title: 86-week-old_ATAC-seq_rep1

city: Fuzhou

first: Wenhui

last: Xie

state: Fujian

address: Gulou District, Xinquan Road, No.29

department: Department of Geriatrics, Fujian Key Laboratory of Vascular Aging (Fujian Medical University)

institute: Fujian Medical University Union Hospital

data_processing:
Single-cell mRNA-sequencing libraries were sequenced using the Illumina NovaSeq sequencer, and single-cell ATAC-sequencing libraries were sequenced using Illumina NovaSeq sequencer with a paired-end 50 bp (PE50) reading strategy (the sequencing depth of at least 25k read pairs per nuclei).
For single-cell mRNA-sequencing data, raw sequencing reads generated using NovaSeq system were aligned to the Cell Ranger pre-processing mm10 reference genome. Reads counts were then obtained using Cell Ranger (version 3.1.0) with the default parameters to generate the filtered read count matrix for subsequent analyses. For single-cell ATAC-sequencing data, raw sequencing reads were converted to FASTQ format and then aligned to the mm10 reference genome using Cell Ranger ATAC software (version 1.2.0). After peak calling using the “cellranger-atac count” function with default parameters, a filtered peak-cell matrix was obtained for subsequent analysis.
For single-cell mRNA-sequencing data, the Seurat package (version 3.1.4) was used for QC, data normalization, dimensional reduction, clustering and identification of markers (differentially expressed genes, DEGs). Cells with a mitochondria ratio higher than 0.1 and fewer than 500 genes were filtered out. Doublets were evaluated and excluded using DoubletFinder package (2.0.2). Read count matrices were normalized using the “NormalizeData” function with default parameters. For single-cell ATAC-sequencing data, the Signac package (version 0.2.4) was then used to perform QC, integration of multiple datasets, data normalization, dimensional reduction, clustering, creation of a gene activity matrix, assignment of cell types, differential peak analysis, and differential motif activity analysis. QC metrics including nucleosome banding pattern, transcriptional start site (TSS) enrichment score, total number of fragments in peaks, fraction of fragments in peaks, and ratio reads in “blacklist” sites for scATAC sequencing data, were assessed. The applied cutoffs for QC metrics were as follows: total number of fragments in peaks > 3,000 and < 100,000; percentage of reads in peaks > 15; ratio of reads in genomic blacklist regions < 0.025; signal intensity of nucleosome < 10; TSS enrichment score > 2. Integration of multiple datasets with the same set of peaks was performed using the standard “merge” function in the Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
Supplementary_files_format_and_content: Peak text files for every cell

extract_protocol:
Whole mouse aortas were harvested from 4-week-old, 26-week-old, and 86-week-old male C57/BL6J mice. The isolated aorta included the aortic arch, as well as the ascending, descending, thoracic, and abdominal portions. Perivascular fat was dissected from the vascular tissue before dissociation. Single cells were captured in droplet emulsions using a GemCode Single-Cell Instrument (10X Genomics). Nuclei were isolated from cells dissociated from the aorta based on the protocol of the Nuclei Isolation for Single-Cell ATAC-Sequencing (10X Genomics).
Single-cell mRNA-sequencing and single-cell ATAC-sequencing:
Libraries for single-cell mRNA-sequencing were constructed as per the 10X Genomics protocol using the Single-Cell 3’ v2 Reagent Kits from 10X Genomics, whereas  single-cell ATAC-sequencing libraries were prepared using the Chromium Single-Cell ATAC Library & Gel Bead Kit (#1000110, 10X Genomics).

value: Aorta


title: trh-GAL4::UAS-GFP – rep 1

status: Public on Feb 15 2022

type: SRA

city: Duluth

first: Matthew

last: Slattery

state: MN

address: 1035 University Drive, SMed 255

department: Biomedical Sciences

country: USA

institute: University of Minnesota Medical School

description: trh-rib-GFP_A_IDR0.1-peaks.narrowPeak.gz

library_source: genomic

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
50 bp single-end sequencing reads were trimmed for adapter sequence and low-quality ends were removed
For the samples with 2 replicates, remaining downstream processing was done using the ENCODE ChIP-seq-pipeline2 v1.8.0 (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with default settings, including macs2 peak-calling and IDR peak threshold of 0.1.  Mapping – bowtie2 v2.3.4.3, map quality filtering > 30 – SAMtools v1.9, duplicate read removal – Picard MarkDuplicates v2.20.7, peak calling – macs2 v2.2.4.  For the final, independent btl-GAL4::UAS-rib-GFP replicate, the same parameters and filtering were used (mapping with bowtie v2.3.4.1 to dm6, map quality filtering > 30 with SAMtools v 1.7, duplicate removal with Picard MarkDuplicates v2.9.0), except no IDR thresholding was used and macs2 (v2.2.4) peaks were called with the following parameters: -q 0.05 -B --SMPR --keep-dup all --call-summits.
The final Tracheal Rib high confidence peak set was obtained by using the bedtools intersect command with the following sets of peaks: 1) the IDR peaks from btl-GAL4::UAS-GFP replicate experiment VERSUS the IDR peaks from the trh-GAL4::UAS-GFP replicate experiment --> 2) the set of intersecting IDR regions from btl- and trh-GAL4::UAS-GFP  (from previous step, 1) VERSUS the third, independent set of btl-GAL4::UAS-GFP peaks.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited genomic interval file of peak locations
Supplementary_files_format_and_content: tab-delimited genomic intervals for peaks (BED)
Supplementary_files_format_and_content: tab-delimited genomic intervals for peaks (narrowPeaks)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Drosophila melanogaster embryo

growth_protocol: Flies were raised at 25°C on a standard yeast/molasses medium (1212.5 mL water, 14.7 mL agar, 20.4 g yeast, 81.8 g cornmeal, 109.1 mL molasses, 10.9 mL Tegosept, 3.4 mL propionic acid, 0.4 mL phosphoric acid). All experiments were conducted on embryos collected at 25°C.

extract_protocol:
Chromatin from multiple independent collections of stage 11 – 16 btl-GAL4::UAS-rib-GFP and trh-GAL4::UAS-rib-GFP embryos were cross-linked at room temperature in 1.8% formaldehyde in 2 ml of homogenization buffer (60 mM KCl, 15 mM NaCl, 15 mM HEPES {pH7.6}, 4 mM MgCl2, 0.5 mM DTT, 0.5% Triton X-100 and cOmplete™ protease inhibitor cocktail [1 tablet per 50 ml buffer]). The cross-linked material was resuspended in 0.1% SDS and 0.5% N-lauroylsarcosine in lysis buffer (140mM NaCl, 15mM HEPES [pH 7.6], 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 1% Triton X-100, 0.5mM DTT and cOmplete™ protease inhibitor cocktail [1 tablet per 50 ml buffer]). Chromatin was sonicated three times at 4°C using the Sonic Dismembrator Model 100 (Fisher Scientific) under the following conditions: power setting 3, 20s ON, 20s OFF. Immediately after sonication, the chromatin extract was stored at −80°C prior to immunoprecipitation. Immunoprecipitations were performed, as described in (Negre et al., 2006), using a polyclonal goat anti-GFP antibody.
DNA libraries were prepared using the NuGen Ovation Ultralow Library System (btl-GAL4::UAS-rib-GFP and trh-GAL4::UAS-rib-GFP experimental replicates 1 & 2 and corresponding input control), or the KAPA DNA HyperPrep Library Prep Kit (independent replicate of btl-GAL4::UAS-rib-GFP).  Illumina sequencing was performed according to the manufacturers specifications at the University of Minnesota Genomics Center (btl-GAL4::UAS-rib-GFP and trh-GAL4::UAS-rib-GFP experimental replicates 1 & 2 and corresponding input control) or at th UCLA Technology Center for Genomics & Bioinformatics (independent replicate of btl-GAL4::UAS-rib-GFP) as 50 bp single-end reads.

tag: tissue

value: whole embryo

tag: genotype

tag: treatment

value: goat anti-GFP immunoprecipitation

tag: age

value: stage 11-15

tag: replicate


title: btl-GAL4::UAS-GFP – input (1&2)

value: input (untreated)


title: MM468bc_primaryH3K27me3_H3K27me3_IgG

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description: H3K27me3_IgG_summits_merged_filtered_by_TSS_and_K27.bed

data_processing: Fastq files for primary (ChIP) and secondary (ChIP-reChIP) immunoprecipitation were processed as for bulk ChIP-seq. In order to detect peaks within secondary ChIP, peaks were called with MACS2 using the primary H3K27me3 signal as input, and the secondary ChIP (H3K4me3 or IgG) as sample with parameters ‘macs2 callpeak --call-summits -p 0.1 --nomodel --extsize 300’. Summits closer to each other by 1,000 bp were merged using Bedtools.

organism: Homo sapiens

source_name: MDA-MB-468 cell line

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106).

extract_protocol: Sequential ChIP-seq:The first ChIP experiments were performed as described previously (Grosselin et al.,  2018) on 30e6 cells using anti-H3K27me3 (Cell signaling, Ref: #9733) or anti-H3 (Cell signaling, Ref: #4620) antibodies. After the washes, samples were eluted twice at 37°C for 15 min under agitation in the first ChIP elution buffer (50mM Tris-Hcl pH8, 5mM EDTA, 20mM DTT, 1%SDS)(Desvoyes et al., 2018). Samples were diluted 10 times to reduce SDS and DTT concentration. 10% of the eluted chromatin were kept as primary ChIP. The second ChIP was performed overnight on the rest of the chromatin using anti-H3K27me3, anti-H3K4me3 (Cell signaling, Ref: #9751) or anti-IgG (Cell signaling, Ref: #3900) antibodies. After the washes, samples were eluted twice at 65°C for 15 min under agitation in the ReChIP elution buffer (0,1M NaHCO3 and 1% SDS)(Desvoyes et al., 2018). As a positive control, we first immunoprecipitated H3 and the H3K27me3 and as a negative control, we first immunoprecipitated H3K27me3 followed by IgG immunoprecipitation.

treatment_protocol: All cell lines were cultured in a humidified 5% CO2 atmosphere at 37 °C, and were tested as mycoplasma negative. GSKJ4 (KDM6A/B inhibitor, Sigma, Ref: SML0701), GSKJ5 (GSK-J4 inactive isomer, Abcam, Ref: ab144397) and UNC1999 (EZH2 inhibitor, Abcam, Ref: ab146152) were used at indicated concentrations. Cells were treated with 5 μM of 5-FU (Sigma, Ref: F6627) alone or in combination with KDM6A/Bi or EZH2i for indicated days.

value: DMSO

tag: day

tag: antibody

value: H3K27me3 - Cell Signaling, Ref:9733


title: MM468_5FU4_day113_a_H3K27me3 [bulk ChIP-seq]

data_processing:
ChIP-seq: Read #1 was aligned to hg38 Human genome reference using bowtie with options ‘-S -k 1 -m 1’
ChIP-seq: After sorting by genomic coordinates, duplicates were removed using Picard tools MarkDuplicates.
ChIP-seq: Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCoverage function with options ‘--normalizeUsing CPM --binSize 50 --smoothLength 500 --extendReads 150 --ignoreForNormalization chrX’.
ChIP-seq: Comparison Coverage BigWigs files were created from sorted deduplicated files using Deeptools bamCompare function with options ‘--binSize 50 --smoothLength 1000 --extendReads 150 --ignoreForNormalization chrX --operation log2 --pseudocount 1 –skipNonCoveredRegions’.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig binary file of coverage and compared coverage

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). HCC38 cell lines were cultured in RPMI 1640 (Gibco-BRL, Ref: 11875085), supplemented with 10% heat-inactivated fetal calf serum.

extract_protocol:
Sequential ChIP-seq:The first ChIP experiments were performed as described previously (Grosselin et al.,  2018) on 30e6 cells using anti-H3K27me3 (Cell signaling, Ref: #9733) or anti-H3 (Cell signaling, Ref: #4620) antibodies. After the washes, samples were eluted twice at 37°C for 15 min under agitation in the first ChIP elution buffer (50mM Tris-Hcl pH8, 5mM EDTA, 20mM DTT, 1%SDS)(Desvoyes et al., 2018). Samples were diluted 10 times to reduce SDS and DTT concentration. 10% of the eluted chromatin were kept as primary ChIP. The second ChIP was performed overnight on the rest of the chromatin using anti-H3K27me3, anti-H3K4me3 (Cell signaling, Ref: #9751) or anti-IgG (Cell signaling, Ref: #3900) antibodies. After the washes, samples were eluted twice at 65°C for 15 min under agitation in the ReChIP elution buffer (0,1M NaHCO3 and 1% SDS)(Desvoyes et al., 2018). As a positive control, we first immunoprecipitated H3 and the H3K27me3 and as a negative control, we first immunoprecipitated H3K27me3 followed by IgG immunoprecipitation.  manufacturer’s instructions.   Bulk ChIP-seq : ChIP experiments were performed as previously described19 on 3x106 MDA-MB-468 cells (DMSO-D67-#2, DMSO-D77-#3, DMSO-D113-#4, 5-FU-D67-#2, 5-FU-D77-#3, 5-FU-D113-#4) using an anti-H3K27me3 antibody (Cell Signaling Technology, Ref: 9733 - C36B11).   Chromatin Indexing : Chromatin isolation, indexing, immunoprecipitation and library preparation was adapted from48. Briefly, 50,000 MDA-MB-468 were lysed and digested with MNase for 20min at 37°C in the following buffer: 46mM Tris-HCl pH 7.4, 0.154M NaCl, 0.1% Triton, 0.1% NaDoc, 4.65mM CaCl2, 0.47x Protease Inhibitor Cocktail (Roche, Ref: 11873580001) and 0.09u/uL MNase (Thermo Scientific, Ref: EN0181). Fragmented nucleosomes were then ligated for at least 24h at 16°C to double-stranded barcoded adapters containing 8bp barcodes to combine samples:  Pac1-T7-Read2-8bpBarcode-linker-Pac1 (Supplementary Table 1). Next, 5 indexed chromatin samples (DMSO, 5-FU, UNC, 5-FU + UNC, GSK-J4) were pooled, each containing a different 8-bp barcode, to perform anti-H3K27me3 ChIP (Cell Signaling, Ref: 9733 - C36B11) on 250,000 cells in total in each pool.
Sequential ChIP-seq : After reverse crosslinking and DNA clean-up, 3 to 15ng of immunoprecipated DNA were used to prepare the sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (NEB, Ref: E7645S) according to theLibraries were sequenced on a NovaSeq 6000 (Illumina) in SE100 mode.  Bulk ChIP-seq : Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, Ref: E7645S) according to the manufacturer’s instructions.  Libraries were sequenced on a NovaSeq 6000 (Illumina) in SE50 mode.  Chromatin Indexing : ChIP and DNA amplification was carried out as for scChIP-seq19 and a sequencing library was produced for both IP and input pools, sequenced on NovaSeq 6000 (Illumina) in PE100 mode.


title: 26-week-old_ATAC-seq_rep1

country: China

organism: Mus musculus

tag: strain


title: MM468bc_reChIP_H3K27me3_IgG

extract_protocol: Sequential ChIP-seq:The first ChIP experiments were performed as described previously (Grosselin et al., 2018) on 30e6 cells using anti-H3K27me3 (Cell signaling, Ref: #9733) or anti-H3 (Cell signaling, Ref: #4620) antibodies. After the washes, samples were eluted twice at 37°C for 15 min under agitation in the first ChIP elution buffer (50mM Tris-Hcl pH8, 5mM EDTA, 20mM DTT, 1%SDS)(Desvoyes et al., 2018). Samples were diluted 10 times to reduce SDS and DTT concentration. 10% of the eluted chromatin were kept as primary ChIP. The second ChIP was performed overnight on the rest of the chromatin using anti-H3K27me3, anti-H3K4me3 (Cell signaling, Ref: #9751) or anti-IgG (Cell signaling, Ref: #3900) antibodies. After the washes, samples were eluted twice at 65°C for 15 min under agitation in the ReChIP elution buffer (0,1M NaHCO3 and 1% SDS)(Desvoyes et al., 2018). As a positive control, we first immunoprecipitated H3 and the H3K27me3 and as a negative control, we first immunoprecipitated H3K27me3 followed by IgG immunoprecipitation.

value: IgG


title: 26-week-old_ATAC-seq_rep2


title: btl-GAL4::UAS-GFP – rep 2

description: btl-rib-GFP_A_IDR0.1-peaks.narrowPeak.gz


title: btl-GAL4::UAS-GFP – rep 1


title: 86-week-old_ATAC-seq_rep2


title: MM468_primaryH3K27me3_H3K27me3_H3K4me3


title: 4-week-old_ATAC-seq_rep1


title: MM468_reChIP_H3K27me3_H3K4me3

description: H3K27me3_H3K4me3_summits_merged_filtered_by_TSS_and_K27.bed

value: H3K4me3 - Cell Signaling, Ref:9751


title: 86-week-old_RNA-seq_rep2

library_source: transcriptomic

molecule: total RNA


title: c55t MCLA158 10ug/ml 48h replicate 2

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

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 GENCODE hsapiens_v34.GRCh38.p13 custom annotation
Genome_build: hg38
Supplementary_files_format_and_content: Raw count matrix in tab separated format

source_name: organoid

growth_protocol: PDOs were cultured at 37 °C with 85–90% humidity, atmospheric O2 and 5% CO2. For PDO passaging, basement-membrane extract drops were washed once with HBSS (Lonza) and treated with Trypsin-EDTA (Sigma) for 5 min at 37 °C, followed by mechanical disaggregation of organoid fragments (by pipetting) until a single-cell suspension was obtained. Trypsin was quenched with FBS, cells were washed with HBSS and replated in cold BME medium on warm plates.

extract_protocol:
Organoids were lyzed with Cell Lysis buffer and RNA was purified using PureLink® RNA Mini Kit
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 12 cycles of amplification.

treatment_protocol: P18 and C55T organoids were dissociated into a single cell suspension with Trypsin/EDTA. The full organoid culture media (Morral et al. 2020) was modified, and did not contain Gastrin or PGE2, and had a reduced concentration of EGF (2.5 ng/mL). Organoids were treated either with PG1337, Cetuximab or MCLA-158 at 1 or 10 µg/mL for 2 days. At day 2, cells were lysed with lysis buffer. Each treatment has 2 technical replicates.

tag: organoid

tag: treatmet

tag: dose


title: c55t MCLA158 1ug/ml 48h replicate 2


title: HBCx95_m43_UNT_H3K4me3 [scChIP-seq]

data_processing:
scChIP-seq: Each #Read 2 was first separated into two parts – a cell barcode part composed of the first 79 nucleotides and the last 22 nucleotides composed of genomic DNA.
scChIP-seq: Full #Read 1 and genomic DNA of #Read 2 were mapped in paired-end mode to hg38 whole genome using STAR v2.6.0c with parameters --alignEndsType EndToEnd --outFilterMultimapScoreRange 2 --winAnchorMultimapNmax 1000 --alignIntronMax 1 --peOverlapNbasesMin 10 --alignMatesGapMax 450 --limitGenomeGenerateRAM 25000000000 --outSAMunmapped Within
scChIP-seq: Barcodes were extracted from the 79bp of Reads #2 by retrieving the three 16-mer indices (respectively  located at positions 1-16, 21-36, 41-56 on Read #2). Each index was independently aligned on the 96 possibles indexes of it’s respective set of indices using Bowtie2 2.2.9  with options ‘-N 1 -L 10 --rdg 0,7 --rfg 0,7 --mp 7,7 --ignore-quals --score-min L,0,-1 -t --no-unal –no-hd’, allowing up to two mismatches / indels on the entire sequence. Full non redundant barcodes were then reconstructed for reads mapping all of the three indexes.
scChIP-seq: For each barcode, aligned reads were deduplicated by removing successively:  1. PCR duplicates, identified if #Read1 + #Read 2 mapped at the same position, 2. RT duplicates, identified if #Read 1 mapped at the same postion and  3. Window duplicates : all the reads falling in the same 50 bp window were stacked into one as reads possibly originating from PCR duplicates or from the same nucleosome. Then, reads were either counted on a ‘consensus peak annotation’  or onto 10kbp regions around Transcript Start Site (TSS) to generate a n x m coverage matrix with n barcodes and m genomic regions used in downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count for each cell genomic bins (scChIP-seq). Single-cell raw BED files can be easily generated from BAM files using the bash script at https://github.com/vallotlab/ChemoPersistance/blob/master/Scripts/scChIPseq/bam_to_single_cell_bed.sh

source_name: PDX model

growth_protocol: For the PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used a xenograft model generated from a residual triple-negative breast cancer post-neoadjuvant chemotherapy (HBCx95) established previously at Institut Curie.

extract_protocol: For the PDX model, prior scChIP-seq and scRNA-seq, PDX were digested at 37°C for 2h with a cocktail of Collagenase I (Roche, # 11088793001) and Hyaluronidase (Sigma, # H3506) as previously described (Petit et al, Lab Investigation 2013). Cells were further individualized at 37°C using a cocktail of 0.25% trypsin/Versen (ThermoFisher Scientific, #15040-033), Dispase II (Sigma, # D4693) and Dnase I (Roche, # 11284932001). Red Blood Cell lysis buffer (ThermoFisher Scientific, # 00-4333-57) was then added to degrade red blood cells. To increase the viability of the cell suspension, we removed dead cells using a Dead Cell Removal kit (Miltenyi Biotec). Cells were re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).  After immunoprecipitation targeting H3K4me3 or H3K27me3, scChIP-seq libraries were prepared as following: barcoded-nucleosomes were amplified by in vitro transcription using the T7 MegaScript kit (ThermoFisher Scientific). The resulting amplified RNA was purified using 1x RNAClean XP beads (Beckman) and reverse transcribed by random priming in cDNA. After RNA digestion, DNA was amplified by PCR using with Illumina Primers for 12 cycles and library fragments ranging from 300 to 600 bp (single-cell barcode plus nucleosomal sequence + PCR primer sequence) were size-selected on an agarose gel. Single-cell ChIP-seq libraries were sequenced on Illumina NovaSeq 6000 in PE100, with 4 dark cycles on Read 2.

value: Untreated


title: 86-week-old_RNA-seq_rep1


title: HBCx95_m43_UNT_H3K27me3 [scChIP-seq]


title: Unheated control Lp replicate 3

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

middle: P

last: Faucher

state: Quebec

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity and local background was measured.

data_processing: Fluorescence data were aquired by mapix software and analyzed using limma package in R. Background correction was performed using normexp and both within-array  and between array normalization were performed with the normalizeVSN inbuilt function.

label: Alexa Fluor 546

organism: Legionella pneumophila subsp. pneumophila ATCC 33215

source_name: Freshwater suspended Lp

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.

growth_protocol: Legionella pneumophila strain Philadelphia-1 was grown from a single colony in AYE media to stationary phase shaking 250 rpm at 37 degrees C and washed three times in Fraquil (defined freshwater simulant) before 2 hour suspension at an OD600 nm of 1.0 in Fraquil

extract_protocol: 8 mL volumes were withdrawn from suspensions and pelleted for RNA extraction by TRIzol reagent (Invitrogen) and reverse-transcribed into cDNA. Genomic DNA was extracted using the Wizard DNA extraction kit (ProMega)

treatment_protocol: 10 mL suspensions were dispensed into 50 mL Erlenmeyer flasks and heat shocked for 5 minutes in a circulating water bath at 55 degrees C or left at room temperature for the same amount of time

label: Alexa Fluor 647


title: 4-week-old_ATAC-seq_rep2


title: Heat shocked Lp replicate 2

source_name: Freshwater suspended Lp after 5 minutes exposure to 55 C


title: c55t Erbitux 1ug/ml 48h replicate 2

value: Erbitux


title: Heat shocked Lp replicate 3


title: Heat shocked Lp replicate 1


title: Unheated control Lp replicate 2


title: 26-week-old_RNA-seq_rep1


title: 26-week-old_RNA-seq_rep2


title: c55t PG1337 10ug/ml 48h replicate 2


title: 4-week-old_RNA-seq_rep2


title: c55t PG1337 1ug/ml 48h replicate 2


title: P18 MCLA158 10ug/ml 48h replicate 2


title: c55t Erbitux 10ug/ml 48h replicate 2


title: MM468_DMSO1_day0_H3K4me3 [scChIP-seq]

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). All cell lines were cultured in a humidified 5% CO2 atmosphere at 37 °C, and were tested as mycoplasma negative.

extract_protocol: For MDA-MB-468 cell line, prior to scChIP-seq cells were  individualized and re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).  For the PDX model, prior scChIP-seq and scRNA-seq, PDX were digested at 37°C for 2h with a cocktail of Collagenase I (Roche, # 11088793001) and Hyaluronidase (Sigma, # H3506) as previously described (Petit et al, Lab Investigation 2013). Cells were further individualized at 37°C using a cocktail of 0.25% trypsin/Versen (ThermoFisher Scientific, #15040-033), Dispase II (Sigma, # D4693) and Dnase I (Roche, # 11284932001). Red Blood Cell lysis buffer (ThermoFisher Scientific, # 00-4333-57) was then added to degrade red blood cells. To increase the viability of the cell suspension, we removed dead cells using a Dead Cell Removal kit (Miltenyi Biotec). Cells were re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).  After immunoprecipitation targeting H3K4me3 or H3K27me3, scChIP-seq libraries were prepared as following: barcoded-nucleosomes were amplified by in vitro transcription using the T7 MegaScript kit (ThermoFisher Scientific). The resulting amplified RNA was purified using 1x RNAClean XP beads (Beckman) and reverse transcribed by random priming in cDNA. After RNA digestion, DNA was amplified by PCR using with Illumina Primers for 12 cycles and library fragments ranging from 300 to 600 bp (single-cell barcode plus nucleosomal sequence + PCR primer sequence) were size-selected on an agarose gel. Single-cell ChIP-seq libraries were sequenced on Illumina NovaSeq 6000 in PE100, with 4 dark cycles on Read 2.


title: MM468_5FU2_day171_H3K27me3 [scChIP-seq]


title: MM468_5FU1_day60_H3K4me3 [scChIP-seq]


title: P18 MCLA158 1ug/ml 48h replicate 2


title: 4-week-old_RNA-seq_rep1


title: MM468_5FU3_day147_H3K27me3 [scChIP-seq]


title: No drug control

city: Köln

first: Martin

last: Lukačišin

state: Deutschland

address: Zülpicher Straße 47a

department: Institute for Biological Physics

country: Germany

institute: Universität zu Köln

description:
87
countsCDS.txt
countsIntrons.txt
countsFivePrimeIntrons.txt

data_processing:
The reads resulting from sequencing were aligned to annotated reference S. cerevisiae genome R64-2 using TopHat (Kim et al., 2013). The reads mapping to introns or CDS of intron-containing genes were quantified using featureCounts (Liao et al., 2014) using custom produced .saf file extracted from the reference .gff annotation file. The intron retention rate was calculated as the ratio of intron counts normalised to the intron length over the CDS counts normalized to the length of the CDS region. For genes containing multiple introns, the introns were treated jointly for CDS introns and separately for 5’-UTR introns.
Genome_build: R64-2
Supplementary_files_format_and_content: countsCDS.txt: RNA seq counts for the protein coding regions of all the annotated genes.
Supplementary_files_format_and_content: countsIntrons.txt: RNA seq counts for the CDS introns.
Supplementary_files_format_and_content: countsFivePrimeIntrons.txt: RNA seq counts for the 5'UTR introns.

organism: Saccharomyces cerevisiae

source_name: Ribodepleted RNA from 200 ul liquid culture

growth_protocol: For RNA isogrowth RNA sequencing, S. cerevisiae strain BY4741 was grown in 7 conditions of varying ratios of LiCl and cycloheximide, ensuring 50% growth inhibition, and in YPD containing no drug. The frozen stock was diluted 130-times into drug containing wells and 100-times more into wells without drug. The cells were incubated as for ~17 hrs to the OD600 of ~0.5.

extract_protocol:
Cells were then harvested and the RNA extraction was performed using RiboPure RNA Purification Kit for yeast (Thermo Scientific, AM1926).
The extracted RNA was sent to the Next Generation Sequencing Facility of the Vienna Biocenter Core Facilities, where it was rRNA depleted using Illumina Ribozero Yeast Kit, multiplexed using Illumina TruSeq adapters, single-end 50bp sequenced using Illumina HiSeqV4 and demultiplexed.

tag: condition

value: No drug


title: Torin1 trerated J774.1 cell replicate 2

type: RNA

city: Tokushima

first: kohta

last: ohnishi

address: Kuramoto-cho 3-18-15

country: Japan

institute: Tokushima University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE Unrestricted Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel was set to Green and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: J774.1 mouse macrophage-like cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Sepasol®-RNA I Super G following the manufacture's decommendations. Quality and concentration of RNA were checked by 2100 Bioanalyzer (Agilent Technologies, CA, USA)

treatment_protocol: J774.1 cells were treated with isorhamnetin (10µM) or tamarixetin (10µM) or Torin1 (1µM) for 6h.

value: hemo-lymphocytic

value: BALB/c

tag: cell line

value: J774.1 cells

value: Torin


title: LiCl only, isobole point no. 7

description:
86
countsCDS.txt
countsIntrons.txt
countsFivePrimeIntrons.txt

value: LiCl only


title: Unheated control Lp replicate 1


title: P18 Erbitux 10ug/ml 48h replicate 2


title: Isobole point no. 6

description:
85
countsCDS.txt
countsIntrons.txt
countsFivePrimeIntrons.txt

value: Cycloheximide and LiCl


title: P18 Erbitux 1ug/ml 48h replicate 2


title: MM468_5FU6_day131_H3K27me3 [scChIP-seq]


title: P18 PG1337 10ug/ml 48h replicate 2


title: Isobole point no. 5

description:
84
countsCDS.txt
countsIntrons.txt
countsFivePrimeIntrons.txt


title: MM468_5FU1_day33_H3K27me3 [scChIP-seq]


title: Isobole point no. 4

description:
83
countsCDS.txt
countsIntrons.txt
countsFivePrimeIntrons.txt


title: Tamarixetin treated J774.1 cell replicate 1

value: TAM


title: Torin1 trerated J774.1 cell replicate 1


title: Isorhamnetin treated  J774.1 cell replicate 2

value: IR


title: human spinal cord organoids, 1month

city: SEOUL

first: Ju-Hyun

last: Lee

address: 73 Inchon-ro

country: South Korea

institute: Korea University College of Medicine

data_processing:
Raw sequencing data were processed via Cell Ranger pipline(version 3.1.0) provided by 10X genomics.
Raw bcl files were demultiplexed to fastq files using cellranger mkfastq with default parameters.
Alignment, filtering, barcode counting, and UMI counting were performed using cellranger count step.
Downstream analysis including QC and visualization were performed with the Seurat R package (version 3.1.5)
Genome_build: GRCh38
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: hPSCs

extract_protocol:
The hSCOs were collected in a petri dish on day 29 and chopped into small pieces. After dissection, the hSCOs were dissociated by using papain containing L-cysteine by incubation at 37℃ with gentle shaking. Papain was removed after 30 min, and the dissociated cells were washed twice with ice-cold HBSS. Libraries were prepared using the Chromium controller according to the 10x Single Cell 3’ v3 protocol (10x Genomics)
The dissociated cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. The cell suspension was mixed with a master mix and loaded with Single-Cell 3′ Gel Beads and Partitioning Oil into a Single Cell 3′ Chip. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled. The cDNA pool was subjected to an end repair process, followed by the addition of a single ‘A’ base and ligation of the adapters. The products are then purified and enriched with PCR to develop the final cDNA library. The purified libraries were quantified using qPCR based on the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies). The libraries were subsequently sequenced using the HiSeq platform (Illumina) with a read length of 28 bp for read 1 (cell barcode and unique molecular identifier, UMI), 8 bp index read (sample barcode), and 91 bp for read 2 (RNA read).
single cell RNA-seq

value: spinal cord organoids, on day 29 (1-month) from hPSC

tag: cell type

value: hPSC-derived caudal neural cells


title: Isobole point no. 3

description:
82
countsCDS.txt
countsIntrons.txt
countsFivePrimeIntrons.txt


title: HepG2_RPUSD4KD_mRNA_Rep2

city: New Haven

first: Wendy

last: Gilbert

state: CT

address: 333 Cedar Street – Room C-129

department: MB&B

institute: Yale University

data_processing:
Library strategy: Pseudo-seq
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed for in vitro Pseudo-seq libraries using fastx_collapser
Reads were mapped to bowtie indices of the pool or GRCh37 for chromatin-associated RNA Pseudo-seq with tophat2. Reads from PUS1 knockout and wild type mRNA-seq were mapped to GRCh37 using STAR
Pseudouridylation was assessed using cutom python scripts (see text)
Differential mRNA level analysis of PUS1 knockout and wildtype mRNA-seq using DEseq2
Differential splicing analysis of PUS1 knockout and wildtype mRNA-seq using rMATS
Genome_build: GRCh37 for sequencing experiments from cellular RNA and Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)
Supplementary_files_format_and_content: rMATS output
Supplementary_files_format_and_content: DEseq2 output

source_name: poly(A)+ mRNA HepG2 RPUSD4 KD

extract_protocol:
HepG2 cells were biochemically fractionated and chromatin-associated RNA was isolated and Pseudo-seq was performed. Total RNA was isolated from PUS1 knockout, PUS7 knockdown, RPUSD4 knockdown and wildtype HepG2 cells with Qiazol and poly(A)+ mRNA-seq was perfomed with TruSeq Stranded mRNA kit.   Oligo pools (human, Twist Biosciences) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
Pseudo-seq samples were treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.

value: PUS7 KD

tag: bowite fasta


title: Isorhamnetin treated J774.1 cell replicate 1


title: Isobole point no. 2

description:
81
countsCDS.txt
countsIntrons.txt
countsFivePrimeIntrons.txt


title: Stimulation AbSeq, Tum051_Cart4

city: Seattle

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

data_processing:
Samples 1-8 (10x) samples were processed using CellRanger pipline version 2.1.1 or 3.0.2
Sample 9 aligned RNA reads using 1342_Fred_Hutch_suppt2_amplicons.fasta
Sample 10 aligned RNA reads using 1342_Fred_Hutch_suppt2_amplicons.fasta and aligned protein reasd using AbSeq_Prlic_NEW_v2.fasta
FASTQ files were processed with BD Rhapsody Analysis Pipeline hosted by SevenBridges Genomics
FASTQ files were processed with CellRanger software v2.1.1 or v3.0.1 and corresponding sample sheet
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

source_name: SCC and Peripheral blood

extract_protocol:
RNA was extracted using BD Rhapsody or 10x genomics protocols
RNA was constructed using BD Rhapsody or 10x genomics protocols

treatment_protocol: T  cells were stimulated for 2 hour with PMA/ Ionomycin or IL-12, IL-15, IL-18

tag: phenotype

tag: donors

value: Squamous Cell Carcinoma and Peripheral Blood


title: MM468_5FU2_day67_H3K27me3 [scChIP-seq]

value: H3K27me3 - Cell Signaling, Ref:9733


title: Tamarixetin treated J774.1 cell replicate 2

tag: tissue


title: c55t MCLA158 10ug/ml 48h


title: MM468_DMSO3_day77_H3K27me3 [scChIP-seq]

value: DMSO


title: MM468_DMSO1_day60_H3K27me3 [scChIP-seq]


title: Cycloheximide only, isobole point no. 1

description:
80
countsCDS.txt
countsIntrons.txt
countsFivePrimeIntrons.txt

value: Cycloheximide only


title: P18 PG1337 1ug/ml 48h replicate 2


title: Stimulation AbSeq, Tum051_Cart3


title: c55t Erbitux 10ug/ml 48h

value: Erbitux


title: MM468_DMSO5_day131_H3K27me3 [scChIP-seq]

growth_protocol: MDA-MB-468 cells were cultured in DMEM (Gibco-BRL, Ref: 11966025), supplemented with 10% heat-inactivated fetal calf serum (Gibco-BRL, Ref: 10270-106). HCC38 cell lines were cultured in RPMI 1640 (Gibco-BRL, Ref: 11875085), supplemented with 10% heat-inactivated fetal calf serum. All cell lines were cultured in a humidified 5% CO2 atmosphere at 37 °C, and were tested as mycoplasma negative.   For the PDX model, female Swiss nude mice were purchased from Charles River Laboratories and maintained under specific-pathogen-free conditions. Mouse care and housing were in accordance with institutional guidelines and the rules of the French Ethics Committee (project authorization no. 02163.02). In this study, we used a xenograft model generated from a residual triple-negative breast cancer post-neoadjuvant chemotherapy (HBCx95) established previously at Institut Curie with informed consent from the patient51,52.


title: Stimulation AbSeq, Tum051_Cart2


title: Control J774.1 cell replicate 2

value: Ctrl


title: Control J774.1 cell replicate 1

value: hemo-lymphocytic


title: rv0500A*, pH 5.7, 250 mM NaCl, replicate 1 [STr121]

city: Boston

first: Shumin

last: Tan

state: MA

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

data_processing:
Illumina bcl2fastq was used for demultiplexing and conversion of reads to FASTQ file format.
Trimmomatic (v0.33) was used with a 4 bp sliding window to trim adapter sequences and low quality bases. Sequence was removed when the sliding window identified read quality below 15 or read length less than 36 bp.
Bowtie (v1.1.1) was used to align trimmed reads to the M. tuberculosis CDC1551 genome (NCBI accession #: AE000516) to produce SAM files.
HTseq (v0.6.1) was used to determine the number of aligned reads that map to each gene feature in the M. tuberculosis genome.
edgeR (v3.2) was used to normalize data.
R was used for differential gene expression and statistical analyses.
Genome_build: M. tuberculosis Erdman genome (GCA_000350205.1) (NCBI accession NC_020559.1).
Supplementary_files_format_and_content: The file is presented in the .csv file format. It contains gene expression analysis from 2 biological replicates for each condition.

organism: Mycobacterium tuberculosis

source_name: Bacterial cell

growth_protocol: Mtb strain Erdman wild type (WT), ∆rv0500A, and rv0500A* (complemented mutant) were grown to an OD600 of ~0.6 (mid-log phase) in standing, filter-capped T-75 flasks in 20 ml of media, originally seeded at an OD600 of 0.05.

extract_protocol:
RNA was extracted as previously described by Rohde, Abramovitch, and Russell (Cell Host and Microbe 2:352-364, 2007). In brief, RNA was stabilized with guanidine-thiocyanate lysis buffer prior to a freeze-thaw step. Once thawed, bacteria were lysed with 5 µg/ml lysozyme, followed by hot Trizol and physical disruption through silica bead agitation in a Beadbeater.  A chloroform extraction was used to further isolate the RNA before purification with an RNAeasy kit (Qiagen). DNA was degraded with Turbo DNAfree DNAse (Ambion). RNA quality was assessed with an Aligent Bioanalyzer.
The cDNA library was constructed with an Illumina Stranded Total RNA with Ribo-Zero Plus kit.

treatment_protocol: Mtb strains at mid-log phase were subcultured in 10 ml of media to an OD600 of 0.3 in standing, filter-capped T-25 flasks containing either standard 7H9, pH 7 media, or 7H9, pH 5.7 media supplemented with 250 mM NaCl. Exposure was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted.

value: Erdman

tag: genotype

value: rv0500A* (complemented mutant)

tag: exposure condition


title: rv0500A*, pH 5.7, 250 mM NaCl, replicate 2 [STr122]


title: c55t PG1337 10ug/ml 48h


title: Stimulation AbSeq, Tum051_Cart1


title: c55t MCLA158 1ug/ml 48h


title: ∆rv0500A, pH 5.7, 250 mM NaCl, replicate 2 [STr120]


title: Stimulation AbSeq, Tum049_Cart4


title: c55t PG1337 1ug/ml 48h


title: HepG2_Ctrl_RPUSD4_mRNA_Rep1

source_name: poly(A)+ mRNA HepG2 Ctrl

value: control PUS7


title: HepG2_PUS7KD_mRNA_Rep3

source_name: poly(A)+ mRNA HepG2 PUS7 KD


title: HepG2_Ctrl_RPUSD4_mRNA_Rep2


title: P18 MCLA158 10ug/ml 48h


title: WT, pH 5.7, 250 mM NaCl, replicate 2 [STr118]

value: wild type


title: ∆rv0500A, pH 5.7, 250 mM NaCl, replicate 1 [STr119]


title: HepG2_Ctrl_PUS7_mRNA_Rep3


title: HepG2_PUS7KD_mRNA_Rep2


title: HepG2_Ctrl_PUS7_mRNA_Rep2


title: P18 MCLA158 1ug/ml 48h


title: HepG2_RPUSD4KD_mRNA_Rep1


title: Stimulation AbSeq, Tum049_Cart2


title: c55t Erbitux 1ug/ml 48h


title: P18 Erbitux 10ug/ml 48h


title: Stimulation AbSeq, Tum049_Cart1


title: HepG2_PUS7KD_mRNA_Rep1


title: WT, pH 5.7, 250 mM NaCl, replicate 1 [STr117]


title: rv0500A*, pH 7, replicate 2 [STr116]


title: P18 Erbitux 1ug/ml 48h


title: HepG2_Ctrl_PUS7_mRNA_Rep1


title: rv0500A*, pH 7, replicate 1 [STr115]


title: T cells - SCC Rhapsody, Cart2

source_name: Cryopreserved SCC-derived T cells

value: SCC004  SCC007  SCC008


title: ∆rv0500A, pH 7, replicate 2 [STr114]


title: T cells - SCC Rhapsody, Cart1


title: WT, replicate 2

city: Basel

first: Daniel

last: Bodmer

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University Hospital Basel

data_processing:
The produced single-end reads which passed Illumina’s chastity filter were subject to de-multiplexing and trimming of Illumina adaptor residuals using Illumina’s bcl2fastq software version 2.20.0.422 (no further refinement or selection).
Raw reads having average Q-values below 20 or incorporating uncalled ‘N’ bases were filtered using the BBTools software suite (version 38.86).
The splice aware RNA mapping software STAR (version 2.7.7a) was used to map the surviving reads to the mm10 reference genome provided by IGenomes.
To count the uniquely mapped reads to annotated genes, the software htseq-count (HTSeq version 0.13.5) was used.
Normalization of the raw counts and differential gene expression analysis was carried out with help of the R software package DESeq2 (version 1.26.0).
Genome_build: mm10 (UCSC) - provided by IGenomes
Supplementary_files_format_and_content: counts.tsv: tab-separated text file with gene counts; column 1: gene symbol, columns 2-7: counts per sample

source_name: stria vascularis

growth_protocol: Stria vascularis for culture studies were obtained from C57BL/6N and Nhe6KO mice on postnatal day 10-12. Endothelial cells were cultured in Endothelial Cell Basal Medium (Sigma, cat#210-500) with  10 % fetal bovine serum (Gibco, cat#10270106), 1 % endothelial cell growth factor (Sigma, cat# E1388) and 1 % penicillin/streptomycin solution (Sigma, cat# P4333) at 37°C and 5% CO2.

extract_protocol:
Cell lysis and total RNA isolation was done according to manufacturer's recommendation (RNeasyPlus 96 kit from Qiagen) in doing so 10 μl of β-mercaptoethanol (14.3M) per ml of buffer RLTplus lysis was added before cell lysis.
Illumina’s TruSeq stranded RNA library preparation kit including polyA enrichment was used to construct libraries from total RNA. Subsequently the Illumina NextSeq 550 platform and a high output v2.5 kit (75 cycles) were used to sequence the libraries.

treatment_protocol: no treatment

tag: strain background

value: Primary Endothelial cells

value: Wild type


title: WT, replicate 3

tag: replicate


title: ∆rv0500A, pH 7, replicate 1 [STr113]


title: P18 PG1337 1ug/ml 48h


title: WT, pH 7, replicate 2 [STr112]


title: Myeloid Cells - Blood (Tumor) 10x SCC027

source_name: Peripheral Blood Myloid Cells (SCC)

value: Peripheral Blood


title: Stimulation AbSeq, Tum049_Cart3


title: WT, replicate 1


title: Chr_Seq shDrosha rep2

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
Library strategy: chromatin-associated RNA-seq (Chr-seq)
build tRNA+-7nt bowtie index
Chr-Seq: kallisto mapping to ensembl 89 ncRNA and cDNA
Chr-Seq: DESeq2 differential expression analysis
Chr-Seq: Tophat2 mapping to hg38
Chr-Seq: extract reads with samflags 0x63, 0x93, 0x53, 0xA3
Chr-Seq: create bedgraph and bigwig files for + and - strands
Genome_build: hg38
Supplementary_files_format_and_content: bigwig, Chr-Seq for + and - strands

growth_protocol: All cells were grown in DMEM.

extract_protocol:
RNA were isolated from cells using TRIzol reagent (Thermo Fisher Scientific)
Chr-Seq: NEBNext Ultra II mRNA kit (NEB)

treatment_protocol: Chr-Seq: Drosha knockdown was induced by transfection of plasmids containing short hairpin RNA against DROSHA mRNA. Dicer and Ago2 knockdown was induced by incubating inducible cell lines which are incorporated with genetic construct containing short hairpin RNA against DICER and AGO2 mRNA with doxycyclin (3 ug/ml) for 72 hours.

tag: genotype/variation

value: Drosha knockdown

tag: molecule subtype

value: Chromatin RNA


title: Chr_Seq shDrosha rep1


title: Myeloid Cells - Blood (Tumor) 10x SCC020


title: T cells - SCC Rhapsody, Cart3

value: Squamous Cell Carcinoma and Peripheral Blood


title: Myeloid Cells - Blood (Tumor) 10x SCC015


title: Chr_Seq shAgo2 rep1

value: Ago2 knockdown


title: KO, replicate 3

tag: strain

value: Nhe6 KO


title: P18 PG1337 10ug/ml 48h

tag: organoid


title: Chr_Seq shAgo2 rep2


title: KO, replicate 1


title: KO, replicate 2


title: Myeloid Cells - SCC 10x SCC020

source_name: SCC-derived Myloid Cells

value: Squamous Cell Carcinoma


title: Chr_Seq shDicer rep1

value: Dicer knockdown


title: PE-rep8

city: Guangzhou

first: Siwen

last: Wang

address: 58# Zhongshan 2nd Rd

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

description:
Biological replicate 8 of 8. Patients Group Circulating CD4+ T Cells.
Patients Experiment Group Circulating CD4+ T Cells Replicate 8

hyb_protocol: The Hy3-labeled samples and Hy5-labeled samples were mixed pair-wise and hybridized on the miRCURYTM LNA Array (v.14.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples and Hy5TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA). Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: miRNAs that two channel intensities>0 and SNR>1(or one of channel SNR>2) were chosen for further normalization. Expression data were normalized using the lowess (Locally Weighted Scatter plot Smoothing) regression algorithm (MIDAS, TIGR Microarray Data Analysis System), which can produce within-slide normalization to minimize the intensity-dependent differences between the dyes. Between slides normalization was performed by scale normalization. After normalization, replicated miRNAs were averaged. Differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: Circulating CD4+ T Cells_CD4+75(1)_Hy5

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3 and Hy5 fluorescent label, respectively, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3 or Hy5), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

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

tag: disease state

value: Atherosclerosis Obliterans

value: Circulating CD4+ T Cells

source_name: common reference pool

tag: sample type

value: pooled sample including all 14 samples


title: HEK293T, ChIP-seq, overexpressing NANOG W8A , NANOG, biological replicate 2

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

data_processing:
FASTQ data were trimmed by Cutadapt and Trimmomatic.
Reads were aligned using bowtie2 with the hg19 build of the human genome.
Peaks for ChIP-Seq  were called by using MACS2.
HiC-Pro was used to process Hi-C data. The Hi-C contact matrix normalized by ICE method was converted into mcool by cooler.
Genome_build: hg19

source_name: Kidney

extract_protocol:
HEK293T  cells were crosslinked in  1% formaldehyde for 10 min at room temperature. After quenching with 0.125M glycine, we collected cell pellets, and extracted the nuclei by using buffer LB1 [50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 10% (v/v) glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1×cocktail protease inhibitor], and then LB2 [10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 1×cocktail protease inhibitor]. After centrifuge, cell nuclei were suspended in buffer LB3 [10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), 0.1% Na-deoxycholate, 0.5% N-lauroyl sarcosine and 1×cocktail protease inhibitor], and fragmented using Q800R3 sonicator (QSONICA).Sheared chromatins were collected by centrifugation, and were incubated with appropriate antibodies at 4°C overnight. The next morning, the antibody-protein-chromatin complex was retrieved by adding 40ul Protein G Dynabeads (Thermo Fisher Scientific, 10004D). Immunoprecipitated DNA was de-crosslinked by 65ºC heating overnight, treated by proteinase-K, and were harvested by phenol chloroform or by Qiagen Quick DNA extraction kit.
ChIP-Seq  library construction using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).

tag: antibody

value: R&D Systems, AF1997

tag: treatment

value: untreated


title: Chr_Seq shDicer rep2

tag: cell line


title: PE-rep4

description:
Biological replicate 4 of 8. Patients Group Circulating CD4+ T Cells.
Patients Experiment Group Circulating CD4+ T Cells Replicate 4

source_name: Circulating CD4+ T Cells_CD4+415(3)_Hy5

tag: cell type


title: Myeloid Cells - SCC 10x SCC015

tag: phenotype


title: T cells - Blood (Tumor) 10x SCC027

source_name: Peripheral Blood T Cells (SCC)

tag: donors


title: PE-rep5

description:
Biological replicate 5 of 8. Patients Group Circulating CD4+ T Cells.
Patients Experiment Group Circulating CD4+ T Cells Replicate 5

source_name: Circulating CD4+ T Cells_CD4+68(1)_Hy5


title: PE-rep7

description:
Biological replicate 7 of 8. Patients Group Circulating CD4+ T Cells.
Patients Experiment Group Circulating CD4+ T Cells Replicate 7

source_name: Circulating CD4+ T Cells_CD4+629(1)_Hy5


title: Chr_Seq Control rep2

value: wild type


title: HEK293T, ChIP-seq, overexpressing NANOG W8A, NANOG, biological replicate 1

data_processing:
FASTQ data were trimmed by Cutadapt and Trimmomatic.
Reads were aligned using bowtie2 with the hg19 build of the human genome.
Peaks for ChIP-Seq were called by using MACS2.
HiC-Pro was used to process Hi-C data. The Hi-C contact matrix normalized by ICE method was converted into mcool by cooler.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Hi-C: mcool files
Supplementary_files_format_and_content: ChIP-seq: bigWig files

extract_protocol:
HEK293T cells were crosslinked in 1% formaldehyde for 10 min at room temperature. After quenching with 0.125M glycine, we collected cell pellets, and extracted the nuclei by using buffer LB1 [50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 10% (v/v) glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1×cocktail protease inhibitor], and then LB2 [10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 1×cocktail protease inhibitor]. After centrifuge, cell nuclei were suspended in buffer LB3 [10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), 0.1% Na-deoxycholate, 0.5% N-lauroyl sarcosine and 1×cocktail protease inhibitor], and fragmented using Q800R3 sonicator (QSONICA). Sheared chromatins were collected by centrifugation, and were incubated with appropriate antibodies at 4°C overnight. The next morning, the antibody-protein-chromatin complex was retrieved by adding 40ul Protein G Dynabeads (Thermo Fisher Scientific, 10004D). Immunoprecipitated DNA was de-crosslinked by 65ºC heating overnight, treated by proteinase-K, and were harvested by phenol chloroform or by Qiagen Quick DNA extraction kit.
ChIP-Seq library construction using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).

tag: overexpression

value: NANOG W8A

tag: chip antibody

value: NANOG (R&D Systems, AF1997)


title: WT, pH 7, replicate 1 [STr111]

value: Erdman

tag: genotype

tag: exposure condition


title: Myeloid Cells - SCC 10x SCC027

tag: tissue


title: PE-rep6

description:
Biological replicate 6 of 8. Patients Group Circulating CD4+ T Cells.
Patients Experiment Group Circulating CD4+ T Cells Replicate 6

source_name: Circulating CD4+ T Cells_CD4+68(2)_Hy5


title: HEK293T, ChIP-seq, overexpressing NANOG W8A, H3K27ac, biological replicate 1

value: H3K27ac (Abcam, AB4927)


title: T cells - SCC 10x SCC027

source_name: SCC-derived T cells


title: pH 5.7, 250mM NaCl, ATC treated, replicate 2

organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

growth_protocol: Mtb strain Erdman harboring a tet inducible N-terminally tagged 6x His-Rv0500A construct was grown to an OD600 of 0.6 (mid-log phase) in standing, filter-capped T-75 flasks in 20 ml of media, originally seeded at an OD600 of 0.05.

extract_protocol:
RNA was extracted as previously described by Rohde, Abramovitch, and Russell (Cell Host and Microbe 2:352-364, 2007). In brief, RNA was stabilized with guanidine-thiocyanate lysis buffer prior to a freeze-thaw step. Once thawed, bacteria were lysed with 5 µg/ml lysozyme, followed by hot Trizol and physical disruption through silica bead agitation in a Beadbeater.  A chloroform extraction was used to further isolate the RNA before purification with an RNAeasy kit (Qiagen). DNA was degraded with Turbo DNAfree DNAse (Ambion). RNA quality was assessed with an Aligent Bioanalyzer before removal of rRNA with a Ribo-Zero rRNA removal kit (bacterial) (Ilumina).
The cDNA library was constructed with the Illumina Tru-Seq Stranded kit. The polyA enrichment procedure was skipped.

treatment_protocol: Mtb at mid-log phase were treated with either anhydrotetracycline (ATC) or ethanol (EtOH) as a carrier control in standing, filter-capped T-75 flasks in 20 ml of 7H9, pH media for 2 hours. Bacteria were then subcultured in 10 ml of media to an OD600 of 0.3 in standing, filter-capped T-25 flasks containing either standard 7H9, pH 7 media, or 7H9, pH 5.7 media supplemented with 250 mM NaCl, with continued prescence of ATC or EtOH as appropriate. Exposure was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted.

value: Inducible 6x His-Rv0500A

value: 7H9, pH 5.7, 250 mM NaCl - ATC


title: PE-rep2

description:
Biological replicate 2 of 8. Patients Group Circulating CD4+ T Cells.
Patients Experiment Group Circulating CD4+ T Cells Replicate 2

source_name: Circulating CD4+ T Cells_CD4+412(1)_Hy5


title: PE-rep3

description:
Biological replicate 3 of 8. Patients Group Circulating CD4+ T Cells.
Patients Experiment Group Circulating CD4+ T Cells Replicate 3

source_name: Circulating CD4+ T Cells_CD4+415(1)_Hy5


title: HEK293T, ChIP-seq, overexpressing NANOG WT, NANOG, biological replicate 1

value: NANOG WT


title: HEK293T, ChIP-seq, overexpressing NANOG W8A, H3K27ac, biological replicate 2


title: T cells - SCC 10x SCC015


title: Chr_Seq Control rep1

tag: genotype/variation

value: Chromatin RNA


title: PE-rep1

description:
Biological replicate 1 of 8. Patients Group Circulating CD4+ T Cells.
Patients Experiment Group Circulating CD4+ T Cells Replicate 1

source_name: Circulating CD4+ T Cells_CD4+410(1)_Hy5


title: T cells - Blood (Tumor) 10x SCC020

value: Peripheral Blood


title: pH 7, ATC treated, replicate 1

source_name: Bacterial cell

value: 7H9, pH 7 - ATC


title: T cells - SCC 10x SCC020

value: Squamous Cell Carcinoma


title: T cells - Blood (Tumor) 10x SCC015


title: HEK293T, ChIP-seq, overexpressing NANOG WT, H3K27ac, biological replicate 1


title: pH 5.7, 250mM NaCl, ATC treated, replicate 1


title: HEK293T, ChIP-seq, overexpressing NANOG WT, H3K27ac, biological replicate 2


title: pH 7, ATC treated, replicate 2


title: HEK293T, ChIP-seq, overexpressing NANOG WT , NANOG, biological replicate 2


title: HC-rep5

description:
Biological replicate 5 of 6. Healthy Control Group Circulating CD4+ T Cells.
Healthy Control Group Circulating CD4+ T Cells Replicate 5

source_name: Circulating CD4+ T Cells_CD4+425(7)_Hy5

value: Healthy


title: HC-rep3

description:
Biological replicate 3 of 6. Healthy Control Group Circulating CD4+ T Cells.
Healthy Control Group Circulating CD4+ T Cells Replicate 3

source_name: Circulating CD4+ T Cells_CD4+425(5)_Hy5

value: Circulating CD4+ T Cells


title: Myeloid Cells - Oral Mucosa 10x OM124

source_name: Mucosa-derived Myloid cells

value: Oral Mucosa


title: HEK293T, Hi-C, overexpressing NANOG W8A, biological replicate 2

description:
HEK293T-NANOG_W8A_HiC_rep2
in situ Hi-C3.0

extract_protocol:
Hi-C 3.0 was performed based on a recent protocol, which is largely modified based on in situ Hi-C. Briefly, ~5 million cells were washed once with PBS to remove debris and dead cells, trypsinized off the culture plates, and were cross-linked using 1% formaldehyde for 10mins at room temperature, quenched with 0.75M Tris-HCl pH 7.5 for 5mins. These cells were further cross-linked with 3mM disuccinimidyl glutarate (DSG) for 50mins, and again quenched with 0.75M Tris-HCl pH 7.5 for 5mins. Cross-linked cell pellets were washed with cold PBS, and then resuspended in 0.5 ml ice-cold Hi-C lysis buffer (10 mM Tris-HCl, pH 8.0; 10mM NaCl, 0.2% NP-40 and protease inhibitor cocktail), and rotated at 4°C for 30 mins. Nuclei were washed once with 0.5 ml ice-cold Hi-C lysis buffer. After pelleting down the nuclei, 100 μl of 0.5% SDS was used to resuspend and permeabilize the nuclei at 62 °C for 10 mins. Then 260 μl H20 and 50 μl 10% Triton-X100 were added to quench the SDS at 37 °C for 15 mins. Subsequently, enzyme digestion of chromatin was performed at 37 °C overnight by adding an additional 50 μl of 10X NEB buffer 2, 100U MboI (NEB, R0147M) and 100U DdeI (NEB, R0175L). After overnight incubation, the restriction enzyme was inactivated at 62 °C for 20 mins. To fill-in the DNA overhangs and add biotin, 35U DNA polymerase I (Klenow, NEB, M0210) together with 10 μl of 1mM biotin-dATP (Jeana Bioscience), 1μl 10mM dCTP/dGTP/dTTP were added and incubated at 37°C for 1 hour with rotation. Blunt end Hi-C DNA ligation was performed using 5000 U NEB T4 DNA ligase with 10X NEB T4 Ligase buffer with 10mM ATP, 90 μl 10% Triton X-100, 2.2 μl 50mg/ml BSA at room temperature for four hours with rotation. After ligation, nuclei were pelleted down and resuspended with 440 μl Hi-C nuclear lysis buffer (50mM Tris-HCl pH7.5, 10mM EDTA, 1% SDS and protease inhibitor cocktail), and further sheared using the parameter of 10/20 secs ON/OFF cycle, 25% Amp, 4 mins by a QSonica 800R sonicator. Around 10% of the sonicated chromatin was subjected to overnight decrosslinking at 65°C, protein K treatment, and DNA extraction.
After DNA extraction, biotin labelled Hi-C 3.0 DNAs were purified by 20 μl Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher 65002). The biotinylated-DNA on C1 beads was used to perform on-beads library making with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L) following manufacturer's instructions. The sequencing was done on a NextSeq 550 platform with PE40 mode.


title: pH 5.7, EtOH treated, 250mM NaCl, replicate 2

value: 7H9, pH 5.7, 250 mM NaCl - EtOH


title: HC-rep6

description:
Biological replicate 6 of 6. Healthy Control Group Circulating CD4+ T Cells.
Healthy Control Group Circulating CD4+ T Cells Replicate 6

source_name: Circulating CD4+ T Cells_CD4+425(13)_Hy5

value: pooled sample including all 14 samples


title: Myeloid Cells - Blood (Oral) 10x OM124

source_name: Peripheral Blood Myloid Cells (OM)


title: pH 7, EtOH treated, replicate 2

value: 7H9, pH 7 - EtOH


title: T cells - Blood (Oral) 10x OM124

source_name: Peripheral Blood T Cells (OM)


title: HC-rep2

description:
Biological replicate 2 of 6. Healthy Control Group Circulating CD4+ T Cells.
Healthy Control Group Circulating CD4+ T Cells Replicate 2

source_name: Circulating CD4+ T Cells_CD4+425(3)_Hy5

source_name: common reference pool


title: HEK293T, Hi-C, overexpressing NANOG W8A, biological replicate 1

description:
HEK293T-NANOG_W8A_HiC_rep1
in situ Hi-C3.0

source_name: Kidney

value: NANOG W8A

value: untreated


title: HC-rep4

description:
Biological replicate 4 of 6. Healthy Control Group Circulating CD4+ T Cells.
Healthy Control Group Circulating CD4+ T Cells Replicate 4

source_name: Circulating CD4+ T Cells_CD4+425(6)_Hy5


title: pH 7, EtOH treated, replicate 1

value: Erdman


title: HEK293T, Hi-C, overexpressing NANOG WT, biological replicate 1

description:
HEK293T-NANOG_WT_HiC_rep1
in situ Hi-C3.0


title: Spleen_Megakaryocyte plus sepsis_2

status: Public on Feb 14 2022

city: San Francisco

first: Colin

last: Valet

state: California

address: 513 Parnassus avenue

institute: UCSF

data_processing:
de-multiplexing raw sequencing results, trimming adapter sequences, and aligning to the reference genome
Sequence alignment and splice junction estimation was performed using STAR software ( 2.7.2b)
genomic alignments were restricted to unique Ensembl IDs (all protein coding mRNAs, coding and noncoding RNAs)
STAR aggregated mappings on a per-gene basis were used as raw input for normalization by DESeq2
Differential expression analysis was performed in the R version 3.6.1 using DESeq2 version 1.26. Significance thresholds were FDR<0.05 and log fold change >1 or <-1
Genome_build: GRCm38.96
Supplementary_files_format_and_content: counts matrix post-alignment contained in: counts.STARMOUSE.txt

source_name: Spleen

extract_protocol:
Bone marrow and Spleen were removed, single cells were harvested, 300 CD45+ Lineage- Pf4-tomato+ CD41+ CD42b+ Megakaryocytes were sorted by flow cytometry and lysed using Takara SMART-Seq HT Lysis Components.
RNA libraries were prepared for sequencing using SmartSeq/NexteraXT

value: Spleen

value: Megakaryocyte

value: Day 5 post Sepsis


title: Bone Marrow_Megakaryocyte minus sepsis_3

source_name: Bone marrow

value: Bone marrow

value: Day 5 post Saline


title: Spleen_Megakaryocyte plus sepsis_1


title: pH 5.7, EtOH treated, 250mM NaCl, replicate 1

value: Inducible 6x His-Rv0500A


title: Spleen_Megakaryocyte minus sepsis_3


title: Bone Marrow_Megakaryocyte plus sepsis_3


title: Bone Marrow_Megakaryocyte minus sepsis_2


title: HEK293T, Hi-C, overexpressing NANOG WT, biological replicate 2

description:
HEK293T-NANOG_WT_HiC_rep2
in situ Hi-C3.0

value: NANOG WT


title: Bone Marrow_Megakaryocyte plus sepsis_2


title: Spleen_Megakaryocyte plus sepsis_3


title: KO_21

first: Vincent

last: Auyeung

state: CA

department: Medicine

institute: University of California, San Francisco

data_processing:
Adapter removal: Cutadapt
Alignment: HISAT2
Genome_build: UCSC Mouse GRCm38
Supplementary_files_format_and_content: Comma-separated file with read counts (rows) and samples (columns)

source_name: Whole lung

extract_protocol:
Trizol
mRNA from eukaryotic organisms was enriched using oligo(dT) beads. mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

tag: mouse identifier

value: EpithelialKO


title: Bone Marrow_Megakaryocyte minus sepsis_1

tag: strain


title: KO_20


title: Spleen_Megakaryocyte minus sepsis_1


title: HC-rep1

description:
Biological replicate 1 of 6. Healthy Control Group Circulating CD4+ T Cells.
Healthy Control Group Circulating CD4+ T Cells Replicate 1

source_name: Circulating CD4+ T Cells_CD4+425(1)_Hy5

value: Healthy


title: T cells - Oral Mucosa 10x OM124

source_name: Mucosa-derived T cells


title: Spleen_Megakaryocyte minus sepsis_2


title: KO_17


title: KO_18


title: Bone Marrow_Megakaryocyte plus sepsis_1


title: Flox_4

value: Flox


title: Flox_3


title: Flox_2


title: Bleomycin3G9_wholelung_228

description: Tagged ribosome immunoprecipitated RNA

data_processing:
Alignment: STAR_2.5.2b
Genome_build: Ensembl Mouse GRCm38
Supplementary_files_format_and_content: Comma-separated file with read counts (rows) and samples (columns)

source_name: Lung epithelial Ribotag immunoprecipitation

extract_protocol:
Anti-HA immunoprecipitation followed by Rneasy Micro kit (Qiagen)
Lexogen Quantseq Forward kit

tag: mouse sex

value: M

tag: tissue compartment

value: Whole Lung

tag: exposure

value: Bleomycin

tag: treatment type

tag: batch


title: KO_22


title: Bleomycin_epithelial_204

description: Tagged ribosome immunoprecipitated RNA

value: Epithelium

tag: treatment

value: Control


title: Flox_5


title: Flox_6


title: Bleomycin3G9_wholelung_219

description: Tagged ribosome immunoprecipitated RNA


title: Saline_epithelial_221

description: Tagged ribosome immunoprecipitated RNA

value: Saline


title: Saline_epithelial_207

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin3G9_wholelung_226R

description: Tagged ribosome immunoprecipitated RNA

value: F


title: Bleomycin_wholelung_206

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_epithelial_225

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin3G9_epithelial_219

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin3G9_wholelung_218

description: Tagged ribosome immunoprecipitated RNA


title: Saline_wholelung_230

description: Tagged ribosome immunoprecipitated RNA


title: Saline_epithelial_230

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin3G9_epithelial_228

description: Tagged ribosome immunoprecipitated RNA


title: Saline_wholelung_207

description: Tagged ribosome immunoprecipitated RNA


title: Saline_wholelung_221

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_epithelial_206

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_wholelung_204

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin3G9_epithelial_218

description: Tagged ribosome immunoprecipitated RNA


title: Saline_wholelung_153

description: Tagged ribosome immunoprecipitated RNA

value: Vehicle


title: Bleomycin_epithelial_208R

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_wholelung_225

description: Tagged ribosome immunoprecipitated RNA


title: Saline_epithelial_152

description: Tagged ribosome immunoprecipitated RNA


title: Saline_epithelial_153

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_wholelung_208R

description: Tagged ribosome immunoprecipitated RNA


title: Saline_epithelial_146

description: Tagged ribosome immunoprecipitated RNA


title: Saline_wholelung_146

description: Tagged ribosome immunoprecipitated RNA


title: BleomycinKIRA8_epithelial_154

description: Tagged ribosome immunoprecipitated RNA


title: BleomycinKIRA8_wholelung_154

description: Tagged ribosome immunoprecipitated RNA


title: BleomycinKIRA8_wholelung_155

description: Tagged ribosome immunoprecipitated RNA


title: BleomycinKIRA8_epithelial_155

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_wholelung_149

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_epithelial_149

description: Tagged ribosome immunoprecipitated RNA


title: Xenograft-LuCaP35CR-Pal-T_tumor2

first: Changmeng

last: Cai

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

description: Xenograft_LuCaP35CR_samples_count_table.txt

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Genome_build: hg19
Supplementary_files_format_and_content: txt file forraw counts of sequence reads

source_name: xenograft

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
RNA-seq libraries of xenograft C4-2-tet-shRB (without Dox) were performed by using TruSeq® Strnd Total RNA LT (Illumina). RNA-seq libraries of the rest of samples were performed by using TruSeq® Stranded mRNA (Illumina).

value: patient derived xenografts

value: 40mg/kg Depo-testosterone (daily) and 150mg/kg palbociclib (daily)


title: Bleomycin_wholelung_148

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_epithelial_148

description: Tagged ribosome immunoprecipitated RNA


title: BleomycinKIRA8_epithelial_041

description: Tagged ribosome immunoprecipitated RNA


title: Saline_wholelung_152

description: Tagged ribosome immunoprecipitated RNA


title: BleomycinKIRA8_wholelung_041

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_epithelial_045

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_wholelung_031

description: Tagged ribosome immunoprecipitated RNA


title: Xenograft-LuCaP35CR-T_tumor1

value: 40mg/kg Depo-testosterone (daily) and sodium D-lactate (daily)


title: BleomycinKIRA8_epithelial_032

description: Tagged ribosome immunoprecipitated RNA


title: Xenograft-LuCaP35CR-Pal_tumor3

value: Corn oil (daily) and 150mg/kg palbociclib (daily)


title: Xenograft-LuCaP35CR-T_tumor3


title: Xenograft-LuCaP35CR-Pal-T_tumor1


title: Bleomycin_epithelial_031

description: Tagged ribosome immunoprecipitated RNA


title: Xenograft-LuCaP35CR-T_tumor2


title: BleomycinKIRA8_wholelung_020

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_wholelung_017

description: Tagged ribosome immunoprecipitated RNA


title: Xenograft-LuCaP35CR-Pal_tumor2


title: Xenograft-LuCaP35CR-Veh_tumor3

value: Corn oil (daily) and sodium D-lactate (daily)


title: Xenograft-LuCaP35CR-Pal_tumor1


title: Xenograft-LuCaP35CR-Veh_tumor2


title: BleomycinKIRA8_epithelial_020

description: Tagged ribosome immunoprecipitated RNA


title: Bleomycin_wholelung_045

description: Tagged ribosome immunoprecipitated RNA


title: Day 42

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

description:
rowData.txt
colData.txt
exprsData.mtx

data_processing:
Illumina software was used for basecalling.
Transcript abundances were obtained from cellranger 3.0.2.
Matrix files were loaded into monocle 3.0 for sample merging and normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Sparse Matrix (mtx) file of merged UMI counts with each row representing a gene and each column a cell barcode, can be read into R with readMM function in the Matrix package
Supplementary_files_format_and_content: Tab-delimited text (txt) files providing gene names (row data) or cell clustering and sample information (column data), matched to the sparse Matrix file

source_name: Distal colon and anus

growth_protocol: C57Bl/6 mice at 6 wks of age were purchased from Jackson Laboratory.

extract_protocol:
Tissue was enzymatically digested in 0.25% trypsin-EDTA for 20 min, cleaned of dead cells using the EasySep Live/Dead Annexin V magnetic selection kit, and passed through a 40-µm filter to obtain a single-cell suspension.
Single-cell 3' libraries were generated using the 10X Chromium platform. Paired-end sequencing with index reads was performed on 2 lanes of a HiSeq 4000.

treatment_protocol: Ten mice were exposed to 3% DSS dissolved in drinking water for 6 d, beginning on experimental day (exp d ) 0. Five additional mice were not treated. Mice were dissected on exp d 0 (untreated mice, n=5), exp d 7 (DSS, n=5 mice), or exp d 42 (DSS, n=5 mice) and their isolated distal colon and anus pooled together.

tag: injury

value: 3% DSS

tag: histological status

value: Recovered


title: Run_2788_Mouse: iKras_3w_ON_3d_OFF

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan

description: Whole iKras* pancreas with PanIN lesions digested to single cell suspension and submitted for single cell RNA sequencing

data_processing:
Sample was run using paired-end 50 cycle reads on HiSeq 400 (Illumina) to a depth of 100,000 reads.
Raw Data was processed and aligned by the University of Michigan Advanced Genomics Core. Files were demulitplexed into FASTQ files using cellranger mkfastq v3.0.0.
FASTQ files were aligned, filtered, and counted by cellranger count v3.0.0 and formed into feature-barcode matrices.
Feature-barcode matrices were read into R using the Seurat package v3.2.2 and were analyzed according to the Seurat pipeline, including normalizing, scaling, filtering based on read counts and mitochondrial gene percentage, and manually labeling cells according to gene expression profiles.
Genome_build: mm10

extract_protocol:
Samples were mechanically and enzymatically digested (Collagenase V; 1 mg/mL in RPMI) under constant agitation. Single cell suspensions were obtained by filtering consecutively through 500 µm, 100 µm, and 40 µm cell strainers. Dead cells were removed using MACS Dead Cell Removal Kit (Miltenyi Biotec).
Single cell cDNA libraries were prepared and sequenced using the 10x Genomics platform at the University of Michigan Advanced Genomics Core.

treatment_protocol: Mice were fed doxycycline water to induce expression of KrasG12D (Kras*) for 3 weeks following induction of acute pancreatitis, then water was replaced with untreated water to turn off Kras* expression for 3 days.

value: Mixed

tag: disease state

value: acute pancreatitis

tag: ikras status

value: Kras* induced, then stopped

tag: time point

value: 3 weeks ON + 3 days OFF

tag: number of mice pooled

value: iKras Pancreatic Intraepthelial Neoplasia (PanIN)


title: Xenograft-LuCaP35CR-Pal-T_tumor3


title: BleomycinKIRA8_wholelung_032

description: Tagged ribosome immunoprecipitated RNA

value: Whole Lung

value: Bleomycin


title: Xenograft-LuCaP35CR-Veh_tumor1


title: Day 00

description:
rowData.txt
colData.txt
exprsData.mtx

value: Normal


title: Day 07

description:
rowData.txt
colData.txt
exprsData.mtx

value: Severe colitis


title: H2030-BrM pooled GFP+ metastases from three nude mice

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

description: Single-cell RNA-seq

data_processing:
RNA-seq processing:
Xenocell (https://gitlab.com/XenoCell/XenoCell) was used to classify reads between host (mouse) and graft (human). The bollito pipeline (https://gitlab.com/bu_cnio/bollito) was used to perform read analysis, as follows: Sequencing quality was checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the human reference genome (GRCh38_p13 from GENCODE) with STARsolo (STAR 2.7.3a). Seurat 3.2.2 was used to check the quality of sequenced cells, explore and quantify single-cell data, obtain cell clusters and specific gene markers. GSEAPreranked was used to perform gene set enrichment analysis for the selected signature collections on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized counts obtained with Seurat

source_name: Human tumor grafted in mouse brain

growth_protocol: H2030-BrM cells grew in nude mice under regular housing conditions

extract_protocol:
After obtaining the GFP+ cells the sample was loaded onto a 10x Chromium Single Cell controller chip B (10x Genomics) as described in the manufacturer’s protocol (Chromium Single Cell 3’GEM, Library & Gel Bead Kit v3, PN-1000075). Intended targeted cell recovery of ~10000 cells. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, cDNA amplification and library construction were all performed as recommended by the manufacturer.
Cell sample was loaded onto a 10x Chromium Single Cell controller chip B (10x Genomics) as described in the manufacturer’s protocol (Chromium Single Cell 3’GEM, Library & Gel Bead Kit v3, PN-1000075). Intended targeted cell recovery of ~10000 cells. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, cDNA amplification and library construction were all performed as recommended by the manufacturer. Single-cell RNA-seq libraries were sequenced with an Illumina NextSeq 550 (using v2.5 reagent kits) in paired-end fashion (28bp + 56bp bases).

treatment_protocol: No treatments added

tag: cell type

value: lung adenocarcinoma

tag: cell line

value: No treatment

tag: sorted

value: GFP and luciferase


title: mSSCs, Injured Rep 3

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

description: Injured 7

data_processing:
Raw FASTQ reads were aligned to GENCODE vM20 reference transcripts (GRCm38.p6) for mouse with Salmon  v0.12.0 using the --seqBias, --gcBias, --posBias, --useVBOpt, -- rangeFactorizationBins 4, and --validateMappings flags and otherwise default parameters for single-end mapping.
Count normalization and differential gene expression analysis was performed using the DESeq2 v1.22.2 package in R .
Counts were size-factor normalized using the ‘DESeq’ function and log2- transformed.
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: Achilles Tendon-To-Bone Interface

extract_protocol:
Achilles Tendon-To-Bone Interfaces were removed and digested under fluorescence-activated cell sorting  for mSSCs. RNA extraction was performed using Qiagen miRNeasy kit (cat. 1071023)  with one column DNAse treatment per the manufacturer’s recommendations. To generate cDNA from 150 pg total RNA, the Clontech Smarter Ultra Low Input RNA kit (Takara Bio, Cat. 634848) was used per the manufacturer’s recommendations. Amplified cDNA was purified using SPRI Ampure Beads (Beckman Coulter, Cat. A63880) and the quality and quantity was measured using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Partial tendon-to-bone interface (TBI) injury

tag: cell name

value: mouse skeletal stem cells (mSSCs)

value: Injured


title: mSSCs, Injured Rep 2

description: Injured 6

tag: strain


title: mSSCs, Injured Rep 1

description: Injured 1


title: mSSCs, Sham Control Rep 2

description: Sham 5

value: Sham Control


title: mSSCs, Uninjured

description: Sham 9

value: Uninjured


title: D20_18_dist

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual transcripts for each sample.

source_name: rectal mucosa

extract_protocol:
Colonic mucosal surfaces were cut and isolated from freshly dissected full-thickness colonic tissue, then placed into Trizol. RNA was precipitated with isopropanol and cleaned with multiple washes of 75% ethanol prior to resuspension in water.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on NextSeq High Output Runs.

treatment_protocol: Mice were exposed to 3% DSS for 6 d, beginning of experimental day (exp d) 0. On the indicated experimental days, 3-4 mice were euthanized from the larger cohort and their colons dissected for analysis.

value: DSS

value: dist


title: D20_19_meta

source_name: squamous neo-epithelium of colon

value: meta


title: D20_18_meta


title: D20_19_anal

source_name: anus

value: anal


title: D20_19_dist


title: D20_18_anal


title: Heart, HF+Med, 3

city: Changchun

first: Yanan

last: Yu

state: Jilin

address: Xiantai Street  No.126

department: Department of Rehabilitation

institute: China-Japan Union Hospital

data_processing:
The data generated from Illumina/BGI platform were used for bioinformatics analysis. All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology.
Quality control Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
Prediction of novel gene The mapped reads were spiced with Stringtie software (http://ccb.jhu.edu/software/stringtie/) , and then use the Gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml) to compare with the reference genome GTF/GFF file to find the original unannotated transcription region and discover new transcripts and new genes of the species.
Quantification of gene expression level FeatureCounts (http://subread.sourceforge.net/) 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. 3.5 Differential expression analysis Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html) , DEGs with |log2FC|>1 and Padj <0.05 were considered to be significantly different expressed genes. 3.6 Enrichment analysis The GO and KEGG enrichment analysis of differential genes can explain the functional enrichment of differential genes and clarify the differences between samples at the gene function level. We use clusterProfiler R software package for GO function enrichment and KEGG pathway enrichment analysis. When P<0.05, it is considered that the GO or KEGG function is significantly enriched.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM and count values for each Sample

organism: Rattus norvegicus

source_name: rats heart --ligation,  anterior descending coronary artery--BAIBA

extract_protocol:
Total RNA was extracted from the heart using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina Novaseq 6000 /MGISEQ-T7 instrument。

value: Sprague-Dawley

tag: tissue

value: heart

value: HF+BAIBA


title: Heart, HF+Med, 2


title: Bleomycin_epithelial_017

description: Tagged ribosome immunoprecipitated RNA

tag: mouse identifier

tag: mouse sex

value: F

tag: tissue compartment

value: Epithelium

value: Bleomycin

value: Vehicle

value: Control


title: D20_17_prox

source_name: mucosa of mid-colon

value: prox


title: Heart, HF+Exe, 3

source_name: rats heart --ligation,  anterior descending coronary artery--Exercise

value: HF+Exercise


title: Heart, HF+Exe, 1


title: D20_19_prox


title: D20_17_meta


title: Heart, HF+Exe, 2


title: Heart, HF+Sed, 3

source_name: rats heart --ligation,  anterior descending coronary artery

value: HF+Sedentary


title: D20_17_anal


title: D20_17_dist


title: D14_16_meta


title: mSSCs, Sham Control Rep 1

description: Sham 4

value: mouse skeletal stem cells (mSSCs)

value: Sham Control


title: D14_16_prox

value: DSS


title: D20_18_prox


title: D14_16_dist

value: dist


title: Heart, HF+Sed, 2


title: Heart, Sham, 3

source_name: rats heart --no ligation,  anterior descending coronary artery

value: Sham operation


title: D14_15_prox


title: Heart, HF+Sed, 1


title: D14_16_anal

value: anal


title: D14_15_meta

value: meta


title: Heart, Sham, 2

value: Sprague-Dawley

value: heart


title: Heart, Sham, 1


title: Heart, HF+Med, 1

value: HF+BAIBA


title: D14_15_dist


title: D14_15_anal


title: D14_14_meta


title: D14_14_prox


title: D14_14_anal


title: Pediatric acute lymphoblastic leukemia [16-221]

city: Montreal

last: Sinnett

state: QC

address: 2900 Edouard Montpetit Blvd

institute: University of Montreal

description:
16-221
Strand-specific RNA-seq

data_processing:
Raw reads were aligned to the GRCh37 genome reference using STAR v2.5.3a.
Expression counts were obtained using htseq-count v0.9.0 on the Ensembl Homo_sapiens.GRCh37.75.gtf.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw expression counts.

source_name: Pediatric acute lymphoblastic leukemia

extract_protocol:
Mini AllPrep DNA/RNA kits from Qiagen.
Ribo-Zero Gold Kit according to Illumina's protocol.

tag: diagnosis

value: bone marrow

tag: gender

value: Male


title: Pediatric acute lymphoblastic leukemia [16-220]

description:
16-220
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-217]

description:
16-217
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-222]

description:
16-222
Strand-specific RNA-seq

value: Female


title: Pediatric acute lymphoblastic leukemia [16-194]

description:
16-194
Strand-specific RNA-seq


title: D14_14_dist

tag: injury


title: D09_13_anal


title: Pediatric acute lymphoblastic leukemia [16-218]

description:
16-218
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-196]

description:
16-196
Strand-specific RNA-seq


title: D09_13_meta


title: Pediatric acute lymphoblastic leukemia [16-161]

description:
16-161
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-170]

description:
16-170
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-191]

description:
16-191
Strand-specific RNA-seq


title: D09_13_dist


title: D09_12_prox


title: Pediatric acute lymphoblastic leukemia [16-167]

description:
16-167
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-139]

description:
16-139
Strand-specific RNA-seq


title: D09_11_prox


title: D09_12_dist


title: D09_12_anal


title: D09_11_meta


title: F_tar_stem_3

city: Shanghai

first: Moyang

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

description:
Fagopyrum tataricum Gaertn.
F_tar_stem_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house SOAPnuke. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2 and paired-end clean reads were aligned to the reference genome using CPC v0.9-r2.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: http://www.mbkbase.org/Pinku1/
Genome_build: a FASTA file with all transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Fagopyrum tataricum

source_name: stem

growth_protocol: Tartary buckwheat (XiQiao 2) were collected in 2016 at the experimental field of College of Life Science, Sichuan Agricultural University (Lat. 29°97’ N, 102°97’ E, Alt. 580 m), China. It had been introduced to the field and grown in the same ecoenvironmental and cultivation conditions for five years. We observed the development process. Samples were hand-collected at flowering stage.

extract_protocol:
Samples were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the transcriptome sampling, samples were collected from the same individual, and samples with the same flowering stage from three plants comprised of three replicates. the collected samples were flash frozen in liquid nitrogen and stored at −80°c until further use.

tag: cultivar

value: XiQiao 2

tag: developmental stage

value: Flowering stage

value: stem


title: F_tar_stem_1

description:
Fagopyrum tataricum Gaertn.
F_tar_stem_1


title: Pediatric acute lymphoblastic leukemia [16-138]

description:
16-138
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-132]

description:
16-132
Strand-specific RNA-seq


title: D09_13_prox

value: prox


title: Pediatric acute lymphoblastic leukemia [16-131]

description:
16-131
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-140]

description:
16-140
Strand-specific RNA-seq


title: F_tar_stem_2

description:
Fagopyrum tataricum Gaertn.
F_tar_stem_2


title: F_tar_root_3

description:
Fagopyrum tataricum Gaertn.
F_tar_root_3

source_name: root

value: root


title: Pediatric acute lymphoblastic leukemia [16-129]

description:
16-129
Strand-specific RNA-seq


title: D09_11_dist


title: F_tar_root_1

description:
Fagopyrum tataricum Gaertn.
F_tar_root_1


title: F_tar_root_2

description:
Fagopyrum tataricum Gaertn.
F_tar_root_2


title: F_tar_flower_3

description:
Fagopyrum tataricum Gaertn.
F_tar_flower_3

source_name: flower

value: flower


title: D06_10_prox

value: DSS


title: F_tar_leaf_2

description:
Fagopyrum tataricum Gaertn.
F_tar_leaf_2

source_name: leaf

value: leaf


title: D09_11_anal


title: F_tar_flower_1

description:
Fagopyrum tataricum Gaertn.
F_tar_flower_1


title: Pediatric acute lymphoblastic leukemia [16-116]

description:
16-116
Strand-specific RNA-seq

value: peripheral blood


title: D09_12_meta


title: D06_09_prox


title: F_tar_leaf_3

description:
Fagopyrum tataricum Gaertn.
F_tar_leaf_3


title: Pediatric acute lymphoblastic leukemia [16-115]

description:
16-115
Strand-specific RNA-seq


title: D06_10_dist

value: dist


title: F_tar_flower_2

description:
Fagopyrum tataricum Gaertn.
F_tar_flower_2


title: D06_10_anal

value: anal


title: AR_C4-2_DHT_pal

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.9a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS2 (version 2.1.0) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 369).
Genome_build: hg19
Supplementary_files_format_and_content: bw, narrowPeak

source_name: C4-2 cell

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

value: prostate cancer cell line

tag: medium condition

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

tag: treatment

value: 1uM palbociclib for 1 day, then treat 10nM dihydrotestosterone (DHT) for 4 hours

tag: chip antibody

value: anti-AR (abcam)


title: Pediatric acute lymphoblastic leukemia [16-108]

description:
16-108
Strand-specific RNA-seq

value: bone marrow


title: D06_09_anal


title: D06_08_prox


title: Pediatric acute lymphoblastic leukemia [16-103]

description:
16-103
Strand-specific RNA-seq

value: Male