies) and selected as per manufacturers instructions. Stable cell lines were grown in DMEM 10% Tet-free FBS at 37 degree celcius and 5% CO2

extract_protocol:
RNA was extracted using TRIzol following manufacturers instructions
Library was constructed using NEBNext Ultra II Directional RNA library prep kit following rRNA depletion with NEBNext rRNA depletion kit.

treatment_protocol: Protein expression was induced with 0.01ug/ml doxycycline for 24 hours

value: Flp-In T-REx 293

tag: tagged protein expressed

value: GRSF1 WT

tag: genome build


title: C1_HEK_147_D3_S37


title: RNAseq_GRSF1_WT3


title: RNAseq_DHX36_WT2

value: DHX36 WT


title: RNAseq_DHX36_WT1


title: C1_HEK_147_D1_S24


title: C1_HEK_147_B2_S29


title: C1_HEK_147_C9_S54


title: C1_HEK_147_D2_S31


title: RNAseq_GRSF1_WT1


title: RNAseq_DHX36_WT3


title: C1_HEK_147_C7_S43


title: 3_prime_mRNASeq_E203Q_shINTS11_ctrl_r2

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

description:
E203Q shINTS11
3' mRNA-Seq

data_processing:
ChIP-seq/3'mRNAseq: FASTQ data were processed with Trimmomatic v0.32 to remove adapters and low-quality reads.
eCLIP: FASTQ data were processed were double adapter trimming with cutadapt v1.14.
ChIP-seq: Reads were aligned to the hg19 human genome using STAR aligner v2.5.3a with default parameters.
eCLIP: Data was processed according to Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810. https://github.com/YeoLab/eclip
3'mRNA: Analysis was performed by using the LexonGen QuantSeq data pipeline. Briefly reads were aligned to the hg19 human genome using STAR aligner v2.5.3a with the following parameters:   --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The processed data files are in bigWig format: ChIP-seq/3'mRNAseq bigwigs were normalized by Count Per Million produced from DeepTools2.

source_name: HeLa

growth_protocol: HeLa stable containing INTS11 shRNA and overexpression E203Q mutant INTS11 cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. DMEM medium was supplemented with 10% FBS, puromycin (2 μg/ml) and G418 (200 μg/ml). Knockdowns were induced by adding of 1 μg/ml doxycycline (Dox) into the culture medium daily for 3 days.

extract_protocol:
Total RNA was extracted with TRizol (Thermo Fisher Scientific) and treated with TURBO DNase for 30min at 37°C. Ribosomal RNA was removed using NEBNext rRNA Depletion Kit v2 (NEB), we used 1ug of RNA as input in the QuantSeq 3’ mRNA-Seq Library Prep Kit REV (Lexogen) to prepare 3’ end libraries.
3'mRNA-seq libraries were generated using 1ug of RNA as input in the QuantSeq 3’ mRNA-Seq Library Prep Kit REV from Lexogen.

value: HeLa (ATCC #CCL-2)

tag: cell type

value: cervical adenocarcinoma

tag: modification


title: 3_prime_mRNASeq_E203Q_shINTS11_dox_r2

description:
E203Q shINTS11
3' mRNA-Seq


title: 3_prime_mRNASeq_WT_shINTS11_dox_r2

description:
WT shINTS11
3' mRNA-Seq

growth_protocol: HeLa stable containing INTS11 shRNA and overexpression WT INTS11 cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. DMEM medium was supplemented with 10% FBS, puromycin (2 μg/ml) and G418 (200 μg/ml). Knockdowns were induced by adding of 1 μg/ml doxycycline (Dox) into the culture medium daily for 3 days.


title: 3_prime_mRNASeq_WT_shINTS11_dox_r1

description:
WT shINTS11
3' mRNA-Seq


title: 3_prime_mRNASeq_E203Q_shINTS11_dox_r1

description:
E203Q shINTS11
3' mRNA-Seq


title: 3_prime_mRNASeq_WT_shINTS11_ctrl_r2

description:
WT shINTS11
3' mRNA-Seq


title: HeLa_shINTS11_dox_r2_H3K36me2_ChIP-seq

growth_protocol: HeLa stable containing INTS11 shRNA cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. DMEM medium was supplemented with 10% FBS and puromycin (2 μg/ml). Knockdowns were induced by adding of 1 μg/ml doxycycline (Dox) into the culture medium daily for 3 days.

extract_protocol:
ChIP-seq was performed as previously described (Gardini, A. et al. 2014, Lai, F. et a.l 2015, Yue, J. et. al 2017) with slight modifications. 2 x 10^7 cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine. Samples were resuspended in ChIP lysis buffer (20 mM Tris-HCl, 50 mM NaCl, 0.1% SDS, 0.5% Triton-X-100, 1 mM EDTA) and sonicated in a Covaris M220 focused sonicator until chromatin fragments of 150-300 bp were produced. Protein A/G magnetic beads were bound with antibody and incubated with 1 mg of sonicated chromatin overnight. The following day, beads were washed twice with Mixed Micelle Buffer (150 mM NaCl, 1% Triton X-100, 0.2% SDS, 20 mM Tris-HCl, 5 mM EDTA, 65% sucrose), Buffer 500 (500 mM NaCl, 1% Triton X-100, 0.1% Na deoxycholate, 25 mM HEPES, 10 mM Tris-HCl, 1 mM EDTA), LiCl/detergent wash (250 mM LiCl, 0.5% Na deoxycholate, 0.5% NP-40, 10 mM Tris-HCl, 1 mM EDTA), and eluted in Decrosslinking Buffer (20 mM Tris-HCl, 300 mM NaCl, 0.5% SDS, 1 mM EDTA) at 65 °C. Eluates were treated with RNase A for 1 hour at 37 °C and then Proteinase K for 3 hours at 56 °C. The DNA was finally purified by phenol/chloroform and eluted in 1x TE.
ChIP-seq libraries were generated using the NEBNext Ultra II DNA library prep kit (New England Biolabs, #E7645S) with at least 10 ng of input DNA.

value: Tet-pLKO_shINTS11 stable cells

tag: antibody


title: HeLa_shINTS11_ctrl_r1_H3K36me2_ChIP-seq


title: HeLa_shINTS11_ctrl_r1_CSTF64_ChIP-seq

value: CSTF64 [Bethyl Laboratories, A301-92A, lot #A301-092A-2]


title: HeLa_shINTS11_dox_r1_CSTF64_ChIP-seq


title: HeLa_shINTS11_dox_r1_CPSF73_ChIP-seq

value: CPSF73 [Bethyl Laboratories, A301-019A, lot #A301-091A-1]


title: HeLa_shINTS11_dox_r2_CPSF73_ChIP-seq


title: HeLa_shINTS11_dox_r1_H3K36me2_ChIP-seq


title: HeLa_shINTS11_ctrl_r1_CPSF73_ChIP-seq


title: 3_prime_mRNASeq_E203Q_shINTS11_ctrl_r1

description:
E203Q shINTS11
3' mRNA-Seq


title: HeLa_shINTS11_ctrl_r1_eCLIP_INTS11_IP

description:
shINTS11
Total RNA (INTS11 IP)

growth_protocol: HeLa stable containing INTS11 shRNA cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. DMEM medium was supplemented with 10% FBS and puromycin (2 μg/ml).

extract_protocol:
After double adapter trimming (cutadapt v1.14), resulting reads were first mapped against the repetitive genome using STAR (v2.7.6a), the unmapped output was aligned against the human genome (hg19). PCR duplicates were removed by umi_tools (v1.0.0) and the samples were visualized in UCSC.
eCLIP was performed according to Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810 Libraries were prepared as described in Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810. In brief, 2 x 10^7 HeLa cells were crosslinked by UV-C irradiation (254 nm, 400 mJ/cm2) and lysed on ice followed by sonication. The lysate was subjected to RNase I (Ambion) digest (40 U/ml) in presence of murine RNase inhibitor (NEB) and 4 U/ml Turbo DNase (Ambion). 4 µg INTS11 antibody (Sigma Prestige, HPA029025) was pre-incubated with Dynabeads M-280 Sheep Anti-Rabbit IgG (Invitrogen, 11204D) for 1 hour and added to the lysates for immunoprecipitation at 4˚C for 16 hours. 2% of the lysate were removed and stored as size-matched input controls. Co-immunoprecipitated RNA was dephosphorylated, followed by on-bead 3'RNA adapter ligation using high concentration T4 RNA Ligase I (NEB). IP efficiency was verified by immunoblot of 20% of the IP samples. Input controls and 80% of the IPed INTS11-RNA complexes were run on a NuPAGETM 4-12% Bis-Tris Gel, transferred to nitrocellulose membrane and the desired size range (INTS11 signal + 75 kDa) was cut from the membrane for both input and IP samples. To extract RNA, nitrocellulose membranes were finely fragmented and treated with Urea/ Proteinase K, followed by acid phenol-chloroform extraction and purification using RNA Clean & Concentrator column cleanup (Zymo Research). Size-matched input samples were also dephosphorylated and ligated to 3’RNA adapter. After reverse transcription (AffinityScript reverse transcriptase, Agilent), excess oligonucleotides were removed with exonuclease (ExoSAP-IT, Affymetrix), and the remaining RNA hydrolyzed by NaOH. A 3' DNA Linker was ligated to the cDNA, and the resulting library was PCR amplified using Q5 Ultra IIMaster Mix (NEB). The library was size selected by agarose gel electrophoresis and purified (MinElute, Qiagen). Single-end sequencing was performed to an average of 40 million reads per sample using Illumina NovaSeq 6000.

value: INTS11 [Sigma#HPA029025]


title: HeLa_shINTS11_ctrl_r2_eCLIP_Input

value: Tet-pLKO_shControl stable cells


title: HeLa_shINTS11_ctrl_r2_H3K36me2_ChIP-seq


title: HeLa_shINTS11_dox_r2_CSTF64_ChIP-seq


title: HeLa_shINTS11_ctrl_r2_CSTF64_ChIP-seq


title: HeLa_shINTS11_ctrl_r2_CPSF73_ChIP-seq


title: NCC_rep2_day5_dmso

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

data_processing:
RNA-seq fastq have been trimmed from adaptors using cutadapt (cutadapt -q 20 -m 20 -a AGATCGGAAGAGC) and alined to hg38 using RSEM (RSEM-1.3.1, rsem-calculate-expression --phred33-quals -p 40 --bowtie2). We used the gene results to further quantify gene expression level in each individual library. TTPM have been generated after quantifying the signal per transcript and scaled by transcript length.
Genes for the differential analysis have been selected only when they showed 1cpm in at least 2 libraries (2 replicates) in any of the experimental conditions. Differential analysis have been performed using EdgeR accounting for the presence of biological replicates. All individual experimental conditions have been contrasted for identifying gened with differential changes.
Differential expressed genes were those with abs(logFC)>2 and FDR<=0.05.
Genome_build: hg38
Supplementary_files_format_and_content: genes.results: count table for gene models based on genecode v.28
Supplementary_files_format_and_content: summary_outcome_all_comparisons.csv: contains the outcome of differential expression. Column names indicate the comparison examined (COND1__VS_COND2. Rows: genes. Cell content: 0 = genes not differentially expressed; 1= genes differentially up-regulaed in COND1; -1: genes differentially down-regulated in COND1.
Supplementary_files_format_and_content: all_cpm.all_libraries.csv: table with all gene counts (expected counts output from Rsem) from all libraries
Supplementary_files_format_and_content: TPM_hg38_phenDC3.csv: table with all gene TPM (Transcript per Million) from all libraries

source_name: hESC NCC Differentiation Day5

growth_protocol: Cranial neural crest cells were generated from H1-hESC OCT4-EGFP using a 5 day procedure as previously described (Gomez et al 2019). 2µM DMSO was included for the duration of the experiment. ROCK inhibitor Y-27632 and ChIRON 99021 was included in the induction media for the first 48 hr only. Induction media was changed daily until day of collection (day 5).

extract_protocol:
Total RNA was extracted from 1 x 10^6 cells using the RNeasy Plus Mini. Kit (Qiagen) as per manufacturer’s instructions. RNA quality (RIN >8) was checked via Bioanalyzer (Aglient) and RNA concentration determined using a Qubit fluorometer (Thermofisher).
Libraries were prepared from 1µg RNA using the NEBNEXT Ultra8482 II Directional RNA Library Prep Kit for Illumina (E7760S) in combination with the NEBNExt Poly(A)mRNA Magnetic isolation module (E7490S) as per manufacturer’s instructions.

tag: cell line of origin

value: H1 ESC OCT4-EGFP

value: 2 uM DMSO


title: ESC_rep3

source_name: human embryonic stem cells (ESC)

growth_protocol: H1 hESC OCT4 EGFP cells (ESC, WiCell) were cultured in mTESR1 media (StemCell Technologies) and grown on Matrigel matrix (Corning).  ESCs were fed daily and routinely passaged every 4-6 days using ReLeSR. Sample was take prior to differentiation.


title: NCC_rep2_day5_phenDC3

growth_protocol: Cranial neural crest cells were generated from H1-hESC OCT4-EGFP using a 5 day procedure as previously described (Gomez et al 2019). 2µM PhenDC3 was included for the duration of the experiment. ROCK inhibitor Y-27632 and ChIRON 99021 was included in the induction media for the first 48 hr only. Induction media was changed daily until day of collection (day 5).

value: 2 uM PhenDC3


title: HeLa_shINTS11_ctrl_r2_eCLIP_INTS11_IP

description:
shINTS11
Total RNA (INTS11 IP)


title: ESC_rep2


title: ESC_rep1


title: NCC_rep3_day5_phenDC3


title: HeLa_shINTS11_ctrl_r1_eCLIP_Input


title: NSC_Rep2_3xBG4_input

data_processing:
Fastq files were trimmed from adapters using cutadapt (-m 10 -q 20 -O 3 -a CTGTCTCTTATACACATCT) and aligned to a the human genome hg38 with bwa-mem. Bam files were generated from the alignment with samtools view. Duplicated reads were marked and removed using picard MarkDuplicates (ver: 2.20.3).Peak calling was performed with macs2 over input (ver. 2.1.2) with fdr 0.05 (default) and --broad option. Regions confirmed across 2 out of 3 tecnical replicates have been assigned to each biological replicate. Regions shared by 2 out of 3 biological replicates have been elected as consensus of the cell type and multiIntersectBed was used for this. Bigwig files have been generated using deeptools bamCoverage --scaleFactor using the 1000000/total_library_size as a  scaling factor.
ATAC-seq: fastq files were trimmed from adapters with cutadapt ( -a AGATCGGAAGAGC -A AGATCGGAAGAG) and aligned to hg38 with bwa-mem for paired-end (-M -t 12 $read1 $read2). Mapped reads have been filtered using samtools view (-Sb -F780 -q 10 -L )  to keep only mapped and properly paired reds. Those reads have been then used to identify accessible reagions using macs2 wih default options. Regions identified in 2 out 3 biolofical replicates have used as consensus each cell type.
RNA-seq fastq have been trimmed from adaptors using cutadapt (cutadapt -q 20 -m 20 -a AGATCGGAAGAGC) and alined to hg38 using RSEM (RSEM-1.3.1, rsem-calculate-expression --phred33-quals -p 40 --bowtie2). We used the gene results to further quantify gene expression level in each individual library. Technical replicates quantification have been summed up before subsequent analysis. TPM have been generated after quantifying the signal per transcript and scaled by transcript length.
Genome_build: hg38
Supplementary_files_format_and_content: broadPeak: broad peak regions obtained with macs2 ( fdr 0.05 and --broad options)
Supplementary_files_format_and_content: narrowPeak: narrowPeak regions obtained with macs2 default options
Supplementary_files_format_and_content: genes.results.txt: count table for gene models based on genecode v.28
Supplementary_files_format_and_content: *ATAC.multi2.sorted.bed: ATAC consensus regions obtained as those observed in 2 out of 3 biologicial replicates
Supplementary_files_format_and_content: bio2out3.bed: G4 consensus regions obtained as regions observed in 2 out of 3 biological replicates
Supplementary_files_format_and_content: TPM_hg38_all_bio_rep_*.csv: Matrix table with expression levels expressed as TPM (transcript per million) for every gene and every sample. In case of multiple technical replicates TPM have been generated from the data obtained after summing up technical replicates.

source_name: neural stem cells (NSC)

extract_protocol: G4-ChIP-seq was performed as previously described (Hansel-Hertsch et al 2018) with the following modifications. 30 million cells were dissociated with Accutase and cross-linked in serum-free media containing 1% (v/v) methanol-free formaldehyde for 10 min and then quenched with 0.12M glycine for 10 min at room temperature. Cross-linked cells were washed with PBS by centrifugation and flash frozen in liquid nitrogen and stored at -80 °C. Chromatin was isolated using the Lysis and Hypotonic Buffer for Sonication kit (Chromatrap). Each lysed nuclei suspension was sonicated for 25-40 cycles (30 sec on/ 60 sec on, high setting) using a water-cooled bath sonicator until an average DNA size of 100-500 bp was reached.  For ChIP, 7.5 µL of 150 ng/mL chromatin was incubated in Blocking Buffer (25 mM HEPES pH 7.5, 10.5mM NaCl, 110m KCl, 1mM MgCl2 and 1% (w/v) bovine serum albumin) supplemented with 3 µL 1mg/ml RNaseA for 30 min at 800 rpm on a thermoshaker at 16 °C. Next 6 µL of 4.8µM BG4 anti-G4 antibody (generated via autoinduction as previously described in Biffi et al 2014) was added and the reaction incubated for 1 h at 16 °C with mixing at 1,400 rpm. After pre-blocking anti-flag M2 magnetic beads (Merck) with Blocking Buffer for 1 hour at 4°C, 150 µL of this bead slurry solution was then added to the CHIP reaction and incubated for 1 h at 16 °C with mixing at 1,400 rpm. Beads containing antibody bound chromatin were magnetically captured, supernatant discarded via vacuum aspiration and washed four times with wash buffer (10 mM Tris pH 7.4, 100 mM KCl, 0.1% (v/v) Tween 20) at 4°C by manual agitation.  Beads were then subjected to two subsequent washes at 37 °C in a thermoshaker at 1,400 rpm for 10 min. The supernatant was then removed, beads resuspended in 150 µL of elution buffer (1 x TE buffer, 3 µL proteinase K) and incubated at 65 °C  with 1,400 rpm shaking for 3 h to digest protein.  DNA from ChIP and input samples was then purified using MinElute Reaction Clean up Kit. For library preparation, samples were quantified by Qubit dsDNA HS assay and 10ng of purified ChIP or input DNA was tagmentated (2.5 µL Tn5 (Illumina) in tagmentation buffer (Illumina)) in total reaction volume of 40 µL at 800 rpm shaking for 20 min at 37 °C. After purification by MinElute Reaction Clean up Kit, libraries were generated by mixing 20 µL tagmentated DNA, 2.5 µL each of Nextera Index i7 and Nextera Index i5 (Nextera index primer kit, Illumina) with 25 µL NEB Next High Fidelity 2 x PCR master mix (NEB) in a PCR reaction using the following conditions: 72 °C for 5 min, 98 °C for 30 sec followed by six cycles of 98 °C for 10 sec, 63 °C for 30 sec and 72 °C for 1 min. Libraries were purified by MinElute reaction clean-up kit and library quality and quantity were assessed by Bioanalyser and Qubit, respectively. Samples were sequences on a NextSeq platform (single-end, 75 bp reads).

value: H9 embryonic stem cell-derived neural stem cell

value: H9 ESCs (WA09)

tag: chip antibody


title: NSC_Rep1_3xBG4_input


title: NCC_rep3_day5_dmso


title: 3_prime_mRNASeq_WT_shINTS11_ctrl_r1

description:
WT shINTS11
3' mRNA-Seq


title: ESC_Rep2_3xBG4_input

value: H9 embryonic stem cells


title: NCC_rep3_day3_phenDC3

source_name: hESC NCC Differentiation Day3

growth_protocol: Cranial neural crest cells were generated from H1-hESC OCT4-EGFP using a 5 day procedure as previously described (Gomez et al 2019). 2µM PhenDC3 was included for the duration of the experiment. ROCK inhibitor Y-27632 and ChIRON 99021 was included in the induction media for the first 48 hr only. Induction media was changed daily until day of collection (day 3).


title: NCC_rep3_day3_dmso

growth_protocol: Cranial neural crest cells were generated from H1-hESC OCT4-EGFP using a 5 day procedure as previously described (Gomez et al 2019). 2µM DMSO was included for the duration of the experiment. ROCK inhibitor Y-27632 and ChIRON 99021 was included in the induction media for the first 48 hr only. Induction media was changed daily until day of collection (day 3).


title: NCC_rep3_day3_ctrl

growth_protocol: Cranial neural crest cells were generated from H1-hESC OCT4-EGFP using a 5 day procedure as previously described (Gomez et al 2019). ROCK inhibitor Y-27632 and ChIRON 99021 was included in the induction media for the first 48 hr only. Induction media was changed daily until day of collection (day 3).


title: NCC_rep3_day5_ctrl

growth_protocol: Cranial neural crest cells were generated from H1-hESC OCT4-EGFP using a 5 day procedure as previously described (Gomez et al 2019). ROCK inhibitor Y-27632 and ChIRON 99021 was included in the induction media for the first 48 hr only. Induction media was changed daily until day of collection (day 5).


title: NCC_rep2_day5_ctrl

growth_protocol: Cranial neural crest cells were generated from H1-hESC OCT4-EGFP using a 5 day procedure as previously described (Gomez et al 2019).  ROCK inhibitor Y-27632 and ChIRON 99021 was included in the induction media for the first 48 hr only. Induction media was changed daily until day of collection (day 5).


title: CNCC_Rep3_3xBG4_input

source_name: cranial neural crest cells (CNCC)

value: H9 embryonic stem cell-derived cranial neural crest cell


title: NCC_rep1_day5_phenDC3


title: NCC_rep2_day3_dmso


title: NSC_ATAC_50_bio3

growth_protocol: H9-derived neural stem cells (NSC; WiCell) were cultured in StemPro NSC SFM complete media (ThermoFisher) on Geltrex (Thermofisher) pre-coated plates. Media was replenished every two days and NSC were passaged every four to five days using StemPro Accutase (ThermoFisher).

extract_protocol: ATAC-seq libraries were generated from whole cells as previously described (Calviello et al., 2019). Briefly, cells were dissociated with StemPro Accutase and 50,000 viable cells (as determined using the Muse Cell Analyzer (Merck) ‘Count and Viability’ assay) were washed in ice cold PBS. Cells were pelleted at 500 xg for 5 min at 4 °C and resuspended in transposition reaction mix (25 µL 2 x TD reaction buffer (Illumina), 2.5 µL Tn5 transposase (Illumina) and 22.5 µL sterile water) and incubated at 37 °C in a thermoshaker at 1,400 rpm for 1 hour. The transposition reaction was immediately purified in 10 µL elution buffer using a MinElute reaction clean-up kit (Qiagen). Transposed DNA fragments were then initially amplified using 2.5 µL each of Nextera Index i7 and Nextera Index i5 (Nextera index primer kit, Illumina) with 25 µL NEB Next High Fidelity 2 x PCR master mix (NEB) under the following conditions: 72 ° for 5 min, 98 °C for 30 sec followed by five cycles of 98 °C for 10 sec, 63 °C for 30 sec and 72 °C for 1 min. To reduce GC and size biases, the total PCR cycle was determined as previously described


title: NSC_ATAC_50_bio2


title: ESC_ATAC_50_bio2

growth_protocol: H9 human embryonic stem cells (ESC, WiCell) were cultured in mTESR1 media (StemCell Technologies) and grown on Matrigel matrix (Corning).  ESCs were fed daily and routinely passaged every 4-6 days using ReLeSR (StemCell Technologies).