title: S116_IHFS_EV_S18

city: Durham

first: Christopher

last: Vann

state: NC

address: 300 N Duke St

department: Molecular Physiology Institute

institute: Duke University School of Medicine

data_processing:
The UMI-tools (Smith et al., 2017) algorithm was used to process miRNAseq data, parsing the Illumina adapters and extracting the unique molecular identifier (UMI) sequence for each read. Reads were then mapped to GRCh38/hg38 using the Bowtie alignment tool (Langmead et al., 2009). Reads were kept for use in subsequent analyses if they mapped to no more than 13 genomic locations.
miR counts were compiled using custom scripts that compared the mapped read coordinates to the miRbase miR database (Kozomara and Griffiths-Jones, 2014).
Deduplication of reads was then completed using UMI-tools, based on the mapping coordinate and the UMI identified from the read. Reads that matched the coordinates of the known mature miR were kept if they perfectly matched the coordinates of the miR seed whilst not varying more than 2nt on the 3’ end of the mature miR
raw data (991 miRs) were read into R (R Core team, 2020) and subsequently filtered to remove low expressors using a counts per million (CPM) threshold of 0.5 (corresponding to ~10 counts) whilst additionally requiring more than one sample to meet this threshold to be included in the filtered data set analyses.
Data were further processed using the edgeR package with normalization being conducted using the trimmed mean of M-values (TMM) method and differential expression analysis being cinducted using GLM-QLF-tests
Assembly: GRCh38/hg38
Supplementary files format and content: raw data files prior to reading into edgeR are in .csv format containing the raw counts per miR for each sample.  The normalized data are in .xlsx format containing the raw reads and normalized reads.

source_name: extracellular vesicles derived from human skeletal muscle primary cells

growth_protocol: muscle samples were minced and digested with 0.05% trypsin at 37C for 30 minutes. Isolated cells were then centrifuged and resuspended in growth media (GM) consisting of low-glucose DMEM, 10% fetal bovine serum (FBS), supplemented with SkGM bulletkit without gentamycin and insulin (Lonza Group LTD; Basel, Switzerland) and subsequently pre-plated for 2 hours to decrease fibroblast numbers. Following pre-plating, cells were seeded onto Matrigel coated flasks (BD Biosciences; Franklin Lakes, NJ, USA) and expanded via passaging once 70% confluence was reached. Cells were detached and used to fabricate myobundles at passage 5

extract_protocol:
The serum-free media in the engineered muscle myobundle culture were collected and replaced with fresh media daily. EVs were isolated from the serum-free media supernatants collected on day 6 following cultures in the absence or presence of electrical stimulation. Briefly, a standard volume of 1 mL of supernatant was used for each corresponding myobundle. Supernatants were completely thawed on ice and subsequently centrifuged at 2000g for 10 minutes at 4C to remove debris. Following debris removal, EVs in the supernatant were separated using ExoQuick-TC (System Biosciences; Palo Alto, CA, USA) in accordance with the manufacturer’s specifications. The estimated size and number, surface marker CD9, bilayer structure (PKH), and cargo mitochondria (MitoTracker Green for total mitochondria and MitoTracker Deep Red for functional respiring mitochondria) of EVs were determined via high resolution flow cytometry (Supplementary Figure 1) as previously described (Zhang et al., 2020). RNA isolation was performed on the muscle myobundles and EVs prior to submitting samples for miRNAseq at the Duke University Center for Genomic and Computational Biology. RNA was extracted from myobundles using the Aurum™ Total RNA Mini Kit (Bio-Rad; Hercules, CA, USA) in accordance with manufacturers specification. Extraction of RNA from EVs was performed using ExoQuick® Exosome RNA Column Purification Kit (System Bioscience; Palo Alto, CA, USA) in accordance with the manufacturer’s specifications. RNA was subsequently dissolved in 20 L RNAse-free water and underwent quantification via the Qubit™ RNA HS Assay Kit (Thermo Fisher Scientific; Waltham, MA, USA) according to the manufacturer’s specifications.
Library preparation of myobundle and EV RNA samples was completed using the NextSeq 500 Mid-Output Library Kit (Illumina Inc.; San Diego, CA, USA). Following library preparation, sequencing was completed on the Illumina NextSeq500 (Illumina; San Diego, CA, USA) yielding 75bp paired-end reads at a depth of 16M

treatment_protocol:
Three-dimensional engineered muscle myobundles were generated within polydimethylsiloxane (PDMS) molds containing two semi-cylindrical wells (7mm long  2mm diameter), cast from 3D- machined Teflon masters as described previously (Madden et al., 2015, Rao et al., 2018). PDMS molds were then coated with 0.2% (w/v) Pluronic™ F-127 (Invitrogen; Waltham, MA, USA) for 1 hour at room temperature to prevent hydrogel adhesion. Laser-cut Cerex® frames (9  9 mm2, 1mm wide rim) were positioned around the wells and served to anchor myobundle ends and facilitate handling and implementation. Briefly, a cell solution (7.5105 cells in 17.2µL media per bundle + 0.5µL 80µg/mL aprotinin in water + 2µL of 50U/mL thrombin in 0.1% BSA in PBS) and a gelling solution (11µL media + 10µL Matrigel + 10µL of 20mg/mL Fibrinogen in DMEM) were prepared on ice in separate vials for up to six myobundles per vial. Excessive fibrinolysis was reduced via the inclusion of aprotinin (Khodabukus and Baar, 2009). Gelling solution was added to the cell solution and each myobundle was individually pipetted within the PDMS mold and onto each frame. The cell/hydrogel mixture was then injected into the PDMS wells and subsequently polymerized at 37°C for 30 min. After formation, myobundles were dynamically cultured in a rocker and fed with GM supplemented with 1.5mg/mL 6-aminocaproic acid (ACA; MilliporeSigma; Burlington, MA) for a period of 4-days. Media were then switched to serum-free differentiation media consisting of low-glucose DMEM, 1% N2-supplement (ThermoFisher, Waltham, MA, USA), 100U/mL penicillin (MilliporeSigma), and 2mg/mL ACA.  Myobundles were cultured in DM for a period of 7-days prior to being subjected to e-stim with media being changed daily
Three myobundles were generated per participant tissue sample and subjected to either a CTL condition, which received no electrical stimulation, or one of two electrical stimulation protocols (CLFS and IHFS), which began after 7 days differentiation. Myobundles subjected to CLFS received continuous electrical stimulation consisting of a 0.5sec 10Hz train followed by a 4.5sec rest. The IHFS protocol consisted of a 0.5sec 40Hz train delivered every 20 seconds for 1hr, followed by a 7hr rest period. E-stim protocols were conducted for a period of 7-days. Electrical impulses delivered to the myobundles were bipolar at an amplitude of 70mA with a duration of 2ms and were delivered using a D330 Multistim System (Digimeter Ltd; Hertfordshire, UK) and programmed using a custom-made pulse generating Labview program (NI; Austin, TX, USA)

value: paraspinal muscle harvested from surgical waste

value: IHFS (0.5 sec 40Hz train followed by 20 sec rest) for 1 hour followed by 7 hours rest

value: 7 days


title: scrambled_7d_of_osteogenesis_2

status: Public on Sep 28 2022

type: SRA

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

library_source: transcriptomic

data_processing:
Quality control for total RNA was performed using TapeStation (Agilent). The RINe value of all samples was in the range of 8.0-9.8, indicates that all samples have a good quality
Quality control was assessed using Fastqc (v0.11.5), reads were trimmed for adapters, low quality 3` and minimum length of 20 using CUTADAPT (v1.12).
80 bp single-end reads were aligned to human reference genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa downloaded from ENSEMBL) and annotation file (Homo_sapiens.GRCh38.92.gtf downloaded from ENSEMBL) using STAR aligner (v2.6.0a).
The number of reads per gene was counted using Htseq (v0.9.1).
A statistical analysis was preformed using DESeq2 R package (version 1.18.1) (Genome Biology 2014 15:550). The number of reads per gene was extracted into Count.xls and NormalizedCounts.xls files for raw counts and normalized counts, respectively
Assembly: Homo_sapiens.GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: mesenchymal stem cells

growth_protocol: hBMSCs were cultured in Minimum Essential Medium-Alpha (αMEM) supplemented with 10% Fetal Bovine Serum (FBS), 2mM L-glutamine and Pen-Strep (both 100U/ml)

extract_protocol:
RNA was extracted with Rneasy Mini Kit (Qiagene)
12 RNAseq libraries (NEBNext UltraII Directional RNA Library Prep Kit for Illumina, cat no. E7760) were produced according to manufacture protocol using 800 ng total RNA. mRNAs pull-up was performed using Magnetic Isolation Module (NEB, cat no. E7490). All 12 libraries were mixed into a single tube with equal molarity. The RNAseq data was generated on Illumina NextSeq500, 75 cycles, high-output mode (Illumina, cat no. FC-404-2005).

treatment_protocol: hBMSCs were cultured in the osteogenic induction conditions (culture medium supplemented with 100ug/ml ascorbic acid-magnesium and 10-8M dexamethasone, 10mM sodium β-glycerophosphate).

tag: cell type

value: mesenchymal stem cells

tag: genotype

value: WT day 7

tag: treatment

value: Osteogenic Differentiation


title: A1266

city: Leicester

first: Shu

last: Ye

state: Leicestershire

address: British Heart Foundation Cardiovascular Research Centre, Department of Cardiovascular Sciences, University of Leicester, Glenfield General Hospital

country: United Kingdom

institute: University of Leicester

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality was checked with FastQC. Adapters were trimmed with BBMap.
Reads were mapped with STAR v2.7.1a
SAMtools v1.9 was used for processing aligned reads.
Rsubread was used to obtain raw read counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Table and individual files of raw gene counts in all samples

source_name: Vascular Smooth Muscle Cells

extract_protocol:
Total RNA was extracted from an aliquot of passage-3 VSMCs stored with the use of the Biobasic EZ-10 DNAaway RNA miniprep kit (Biobasic), according to the manufacturer’s protocol with additional wash steps to ensure complete removal of residual salts from the samples
A strand specific library with rRNA removal was prepared from total RNA of each of the 1,499 VSMC samples, and 150bp paired-end sequencing at 30 million read depth was performed.

tag: source tissue

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: S111_IHFS_EV_S15

country: USA

value: extracellular vesicles derived from human skeletal muscle primary cells

tag: time


title: S110_IHFS_EV_S12


title: siRNAaRNF4_untreated_2

value: KD RNF4 day 0


title: siRNAaRNF4_7d_of_osteogenesis_2

value: KD RNF4 day 7


title: siRNAaRNF4_untreated_1


title: A1268


title: A1265


title: S116_CTL_EV_S16

value: CTL (no electrical stimulation)


title: A1262


title: S111_CTL_EV_S13


title: scrambled_untreated_1

value: WT day 0


title: A1258


title: A1264


title: A1261


title: A1263


title: S116_CLFS_EV_S17

value: CLFS (0.5 sec 10Hz train followed by 4.5 sec rest) for 1 hour followed by 7 hours rest


title: S110_CLFS_EV_S11


title: S110_IHFS_bundle_S3

source_name: human skeletal muscle primary cells

value: human skeletal muscle primary cells


title: S111_CLFS_bundle_S5


title: A1257


title: S116_IHFS_bundle_S9


title: A1260


title: A1253


title: A1259


title: A1256


title: S111_IHFS_bundle_S6


title: A1254


title: S111_CLFS_EV_S14


title: S110_CTL_EV_S10


title: A1252


title: S111_CTL_bundle_S4


title: S110_CLFS_bundle_S2


title: S116_CTL_bundle_S7


title: A1249


title: S110_CTL_bundle_S1


title: S116_CLFS_bundle_S8


title: A1251


title: HEMF_RR_A

city: Los Angeles

first: Anisa

last: Shaker

address: 2011 Zonal Avenue

institute: Keck School of Medicine of USC

data_processing:
Raw sequencing reads were trimmed based on their quality scores (minimum Phred score 20, minimum read length 25 nt from both end) before being mapped to the human genome hg38 using STAR version 2.7.3a with default parameter settings
Aligned reads were then quantified to Gencode annotation release 34 usingPartek E/M method and genes with fewer than 10 reads in all samples wereexcluded from the subsequent analyses
Gene counts were offset by 1 then normalized using Upper Quartile normalization (Bullard et al. 2010) before being subjected to differential expression analysis using ANOVA
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file with raw read counts

source_name: esophagus

growth_protocol: HEMFs were grown as previously described in myofibroblast media in 6 well plates

extract_protocol:
RNA was harvested using GeneElute Mammalian Total RNA miniprep
RNA libraries were prepared using poly-A kit for mRNA enrichment and sequenced with Illumina NextSeq 500

treatment_protocol: HEMFs were treated with control media or acidic bile salts for 8 minutes every 2 hours for total of 4 times

value: control

tag: subject

value: RR

tag: tissue

value: normal HEMF


title: HEMF_NDRI_B

value: acidic bile salts

value: NDRI


title: HEMF_RR_B


title: A1248


title: A1255


title: A1247


title: A1245


title: HEMF_M17_B


title: HEMF_M17_A


title: HEMF_NDRI_A


title: HEMF_JR_A

value: JR


title: A1243


title: A1241


title: A1250


title: HEMF_JR_B


title: HepG2 cells, TFAM KD, H3K27ac

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

library_source: genomic

data_processing:
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
Sequence data were alignmened onto the human reference genome hg19 using the Burrows-Wheeler alignment algorithm.
Low read/mapping quality reads were trimmed out with Galaxy.
Genome_build: hg19
Supplementary_files_format_and_content: The bigwig files were generated using CONVERTER bam to bigwig (Galaxy).

molecule: genomic DNA

growth_protocol: HepG2 cells were cultured in high glucose (25mM D-glucose) Dulbecco-modified Eagle's Medium (DMEM) (Sigma) supplemented with 10% (v/v) heat-inactivated fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Crosslinking and fragmentation were conducted as described for the ChIP-pPCR. Chromatin fragments were incubated at 4 °C overnight with 2 µg of appropriate antibodies and immunoprecipitated with Dynabeads protein A/G (Life Technologies). After decrosslinking, the DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
The ChIP-seq library was prepared using a NEBNext Ultra DNA Library Prep Kit.

treatment_protocol: For the knockdown experiments, specific siRNAs were introduced to the cells using RNAiMAX reagent (Thermo Fisher Scientific).

tag: cell line

tag: disease state

value: hepatocellular carcinoma

value: siRNA TFAM#1 for 72 hours

value: TFAM knockdown

tag: chip antibody

value: anti-Histone H3 (acetyl K27) antibody - ChIP Grade (ab4729)


title: A1246

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: HepG2 cells, TFAM KD, Input


title: A1240


title: A1238


title: HepG2 cells, Cont KD, H3K4me1

value: siRNA GL3 for 72 hours

value: anti-Histone H3 (mono methyl K4) antibody - ChIP Grade (ab8895)


title: A1236


title: A1244


title: HepG2 cells, Cont KD, H3K27ac


title: HepG2 cells, TFAM KD, H3K4me1


title: A1235


title: 20180928-1-ZYQ

city: Fuzhou

first: Jinyan

last: Chen

address: No.7 Wusi Road

country: China

institute: Fufian Academy of Medical Sciences

description: microRNA

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads where normalized by dividing the number of reads by the total number of mapped reads in millions, i.e., RPM
Genome_build: miRBase Release 22
Supplementary_files_format_and_content: Supplementary_files_format_and_content:

source_name: plasma

extract_protocol:
Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: plasma

tag: diagnosis

value: Normal control


title: A1239


title: scrambled_7d_of_osteogenesis_1

value: mesenchymal stem cells

value: WT day 7

value: Osteogenic Differentiation


title: A1233


title: A1242


title: 20180926-3-SXS

description: microRNA


title: CQH

description: microRNA

value: Human with familial hypertrophic cardiomyopathy

value: MYBPC3 gene mutations


title: A1237


title: HepG2 cells, Cont KD, Input

value: control


title: A1227


title: A1228


title: A1231


title: A1234


title: A1230


title: A1232


title: MLF

description: microRNA


title: 20180930-1-TXZ

description: microRNA


title: 4C-seq wild-type repeat 1

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

country: Germany

institute: University of Tuebingen

data_processing:
Library strategy: 4C-Seq
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Raw reads were separated into individual sample FastQ Files by barcode sequences.
Raw reads were filtered by retaining VP-specific PR amplicons (GGAGGGGGTGGTGCTGC), trimmed to remove nucleotide sequences belongs to the VP restriction fragment,
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files showed the distribtuion of raw reads in whole genome

source_name: SH-SY5Y cells

growth_protocol: SH-SY5Y cells were cultured in DMEM medium with 10% FBS and 1% Glutmax at 37℃ in a humidified atmosphere containing 5% CO2.

extract_protocol:
The 4C-seq was performed as previously reported with some modifications (van de Werken et al, Methods Enzymol. 2012; 513:89-112.). NlaIII and BfaI were selected as the first and second restriction enzymes, respectively.
Before generating 4C-seq libraries for sequencing, 4C template of viewer point (VP: SNCA promoter) were PCR amplified by 6 cycles using specific primers. Final 4C-seq libraries were generated by PCR amplified by 24 cycles using indexed primers (P5 and P7).

value: SH-SY5Y cells

tag: restriction enzyme

value: NlaIII

tag: condition

value: wild-type


title: 4C-seq THAP1 KD repeat 2

value: THAP1 knock-down


title: THAP1 KD Mouse IgG control

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
ChIP-seq data analysis was performed in Galaxy platform (Galaxy Version 1.2.0) (https://usegalaxy.org/).
ChIP-seq raw reads were aligned to the hg19 genome assembly using Bowtie. Only reads that uniquely mapped to the genome were used for further analysis.
ChIP-seq peaks were identified using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: bed files with all peaks information

extract_protocol:
Cells were crosslinked by 1% formaldehyde (ThermoFisher scientific) and sonicated in RIPA buffer (10 mM Tris-HCl, 1 mM EDTA, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40, 1× Protease inhibitor cocktail (Roche), pH 8.0) to 200-500 bp. The sonicated lysate was subjected to immunoprecipitation with specific antibody. The immunoprecipitated DNA (at least 1ng) was purified and subjected to libraries generation.
ChIP-seq libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

tag: conditions

tag: antibody

value: anti-mouse IgG (Invitrogen, 31903)


title: THAP1 KD Rabbit IgG control

value: anti-rabbit IgG (Cell signaling, 2729)


title: A1224

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: THAP1 KD H3K27ac ChIP-seq

value: anti-H3K27ac (Cell signaling, D5E4)


title: Wild-type Rabbit IgG control

value: Wild-type


title: 20180926-4-LBL

description: microRNA

value: plasma


title: Rep2, BF, RPB1, set27 DKO, IP

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent

institute: Wellcome Centre for Cell Biology

data_processing:
Collapsing. Command: pyFastqDuplicateRemover.py -f paired-end_file_1.fastq -r paired-end_file_2.fastq -o collapsed_file
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  collapsed_paired-end_file_1.fasta - 2 collapsed_paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Normalization of IP to input and to library size. Command: bamCompare --operation ratio -b1 aligned_sorted_IP_file.bam -b2 aligned_sorted_input_file.bam -o IP_to_input_ratio.bw --outFileFormat bigwig --binSize 50 --normalizeUsing CPM --scaleFactorsMethod None
Assembly: HGAP3_Tb427v9.2
Supplementary files format and content: bigWig files contain information about the peak distribution of each protein across the T. brucei genome

organism: Trypanosoma brucei brucei

source_name: Lister 427

growth_protocol: Bloodstream form cells were grown at 37 oC and 5% CO2 in HMI-9 medium supplemented with 10% Fetal Calf Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). Procyclic form T. brucei 427 cells were grown at 27oC in SDM-79 medium supplemented with hemin, 10% Fetal Calf Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
3-5 x 10^8 cells were harvested and fixed with 0.8% formaldehyde (final concentration) for 20 min at room temperature. Cells were lysed and sonicated for 30 cycles (30 s on, 30 s off; high setting) in a Bioruptor sonicator (Diagenode) in the presence of 0.2% SDS. Inputs (0.8% of total volume/sample) were taken before incubating the rest of the cell lysates overnight with 10 µg anti-GFP antibody (A-11122, Invitrogen) and Protein G Dynabeads. The beads were washed first in the presence of 500 mM NaCl, and then in the presence of 250 mM LiCl. The DNA was eluted from the beads with 1% SDS and treated with RNAse and Proteinase K. Finally, the DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
Immunoprecipitated and input DNA was blunt ended using a Quick Blunting Kit (NEB). DNA was then purified using AMPure beads (Beckman Coulter) with a beads:DNA ratio of 1.6:1 (v/v). DNA was A-tailed using Klenow Fragment exo (NEB) and NEXTflex adapters (Bioo Scientific) were ligated to the DNA fragments using a Quick Ligation Kit (NEB). Samples were purified twice with AMPure beads:DNA ratio of 1:1 (v/v), and DNA was then amplified by PCR (14-18 cycles). Following PCR, DNA was purified with AMPure beads:DNA ratio of 0.65:1 (v/v), and the resulting supernatant was taken for a 0.7:1 bead:sample purification (v/v). Finally, two 1:1 (v/v) DNA:AMPure beads purifications were performed. The DNA amount in each library was quantified using Qubit dsDNA HS Assay Kit (Invitrogen). Fragment size distribution in each library was assessed using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent).

tag: developmental stage

value: bloodstream form

value: Lister 427

tag: yfp-tagged protein

value: anti-GFP (A-11122, Invitrogen)


title: Rep2, BF, RPB1, WT, IP


title: 4C-seq CTCF KO repeat 2

tag: cell type

value: CTCF knock-out


title: A1225


title: A1223


title: 4C-seq CTCF KO repeat 1


title: Rep1, BF, RPB1, set27 DKO, IP


title: 4C-seq THAP1 KD repeat 1


title: Rep1, BF, RPB1, WT, IP


title: A1229


title: anti-flag ChIP-seq empty vec

value: Empty vector expression control

value: anti-flag (Sigma, F1804)


title: Rep2, BF, RPB1, set27 SKO, IP


title: T2-1-methylation

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

description: Flag leaves,FIX_T2

data_processing:
For the RNA sequencing data analysis, raw reads of fastq format were firstly processed.FastQC was used to estimate the raw reads and assess their quality. Trimming of reads was carried in Trimmomatic (v0.39) and reads containing contaminant primer/adapters and long stretches of poor-quality bases were removed. Index of the reference genome was built using Hisat2 (v2.1.0)(Kim et al., 2015) and paired-end clean reads were aligned to the reference genome using Hisat2. The mapped reads of each sample were assembled by StringTie (v1.3.4d) in a reference-based approach (Pertea et al., 2015). FeatureCounts (v1.6.4) 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. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.30.1). Genes with an adjusted padj<0.01 and |log2FoldChange| > 1 found by DESeq2 were assigned as differentially expressed.
Fastp (v0.21.0) was used to estimate the raw reads and assess their quality. And low quality reads and adapters were removed from the raw data by using fastp. Clean data was mapped to the rice reference genome (MSU7.0) using Bismark (v0.23.0). Uniquely mappable reads were used to calculate the methylated cytosines using the bismark methylation extractor program. We estimated the DNA methylation level at each cytosine only when the total number of all C+T counted for that position was no less than 5. The methylation ratio for each single cytosine nucleotide was calculated as the number of unconverted cytosines divided by the total number of the uniquely mappable reads at each targeted locus. To calculate the DNA methylation levels in different regions, we split each region into small windows (20 bp each), and the DNA methylation levels were calculated by averaging the DNA methylation ratios of all cytosine sites in each window.
Assembly: MSU v7.0

organism: Oryza sativa

source_name: Flag leaves

growth_protocol: Previously, the Fix-T0 plants were generated in the hybrid rice Chunyou84 (CY84) genetic background, an elite inter-subspecific hybrid rice from a cross between the maternal Chunjiang 16 A (16 A), a japonica male-sterile line, and the paternal C84, an indica-japonica intermediate-type line17. The Fix-T0 plants self-pollinated to T3 generation with screening diploids at each generation. The Fix-T0 and CY84 (corresponding control for Fix T0) plants were preserved to next generation via roots. The seeds from Fix offsprings (Fix T01th, T12th, T23th and T34th; Fix T0, T1, T2, T3 and T4), MiMe-T1 and Nipponbare variety (continuous self-pollinated four generations materials, coded as 1th, 2th, 3th and 4th) were soaked in deionized water at 37 °C in the dark for 2 d, and then transferred to a net floating on deionized water for further 5 d. The seedlings were cultured in a half-strength Kimura B nutrient solution (pH 5.4) for 21 d. Plant ploidy of the Fix offspring seedlings were identified using flow cytometry as described followings. All the confirmed seedlings were transferred to paddy field in Hangzhou. Plant growth in the field was managed according to local cultivation practices.

extract_protocol:
Flag leaves from the descendant Fix clonal plants (Fix-T1, T2, T3 and T4), Fix-T0 and CY84 at heading time were ground to a fine powder in liquid nitrogen using a mortar and pestle. Genomic DNA was isolated using a Plant Genomic DNA Purification Kit (Tiangen) and sent to the GENEWIZ (Suzhou, China) for bisulfite treatment, library preparation, and next-generation sequencing on an Illumina HiSeq. 2000 platform (Illumina).Flag leaves from the descendant Fix clonal plants (Fix-T1, T2, T3 and T4), Fix-T0, CY84 and four generations Nipponbare variety (1th, 2th, 3th and 4th) at heading time were ground to a fine powder in liquid nitrogen using a mortar and pestle. Total RNA was isolated using TRIzol reagent (Invitrogen, 15596026) and sent to the GENEWIZ (Suzhou, China) for RNA-seq library construction and sequencing on an Illumina HiSeq. 2000 platform.
Genomic DNA was isolated using a Plant Genomic DNA Purification Kit (Tiangen) and sent to the GENEWIZ (Suzhou, China) for bisulfite treatment, library preparation, and next-generation sequencing on an Illumina HiSeq. 2000 platform (Illumina).e. Total RNA was isolated using TRIzol reagent (Invitrogen, 15596026) and sent to the GENEWIZ (Suzhou, China) for RNA-seq library construction and sequencing on an Illumina HiSeq. 2000 platform.

treatment_protocol: For comparison of agronomic traits in Fix-T0, CY84 and Fix offspring rice plants (T1, T2, T3 and T4) were grown to maturity

value: Flag leaves

tag: cultivar

value: the hybrid rice Chunyou84 (CY84)

tag: generation

value: T2 generation


title: T2-2-methylation

description: Flag leaves,FIX_T2


title: T3-1-methylation

description: Flag leaves,FIX_T3

value: T3 generation


title: T1-2-methylation

description: Flag leaves,FIX_T1

value: T1 generation


title: POI patient without Turner syndrome POI_1

city: Incheon

first: meesup

last: Yoon

address: 155,Gaebeol-ro, yenosu-gu

country: South Korea

institute: Gachon university

description: Exosomal RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (miRBase) using Bowtie2
Read count extraction using bedtools.
Assembly: has
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: POI patient without Turner syndrome

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Exosomal RNA was isolated using TRIzol LS reagent (Ambion). Total RNA was extracted from 200㎕ serum/plasma using miRNeasy Serum/Plasma Kit (Quaigen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex SmallRNA Library Prep Kit (New England BioLabs) standard protocols.

tag: sample type

value: urine


title: Rep1, BF, RPB1, set27 SKO, IP


title: T1-1-methylation

description: Flag leaves,FIX_T1


title: THAP1 KD CEBPD ChIP-seq

value: SH-SY5Y cells

value: THAP1 knock-down

value: anti-CEBPD (Santa Cruz Biotechnology, C-6)


title: Rep2, BF, RPB1, WT, input


title: Wild-type H3K27ac ChIP-seq

value: Wild-type

value: anti-H3K27ac (Cell signaling, D5E4)


title: A1218

tag: source tissue

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: Rep1, BF, RPB1, WT, input

value: bloodstream form

value: Lister 427


title: T4-1-methylation

description: Flag leaves,FIX_T4

value: T4 generation


title: T4-2-methylation

description: Flag leaves,FIX_T4


title: T3-2-methylation

description: Flag leaves,FIX_T3


title: A1226


title: FIX-T0-2-methylation

description: Flag leaves,FIX_T0

value: T0 generation


title: A1222


title: A1217


title: anti-flag ChIP-seq THAP1

value: THAP1-flag overexpression

value: anti-flag (Sigma, F1804)


title: A1221


title: FIX-T0-1-methylation

description: Flag leaves,FIX_T0

value: Flag leaves

value: the hybrid rice Chunyou84 (CY84)


title: Rep1, BF, RPB1, set27 SKO, input


title: A1216


title: A1219


title: Rep1, BF, RPB1, set27 DKO, input


title: A1220


title: Rep2, BF, RPB1, set27 SKO, input


title: T2-1

description: Flag leaves,FIX_T2

value: T2 generation


title: Rep2, BF, RPB1, set27 DKO, input


title: T2-2

description: Flag leaves,FIX_T2


title: T4-2

description: Flag leaves,FIX_T4


title: T3-2

description: Flag leaves,FIX_T3

value: T3 generation


title: CY84-1-methylation

description: Flag leaves,CY84

value: the an elite inter-subspecific hybrid rice from a cross between the maternal Chunjiang 16 A (16 A), a japonica male-sterile line, and the paternal C84, an indica-japonica intermediate-type linehybrid rice Chunyou84 (CY84)


title: T1-2

description: Flag leaves,FIX_T1

value: T1 generation


title: CY84-2-methylation

description: Flag leaves,CY84


title: A1214


title: T4-1

description: Flag leaves,FIX_T4


title: A1211


title: A1215


title: Rep2, BF, RNAseq, WT

data_processing:
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  paired-end_file_1.fasta - 2 paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Selection of minus strand reads and normalization to library size. Command: bamCoverage  -b aligned_sorted_file.bam -o normalized_RNA_sample_CPM_minus_strand.bw --filterRNAstrand=forward --outFileFormat bigwig --binSize 1 --normalizeUsing CPM
Selection of plus strand reads and normalization to library size. Command: bamCoverage  -b aligned_sorted_file.bam -o normalized_RNA_sample_CPM_plus_strand.bw --filterRNAstrand=reverse --outFileFormat bigwig --binSize 1 --normalizeUsing CPM
Assembly: HGAP3_Tb427v9.2
Supplementary files format and content: bigWig files showing distribution of polyadenylated transcripts across the T. brucei genome

molecule: polyA RNA

growth_protocol: Bloodstream form cells were grown at 37 oC and 5% CO2 in HMI-9 medium supplemented with 10% Fetal Calf Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
RNA was extracted from 1-4 x 10^7 cells using Trizol (Thermo Fisher Scientific) according to the manufacturer's protocol. The RNA was treated with DNase and then purified using Phenol/Chloroform/Isoamyl alcohol pH 4.
Libraries were constructed using NEBNEXT Ultra II Directional RNA Library Prep kit (NEB) with a Poly-A mRNA magnetic isolation module (NEB).

tag: genotype

value: WT


title: A1210


title: A1213


title: Rep3, BF, RNAseq, set27, DKO

value: set27 DKO


title: Rep3, BF, RNAseq, set27, SKO

value: set27 SKO


title: T1-1

description: Flag leaves,FIX_T1

tag: tissue


title: A1212

value: Umbilical cord artery


title: T3-1

description: Flag leaves,FIX_T3


title: Rep2, BF, RNAseq, set27, DKO

tag: cell line


title: Rep2, BF, RNAseq, set27, SKO


title: FIX-T0-2

description: Flag leaves,FIX_T0


title: CY84-1

description: Flag leaves,CY84


title: FIX-T0-1

description: Flag leaves,FIX_T0


title: A1209

value: Vascular Smooth Muscle Cells


title: CY84-2

description: Flag leaves,CY84


title: A1208


title: EE501F2_641 Rep3

city: East Lansing

first: Natalie

last: Kaiser

state: MI

address: 1066 Bogue Street

department: PSM

institute: Michigan State University

data_processing:
Raw reads were processed with Trimmomatic (v0.35) (MINLEN = 36, LEADING = 20, TRAILING = 20) to remove low-quality bases, adapters, and primers
Cleaned reads were aligned to the M6 genome and read groups were assigned to enable merging of reads from the same sample using STAR (v2.6.0)
The resulting alignments were merged by read group using picardTools (v 2.18) MergeSamFiles
Reads aligning to annotated M6 reference genes were counted using subread package feature Counts (v1.5.3) in reverse stranded mode
Counts were then analyzed using R package DESeq2 to determine normalized expression values
Genome_build: Solanum Chacoense M6 (Leisner et al., 2018)
Supplementary_files_format_and_content: tab delimited text file containing read counts aligning to genes for each sample

organism: Solanum chacoense

source_name: EE501F2_641_leaf tissue

growth_protocol: Three in vitro plants of each individual were grown in a growth chamber (20°C, 16-hr photoperiod, 70% relative humidity) (N = 24). For each genotype, three biological replicates were prepared from equal quantities of leaflets from the fourth fully-expanded leaf.

extract_protocol:
RNA was isolated from leaf tissue at 16-wks post-transplant using the Qiagen RNeasy Plant Mini Kit. Samples were Turbo DNase (Thermo Fisher Scientific, Waltham, MA, USA) treated, and RNA concentration and quality were measured using Qubit 2.0 Fluorometer (Life Technologies, Inc., Carlsbad, CA, USA) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All samples had a minimum RNA integrity number (RIN) score of 8.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

tag: colorado potato beetle resistance

value: Resistant

value: leaf


title: A1207


title: Rep2, BF, RNAseq, jbp2, SKO

value: bloodstream form

value: Lister 427

value: jbp2 SKO


title: Rep2, BF, RNAseq, jbp2, DKO

value: jbp2 DKO


title: cpxAR_2

city: Wuhan

first: Feng

last: Liu

state: Hubei

address: No.1, Shizishan Street, Hongshan District, Wuhan City, Hubei Province, PRC

department: State Key Laboratory of Agricultural Microbiology

institute: Huazhong Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads  containing N base 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. Both building index of reference genome and aligning clean reads to  reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then   2  FPKM of each gene was calculated based on the length of the gene and reads count mapped  to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels .
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq R  package (1.18.0). DESeq provide statistical routines for determining differential expression in  digital gene expression data using a model based on the negative binomial distribution. The  resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling  the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned  as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the GOseq R package, in which gene length bias was corrected. GO terms  with corrected Pvalue less than 0.05 were considered significantly enriched by differential  expressed genes.
Assembly: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/290/385/GCF_003290385.1_ASM329038v1/
Supplementary files format and content: tab-delimited text files include FPKM values for all sample
Supplementary files format and content: tab-delimited text files include FPKM values for all sample

organism: Actinobacillus pleuropneumoniae

source_name: serotype 1

extract_protocol:
The WT (S4074) and ∆cpxAR mutant strains were grown in TSB overnight, then transferred (at a 1:1000 dilution) into fresh medium and grown to an OD600 of 0.6 at 37°C or 42°C. Total RNA was extracted from the bacterial solution using a Bacteria Total RNA Isolation Kit (Sangon Biotech, China) following the manufacturer’s protocol.
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was purified from total RNA using probes to remove rRNA. 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, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. 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. Then USER Enzyme was used to degrade the second strand of cDNA containing U, 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.

value: serotype 1

value: cpxAR


title: EE501F2_500 Rep3

source_name: EE501F2_500_leaf tissue

value: Susceptible


title: cpxAR_3


title: EE501F2_516 Rep3

source_name: EE501F2_516_leaf tissue


title: EE501F2_500 Rep2


title: cpxAR_1


title: A1206


title: EE501F2_516 Rep2


title: EE501F2_500 Rep1


title: A1205


title: WT_3


title: EE501F2_641 Rep1


title: EE501F2_641 Rep2


title: EE501F2_093 Rep3

source_name: EE501F2_093_leaf tissue


title: A1203


title: EE501F2_099 Rep2

source_name: EE501F2_099_leaf tissue


title: EE501F2_099 Rep1


title: EE501F2_099 Rep3


title: A1204


title: WT_1


title: A1202


title: EE501F2_516 Rep1


title: EE501F2_093 Rep1


title: A1200


title: WT_2


title: EE501F2_089 Rep3

source_name: EE501F2_089_leaf tissue


title: 4C-seq wild-type repeat 2

value: SH-SY5Y cells

value: NlaIII

value: wild-type


title: M6 Rep2

source_name: M6 _leaf tissue


title: EE501F2_093 Rep2


title: EE501F2_089 Rep1


title: M6 Rep3


title: 80-1 Rep1

source_name: USDA8380-1 (80-1) _leaf tissue


title: 80-1 Rep3


title: A1198

source_name: Vascular Smooth Muscle Cells


title: P. syringae - WT rep-1

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to P. aeruginosa and P. syringae whole genome using bowtie2
The Deeptools was used to visulized the RNA desinty
Genome_build: P. syringae 1448A
Genome_build: P. aeruginosa PAO1
Supplementary_files_format_and_content: Bigwig files for RNA density for each strand

organism: Pseudomonas syringae

extract_protocol:
The LM-seq procedure was done following a previous study with slight modification (Hou et al., 2015). In brief, the overnight culture was transferred to a fresh medium (1:100). Until the OD600 reached 0.6, the strain was pelleted and washed before RNA extraction using bacteria total RNA isolation kit (Sangon Biotech).
RNA libraries were prepared for sequencing using LM-seq protocols

value: wild type

tag: strain


title: A1196


title: A1201


title: A1199


title: EE501F2_089 Rep2


title: 80-1 Rep2


title: S2_unstimulated

city: Boston

first: Magali

last: Soumillon

state: MA

address: 38 Wareham Street, Fl3

institute: Flexomics

data_processing:
Sample barcode and UMIs were extracted from read 1 and appended to read 2.
All second sequence reads (read2) were aligned to a reference database consisting of all human RefSeq mRNA sequences (obtained from the UCSC Genome Browser GRCh37 reference set) and the human mitochondrial reference sequence using bwa version 0.7.4 with non-default parameter "-l 24"
Read pairs for which the second read aligned to a human RefSeq gene were kept for further analysis if 1) the initial ten bases of the first read all had quality scores of at least 10 and corresponded exactly to a designed sample-barcode and 2) the next ten bases of the first read (the UMI) all had quality scores of at least 30.
Digital gene expression (DGE) profiles were then generated by counting, for each sample and RefSeq gene, the number of unique UMIs associated with that gene in that well.
Assembly: GRCh37
Supplementary files format and content: Processed data contain for each sample a text file containing gene count for all refseq sequences
Supplementary files format and content: PCR duplicates are filtered in the provided count table by providing UMI counts for each gene

source_name: Donor 2, CD8+ T-cells, unstimulated

extract_protocol:
Total RNA was extracted using Zymo Research Direct-zol RNA extraction kit
RNA-seq libraries were prepared according to the SCRB-seq/3'DGE protocol, using oligo-dT capture followed by template switching and barcoded cDNA generation. Final libraries underwent hybrid capture enrichment based targeting 17 T-cell specific genes (IL2,IFNG,TNF,TGFB1,PRF1,GZMB,GATA3,TBX21,FOXP3,RORC,RUNX1,RUNX3,BCL6,IL10,IL12A,IL13,IL17A)

value: CD8+ T cells

value: WT

tag: treatment

value: unstimulated


title: M6 Rep1


title: P. syringae - WT rep-2


title: S1_CEF_stimulated

source_name: Donor 1, CD8+ T-cells, stimulated with the Cytomegalovirus, Epstein-Barr Virus and Influenza Virus (CEF) control peptide pool

value: CEF stimulated


title: P. syringae - ∆rhpS rep-2

value: {delta}rhpS


title: S2_CEF_stimulated

source_name: Donor 2, CD8+ T-cells, stimulated with the Cytomegalovirus, Epstein-Barr Virus and Influenza Virus (CEF) control peptide pool


title: A1197

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: S1_unstimulated

source_name: Donor 1, CD8+ T-cells, unstimulated


title: A1195


title: P. syringae - ∆rhpS rep-1


title: C

type: RNA

city: Farmington

first: Mohammed

last: Toufiq

state: Connecticut

address: 10 Discovery Drive, Farmington, CT 06032

department: Research Department

institute: The Jackson Laboratory for Genomic Medicine

scan_protocol: After hybridization, samples were transferred to the nCounter Prep Station, where excess probes were removed, and samples were aligned and immobilized on the nCounter cartridge. The cartridge was placed on the nCounter Digital Analyzer for data collection.

data_processing: The nSolver data analysis software version 4.0 (NanoString Technologies) was used for the assessment of QC and the normalization of the raw gene expression counts. We used the recommended default parameters for quality control flagging; briefly, flags were generated if samples did not meet the following QC criteria: imaging threshold with FOV registration of at least 75%, binding density between 0.05 and 2.25, positive control and ligation control linearity with R2>0.95, positive control limit of detection 0.5fM, positive control > or = 2 standard deviations above the mean of the negative controls

source_name: Healthy Control

extract_protocol: A total of 150 ng of RNA was used as input for NanoString miRNA profiling. The samples' preparation, ligation, hybridization, detection and scanning were perforned as per NanoString recommendations the Omics Core at Sidra Medicine.

tag: subject

value: Healthy Control

value: PBMC


title: BR39

city: Milan

first: Giorgio

last: Scita

state: Mi

address: via Adamello, 16

country: Italy

institute: IFOM, The AIRC Institute of Molecular Oncology

data_processing:
Reads were aligned to the GRCh38/hg38 assembly human reference genome using the STAR aligner (Dobin et al. 2013) with default settings with the parameter --quantMode GeneCounts in order to obtain gene counts.
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: raw counts of sequencing reads for the features of interest (genes)

source_name: Breast

growth_protocol: Organoids were cultured following the protocol reported in Sachs N. et al . Cell 2018

extract_protocol:
Organoids were lysed using TRIzol reagent and  processed for total RNA extaction with PureLINK RNA Mini Kit according to manufacturer's  instructions
Library preparation was performed starting from 500 ng of total mRNA (Illumina, TruSeq Stranded mRNA, 20020594) according to the manufacturer’s instructions. Indexed libraries were quality controlled on Agilent Bioanalyzer 2100 (High Sensitivity DNA kit), quantified (Qubit dsDNA HS Assay, Q32851), normalized and pooled to perform a multiplexed sequencing run.

value: Breast

tag: Sex

value: female

value: Organoids

tag: disease state

value: Breast cancer

value: Non rotating organoids


title: BR25

value: Rotating organoids


title: A1193


title: A1192


title: B20/0654; pTINCR 3 4D L20_4478_S7

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description:
B20/0654; pTINCR 3 4D
L20_4478_S7

data_processing:
Reads were aligned to the human genome version hg38 using STAR (v2.5.2) with default parameters. SAM files were converted to BAM and sorted using Sambamba (v0.7.1)
Count matrices were generated using The Rsubread R package with the hg38 inbuilt annotation.
Genome_build: hg38
Supplementary_files_format_and_content: Raw count matrix in tab separated format

source_name: pTINCR 3 4D

extract_protocol:
All samples were treated with 1ug/ml of doxycycline at the indicated time points
RNA was isolated using Trizol reagent, following manufacturer's protocol
Stranded RNA-Seq libraries were prepared by first depleting cytoplasmatic and mitochondrial ribosomal RNAs using the RiboZero Magnetic Gold Kit (Illumina Inc). Then, cDNA from fragmented rRNA-depleted samples was synthesized using reverse transcriptase and random hexamer primers and converted into sequentiable libraries using the TruSeq Stranded Total RNA kit protocol (Illumina Inc.). Double-stranded cDNA were created by removing the RNA template and synthesizing the second strand in the presence of dUTP in place of dTTP. cDNAs were then end-repaired, index adapter-ligated and PCR amplified. Finally, the prepared libraries were quantified by qPCR using KAPA kit as manufacturer’s protocol (KAPA Library Quant Kit, KAPA Biosystems). Based on qPCR concentrations, RNA-Seq libraries were loaded on the Illumina NextSeq 550 and sequenced with 2 × 75 bp paired-end reads at an average depth of 100 million paired reads per library

tag: vector

value: pTINCR

tag: time

tag: replicate


title: M

hyb_protocol: per NanoString recommendations the Omics Core at Sidra Medicine.

source_name: Mother

value: Mother

tag: cell type


title: BR40


title: B20/0648; pTINCR 2 14D L20_3320_S10

description:
B20/0648; pTINCR 2 14D
L20_3320_S10

source_name: pTINCR 2 14D


title: B20/0646; pTINCR 2 4D L20_4477_S6

description:
B20/0646; pTINCR 2 4D
L20_4477_S6

source_name: pTINCR 2 4D


title: P

source_name: Patient

label_protocol: per NanoString recommendations the Omics Core at Sidra Medicine.

value: Patient


title: ZS-Ghd7-Ghd8:GFP-hd1 Rep2

first: yue

last: li

address: Shizishan Street

institute: HUAZHONG Agriculture University

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: bogWig file by deepTools bamCoverage

organism: Oryza sativa Indica Group

source_name: mature leaf

extract_protocol:
Rice tissues were crosslinked with 1% formaldehyde and quenched with 0.2 M glycine.
0.5 to 1g of the sample was ground into a fine powder in liquid nitrogen, the chromatin was fragmented into 200-600 bp by ultrasound processing using Bioruptor (Diagenode). The lysates were incubated at 4 °C for 1 to 6 h and rotated to form antibody-bead complexes. After reverse cross-linking of DNA and protein, ChIP-DNA was extracted using phenol: chloroform: isoamyl alcohol (P3803; Sigma-Aldrich). ChIP-DNA libraries were prepared by Illumina® (New England BioLabs, E7645) using the NEBNext® Ultra™ II DNA Library Preparation Kit. AMPure XP beads (Beckman, A63881) were used to select 250-650 bp library fragments.

tag: cultivar

value: Zhenshan 97

value: mature leaf

tag: chip antibody

value: GFP antibodies (Chromotec, gtma-20)


title: ZS-Ghd7-Ghd8:GFP-hd1 Rep1


title: BR44


title: B20/0645; pTINCR 2 1D L20_3318_S9

description:
B20/0645; pTINCR 2 1D
L20_3318_S9

source_name: pTINCR 2 1D


title: BR30


title: ZS Ghd7-Ghd8:GFP-Hd1_Rep2


title: B20/0654; pTINCR 3 4D L20_4478_S8

description:
B20/0654; pTINCR 3 4D
L20_4478_S8


title: A1189

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality was checked with FastQC. Adapters were trimmed with BBMap.
Reads were mapped with STAR v2.7.1a
SAMtools v1.9 was used for processing aligned reads.
Rsubread was used to obtain raw read counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Table and individual files of raw gene counts in all samples

extract_protocol:
Total RNA was extracted from an aliquot of passage-3 VSMCs stored with the use of the Biobasic EZ-10 DNAaway RNA miniprep kit (Biobasic), according to the manufacturer’s protocol with additional wash steps to ensure complete removal of residual salts from the samples
A strand specific library with rRNA removal was prepared from total RNA of each of the 1,499 VSMC samples, and 150bp paired-end sequencing at 30 million read depth was performed.

tag: source tissue


title: ZS Ghd7-Ghd8:GFP-Hd1_Rep1


title: A1194


title: B20/0646; pTINCR 2 4D L20_4477_S7

description:
B20/0646; pTINCR 2 4D
L20_4477_S7


title: ZS-ghd7-Ghd8:GFP-Hd1_Rep2


title: A1187


title: B20/0638; pTINCR 1 4D L20_4476_S6

description:
B20/0638; pTINCR 1 4D
L20_4476_S6

source_name: pTINCR 1 4D

value: Empty


title: ZS-ghd7-Ghd8:GFP-Hd1_Rep1


title: A1191

value: Umbilical cord artery


title: B20/0632; Empty 3 14D L20_4475_S5

description:
B20/0632; Empty 3 14D
L20_4475_S5

source_name: Empty 3 14D


title: A1186

value: Vascular Smooth Muscle Cells


title: A1190


title: A1185


title: A1184


title: ZS_root_H3K27me3_ChIA_Rep1

data_processing:
Raw ChIA-PET data were analysed using the ChIA-PET pipeline
PETs were  used for further classification as self-ligation,inter-ligation, and other PETs
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: cluster.bedpe file was filtered with false discovery (FDR) > 0.05

source_name: root

extract_protocol:
Rice tissues were dual cross-linked with 1% formaldehyde (SIGMA, F8775) for 10 min and 1.5 mM ethylene glycol bis (succinimidylsuccinate) (Thermo Fisher Scientific, 21565) for 30 min at 25 ℃, after which glycine was added to a final concentration of 0.2 M to stop the cross-linking reaction.
pl-DNA was end-repaired, A-tailed, and proximity ligated using a single biotinylated bridge-linker (Forward strand: 5′-[5Phos]CGCGATATC/iBIOdT/TATCTGACT-3′, Reverse strand: 5′-[5Phos]GTCAGATAAGATATCGCGT-3′). Proximity ligated protein-DNA complexes were eluted and reverse cross-linked (similar to that in eChIP-Seq). Tn5 transposase (VAHTS， TD501) was used to prepare ChIA-PET libraries according to the operation manual, and the libraries were sequenced (paired end 150 bp) using an Illumina HiSeq X-Ten (AnnoRoad Company, Beijing, China).

value: root

value: H3K27me3 antibodies (Abclonal, A2363)


title: A1182

source_name: Vascular Smooth Muscle Cells


title: B20/0630; Empty 3 4D L20_4473_S3

description:
B20/0630; Empty 3 4D
L20_4473_S3

source_name: Empty 3 4D


title: B20/0628; Empty 3 12H L20_4471_S1

description:
B20/0628; Empty 3 12H
L20_4471_S1

source_name: Empty 3 12H


title: A1181


title: A1188


title: B20/0631; Empty 3 7D L20_4474_S4

description:
B20/0631; Empty 3 7D
L20_4474_S4

source_name: Empty 3 7D


title: ZS_seedling_H3K27me3_ChIA_Rep2

source_name: seedling

value: seedling


title: B20/0627; Empty 3 6H L20_4470_S10

description:
B20/0627; Empty 3 6H
L20_4470_S10

source_name: Empty 3 6H


title: ZS_seedling_H3K27me3_ChIA_Rep1


title: MH_root_H3K27me3_ChIA_Rep2

value: Minghui 63


title: MH_root_H3K27me3_ChIA_Rep1


title: ZS-ghd7-ghd8-Hd1


title: A1180


title: A1178


title: B20/0624; Empty 2 14D L20_4468_S8

description:
B20/0624; Empty 2 14D
L20_4468_S8

source_name: Empty 2 14D


title: ZS_root_H3K27me3_ChIA_Rep2


title: MH_seedling_H3K27me3_ChIA_Rep2


title: A1179


title: A1176


title: MH_seedling_H3K27me3_ChIA_Rep1


title: A1175


title: B20/0629; Empty 3 1D L20_4472_S2

description:
B20/0629; Empty 3 1D
L20_4472_S2

source_name: Empty 3 1D


title: B20/0623; Empty 2 7D L20_4467_S7

description:
B20/0623; Empty 2 7D
L20_4467_S7

source_name: Empty 2 7D


title: B20/0622; Empty 2 4D L20_4466_S6

description:
B20/0622; Empty 2 4D
L20_4466_S6

source_name: Empty 2 4D


title: B20/0621; Empty 2 1D L20_4465_S5

description:
B20/0621; Empty 2 1D
L20_4465_S5

source_name: Empty 2 1D


title: B20/0620; Empty 2 12H L20_4464_S4

description:
B20/0620; Empty 2 12H
L20_4464_S4

source_name: Empty 2 12H


title: A1173


title: A1174


title: B20/0619; Empty 2 6H L20_4463_S3

description:
B20/0619; Empty 2 6H
L20_4463_S3

source_name: Empty 2 6H


title: B20/0626; Empty 3 0H L20_4469_S9

description:
B20/0626; Empty 3 0H
L20_4469_S9

source_name: Empty 3 0H


title: B20/0616; Empty 1 14D L20_4461_S1

description:
B20/0616; Empty 1 14D
L20_4461_S1

source_name: Empty  1 14D


title: A1170


title: A1171


title: A1172


title: B20/0618; Empty 2 0H L20_4462_S2

description:
B20/0618; Empty 2 0H
L20_4462_S2

source_name: Empty 2 0H


title: WT ILC1-3

city: Hefei

first: Zhigang

last: Tian

state: Anhui

address: Huangshan Road，number 443

institute: Univerity of Science and Technology of China

data_processing:
Illumina Casava1.7 software used for basecalling. 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
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.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of two groups (three biological replicates per condition) was performed using the edgeR R package (3.34.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression txt file

organism: Mus musculus

source_name: Liver ILC1 cell

extract_protocol:
ILC1 cells were lysed in TRIZOL, followed by total mRNA extraction using Direct-zol RNA Miniprep kit (Zymo Research)
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.

value: liver

tag: genotype

value: WT


title: A1167

first: Shu

last: Ye

address: British Heart Foundation Cardiovascular Research Centre, Department of Cardiovascular Sciences, University of Leicester, Glenfield General Hospital

institute: University of Leicester

source_name: Vascular Smooth Muscle Cells


title: cKO ILC1-1

tag: tissue

value: cKO (Ncr1Cre-Rorafl/fl)


title: B20/0615; Empty 1 7D L20_4460_S9

description:
B20/0615; Empty 1 7D
L20_4460_S9

source_name: Empty  1 7D


title: het clutch 7

city: Bethesda

first: Kai

last: Yu

state: Maryland

address: 50 South Drive, Bldg 50, Room 5151

institute: NHGRI

description: Total RNA-seq of sample het_7_1

data_processing:
Low quality reads, identified by having N-base ratios above 10% or low-quality bases ratio above 50%, and reads containing adapter sequences were removed.
The clean reads were aligned to GRCz11 with hisat2 (2.2.1.0)(Kim, Paggi, Park, Bennett, & Salzberg, 2019) and sorted with sambamba (0.7.1).(Tarasov, Vilella, Cuppen, Nijman, & Prins, 2015)
Reads were counted with Stringtie (2.0.3)(Kovaka et al., 2019) base on GRCz11.99 annotation.
Genome_build: GRCz11
Supplementary_files_format_and_content: Transcript level ctab table from stringtie

organism: Danio rerio

source_name: decapitated embryo

extract_protocol:
Heads were removed from 3dpf zebrafish embryos, and bodies were stored in RNAlater. Bodies were pooled into groups of 10, and RNA was extracted using miRNeasy Kit
500 nanograms of total RNA was used in conjunction with the TruSeq® Stranded Total RNA Library Prep kit

tag: age

value: 3 days post fertilization


title: B20/0614; Empty 1 4D L20_4459_S8

description:
B20/0614; Empty 1 4D
L20_4459_S8

source_name: Empty  1 4D


title: WT ILC1-2


title: A1169

city: Leicester


title: B20/0612; Empty 1 12H L20_4457_S6

description:
B20/0612; Empty 1 12H
L20_4457_S6

source_name: Empty  1 12H


title: B20/0613; Empty 1 1D L20_4458_S7

description:
B20/0613; Empty 1 1D
L20_4458_S7

source_name: Empty  1 1D


title: het clutch 3

description: Total RNA-seq of sample het_3_1


title: WT ILC1-1


title: A1166


title: het clutch 4

description: Total RNA-seq of sample het_4_1


title: A1168


title: A1165


title: A1164


title: wt clutch 15

description: Total RNA-seq of sample WT_clutch_15_1

value: Wild-type


title: wt clutch 13

description: Total RNA-seq of sample WT_clutch_13_1


title: wt clutch 12

description: Total RNA-seq of sample WT_clutch_12_1


title: A1163


title: B20/0611; Empty 1 6H L20_4456_S5

description:
B20/0611; Empty 1 6H
L20_4456_S5

source_name: Empty  1 6H


title: B20/0657; pTINCR 3 21D L20_3328_S3

description:
B20/0657; pTINCR 3 21D
L20_3328_S3

source_name: pTINCR 3 21D

value: pTINCR


title: B20/0610; Empty 1 0H L20_4455_S4

description:
B20/0610; Empty 1 0H
L20_4455_S4

source_name: Empty 1 0H


title: E : trm1 deletion

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

data_processing:
demultiplexing and base call to fastq conversion using illumina’s bcl2fastq v2.19.0.316
Adapter trimming using fastp 0.19.6
Read alignment to reference GCA_900235035.1_ASM90023503v1 using bowtie2
Counts per gene were obtained using featureCounts v1.6.4
Differential expression analysis was performed using DESeq2.
Genome_build: GCA_900235035.1_ASM90023503v1
Supplementary_files_format_and_content: read counts per gene in excel file

organism: Komagataella pastoris

source_name: Cells cultured in YNBM for 14 hrs

growth_protocol: cells cultured in YNBM media for 14 hours

extract_protocol:
RNeasy Mini Kit Qiagen
NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare the library after depleting rRNA from the total RNA  using RiboMinus™ Transcriptome Isolation Kit, bacteria.

tag: synonym

value: Pichia pastoris

value: trm1 deletion


title: A1162


title: B20/0655; pTINCR 3 7D L20_3326_S1

description:
B20/0655; pTINCR 3 7D
L20_3326_S1

source_name: pTINCR 3 7D


title: D1: gcn5 deletion

value: gcn5 deletion


title: A1161


title: B20/0653; pTINCR 3 1D L20_3325_S1

description:
B20/0653; pTINCR 3 1D
L20_3325_S1

source_name: pTINCR 3 1D


title: Induced sample by the SARS-CoV-2 Nucleocapside (N) protein replicate 2

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

institute: Centro de Investigación Biomédica de La Rioja

data_processing:
Raw sequencing reads were analysed to asses their quality with FastQC v0.11.9 and MultiQC v1.9.
Trimming, filtering (Phred score <25) and removing adapters with TrimGalore v0.5.0
Depletion of 18S and 28S rRNA residues with SortMeRNA v2.1
Alignment to reference genome with HISAT2 v2.2.1, resulting alignments were analyzed with Qualimap2 and sorted and indexed with Samtools.
Read count on gene features with Feature Counts tool
Quantitative differential expression analysis: DESeq2 and SARTools (Varet et al., 2016) pipeline
Enrichment in terms of WikiGenes, Gene Ontology, KEGG and Reactome pathways with enrichGO tool from the R package clusterProfiler (Yu et al., 2012).
Genome_build: GRCm38.p6 / GCA_000001635.8
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Immortalized murine olfatory bulb cells OBC1

growth_protocol: Immortalized murine OBC1 cells were cultured in DMEM supplemented with 10% FBS adn 1% penicillin/streptomycin and grown in a 5% CO2 humidified atmosphere at 37ºC.

extract_protocol:
totalRNA was extracted and purified using the Rneasy Mini Kit (Qiagen, Hilden, Germany), as indicated.
RNA libraries were prepared for sequencing using standard Illumina protocols for the Illumina Stranded Total RNA Prep with Ribo-Zero Plus, from 100 ng of total RNA.

treatment_protocol: For transfection, OBC1 cells were seeded in 6-well plates at a confluency of 80%. 20uL of Fugene HD were incubated separately in 50uL of DMEM without FBS and then mixed with 3 ug of M-GFP, E-GFP, N-GFP, S-GFP and control GFP plasmid DNA, followed by 15 min incubation at room temperature. The cell were transfected in a 3 mL total volume for 72 hours. After three days, the culture medium was replaced with DMEM supplemented with 1ug/mL puromycin.

value: Immortalized murine olfatory bulb cells

value: Transfected with the N-GPF protein


title: Induced sample by the SARS-CoV-2 Spike (S) protein replicate 3

value: Transfected with the S-GPF protein


title: Induced sample by the SARS-CoV-2 Nucleocapside (N) protein replicate 1


title: Induced sample by the SARS-CoV-2 Spike (S) protein replicate 2


title: Induced sample by the SARS-CoV-2 Nucleocapside (N) protein replicate 3


title: C2: gal83 deletion

value: gal83 deletion


title: A1160

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: Induced sample by the SARS-CoV-2 Spike (S) protein replicate 1


title: C1: gal83 deletion


title: A1159


title: B20/0656; pTINCR 3 14D L20_3327_S2

description:
B20/0656; pTINCR 3 14D
L20_3327_S2

source_name: pTINCR 3 14D


title: Induced sample by the SARS-CoV-2 Membrane (M) protein replicate 3

value: Transfected with the M-GPF protein


title: D2: gcn5 deletion


title: B2: mxr1  deletion

value: mxr1  deletion


title: A1157


title: HeLa_siTFAM#1

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

description: HeLa, cervix adenocarcinoma, siRNA: TFAM#1

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: GCS3000 Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling, and baseline transformed to the median of all 6 samples. GeneSpring GX12 software was used for summarization by MAS5.0 algorithm and baseline transformation (median shift).

label: biotin

source_name: HeLa cells introduced with siRNA against cording sequence of TFAM

label_protocol: GeneChip 3' IVT Express Kit.

growth_protocol: HepG2 cells or HeLa cells were cultured in high glucose (25mM D-glucose) Dulbecco-modified Eagle's Medium (DMEM) (Sigma) or DMEM/F-12 Ham medium (Sigma) supplemented with 10% (v/v) heat-inactivated fetal bovine serum and penicillin/streptomycin, respectively.

extract_protocol: After cultured for 72 hours, cells were harvested for RNA extraction using RNeasy kit.

tag: cell line

value: HeLa


title: Induced sample by the SARS-CoV-2 Membrane (M) protein replicate 2

tag: strain


title: B1: mxr1  deletion


title: Induced sample by the SARS-CoV-2 Membrane (M) protein replicate 1

tag: treatment


title: B20/0651; pTINCR 3 6H L20_3323_S9

description:
B20/0651; pTINCR 3 6H
L20_3323_S9

source_name: pTINCR 3 6H


title: A1156


title: B20/0650; pTINCR 3 0H L20_3322_S8

description:
B20/0650; pTINCR 3 0H
L20_3322_S8

source_name: pTINCR 3 0H


title: A2: GS115 WT

value: GS115 WT


title: B20/0652; pTINCR 3 12H L20_3324_S10

description:
B20/0652; pTINCR 3 12H
L20_3324_S10

source_name: pTINCR 3 12H


title: B20/0648; pTINCR 2 14D L20_3320_S6

description:
B20/0648; pTINCR 2 14D
L20_3320_S6

source_name: pTINCR 2 14D


title: Induced sample by the SARS-CoV-2 Envelope (E) protein replicate 3

value: Transfected with the E-GPF protein


title: A1155

source_name: Vascular Smooth Muscle Cells


title: A1: GS115 WT


title: Induced sample by the SARS-CoV-2 Envelope (E) protein replicate 2


title: A1154


title: A1153


title: Induced sample by the SARS-CoV-2 Envelope (E) protein replicate 1


title: B20/0645; pTINCR 2 1D L20_3318_S4

description:
B20/0645; pTINCR 2 1D
L20_3318_S4

source_name: pTINCR 2 1D


title: B20/0647; pTINCR 2 7D L20_3319_S5

description:
B20/0647; pTINCR 2 7D
L20_3319_S5

source_name: pTINCR 2 7D


title: elf7-3_Salt_rep3

city: Beijing

first: Zhang

last: Huairen

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1 (Chen et al., 2018).
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10 (Kim et al., 2019).
Reads per gene were counted by HTseq version 0.11.2 (Anders et al., 2015).
The coverage track(bigwig) for each sample was computed by DeepTools bamCoverage  with RPKM normalization
Transcripts per million (TPM) values were generated using R.
Differential gene expression analysis was performed using DESeq2 version 1.26.0 (Love et al., 2014).Genes were considered as differentially expressed in RNA-seq if they exhibited a more than two-fold change in expression and had a P-adjust value<0.05.
Assembly: tair10
Supplementary files format and content: *.bw, normlized transcripts coverage files

organism: Arabidopsis thaliana

source_name: 7-day-old seedlings

extract_protocol:
Total RNA was extracted from seedlings with Trizol (Thermo Fisher Scientific) and treated with Turbo DNase (Thermo Fisher Scientific) to remove any remaining genomic DNA
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to manufacture’s instruction.

treatment_protocol: 7-day-old seedlings were transferred into liquid 1/2 MS medium (Control) or liquid 1/2 MS medium containing 200mM NaCl (Salt). Plants were collected after four hours of treatment.

value: 7-day-old seedlings

value: Salt


title: HeLa_siCont

description: HeLa, cervix adenocarcinoma, siRNA: GL3

source_name: HeLa cells introduced with siRNA against GL3


title: A1158


title: Control sample replicate 3

value: Control-GFP


title: elf7-3_Salt_rep2


title: B20/0644; pTINCR 2 12H L20_3317_S3

description:
B20/0644; pTINCR 2 12H
L20_3317_S3

source_name: pTINCR 2 12H

value: pTINCR


title: HepG2_siTFAM#1

description: HepG2, hepatocellular carcinoma, siRNA: TFAM#1

source_name: HepG2 cells introduced with siRNA against cording sequence of TFAM


title: A1152


title: B20/0649; pTINCR 2 21D L20_3321_S7

description:
B20/0649; pTINCR 2 21D
L20_3321_S7

source_name: pTINCR 2 21D


title: Control sample replicate 2


title: Control sample replicate 1


title: A1151


title: A1150


title: B20/0641; pTINCR 1 21D L20_3314_S1

description:
B20/0641; pTINCR 1 21D
L20_3314_S1

source_name: pTINCR 1 21D


title: B20/0643; pTINCR 2 6H L20_3316_S2

description:
B20/0643; pTINCR 2 6H
L20_3316_S2

source_name: pTINCR 2 6H


title: HeLa_siTFAM#2

description: HeLa, cervix adenocarcinoma, siRNA: TFAM#2

source_name: HeLa cells introduced with siRNA against 3’-untranslated sequence of TFAM


title: Col_Salt_rep2

value: Col


title: HepG2_siCont

description: HepG2, hepatocellular carcinoma, siRNA: GL3

source_name: HepG2 cells introduced with siRNA against GL3


title: HepG2_siTFAM#2

description: HepG2, hepatocellular carcinoma, siRNA: TFAM#2

source_name: HepG2 cells introduced with siRNA against 3’-untranslated sequence of TFAM


title: Col_Salt_rep3


title: A1149


title: Col_Salt_rep1


title: B20/0648; pTINCR 2 14D L20_3320_S8

description:
B20/0648; pTINCR 2 14D
L20_3320_S8


title: B20/0647; pTINCR 2 7D L20_3319_S7

description:
B20/0647; pTINCR 2 7D
L20_3319_S7


title: cbp20_Salt_rep3


title: elf7-3_Salt_rep1


title: BMDC, KO, LPStreated, rep1

city: Freiburg im Breisgau

first: Katharina

last: Glaser

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
KO_stim_1
stim_featurecounts.tsv

data_processing:
snakePipes 2.1.0 was used to generate the count files
Assembly: GRCm38
Supplementary files format and content: tsv file, read counts generated by featureCounts

source_name: BMDC

extract_protocol:
Phenol-chloroform extraction
TruSeq Stranded mRNA protocol

value: BMDC

value: Grk 3xKO

value: LPS


title: BMDC, KO, untreated, rep1

description:
KO_unstim_1
unstim_featurecounts.tsv

value: untreated


title: BMDC, KO, untreated, rep2

description:
KO_unstim_2
unstim_featurecounts.tsv


title: A1147


title: A1146


title: BMDC, KO, LPStreated, rep2

description:
KO_stim_2
stim_featurecounts.tsv


title: B20/0644; pTINCR 2 12H L20_3317_S5

description:
B20/0644; pTINCR 2 12H
L20_3317_S5


title: cbp20_Salt_rep2


title: B20/0645; pTINCR 2 1D L20_3318_S6

description:
B20/0645; pTINCR 2 1D
L20_3318_S6


title: BMDC, WT, LPStreated, rep2

description:
WT_stim_2
stim_featurecounts.tsv

value: WT


title: B20/0643; pTINCR 2 6H L20_3316_S4

description:
B20/0643; pTINCR 2 6H
L20_3316_S4


title: A1145

value: Umbilical cord artery


title: cbp20_Salt_rep1


title: BMDC, WT, LPStreated, rep1

description:
WT_stim_1
stim_featurecounts.tsv


title: BMDC, WT, untreated, rep1

description:
WT_unstim_1
unstim_featurecounts.tsv


title: B20/0640; pTINCR 1 14D L20_3313_S1

description:
B20/0640; pTINCR 1 14D
L20_3313_S1

source_name: pTINCR 1 14D


title: A1144

value: Vascular Smooth Muscle Cells


title: B20/0642; pTINCR 2 0H L20_3315_S3

description:
B20/0642; pTINCR 2 0H
L20_3315_S3

source_name: pTINCR 2 0H


title: elf7-3_Control_rep3

value: Control (no salt)


title: A1143


title: A1142


title: A1148


title: BMDC, WT, untreated, rep2

description:
WT_unstim_2
unstim_featurecounts.tsv


title: elf7-3_Control_rep1


title: elf7-3_Control_rep2


title: Col_Control_rep3


title: B20/0639; pTINCR 1 7D L20_3312_S8

description:
B20/0639; pTINCR 1 7D
L20_3312_S8

source_name: pTINCR 1 7D


title: Col_Control_rep1


title: A1139

source_name: Vascular Smooth Muscle Cells


title: B20/0636; pTINCR 1 12H L20_3310_S6

description:
B20/0636; pTINCR 1 12H
L20_3310_S6

source_name: pTINCR 1 12H


title: Col_Control_rep2


title: B20/0637; pTINCR 1 1D L20_3311_S7

description:
B20/0637; pTINCR 1 1D
L20_3311_S7

source_name: pTINCR 1 1D


title: B20/0635; pTINCR 1 6H L20_3309_S5

description:
B20/0635; pTINCR 1 6H
L20_3309_S5

source_name: pTINCR 1 6H


title: A1141


title: TP-DSCs [4140-JM-2]

city: Nashville

first: Eunyoung

last: Choi

state: TN

address: 2213 Garland ave, 10445 MRB4

institute: Vanderbilt University Medical Center

data_processing:
Sequencing reads were trimmed, aligned by STAR (2.7.3a) with reference mouse genome, mm10, and normalized using the PartekFlow (Partek).
Differentially-expressed genes were obtained using DESeq2 (3.5) package and filtered by fold change (> 2) and adjusted P value (< 0.05).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: Meta4 organoids

extract_protocol:
Total RNAs were extracted from the three independent DP- and TP-DSC samples using the Trizol (Invitrogen) reagent.
cDNA libraries were constructed utilizing the stranded mRNA (polyA-selected) library preparation kit (Illumina).

value: Epithelial organoids

value: Meta4 organoids

tag: cell subtype

value: TP-DSCs


title: A1138


title: TP-DSCs [4140-JM-4]


title: cbp20_Control_rep2

source_name: 7-day-old seedlings


title: cbp20_Control_rep3


title: B20/0634; pTINCR 1 0H L20_3308_S4

description:
B20/0634; pTINCR 1 0H
L20_3308_S4

source_name: pTINCR 1 0H


title: B20/0633; Empty 3 21D L20_3307_S3

description:
B20/0633; Empty 3 21D
L20_3307_S3

source_name: Empty 3 21D

value: Empty


title: DP-DSCs [4140-JM-1]

value: DP-DSCs


title: cbp20_Control_rep1

value: 7-day-old seedlings


title: Tubular adenocarcinoma

library_source: transcriptomic single cell

data_processing:
Sequencing reads were trimmed and aligned by STAR (2.7.3a) with reference mouse genome, mm10 using the PartekFlow (Partek).
Differentially-expressed genes were obtained using DESeq2 (3.5) package and filtered by fold change (> 2) and adjusted P value (< 0.05).
After unique molecular identifiers (UMI) deduplication, reads were filtered, sorted by their barcode of origin and quantified into UMI-filtered counts per gene.
Gene expression profiles of 2,058 cells (1,047 cells from cystic type and 1,011 cells from tubular type) were retrieved corresponding to high-quality cells.
Cells from the two samples were clustered using graph-based clustering on the informative principal-component analysis (PCA) space (n=5) and visualization with t-Distributed Stochastic Neighbor Embedding (t-SNE).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes fold changes for each gene in each cluster

source_name: Tubular type adenocarcinoma

extract_protocol:
Dissociated cells from fresh cystic or tubular adenocarcinoma tissues originated from DP-DSCs were used for single-cell encapsulation with barcoded beads in individual droplets using the inDrop platform (1CellBio).
Sequencing libraries were prepared following TruDrop library preparation protocol as previously reported (Southard-Smith et al., BMC Genomics, 2020)

value: Tubular type adenocarcinoma

value: Tumor cells

value: NuJ

tag: Sex

value: Female

value: 13 weeks after DP-DSC injection


title: A1136


title: ref6c-H3K27me3-72h_rep2

first: Jie

last: Pan

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Duplicated reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
The correlation coefficients between biological replicates were examined using deepTools version 3.1.3 utility multiBamSummary, and subsequently biological replicates were merged with SAMtools version 1.9
For data visualization, bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to sequencing depth using RPKM
ChIP-seq peaks were identified using MACS2 version 2.1.2 with default parameters. The parameter ‘--broad’ was used for the calling of H3K27me3 peaks. The q-value cutoff for peak calling was 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: *.bw: Normalized H3K27me3 coverage files. Data is generated from merged replicates

source_name: ref6c 72h imbibed seeds

growth_protocol: After-ripened Col and ref6c seeds (seeds harvested and stored at room temperature for at least three months) collected at the same time and growth conditions were sown on 1/2 MS medium, and subsequently subjected for germination in long days at ~22°C, and collected at different imbibition time points.

extract_protocol:
Materials were ground with liquid nitrogen into fine powder and fixed with 1% formaldehyde. To profile H3K27me3, nuclei were extracted and mononucleosomes were generated with micrococcal nuclease (MNase)(Sigma, N5386) digestion. Immunoprecipitation was conducted with anti-H3K27me3 antibody (Merck, 07-449). After antibody incubation, Protein A Dynabeads (Life technologies, 10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification.
Library was prepared with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607) according to the manufacture’s instruction

tag: ecotype

value: Col

value: anti-H3K27me3 antibody (Merck, 07-449)


title: ref6c-H3K27me3-72h_rep1


title: A1135


title: Cystic adenocarcinoma

source_name: Cystic type adenocarcinoma

value: Cystic type adenocarcinoma

value: 10 weeks after DP-DSC injection


title: TP-DSCs [3840-JM-2]


title: B20/0625; Empty 2 21D L20_3306_S2

description:
B20/0625; Empty 2 21D
L20_3306_S2

source_name: Empty 2 21D

tag: vector


title: DP-DSCs [4140-JM-3]


title: A1140

value: Umbilical cord artery

value: Vascular Smooth Muscle Cells


title: DP-DSCs [3840-JM-1]

value: Epithelial organoids


title: B20/0617; Empty 1 21D L20_3305_S1

description:
B20/0617; Empty 1 21D
L20_3305_S1

source_name: Empty  1 21D

tag: time


title: ref6c-H3K27me3-24h_rep2

source_name: ref6c 24h imbibed seeds


title: A1133


title: B20/0641; pTINCR 1 21D L20_3314_S2

description:
B20/0641; pTINCR 1 21D
L20_3314_S2

source_name: pTINCR 1 21D

value: pTINCR

tag: replicate


title: ref6c-H3K27me3-24h_rep1


title: A1134

tag: cell type


title: WT M 15 AOM/DSS rep5

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

country: Sweden

institute: Karolinska Institute

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.6.0/RTA v3.4.4) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for adaptor sequence and trimming for low-quality regions using TrimGalore, then mapped to mm10 whole genome using STAR
FeatureCounts were used to generate the raw counts and FPKM and TPM values were generated with StringTie
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and TPM values for each Sample

source_name: Colon

extract_protocol:
Colons were removed (epithelial-layer scrape), snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent with the RNeasy Mini Kit (Qiagen). Illumina TruSeq Stranded mRNA Library Prep Kit with poly-A tail selection was used for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were injected once (i.p.) with 10mg/kg body weight (BW) AOM at day one on the first week, 2.5 % DSS in the drinking water ad libitum the second week, followed by two weeks of normal drinking water, before repeating the DSS three times in total. Mice were sacrificed 9- or 15-weeks after AOM injection.

value: C57BL/6J WT

value: Male

value: Colon

tag: weeks

value: AOM/DSS

tag: sample type

value: Colon scrape


title: Rep3, PF, SET27, IP

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent

institute: Wellcome Centre for Cell Biology

data_processing:
Collapsing. Command: pyFastqDuplicateRemover.py -f paired-end_file_1.fastq -r paired-end_file_2.fastq -o collapsed_file
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  collapsed_paired-end_file_1.fasta - 2 collapsed_paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Normalization of IP to input and to library size. Command: bamCompare --operation ratio -b1 aligned_sorted_IP_file.bam -b2 aligned_sorted_input_file.bam -o IP_to_input_ratio.bw --outFileFormat bigwig --binSize 50 --normalizeUsing CPM --scaleFactorsMethod None
Assembly: HGAP3_Tb427v9.2
Supplementary files format and content: bigWig files contain information about the peak distribution of each protein across the T. brucei genome

source_name: Lister 427

extract_protocol:
3-5 x 10^8 cells were harvested and fixed with 0.8% formaldehyde (final concentration) for 20 min at room temperature. Cells were lysed and sonicated for 30 cycles (30 s on, 30 s off; high setting) in a Bioruptor sonicator (Diagenode) in the presence of 0.2% SDS. Inputs (0.8% of total volume/sample) were taken before incubating the rest of the cell lysates overnight with 10 µg anti-GFP antibody (A-11122, Invitrogen) and Protein G Dynabeads. The beads were washed first in the presence of 500 mM NaCl, and then in the presence of 250 mM LiCl. The DNA was eluted from the beads with 1% SDS and treated with RNAse and Proteinase K. Finally, the DNA was purified using a QIAquick PCR Purification Kit (Qiagen).
Immunoprecipitated and input DNA was blunt ended using a Quick Blunting Kit (NEB). DNA was then purified using AMPure beads (Beckman Coulter) with a beads:DNA ratio of 1.6:1 (v/v). DNA was A-tailed using Klenow Fragment exo (NEB) and NEXTflex adapters (Bioo Scientific) were ligated to the DNA fragments using a Quick Ligation Kit (NEB). Samples were purified twice with AMPure beads:DNA ratio of 1:1 (v/v), and DNA was then amplified by PCR (14-18 cycles). Following PCR, DNA was purified with AMPure beads:DNA ratio of 0.65:1 (v/v), and the resulting supernatant was taken for a 0.7:1 bead:sample purification (v/v). Finally, two 1:1 (v/v) DNA:AMPure beads purifications were performed. The DNA amount in each library was quantified using Qubit dsDNA HS Assay Kit (Invitrogen). Fragment size distribution in each library was assessed using a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent).

tag: developmental stage

value: procyclic form

value: Lister 427

tag: yfp-tagged protein

tag: chip antibody

value: anti-GFP (A-11122, Invitrogen)


title: ref6c-H3K27me3-6h_rep2

source_name: ref6c 6h imbibed seeds

tag: genotype


title: Rep3, BF, JBP2, IP

value: bloodstream form


title: WT M 15 AOM/DSS rep3

tag: tissue


title: WT M 15 AOM/DSS rep4


title: A1137

source_name: Vascular Smooth Muscle Cells

tag: source tissue


title: A1131


title: Rep2, PF, SET27, IP

tag: cell line


title: Rep2, PF, CRD1, IP


title: A1129


title: ref6c-H3K27me3-0h_rep2

source_name: ref6c 0h imbibed seeds

value: Col


title: WT M 15 AOM/DSS rep2

tag: strain

tag: treatment


title: WT M 15 AOM/DSS rep1

tag: Sex


title: A1132


title: A1127


title: A1128


title: Rep2, PF, untagged, IP


title: ref6c-H3K27me3-6h_rep1

tag: ecotype

value: anti-H3K27me3 antibody (Merck, 07-449)


title: A1130


title: ref6c-H3K27me3-0h_rep1


title: A1126


title: Rep2, PF, JBP2, IP


title: A1125


title: WT F 15 AOM/DSS rep4

value: Female


title: Rep2, BF, PWWP1, IP


title: WT F 15 AOM/DSS rep3


title: ref6c-Input-72h_rep2


title: ref6c-Input-6h_rep2


title: A1123


title: ref6c-Input-24h_rep2


title: ref6c-Input-6h_rep1


title: WT M 9 AOM/DSS rep4


title: WT F 15 AOM/DSS rep5


title: ref6c-Input-72h_rep1


title: Rep2, BF, PHD6, IP


title: A1122


title: Rep1, PF, SET27, IP


title: WT F 15 AOM/DSS rep1


title: A1121


title: WT M 9 AOM/DSS rep3


title: WT F 15 AOM/DSS rep2


title: ref6c-Input-24h_rep1


title: A1124


title: WT M 9 AOM/DSS rep2


title: WT M 9 AOM/DSS rep5


title: Rep2, BF, CSD1, IP


title: A1120


title: Rep2, BF, PBP1, IP


title: Rep2, BF, JBP2, IP


title: Rep1, PF, untagged, IP


title: ref6c-Input-0h_rep2


title: Rep1, PF, CRD1, IP


title: ref6c-Input-0h_rep1


title: Rep1, PF, JBP2, IP


title: WT M 9 AOM/DSS rep1


title: A1117


title: WT F 9 AOM/DSS rep4


title: WT F 9 AOM/DSS rep3


title: Col-H3K27me3-48h_rep1

source_name: Col 48h imbibed seeds

value: wild type


title: Rep1, BF, PBP1, IP


title: A1119

value: Umbilical cord artery


title: A1118

value: Vascular Smooth Muscle Cells


title: Rep1, BF, PHD6, IP


title: Rep1, BF, PWWP1, IP


title: Col-H3K27me3-72h_rep2

source_name: Col 72h imbibed seeds


title: Col-H3K27me3-48h_rep2


title: WT F 9 AOM/DSS rep2


title: Rep3, PF, SET27, input


title: Col-H3K27me3-24h_rep2

source_name: Col 24h imbibed seeds


title: Col-H3K27me3-6h_rep2

source_name: Col 6h imbibed seeds


title: A1115


title: A1116


title: WT M Veh rep4

value: Vehicle


title: Col-H3K27me3-24h_rep1


title: Rep1, BF, JBP2, IP


title: WT M Veh rep3


title: WT F 9 AOM/DSS rep5


title: A1111


title: Rep1, BF, CSD1, IP


title: A1113


title: Col-H3K27me3-6h_rep1


title: WT F 9 AOM/DSS rep1


title: A1110


title: Col-H3K27me3-72h_rep1


title: Col-H3K27me3-0h_rep2

source_name: Col 0h imbibed seeds


title: Rep2, PF, SET27, input


title: WT M Veh rep5


title: A1112


title: Col-Input-72h_rep2


title: Rep3, BF, JBP2, input


title: Rep2, PF, JBP2, input


title: A1108


title: Col-H3K27me3-0h_rep1


title: Rep2, PF, CRD1, input


title: A1106


title: A1109


title: Col-Input-48h_rep1


title: Rep2, BF, PHD6, input


title: A1105


title: WT M Veh rep1


title: Rep2, PF, untagged, input


title: Rep2, BF, CSD1, input


title: WT F Veh rep1


title: Rep2, BF, JBP2, input


title: Col-Input-6h_rep2


title: Col-Input-72h_rep1


title: WT F Veh rep3


title: WT F Veh rep5


title: A1103


title: WT M Veh rep2


title: WT F Veh rep2


title: A1102


title: Col-Input-24h_rep1


title: A1101


title: A1104


title: A1100


title: WT F Veh rep4


title: Col-Input-0h_rep1


title: A1099


title: Col-Input-6h_rep1


title: Rep2, BF, PBP1, input


title: A1107


title: Rep2, BF, PWWP1, input


title: Rep1, PF, SET27, input


title: A1098


title: Rep1, PF, JBP2, input


title: Rep1, PF, untagged, input


title: Col-Input-0h_rep2


title: Col-Input-48h_rep2


title: REF6-HA-10d_rep2

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Duplicated reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
The correlation coefficients between biological replicates were examined using deepTools version 3.1.3 utility multiBamSummary, and subsequently biological replicates were merged with SAMtools version 1.9
For data visualization, bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to sequencing depth using RPKM
ChIP-seq peaks were identified using MACS2 version 2.1.2 with default parameters. Narrow peaks were called for REF6-HA ChIP-seq data. The q-value cutoff for peak calling was 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: *.bw: Normalized REF6-HA coverage files. Data is generated from merged replicates except for Col control

source_name: REF6-HA 10-day old seedlings

growth_protocol: After-ripened ref6-1;REF6-HA seeds (seeds harvested and stored at room temperature for at least three months) were sown on 1/2 MS medium,and subsequently subjected for germination in long days at ~22°C,and collected at different imbibition time points

extract_protocol:
For REF6-HA binding ChIP, chromatin was resuspended with ChIP lysis buffer (50mM HEPES (pH7.5), 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.5% SDS, and 1×protease inhibitor cocktail (Sigma, S8830)) and sheared to generate 200-500bp fragments with Bioruptor (Diagenode) for 30 cycles (30s/on, 30s/off) at high power. Sheared chromatin was diluted four times with ChIP dilution buffer (50mM HEPES (pH7.5), 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.01% SDS, and 1×protease inhibitor cocktail (Sigma, S8830)) and subjected to immunoprecipitation with anti-HA antibody (CST, 3724). After antibody incubation, Protein A Dynabeads (Life technologies, 10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification.
Library was prepared with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607) according to the manufacture’s instruction

value: 10-day old seedlings

value: anti-HA antibody (CST, 3724)


title: A1096


title: REF6-HA-10d_rep1


title: Col-HA-10d

source_name: Col 10-day old seedlings


title: Rep1, BF, PHD6, input


title: REF6-HA-48h_rep2

source_name: REF6-HA 48h imbibed seeds

value: seeds


title: A1094


title: REF6-HA-48h_rep1


title: TA - Mobile scRNA-seq

city: Urbana

first: Marni

last: Boppart

address: 405 N Matthews

department: Kinesiology

institute: University of Illinois at Champaign-Urbana

data_processing:
Fastq.gz files were generated and demultiplexed with 10X Genomic’s Cell Ranger 3.0.2. Each sample’s R1 and R2 fastq files were run through cellranger count using a custom reference made from Gencode M21 gene set and --expect-cells=5000 to call cells and de-duplicate individual reads to unique UMI counts per gene.
The UMI counts were then read into R (v 3.6.3) using Seurat (v. 3.1.4) (Stuart et al., 2019). Genes were filtered out if they did not have at least 1 UMI in at least 10 cells combined between the two samples. Cells with ≥ 50% mitochondrial UMIs were filtered out and then additional QC was performed based on the number of UMIs and genes detected. Cells that had > 4 median absolute deviations of the total UMI counts were excluded as possible doublets and cells were filtered out if they had fewer than 250 genes detected.
Cluster analysis was performed with the Seurat package. First, normalization was performed using the SCTransform method then linear dimensional reduction was done using Principal Components Analysis and the first 40 PCs were used as input to find clusters using a k-nearest neighbor graph and also for non-linear dimensional reduction using tSNE. Cell type identification was completed using candidate marker genes curated from the literature and the top unique genes for each cluster.
Within each cluster, differential expression testing was evaluated between Mobile and Immobile cells using the non-parametric Wilcoxon Rank Sum test.
Genome_build: Gencode M21
Supplementary_files_format_and_content: 10X Genomics cellranger count's filtered_feature_bc_matrix output in HDF5 format

source_name: tibialis anterior muscle

extract_protocol:
TAs were pooled according to treatment (Mobile vs. Immobile). The cleaned muscles were minced and then enzymatically digested for ~60 minutes at 37°C. The tissue solution was filtered (70 μm and 40 μm) to obtain mononuclear cell suspension, and the filtrate was centrifuged at 300 RCF for 5 minutes. Supernatant was decanted, and cell pellet was resuspended in PBS with 5% FBS.
Two single-cell libraries (one for the pooled mobile TAs and the other for the pooled immobile TAs) were constructed with the Chromium Single-Cell Gene Expression Kit Version 3 and sequenced on two 2x150nt SP lanes in a NovaSeq 6000.

treatment_protocol: Mice were subjected to unilateral hindlimb immobilization for two weeks by putting one tine of a staple into the plantar of the right foot and the other tine inserted into the distal gastrocnemius, which restrained the foot in full dorsiflexion and immobilized the tibialis anterior (TA) muscle at a shortened position. On day 14 of immobilization the TA muscles from mobile (“Mobile”; control) and previously immobilized (“Immobile”) limbs were excised and washed in cold 1X PBS with penicillin-streptomycin antibiotic.

value: male

tag: age

value: 14 weeks

value: mobile

value: Pool of 6 tibialis anterior muscles from the left leg that had not been immobilized


title: REF6-HA-24h_rep2

source_name: REF6-HA 24h imbibed seeds

tag: time


title: Col-Input-24h_rep2


title: Rep1, BF, CSD1, input

value: Lister 427


title: A1097


title: Rep1, PF, CRD1, input

value: procyclic form


title: Rep1, BF, RNAseq, WT

data_processing:
Alignment. Command: bowtie2 -f -x Tbruceibrucei427  -1  paired-end_file_1.fasta - 2 paired-end_file_2.fasta > aligned_file.sam
Converting from SAM to BAM format. Command: samtools view -bt Tbruceibrucei427.fasta.fai aligned_file.sam -o aligned_file.bam
Sorting. Command: samtools sort aligned_file.bam -o aligned_sorted_file.bam
Indexing.Command: samtools index aligned_sorted_file.bam
Selection of minus strand reads and normalization to library size. Command: bamCoverage  -b aligned_sorted_file.bam -o normalized_RNA_sample_CPM_minus_strand.bw --filterRNAstrand=forward --outFileFormat bigwig --binSize 1 --normalizeUsing CPM
Selection of plus strand reads and normalization to library size. Command: bamCoverage  -b aligned_sorted_file.bam -o normalized_RNA_sample_CPM_plus_strand.bw --filterRNAstrand=reverse --outFileFormat bigwig --binSize 1 --normalizeUsing CPM
Assembly: HGAP3_Tb427v9.2
Supplementary files format and content: bigWig files showing distribution of polyadenylated transcripts across the T. brucei genome

extract_protocol:
RNA was extracted from 1-4 x 10^7 cells using Trizol (Thermo Fisher Scientific) according to the manufacturer's protocol. The RNA was treated with DNase and then purified using Phenol/Chloroform/Isoamyl alcohol pH 4.
Libraries were constructed using NEBNEXT Ultra II Directional RNA Library Prep kit (NEB) with a Poly-A mRNA magnetic isolation module (NEB).

value: bloodstream form

value: WT


title: Rep1, BF, PBP1, input


title: REF6-HA-0h_rep2

source_name: REF6-HA 0h imbibed seeds

value: Col


title: Rep1, BF, PWWP1, input


title: Rep1, BF, RNAseq, set27, SKO

value: set27 SKO