title: SRSF7 polyA RNA pulldown Rep2

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description: SRSF7_polyA_vs_rRNA_depleted_APEX_seq_gene_counts.txt

data_processing:
Library strategy: RNA pull-down
The raw reads were mapped to the human genome using STAR 2.7.4a (PMID: 23104886), and the uniquely-mapped reads were counted using the featurecounts package (PMID:  24227677).
For splicing analysis, the data was processed using vast-tools v2.5.1 (PMID: 28855263).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt file containing gene counts from APEX pulldown and pre-pulldown input samples, as well as polyA and rRNA-depleted SRSF7 pulldown samples

molecule: polyA RNA

source_name: Flp-in HEK293 cells

growth_protocol: HEK293 cells were grown in DMEM (high glucose; Sigma-Aldrich) supplemented with 10% FBS, non-essential amino acids, and penicillin/streptomycin. Mouse neuroblastoma (N2A) cells were grown in DMEM (high glucose; Sigma-Aldrich) supplemented with 10% FBS, non-essential amino acids, sodium pyruvate and penicillin/streptomycin. Cells were maintained at sub-confluent conditions, maintained at 37°C with 5% CO2 and were passaged every 2-3 days.

extract_protocol:
After the second wash with 2X quench buffer in the APEX labeling protocol, the cells were harvested by scraping them down in 2X quench buffer including 4 uL Ribolock RNase inhibitor (Thermo Fisher).  The cells were centrifuged for 5 minutes at 200xg at 4 oC.  Next, after aspirating the quench buffer, cells were lysed and processed using the RNeasy plus mini kit (Qiagen) following the manufacture protocol with minor modifications, including adding ß-mercaptoethanol to the RLT lysis buffer, washing with the RWT Buffer (Qiagen #1067933) instead of RW1 buffer, and application of the on-column DNaseI digestion (Qiagen #79256). The RNA was eluted in RNase-free water and quantified using Nanodrop. Same amounts of RNA were aliquoted before the streptavidin pull down of the RNA for downstream applications.  To enrich for biotinylated RNAs, Dynabeads™ MyOne™ Streptavidin C1 magnetic beads (Thermo Fisher) were used with 10 μl of beads per 25 μg of RNA. The beads were washed 3 times in B&W buffer (5 mM Tris-HCl, pH = 7.5, 0.5 mM EDTA, 1 M NaCl, 0.1% TWEEN 20 (Sigma Aldrich)), followed by 2 times in Solution A (0.1 M NaOH and 0.05 M NaCl), and 1 time in Solution B (0.1 M NaCl). Beads were then incubated with purified RNA (25-50ug) in 0.05M NaCl at 4oC for 2 hours with gentle agitations. Following the incubation step, beads were washed 3 times with B&W buffer, followed by the elution of RNA from the beads by adding the TRI Reagent (Sigma-Aldrich T9424) on the beads and extracting according to the manufacturer’s protocol.
The libraries were prepared by using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® with ribosome-depleted and polyA+ selected RNA

treatment_protocol: The APEX procedure was carried out based on a published protocol with slight modifications (https://protocolexchange.researchsquare.com/article/pex-71/v1).  Briefly, 24 hours after plating the cells stably expressing the APEX2 fusion construct, APEX labeling was initiated by changing the medium to fresh medium containing 500 μM biotin-phenol (Sigma-Aldrich), followed by incubation at 37oC under 5% CO2 for 30 minutes. H2O2 (Sigma Aldrich) was then added to each well to a final concentration of 1 mM, and the plate was gently agitated for 1 minute (Hung et al., 2016). The reaction was quenched by replacing the medium with an equal volume of 2X quench buffer (10 mM Trolox (Sigma-Aldrich), 20 mM sodium ascorbate (Sigma-Aldrich), and 20 mM sodium azide (BioShop) in Dulbecco's phosphate-buffered saline (DPBS)). The cells were washed one more time with 2X quench buffer before proceeding to imaging, RT-qPCR or RNA-seq experiments.

tag: protein tag

value: FLAG-APEX2 tagged

tag: cell line

value: Flp-in HEK293

tag: molecule subtype

value: polyA RNA


title: SRSF7 polyA RNA pulldown Rep1

status: Public on Feb 18 2022

type: SRA

country: USA

library_source: transcriptomic

organism: Homo sapiens


title: VIP-U603

city: Toronto

first: Etienne

last: Sibille

state: Ontario

address: RM,133, 250 college street

department: Neuroscience of Aging and Depression

country: Canada

institute: Center for Addiction and Mental Health

data_processing:
Sequencing performed on Illumina HiSeq 2500 platform. Run mode: High Output (2x125 cycles), 8 lanes. Yield (GBp): 286, Q30: Read 1=90.5%, Read 2=82.9%
Reads were trimmed 9bp on 5' and 21bp on 3' end based on Phred score distribution, and Read 2 was excluded from genomic mapping. Reads were mapped to the mouse genome (build GRCm38-mm10) using HiSat2.
BAM files were processed using SAMTOOLS v1.3
Counts were summarized at the gene level (i.e. meta-analysis of all transcript variants). Count normalization and differential expression was performed using DESeq2 R package. Co-expression analyses were performed using WGCNA R package.
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: Comma seperated values files include Ensembl gene identifiers (ENSMUSG), HUGO gene symbols, and DESeq2-normalized counts

molecule: total RNA

organism: Mus musculus

source_name: Vasoactive intestinal peptide-expressing interneurons isolated from medial prefrontal cortex

extract_protocol:
Mice were sacrificed by cervical dislocation and decapitation. Brains were removed and snap-frozen at -80C. Samples of 130 cells of either pyramidal, somatostatin, parvalbumin, or vasoactive-intestinal-peptide types were collected from 12uM coronal sections of the medial prefronal cortex using RNAscope to visualize (using cell-type specific cDNA probes) and laser-capture microdissection to extract. Extracted cells were collected in PicoPure extraction buffer, incubated at +40C for 30 minutes and frozen on dry ice and stored at -80C until library preparation.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Pico Input Kit (Clontech) according to the manufacturer's directions.

treatment_protocol: All experiments were performed with male C57Bl/6J mice exposed to UCMS (n=10) or control housing (n=10). Controls were group-housed with littermates whereas UCMS-exposed mice were single-housed. All mice were provided with food and water ad libitum. UCMS consisted of a variable sequence of mild social-environmental stressors occurring 1-4 times daily for 5 weeks , as previously described. Stressors included forced bath, light cycle disruptions, predator odor, wet bedding, tilted cage, and restraint. Behavioural testing occurred during week 4 and 5, during which UCMS was continued with 1-2 daily stressors to attenuate their acute effects on test outcomes. Behavioural tests including elevated plus maze (EPM), open-field (OF), novelty-suppressed feeding (NSF), novelty-induced hypophagia (NIH), sucrose preference test (SPT), phenotyper test (PT), and a general locomotor activity test were used to assess anxiety-like and depressive-like behaviours.

tag: strain

tag: experimental group

value: UCMS (5-weeks)

tag: cell-type

value: VIP neurons

tag: tissue

value: brain


title: SRSF7 ribosome-depleted RNA pulldown Rep2

value: ribosome-depleted RNA


title: SRSF7 ribosome-depleted RNA pulldown Rep1


title: ha-h3x2-vps75-HU070-s47

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64 with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-200 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2, for samples ending with X39, S43, S44 and S47c ombined S. cerevisiae (GCA_000146045.2) and C. glabrata (GCF_000002545.3_ASM254v2) genome
Supplementary_files_format_and_content: *.out.txt file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (CHr 1-16+mitochondria); or 24,495,413 bases in the combined genome (first S.cerevisae then C. glabrata). The chromosomes are included sequentially in the outfile. If the C. glabrata genome was included it also goes sequentially after the S.cerevisae genome.

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: Sensor-carrying cells

growth_protocol: yeast cells were grown to saturation overnight in YPD and then dilute in fresh,pre-warmed YPD and incubated for at least 6 hours at 30deg before G1 arrest (alpha factor). After 3 hours in alpha factor, cells were released into HU and samples for ChIP taken in 10-20 minute intervals. The number after 'HU' in the sample title indicates the minutes after release into HU.

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.  SLIM-Chip, as per Gutin et al, Cell Reports 2019
SLIM-Chip, as per Gutin et al, Cell Reports 2019

tag: genotype

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, vps75::HYG

tag: sensor

tag: antibody

value: ha

tag: growth condition


title: ha-h3x2-vps75-HU050-s47


title: ha-h3x2-vps75-HU110-s47


title: FLAG pre-pulldown input Rep2


title: VIP-U606


title: VIP-U609


title: ha-h3x2-vps75-HU040-s47


title: VIP-U6

value: Control


title: VIP-U601


title: FLAG pre-pulldown input Rep1


title: GFP pre-pulldown input Rep2


title: ha-h3x2-vps75-HU015-s47


title: ha-h3x2-vps75-HU030-s47


title: VIP-U5


title: GFP pre-pulldown input Rep1


title: VIP-U2


title: NLS pre-pulldown input Rep2


title: ha-h3x2-vps75-HU190-s44


title: ApoE-/- PX-478 3

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive NE

department: Biomedical Engineering

institute: Georgia Tech & Emory University

data_processing:
Reads were aligned to mm10, counted, filtered, and normalized using R packages Rsubread and edgeR as described in Lun et al, Statistical Genomics pp 391-416, 2016
Alignment was performed with the align command and the mapped reads were counted by using the featureCounts function with the set of BAM files as the input.
Genes with low counts across libraries were filtered using the keep function. Genes with count-per-million > 0.5 in at least 2 samples were retained.
The calcNormFactors function was utilized to generate factors for normalization
The makeContrasts and qlmQLFTest functions were used to genearte a porcessed data matrix and test for significant differential expression in each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Following sacrifice, livers were removed, flash frozen using liquid nitrogen, and RNA was harvested using Qiazol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All ApoE-/- mice were fed Western diet for 3 months. Saline or PX-478 (40 mg/kg) were injected intraperitoneally bi-weekly thorughout the course of the study.

value: liver

tag: age

value: 4 months

value: ApoE-/-

tag: treatment

value: PX-478 (40mg/kg) IP bi-weekly + Western Diet 3 months


title: ha-h3x2-vps75-alpha-s47

value: alpha


title: SST-U9

source_name: Somatostatin-expressing interneurons isolated from medial prefrontal cortex

value: SST neurons


title: ha-h3x2-vps75-async-s47

value: async


title: LMNA pre-pulldown input Rep1

value: FLAG-APEX2 tagged


title: VIP-U3


title: LMNA pre-pulldown input Rep2

value: Flp-in HEK293


title: ha-h3x2-vps75-HU110-s44


title: NLS pre-pulldown input Rep1


title: ha-h3x2-vps75-HU130-s44


title: VIP-U10


title: ha-h3x2-vps75-HU070-s44


title: VIP-U4


title: VIP-U1


title: NPAT pre-pulldown input Rep2


title: FBL pre-pulldown input Rep1


title: NPAT pre-pulldown input Rep1


title: ha-h3x2-vps75-HU040-s44


title: ha-h3x2-vps75-HU150-s44


title: ha-h3x2-vps75-HU030-s44


title: SST-U610


title: SST-U609


title: FBL pre-pulldown input Rep2


title: SST-U7


title: ha-h3x2-vps75-HU015-s44


title: WRAP53 pre-pulldown input Rep2


title: WRAP53 pre-pulldown input Rep1


title: SST-U607


title: SMN2 pre-pulldown input Rep2


title: SST-U606


title: SMN2 pre-pulldown input Rep1


title: ha-h3x2-rtt-HU180spike-x39

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, rtt109::NAT


title: ha-h3x2-rtt-HU130spike-x39


title: ha-h3x2-rtt-HU150spike-x39


title: ha-h3x2-rtt-HU110spike-x39


title: PML pre-pulldown input Rep2


title: SP100 pre-pulldown input Rep2


title: SST-U604

value: UCMS (5-weeks)


title: SST-U8


title: SST-U605


title: SP100 pre-pulldown input Rep1


title: SST-U603


title: ha-h3x2-rtt-HU90spike-x39


title: PML pre-pulldown input Rep1


title: SST-U601


title: ha-h3x2-rtt-HU70spike-x39


title: ha-h3x2-vps75-alpha-s44


title: ha-h3x2-rtt-HU50spike-x39


title: SAM68 pre-pulldown input Rep2


title: SAM68 pre-pulldown input Rep1


title: SST-U6


title: SST-U5


title: MECp10X scRNA-seq

city: Beijing

first: Ruiqi

last: Liu

address: No. 2, Yuanmingyuan West Road, Haidian District

country: China

institute: China Agricultural University

description: Nfatc1-marked cell-derived prognanythe at pregnancy day 14.5

data_processing:
Chromium Single Cell 3’ v2 libraries were sequenced with a Novaseq 6000 sequencer, with the following sequencing parameters: read 1, 150 cycles; i7 index, 8 cycles and read 2, 150 cycles.
Raw Illumina data were demultiplexed and processed using Cell Ranger (10X Genomics version Cell Ranger 2.0.1)
In order to remove partial cells and doublets, cells with less than 500 genes or more than 6000 genes were removed.
Cells with more than 10% of mitochondrial unique molecular identifiers (UMIs) were removed, as a high proportion of mitochondrial expression in cells is indicative of cell stress/damage during isolation.
Genome_build: mm10

source_name: mammary gland

extract_protocol:
Mammary gland were digested into single cells, the Dyeflour450-BV421-, CD45-APC-, CD31-APC-, Ter119-APC-, CD29-FITC+, CD24-PeCy7+ cells were sorted by FACS. for Nfatc1+ cells, the RFP+ cells were sorted by FACS.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry. Cell capture, library preparation, quality control, and sequencing was performed at beijing capitalBio technology

treatment_protocol: breed with WT male mice until they are pregant

tag: cell type

value: mammary gland primary cells

value: pergnancy day14.5

tag: genetype

value: Nfatc1-CreERT2; R26-tdTomato


title: RNPS1 pre-pulldown input Rep2

value: ribosome-depleted RNA


title: ha-h3x2-rtt-HU30spike-x39

value: ha


title: SST-U4

value: Control

value: brain


title: RNPS1 pre-pulldown input Rep1


title: SST-U3


title: ha-h3x2-rtt-HU15spike-x39


title: ha-h3x2-rtt-alpha2spike-x39


title: 10X Adult SVZ 02

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

description: 10X Adult SVZ 02

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v3.0.2 using default parameters to obtain the gene expression matrices
Genome_build: mm10
Supplementary_files_format_and_content: mtx matrix files

source_name: brain

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: Adult


title: SRSF1 pre-pulldown input Rep2


title: ha-h3x2-rtt-alpha1spike-x39


title: MECv 10X scRNA-seq

description: Nfatc1-marked cells at 8-week-old

value: untreated


title: SST-U10


title: SST-U2


title: SRSF1 pre-pulldown input Rep1


title: 10X Adult SVZ 01

description: 10X Adult SVZ 01


title: SST-U608


title: ha-h3x2-rtt-HU40spike-x39


title: 10X P14 SVZ 02

description: 10X P14 SVZ 02


title: 10X P14 SVZ 01

description: 10X P14 SVZ 01


title: SST-U1


title: SRSF7 pre-pulldown input Rep2


title: HVO_oxsRHA_4_NaOCl_WCE

first: Amy

middle: K

last: Schmid

address: 125 Science Dr.

department: Biology

institute: Duke University

data_processing:
Sequencing reads were trimmed and controlled their quality (Phred score > 30) by TrimGalore! wrapper pipeline (https://github.com/FelixKrueger/TrimGalore) with default parameters.
The preprocessed reads were mapped (alignment rate > 95%) using Bowtie2 to the H. volcanii DS2 reference genome (https://www.ncbi.nlm.nih.gov/genome/1149?genome_assembly_id=170797). The mapped reads were then sorted and indexed by Samtools.
Peaks (cutoff, Qval < 0.05) were called by MOSAiCS and checked for quality by ChIPQC. DiffBind was used to identify significant peaks that were present at least three of four biological replicates, and ChIPseeker was used to annotate the peaks.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/1149?genome_assembly_id=170797
Supplementary_files_format_and_content: bed

organism: Haloferax volcanii

source_name: Haloferax volcanii cell culture

growth_protocol: Four single colonies of SH126 (oxsR-HA integrant) and two colonies of H26 were inoculated in 5-mL GMM and grown aerobically at 42 °C to early stationary phase to synchronize growth phase (OD600nm, ~1.0) with shaking (200 rpm).

extract_protocol:
ChIP-seq samples were prepared as the previous method with modifications (Wilbanks et al., 2012; DOI: 10.1093/nar/gks063). Briefly, to crosslink, 37% formaldehyde was added to the culture at the final concentration of 1% and the cell culture was incubated on a rocking platform for 20 min at room temperature. A final concentration of 0.125 M glycine was added to stop the crosslinking reaction and the whole cells were washed three times with cold basal salts buffer followed by storage at -80°C until sonication. The cell pellet was thawed and resuspended in 800 μl lysis buffer (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate, pH 7.5) containing protease inhibitor cocktail (Thermo Scientific) to shear DNA by Bioruptor 300 sonication system (Diagenode) with 15 cycles of 30 s on and 90 s off at high magnitude. The sheared DNA was monitored to confirm the genomic DNA was a smear between 200-800 bp with the highest concentration of fragments ~500 bp by 1.2% (w/v) agarose gel electrophoresis. For immunoprecipitation, the sheared DNA was immediately incubated overnight with the complex anti-HA tag antibody (Abcam, ab9110) and Dynabeads protein A (Invitrogen) at 4°C. Enriched DNA/OxsR complexes were eluted by adding 50 µl elution buffer (50 mM Tris, 10 mM EDTA, 1% SDS (w/v), pH 8.0) and incubation at 65°C for 10 min. Reverse crosslinking was performed by incubating in TE/SDS (10 mM Tris, 1 mM EDTA, 1% SDS) overnight at 65°C. DNA, of which the RNA was removed, was subsequently extracted by a phenol-chloroform method.
Library preparation and deep sequencing were carried out at Duke Sequencing and Genomics Technologies core facility.

treatment_protocol: Cells were transferred to fresh 100-mL GMM, and 2.5 mM NaOCl was added for 20 min when cells reached log phase (OD600nm, 0.3~0.5) for the oxidative stress group. A mock control was included for comparison.

value: 2.5 mM hypochlorite (NaOCl)

tag: epitope tag

value: hemagglutinin (HA)

value: none (input control)

tag: growth medium

value: GMM (glycerol minimal medium)


title: SRSF7 pre-pulldown input Rep1

tag: protein tag

value: FLAG-APEX2 tagged


title: 10X E18.5 VT 02

description: 10X E18.5 VT 02


title: Pyr-U9

source_name: Pyramidal neurons isolated from medial prefrontal cortex

value: Pyramidal neurons


title: ha-h3x2-rtt-asyncspike-x39

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-TEV, HHT1-HA-TEVsite-MYC, HHT2-HA-TEVsite-MYC, bar1, rtt109::NAT

value: asyncspike


title: FLAG pulldown Rep2

tag: cell line

value: Flp-in HEK293


title: Pyr-U8


title: SST-U602

value: UCMS (5-weeks)

value: SST neurons


title: FLAG pulldown Rep1

tag: molecule subtype

value: ribosome-depleted RNA


title: HVO_oxsRHA_3_NaOCl_WCE

tag: strain


title: Pyr-U7

tag: experimental group


title: GFP pulldown Rep1


title: HVO_WT_2_NaOCl_WCE


title: BatchC - lumbar spinal cord - mixed sample

city: New York

first: Paul

middle: Francis

last: Gugger

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone Health

description:
1 female C57BL/6J wild-type control, 1 male C57BL/6J wild-type control, 1 female B6.Cg-Tg(SOD1*G93A)1Gur/J amyotrophic lateral sclerosis-like phenotype, and 1 male B6.Cg-Tg(SOD1*G93A)1Gur/J amyotrophic lateral sclerosis-like phenotype
umi.tsv
umi.sctransform.tsv
metadata.samples.tsv
metadata.nuclei.tsv
readme.txt

data_processing:
Illumina base call (bcl) files for the samples were converted to FASTQ files using CellRanger bcl2fastq 2.20.0.422.
Read data were aligned to mm10 pre-mRNA using STAR_2.5.1b and including the following arguments: --outSAMmultNmax -1 --outSAMunmapped Within KeepPairs --outSAMorder PairedKeepInputOrder
Matrices of unique molecular identifier (UMI) gene expression counts for each gene and hastag oligo counts in each nucleus in each 10X batch were generated with CellRanger 3.1.
UMIs from each nucleus were assigned to individual mice using the HTODemux function on the hashtag data in Seurat 4.0.3 in R 4.0.3.
Low-quality nuclei with fewer than 200 genes or greater than 10% mitochondrial data, and “doublets” with ambiguous hashtag signals, and hashtag-negative nuclei were discarded, yielding 14,662 high-quality nuclei for analyses. Mitochondrial genes were discarded.
The three filtered 10X batches were integrated and normalized using the sctransform method, generating a normalized count matrix.
The integrated data for nuclei passing filters were used for PCA and UMAP dimensionality reduction and clustering analysis in Seurat 4.0.3 (FindNeighbors with 100 PCs and FindClusters with resolution 1.6), followed by initial assignment of cell types to these clusters with SingleR 1.4.1, which were refined by marker gene analysis, subclustering, and mapping to reference data.
Genome_build: mm10
Supplementary_files_format_and_content: filtered_feature_bc_matrix.*.tar.gz include the output from CellRanger 3.1 for each batch A, B, and C as tab-separated text files.
Supplementary_files_format_and_content: umi.tsv.gz is a tab-separated text file that contains the raw UMI count matrix for nuclei that passed filtering.
Supplementary_files_format_and_content: umi.sctranform.tsv.gz is a tab-separated text file that contains the UMI data integrated across batches and normalized using the sctranform method for nuclei that passed filtering.
Supplementary_files_format_and_content: metadata.samples.tsv is a tab-separated text file that defines the 10X batch, sex, genotype, and nuclear hashtag of each sample.
Supplementary_files_format_and_content: metadata.nuclei.tsv is a tab-separated text file that contains the metadata for nuclei that passed filtering (rows here match columns in umi*.tsv), including UMI and hashtag oligo (HTO) count summaries, HTO demultiplexing results, sample ID, batch, sex, genotype, Seurat clusters, SingleR cell type assignments, Seurat subclustering, final cell types based on further refinements with marker genes, UMAP coordinates, and the first 100 principal components from PCA.
Supplementary_files_format_and_content: readme.txt contains instructions for how to demultiplex nuclei and assign to biological samples starting from BAM files using CellRanger and then the Seurat HTODemux function in R.

molecule: nuclear RNA

source_name: lumbar spinal cord

growth_protocol: All experiments were performed on B6.Cg-Tg(SOD1G93A)1Gur/J (JAX Stock No:004435) and C57BL/6J littermate controls 6,25. In accordance with high-copy number transgenics, mice were checked for copy number alterations and any mice with alterations were not enrolled in the study. All mice were maintained under pathogen-free conditions and all experiments were performed under protocols approved by the New York University Grossman School of Medicine Institute Animal Care Committee (IACUC) in accordance with international and NIH guidelines. All mice were housed in a temperature (19–23°C) and humidity (30–70% relative humidity)-regulated environment with 12-hour light/dark cycle, lights on/off at 6:30, and received standard chow food (Lab Diets, 5053) pellets and water ad libitum. Three male and three female SOD1G93A mice and three male and three female littermate control mice were employed for these studies at age day 90.

extract_protocol:
Mice were anesthetized with Ketamine and Xylazine and then underwent rapid cardiac perfusion with PBS. The spinal column was rapidly removed, and the lumbar spinal cord was retrieved. Tissue was flash-frozen in liquid nitrogen and stored at −80°C until sample processing. Single-nucleus pools from frozen lumbar spinal cord were completed as detailed previously with several modifications 24. Briefly, frozen tissue was dounce homogenized with 5 strokes of the loose pestle followed by 10 strokes with the tight pestle at 4°C in a low sucrose buffer (0.32 M sucrose, 10 mM HEPES (pH 7.5), 5 mM CaCl2, 0.1 mM EDTA, 3 mM MgAc, 1 mM DTT) with 0.1% Triton X-100 added. The crude nuclei prep was gently mixed with additional low sucrose buffer and was subsequently passed over a pre-wet 30 μm strainer. The filtered crude nuclei prep was centrifuged at 2613 × g for 10 min at 4°C. Supernatant was decanted and the pellet was re-suspended in low sucrose buffer. An additional homogenization step using a TissueRuptor II (Qiagen Inc.) set to the lowest power was completed on each sample for 15 s. High sucrose buffer (1 M sucrose, 10mM HEPES (pH 7.5), 3 mM MgAc, 1 mM DTT) was then layered underneath the crude prep. The crude prep was centrifuged for 25 min at 2613 × g at 4°C. The supernatant was decanted and re-suspended in resuspension buffer, 1% BSA in PBS with 0.2 U/μL of Ambion RNase Inhibitor (Invitrogen, Cat:AM2684), and transferred to a low-bind conical tube. The nuclei were washed of any residual sucrose by centrifugation at 500 × g for 5 min at 4°C. The pellet was re-suspended in PBS containing 20 μg/mL Fc Block CD16/CD32 (Biolegend, Cat: 101301) and incubated for 5 min at 4°C. 0.5 μg of a nuclear hashing antibody was added to each sample and incubated for 30 min at 4°C. Nuclei were washed three times and finally counted using a Countess Automated Cell Counter (ThermoFisher). Three pools of nuclei were generated, each containing 40,000 nuclei from samples representing each of the four experimental groups. Nuclear hashtag antibodies used included: 10μg/mL anti-Nuclear Pore Complex Proteins Hashtag Antibodies 1–4 (BioLegend, Catalog numbers: TotalSeq-A0451, TotalSeq-A0452, TotalSeq-A0453, TotalSeq-A0454).
The 10X Chromium controller (10X Genomics) with v3 chemistry was used to capture, barcode and prepare single- nucleus libraries from each of the three pools of nuclei as per manufacturer’s instructions. The resulting libraries were sequenced on a full lane of an Illumina NovaSeq 6000 S2 flow cell.

value: lumbar spinal cord

tag: Sex

value: Female and Male

value: C57BL/6J and B6.Cg-Tg(SOD1*G93A)1Gur/J

value: wild type and SOD1G93A transgenic

tag: batch

value: C


title: BatchB - lumbar spinal cord - mixed sample

tag: tissue

tag: genotype

value: B


title: BatchA - lumbar spinal cord - mixed sample

value: A


title: Pyr-U609

tag: cell-type

value: brain


title: HVO_oxsRHA_4_NaOCl_IP

value: 2.5 mM hypochlorite (NaOCl)

value: hemagglutinin (HA)

tag: antibody

value: Abcam, ab9110

value: GMM (glycerol minimal medium)


title: NLS pulldown Rep1

value: FLAG-APEX2 tagged


title: HVO_WT_1_NaOCl_WCE

value: none (input control)


title: Control mice for NEHI model

city: San Diego

first: Xin

last: Sun

state: CA

address: 9500 Gilman Dr., CMME, Room 1055

department: Department of Pediatrics, Department of Biological Sciences

institute: UNIVERSITY OF CALIFORNIA AT SAN DIEGO

description: primary epithelial cells and endothelial cells from 3 dissociated lungs

data_processing:
Sequencing was carried out on NovaSeq (Illumina) platform at the Institute for Genomic Medicine, UCSD.
Cell Ranger package (version 3.0.2) was used to align the raw reads onto the mouse reference genome (GRCm38) with default parameters and generate the feature-barcode matrix.
R package Seurat (version 3.0) was used to perform data quality control, normalization, principal components analysis and uniform manifold approximation and projection  (UMAP method).
Cells with fewer than 200 or more than 2,500 unique feature counts, or more than 7% mitochondrial counts were considered low quality cells and removed from further analysis. Then global-scaling method "LogNormalize" was used to normalize the feature expression. A total of 2,000 top variable features were identified by function FindVariableFeatures and selected for subsequent principal components analysis
Top 20 significant components were chosen to conduct cell clustering by using the algorithm of uniform manifold approximation and projection (UMAP) with default settings. The expression level and feature of selected genes were profiled and visualize by R package ggplot2 (version 3.3.2)
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: For control and mutant: UMI count matrix files from cellranger. Reads alignment files in bam format. Seurat object in R object.

source_name: Lung

growth_protocol: All Mice used in this experiment are bred in the standard facility of UCSD with approval protocol from IACUC

extract_protocol:
Cellular suspensions were loaded on a 10X Genomics Chromium Controller (10x Genomics, Pleasanton, CA) to generate single cell GEMs. And ~1200 cells were loaded per well. cDNA extraction and amilification were excecuted using Chromium Single Cell 3' Reagent Kits (v3 Chemistry, PN-1000075, 10X Genomics) folloing User Guide provided by 10X Genomics.
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit v3 (PN-1000075, 10x Genomics) following User Guide provided by 10X Genomics.
scRNA-seq library for 10X Genomics sequencing

treatment_protocol: No treatment involved

value: Lung

tag: age

value: post natal day 22

value: wild type


title: ha-h3x2-wt-HU015-s43

value: MATa his3delta1 leu2delta0 LYS2 met15delta0 ura3delta0 HTB2-GGS-TEV  HHT1-GGS-HA-Fast-MYC HHT2-GGS-HA-Fast-MYC, bar1

tag: sensor

value: ha

tag: growth condition

value: wt


title: 10X E18.5 VT 01

description: 10X E18.5 VT 01


title: Mutant mice for NEHI model


title: HVO_oxsRHA_3_NaOCl_IP

tag: treatment


title: Pyr-U606

value: UCMS (5-weeks)

value: Pyramidal neurons


title: LMNA pulldown Rep2

value: Flp-in HEK293

value: ribosome-depleted RNA


title: Pyr-U607

value: brain


title: Hottip-Tg-LK-ChIRP-seq

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

description: Hottip-Tg-LK-ChIRP-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end ChIRP-seq, HiC-seq and scRNA-seq and scATAC-seq reads from mice were aligned to the mm9 genome assembly using BWA, and NG capture-C-seq, ChIP-seq, DRIP-seq and DRIPc-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for scRNA-seq and scATAC-seq Samples and peaks for DRIP-seq , DRIPc-seq,ChIRP-seq, ChIP-seq, NG-capture-C and HIC-seq.

source_name: Bone marrow Lin-  Kit+ cells

growth_protocol: Total bone marrow cells were isolate from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers.  Human MOLM13 leukemia cells were culture at RMPI1640 medium with 10% FBS media.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with CTCF, SA1, SA2, RAD21, H3K4me3 and H3K27me3 antibody (antibody: Anti-CTCF, Cell Signaling Technology, Cat# 2899; Anti-SA1, Abcam, Cat# ab4457; Anti-SA2, Abcam, Cat# ab4464;  Anti-RAD21, Abcam, Cat# ab992;  Anti-H3K4me3, Millipore, Cat No. 04-745;   Anti-H3K27me3, Millipore, Cat No. 07-449).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits. DNA:RNA immunoprecipitation sequencing (DRIP-seq) was performed as described previously with s9.6 antibody (Anti-DNA-RNA Hybrid [S9.6] Antibody, Kerafast, Cat# ENH001). ChIRP libraries were prepared using Illumina’s TruSeq ChIP Sample Preparation Kit according to the manufacturer’s instructions. The quality of the library was checked with Agilent Bioanalyzer. NG-Capture-C assay was performed as previously described. Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/) with minor modifications. Single cells were generated using Chromium Controller (10x Genomics), and scRNA-seq and scATAC-seq libraries were constructed using chromium single cell 3’ reagent kits v2 (10x Genomics, California USA) according to the manufacturer’s recommendations.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ChIRP libraries were prepared using Illumina’s TruSeq ChIP Sample Preparation Kit according to the manufacturer’s instructions. The quality of the library was checked with Agilent Bioanalyzer.  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). NG-Capture-C-seq libraries were prepared according to  using the Herculase II PCR kit (Agilent). . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
single cell RNA-seq, ATAC-seq, ChIP-seq, ChIRP-seq, DRIP-seq, DRIPc-seq, NG-Capture-C-seq and HiC-seq

treatment_protocol: Immediately extract RNA from LK, LSK cells and MOLM13 AML cells without any treatment

tag: genotype/variation

value: Hottip transgenic

value: Bone marrow

tag: cell type

value: Lin-  Kit+ cells


title: LMNA pulldown Rep1

tag: protein tag


title: HVO_oxsRHA_2_NaOCl_IP

value: 2.5 mM hypochlorite (NaOCl)

tag: epitope tag

value: hemagglutinin (HA)

value: Abcam, ab9110

tag: growth medium

value: GMM (glycerol minimal medium)


title: HVO_oxsRHA_2_NaOCl_WCE

tag: strain

value: none (input control)


title: GFP pulldown Rep2

value: FLAG-APEX2 tagged

tag: cell line

tag: molecule subtype


title: HVO_oxsRHA_1_NaOCl_WCE


title: FBL pulldown Rep2


title: Pyr-U605

tag: experimental group


title: Pyr-U610

tag: tissue


title: HVO_oxsRHA_1_NaOCl_IP


title: Hottip-Tg-LK-CTCF-ChIP-seq

description: Hottip-Tg-LK-CTCF-ChIP-seq

tag: chip antibody

value: Anti-CTCF, Cell Signaling Technology, Cat# 2899


title: WT-LK-ChIRP-seq

description: WT-LK-ChIRP-seq

value: wild type


title: Pyr-U603

tag: cell-type


title: WT-LK-CTCF-ChIP-seq

description: WT-LK-CTCF-ChIP-seq


title: HVO_WT_2__NaOCl_IP

description: HVO_WT_2__NaOCl_IP.  There were no peaks identified for this control sample.

tag: antibody


title: Pyr-U608


title: Pyr-U604


title: FBL pulldown Rep1


title: HVO_WT_1_NaOCl_IP

description: HVO_WT_1_NaOCl_IP. There were no peaks identified for this control sample.


title: NPAT pulldown Rep2


title: NPAT pulldown Rep1


title: Pyr-U602


title: Hottip-Tg-LK-scATAC-seq

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end HiC-seq and scRNA-seq and scATAC-seq reads from mice were aligned to the mm9 genome assembly using BWA, and NG capture-C-seq, ChIP-seq, DRIP-seq and DRIPc-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for scRNA-seq and scATAC-seq Samples and peaks for DRIP-seq , DRIPc-seq, ChIP-seq, NG-capture-C and HIC-seq.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with CTCF, SA1, SA2, RAD21, H3K4me3 and H3K27me3 antibody (antibody: Anti-CTCF, Cell Signaling Technology, Cat# 2899; Anti-SA1, Abcam, Cat# ab4457; Anti-SA2, Abcam, Cat# ab4464;  Anti-RAD21, Abcam, Cat# ab992;  Anti-H3K4me3, Millipore, Cat No. 04-745;   Anti-H3K27me3, Millipore, Cat No. 07-449).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits. DNA:RNA immunoprecipitation sequencing (DRIP-seq) was performed as described previously with s9.6 antibody (Anti-DNA-RNA Hybrid [S9.6] Antibody, Kerafast, Cat# ENH001).  NG-Capture-C assay was performed as previously described. Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/) with minor modifications. Single cells were generated using Chromium Controller (10x Genomics), and scRNA-seq and scATAC-seq libraries were constructed using chromium single cell 3’ reagent kits v2 (10x Genomics, California USA) according to the manufacturer’s recommendations.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). NG-Capture-C-seq libraries were prepared according to  using the Herculase II PCR kit (Agilent). . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
single cell RNA-seq, ATAC-seq, ChIP-seq, DRIP-seq, DRIPc-seq, NG-Capture-C-seq and HiC-seq

value: Mouse-derived Bone marrow cells

tag: cell subtype

tag: genotype

value: Hottip-Tg


title: HVO_oxsRHA_4_WCE

value: untreated


title: Pyr-U6

value: Control

value: Pyramidal neurons


title: Pyr-U601

value: UCMS (5-weeks)

value: brain


title: HVO_oxsRHA_3_WCE


title: WRAP53 pulldown Rep1

value: Flp-in HEK293

value: ribosome-depleted RNA


title: Pyr-U5


title: WT-LK-scRNA-seq

value: Bone marrow

value: Lin-  Kit+ cells

value: WT


title: Pyr-U4


title: WRAP53 pulldown Rep2


title: SMN2 pulldown Rep2


title: WT-LK-scATAC-seq


title: SMN2 pulldown Rep1


title: Pyr-U2


title: HVO_oxsRHA_1_WCE

value: hemagglutinin (HA)

value: GMM (glycerol minimal medium)


title: HVO_WT_1_WCE

value: none (input control)


title: Hottip-Tg-LK-scRNA-seq


title: WT-LSK-scRNA-seq

source_name: Bone marrow Lin- Sca1+ Kit+ cells

value: Lin- Sca1+ Kit+ cells


title: SP100 pulldown Rep1

value: FLAG-APEX2 tagged


title: HVO_WT_2_WCE


title: SP100 pulldown Rep2


title: Hottip-Tg-LSK-scRNA-seq

value: Mouse-derived Bone marrow cells


title: Hottip-Tg-LSK-HiC-seq

value: Hottip-Tg


title: HVO_oxsRHA_2_WCE

value: untreated


title: WT-LSK-HiC-seq


title: HVO_oxsRHA_4_IP

value: Abcam, ab9110


title: Pyr-U10

value: Control

value: Pyramidal neurons


title: Pyr-U1

value: brain


title: PML pulldown Rep1

value: Flp-in HEK293


title: HVO_oxsRHA_3_IP


title: mHSPC PML/RARa (2KR)

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

data_processing:
Raw Reads were filtered to get high-quality Reads using Seqtk. (https://github.com/lh3/seqtk)
Genome mapping: High-quality Reads were then imported into Hisat2 (version:2.0.4) for alignment into BAM files. (Nat Methods 2015, 12(4):357-360)
FPKM calculation: The number of fragments for each gene obtained from Hisat2 are counted, and normalized using TMM (trimmed mean of M values). Next, the FPKM value is calculated using Perl script. (Nat Methods 2008, 5(7):621-628; Nat Biotechnol 2015, 33(3):290-295; Nat Protoc 2016, 11(9):1650-1667)
Genome_build: GRCm38
Supplementary_files_format_and_content: Table with raw gene count and FPKM for every gene

source_name: mHSPCs

growth_protocol: mHSPCs were cultured in liquid myeloid medium (IMDM supplemented with recombinant mouse SCF (50 ng/ml; Peprotech), recombinant mouse IL-3 (10 ng/ml; Peprotech), recombinant mouse IL-6 (10 ng/ml; Peprotech), 1% bovine serum albumin (Yeasen Biotech Co., Ltd.), hydrocortisone (1 mM; Sigma-Aldrich), 2-mercaptoethanol  (100 mM; Sigma-Aldrich), L-glutamine (2 mM), 20% fetal bovine serum (Gibco BRL) and 1% penicillin/streptomycin.

extract_protocol:
Transduced mHSPCs were collected for RNA extraction and RNA-sequencng.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mHSPCs were cultured in a six-well plate and exposed to concentrated lentivirus (pMSCV, PML/RARa(WT) or PML/RARa(2KR)) in the presence of 6 µg/ml of polybrene. Infection was obtained by centrifugation of the cells in viral supernatant at 1,800 rpm for 40 min. The cells were cultured for 24 h at 37 °C. The following day, the medium was removed and replaced with fresh culture medium.

value: mouse haematopoietic stem/progenitor cells

tag: infection

value: PML/RARa (2KR)


title: Pyr-U3


title: HVO_oxsRHA_2_IP

tag: treatment


title: PVALB-U8

source_name: Parvalbumin-expressing interneurons isolated from medial prefrontal cortex

value: PV neurons


title: DT40

city: Paris

first: Chunlong

last: Chen

address: 26 rue d’Ulm

country: France

institute: Institut Curie

description: DT40 OK-seq

data_processing:
Library strategy: OK-seq
bcl2fastq2 v2.15.0 (demultiplex)
Cutadapt 1.3 (adapter trimming)
FastQC 0.10.1 (quality control)
BWA 0.7.4 (mapping) then merge the original BAM with re-amplificated BAM together by samtools
home-made script for replication fork direction (RFD)
Genome_build: Galgal4
Supplementary_files_format_and_content: bigwig file for forward and reverse strand and RFD profile

organism: Gallus gallus

source_name: lymphoblast

growth_protocol: DT40 cells were cultured in RPMI 1640 medium supplemented with 10% Fetal Bovine Serum (FBS), 1% chicken serum, 50µM of betamercaptoethanol and penicillin/streptomycin.

extract_protocol:
Okazaki fragments were isolated by sucrose gradient size-fractionation of genomic DNA followed by click-chemistry biotinylation and streptavidin capture of EdU-labelled DNA as described previously (PMID: 26751768).
Okazaki fragments were treated with NaOH to remove 5' RNA, 5' phosphorylated with T4 polynucleotide kinase (PNK), hydridized and ligated to double-stranded adapters, followed by ampfication and bar-coding in PCR.

treatment_protocol: Asynchronously growing cells were treated with 20 µM  of 5-ethynyl-2′-deoxyuridine (EdU) for 2 min when 70-80 % confluent (0.8 millions of cells per ml)

value: avian leukosis virus (ALV)-induced bursal lymphoma


title: PVALB-U7


title: PVALB-U9


title: HVO_oxsRHA_1_IP

value: hemagglutinin (HA)


title: SAM68 pulldown Rep2

value: ribosome-depleted RNA


title: HVO_WT_1_IP

value: GMM (glycerol minimal medium)


title: SAM68 pulldown Rep1


title: HOTTIP-KO-DRIPc-seq

data_processing:
Library strategy: DRIPc-seq
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end HiC-seq and scRNA-seq and scATAC-seq reads from mice were aligned to the mm9 genome assembly using BWA, and NG capture-C-seq, ChIP-seq, DRIP-seq and DRIPc-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for scRNA-seq and scATAC-seq Samples and peaks for DRIP-seq , DRIPc-seq, ChIP-seq, NG-capture-C and HIC-seq.

source_name: MOLM13 leukemia cells

value: peripheral blood

value: Human-derived acute myeloid leukemia cells

value: MOLM13 leukemia cells

tag: gene fusion

value: Gene fusion KMT2A-MLLT3 (MLL-MLLT3; MLL-AF9)

value: HOTTIP-KO

value: Anti-DNA-RNA Hybrid [S9.6] Antibody, Kerafast, Cat# ENH001


title: RNPS1 pulldown Rep1

source_name: Flp-in HEK293 cells

value: FLAG-APEX2 tagged


title: RNPS1 pulldown Rep2


title: PVALB-U608

value: UCMS (5-weeks)


title: PVALB-U610

value: brain


title: WT-DRIP-seq

data_processing:
Library strategy: DRIP-seq
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end HiC-seq and scRNA-seq and scATAC-seq reads from mice were aligned to the mm9 genome assembly using BWA, and NG capture-C-seq, ChIP-seq, DRIP-seq and DRIPc-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for scRNA-seq and scATAC-seq Samples and peaks for DRIP-seq , DRIPc-seq, ChIP-seq, NG-capture-C and HIC-seq.

tag: cell type

value: WT


title: HVO_WT_2_IP

value: untreated

value: Abcam, ab9110


title: SRSF1 pulldown Rep2

tag: protein tag

value: Flp-in HEK293


title: WT-DRIPc-seq


title: mHSPC PML/RARa (WT)

value: Bone marrow

value: mouse haematopoietic stem/progenitor cells

value: PML/RARa (WT)


title: SRSF1 pulldown Rep1

value: ribosome-depleted RNA


title: PVALB-U606

value: PV neurons


title: PVALB-U607


title: SRSF7 pulldown Rep2


title: MYC-3CBS-RH-NG-Capture-C-seq

data_processing:
Library strategy: Capture-C-seq
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end HiC-seq and scRNA-seq and scATAC-seq reads from mice were aligned to the mm9 genome assembly using BWA, and NG capture-C-seq, ChIP-seq, DRIP-seq and DRIPc-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for scRNA-seq and scATAC-seq Samples and peaks for DRIP-seq , DRIPc-seq, ChIP-seq, NG-capture-C and HIC-seq.

value: peripheral blood

value: Human-derived acute myeloid leukemia cells


title: PVALB-U604


title: SRSF7 pulldown Rep1


title: PVALB-U603


title: PVALB-U605


title: HOTTIP-KO-SA1-ChIP-seq

value: MOLM13 leukemia cells

value: Gene fusion KMT2A-MLLT3 (MLL-MLLT3; MLL-AF9)

value: Anti-SA1, Abcam, Cat# ab4457


title: HOTTIP-KO-SA2-ChIP-seq

value: HOTTIP-KO

value: Anti-SA2, Abcam, Cat# ab4464


title: WT-SA2-ChIP-seq


title: PML pulldown Rep2

value: FLAG-APEX2 tagged


title: WT-SA1-ChIP-seq

value: WT


title: spermatozoa - CD-F0 - rep5

city: Shanghai

first: Yunfang

last: Zhang

address: 1239 Siping Road

department: Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology

institute: Tongji University

description: small non-coding RNA

data_processing:
Sequencing reads were processed by using the software SPORTS [34]. Briefly, clean reads were aligned to mouse reference genome, miRNA datasets, rRNA and YRNA datasets, the genomic tRNA datasets, the mitochondrial tRNA datasets, piRNA datasets, the non-coding RNA datasets by using Bowtie [35] with one mismatch allowance.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include sncRNA reads for each smaple

source_name: spermatozoa

growth_protocol: Two groups of 4-week-old male mice were randomly assigned to receive a control diet (CD; 10% kcal fat) or a high-fat diet (HFD; 42% kcal fat).

extract_protocol:
Mature sperms were isolated from the epididymal tail and vas deferens of F0 father
Small RNA library construction and sequencing were performed by BGI (Shenzhen, China). According to the NEB Small RNA Sample Pre Kit (NEB), the small RNA library was prepared, and then the library quality was verified for sequencing.

value: control diet

value: spermatozoa

tag: generation


title: HOTTIP-KO-RAD21-ChIP-seq

value: Anti-RAD21, Abcam, Cat# ab992


title: spermatozoa - CD-F0 - rep4

description: small non-coding RNA


title: CBS-u2-KO--NG-Capture-C-seq


title: PVALB-U602

value: UCMS (5-weeks)

value: brain


title: WT-RAD21-ChIP-seq


title: PVALB-U601


title: spermatozoa - CD-F0 - rep3

description: small non-coding RNA


title: HOTTIP-KO-NG-Capture-C-seq


title: HOTTIP-KO-CTCF-ChIP-seq

value: Anti-CTCF, Cell Signaling Technology, Cat# 2899


title: CBS-u2-RH-NG-Capture-C-seq


title: PVALB-U6

value: Control


title: T24 cells, OXLDL_rep3

type: RNA

first: Jingya

address: 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

description: Gene expression data of bladder cancer cells T24 treated with G9a siRNA

hyb_protocol: Following Fragment and Label Single-Stranded cDNA, 27ul of biotin-labeled ss-cDNA sample were hybridized for 16 hr at 45℃ on GeneChip Clariom S Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with robust multi-array average (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: T24, ox-LDL, 24 h

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChipTM WT PLUS Reagent Kit, 2017, Affymetrix)

growth_protocol: T24 cells were maintained in RPMI 1640 medium containing 10% fetal bovine serum.

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

treatment_protocol: T24 cells were seeded in 6-well plates at 30% conference. After adhering, cells were starved with RPMI 1640 medium without fetal bovine serum for 12 h. Then cells were treated with 20 μg/mL ox-LDL or vehicle. Then, the cells were cultured for another 24 h and then prepared using Trizol.

value: bladder cancer cells T24

value: 20 μg/mL ox-LDL


title: T24 cells, OXLDL_rep1


title: T24 cells, CON_rep3

description: Gene expression data of bladder cancer cells T24 treated with negative control siRNA

source_name: T24, vehicle, 24 h

value: Vehicle


title: T24 cells, OXLDL_rep2


title: T24 cells, CON_rep2


title: spermatozoa - CD-F0 - rep1

description: small non-coding RNA


title: spermatozoa - CD-F0 - rep2

description: small non-coding RNA


title: g_2

city: china

first: wei

last: hanhantian

state: china

address: wusu street

institute: zhejiang A&F university

description:
Phyllostachys violascens cv. Viridisulcata
merged.readcount.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr M G, Haas B J, Yassour M, et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29, 644-652. (Trinity)) with min_kmer_cov set to 2 by default and all other parameters set default.
Differential expression analysis of two samples was performed using the DEGseq (Anders S, Huber W. (2010). Differential expression analysis for sequence count data. Genome Biology, doi:10.1186/gb-2010-11-10-r106. (DESeq)) R package. Pvalue was adjusted using q value (Storey et al., 2003). qvalue1 was set as the threshold for significantly differential expression.
Genome_build: cluster_all.fasta
Supplementary_files_format_and_content: merged.readcount.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: cluster_all.fasta: FASTA file

organism: Phyllostachys violascens

source_name: the longest internodes' culm

extract_protocol:
Total samples were washed by 75% ethanol, and wiped with filter paper, then frozen in liquid nitrogen until analysis. RNAs were extracted by using the RNAiso Plus Kit (TaKaRa).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cultivar

value: Viridisulcata

value: wild type

value: yellow culm


title: PVALB-U4

data_processing:
Sequencing performed on Illumina HiSeq 2500 platform. Run mode: High Output (2x125 cycles), 8 lanes. Yield (GBp): 286, Q30: Read 1=90.5%, Read 2=82.9%
Reads were trimmed 9bp on 5' and 21bp on 3' end based on Phred score distribution, and Read 2 was excluded from genomic mapping. Reads were mapped to the mouse genome (build GRCm38-mm10) using HiSat2.
BAM files were processed using SAMTOOLS v1.3
Counts were summarized at the gene level (i.e. meta-analysis of all transcript variants). Count normalization and differential expression was performed using DESeq2 R package. Co-expression analyses were performed using WGCNA R package.
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: Comma seperated values files include Ensembl gene identifiers (ENSMUSG), HUGO gene symbols, and DESeq2-normalized counts

tag: strain

value: PV neurons


title: spermatozoa - HFD-F0 - rep5

description: small non-coding RNA

value: high-fat diet


title: MYC-3CBS-RH-H3K27me3-ChIP-seq

value: peripheral blood

value: Human-derived acute myeloid leukemia cells

tag: cell line

value: MOLM13 leukemia cells

value: Gene fusion KMT2A-MLLT3 (MLL-MLLT3; MLL-AF9)

value: Anti-H3K27me3, Millipore, Cat No. 07-449


title: CBS-u2-RH-H3K27me3-ChIP-seq


title: g_1


title: PVALB-U3


title: CBS-u2-KO-H3K27me3-ChIP-seq


title: spermatozoa - HFD-F0 - rep3

description: small non-coding RNA

value: spermatozoa


title: c_3

source_name: the longest internodes' sulcus

value: green sulcus


title: MYC-3CBS-RH-H3K4me3-ChIP-seq

value: Anti-H3K4me3, Millipore, Cat No. 04-745


title: PVALB-U10

value: Control

value: brain


title: WT-NG-Capture-C-seq

value: WT


title: WT-CTCF-ChIP-seq

value: Anti-CTCF, Cell Signaling Technology, Cat# 2899


title: g_3

value: Viridisulcata


title: spermatozoa - HFD-F0 - rep2

description: small non-coding RNA


title: c_2

value: wild type


title: PVALB-U5


title: spermatozoa - HFD-F0 - rep1

description: small non-coding RNA


title: PVALB-U1


title: c_1


title: CBS-u2-RH-H3K4me3-ChIP-seq


title: T24 cells, CON_rep1

value: bladder cancer cells T24

value: Vehicle


title: CBS-u2-KO-H3K4me3-ChIP-seq


title: spermatozoa - HFD-F0 - rep4

description: small non-coding RNA

value: high-fat diet


title: sj_dcr1_sRNA_Seq_1

status: Public on Feb 17 2022

city: Edinburgh

first: Elizabeth

middle: H

last: Bayne

address: Alexander Crum Brown Road

department: Institute of Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Raw reads were filtered for quality and adapter using Trim Galore! (v0.4.3.1), reads that became shorter than 12nt were discarded
Trimmed reads were aligned to a FASTA file containing the sequence of all annotated ncRNAs in S. japonicus (SJ5) using Bowtie2 (v2.3.4.3). Unaligned reads were output to a separate file.
ncRNA filtered reads were then aligned to the S. japonicus reference genome (SJ5) using Bowtie2 (v2.3.4.3)
Coverage bedgraph files were generated using bamCoverage (v3.3.2.0.0). RPKM was used for normalisation with a bin size of 50bp. Separate files were generated for the forward and reverse strand mapping reads using the filterRNAstrand option.
Genome_build: GCA_000149845.2
Supplementary_files_format_and_content: bedgraph files plotting read coverage for the forward and reverse strand individually for each indidual sample

organism: Schizosaccharomyces japonicus

source_name: S. japonicus cell culture

growth_protocol: Cells were grown in YES at 32C

extract_protocol:
Total RNA was extracted by resuspending 50ml of pelleted cells at OD595 = 0.8-1.0 in 50 mM Tris–HCl pH 7.5, 10 mM EDTA pH 8, 100 mM NaCl, 1% SDS, adding equal volumes of phenol:chloroform 5:1 and acid washed beads. Cells were lysed using a bead beater (Biospec products) for 2 x 2 min at 4°C. The soluble fraction was extracted with phenol/chloroform and long RNAs precipitated with 10% polyethylene glycol 8000 and 0.5 M NaCl on ice for 30 min. The supernatant was recovered and small RNAs precipitated with ethanol overnight at −20°C.
Libraries were prepared using lllumina TruSeq small RNA library preparation kit according to manufacturer's instructions.

value: h- mat-P2028 dcr1-dis::natMX6 mpe1-R77W ura4-D3 ade6(sj)-domE


title: sj_wt_sRNA_Seq_1

value: h- mat-P2028 ura4-D3 ade6(sj)-domE


title: sj_dcr1_sRNA_Seq_2


title: sj_wt_sRNA_Seq_2


title: PVALB-U2

value: PV neurons


title: MEDA17-P-T14-R6

city: Castanet Tolosan

first: Bernard

last: Dumas

address: Chemin de Borde Rouge

institute: LRSV

data_processing:
Quality check with FastQC
htseq-counts files were analyzed with the R software using also EdgeR package version 3.24.3
First, genes which did not have at least 1 read after a count per million normalization in at least one half of the samples, were discarded
raw counts were normalized using TMM method and count distribution was modelled with a negative binomial generalized linear model where the treatment, the time and the double interaction between treatment and time were taken into account and where the dispersion is estimated by the edgeR method. A likelihood ratio test was performed to evaluate an infection effect at a given time point
Raw p-values were adjusted with the Benjamini–Hochberg procedure to control the False Discovery Rate (FDR). A gene was declared differentially expressed if it’s adjusted p value ≤ 0.05
Genome_build: Medicago truncatula A17 r5.0 genome annotation
Supplementary_files_format_and_content: Processed data file contain gene accession, gene annotation and gene expression (raw counts were normalized using TMM method )

organism: Medicago truncatula

source_name: Five seedlings

growth_protocol: A17 M. truncatula seeds were soaked in 3 ml of sulphuric acid for 5 min and then followed by 3 min of soak in 5 ml of Javel 2.6% (v/v) with intensive wash by sterile water at the end of each step. They were then placed on water/agar 1% plates in dark at 22 ◦C for 2 days.

extract_protocol:
Total RNA was then extracted by RNeasy plant mini kit (Qiagen) according to manufacturer’s instruction and rough RNA purity was checked using NanoDrop (Thermo Fisher).
Librairy prepared with Kit Illumina TruSeq Stranded mRNA, Sequencing with High throuput illumina Novaseq (2x150 pb).

treatment_protocol: pre-germinated A17 M. truncatula seedlings were placed on M media plates for each modality (with and without P. oligandrum). Seedlings were maintained in a phytotron at 22 °C and a 16 h light, 8 h dark photoperiod for 14 days. Six replications, which all were a pool of 5 seedings, were used for extraction with a kinetic of 3,5,7,14 days.

tag: treatment group

value: P. oligandrum

tag: time point

value: 14 days post treatment

value: Five seedlings

tag: replicate

value: Biological replicate 6


title: MEDA17-P-T14-R5

tag: tissue

value: Biological replicate 5


title: MEDA17-P-T14-R3

value: Biological replicate 3


title: MEDA17-P-T14-R4

value: Biological replicate 4


title: MEDA17-P-T14-R2

value: Biological replicate 2


title: MEDA17-P-T14-R1

value: Biological replicate 1


title: MEDA17-C-T14-R5

value: A17 (Control)


title: MEDA17-C-T14-R6


title: MEDA17-C-T14-R4


title: MEDA17-C-T14-R2


title: MEDA17-C-T14-R1


title: MEDA17-P-T7-R6

value: 7 days post treatment


title: MEDA17-C-T14-R3


title: MEDA17-P-T7-R1


title: MEDA17-P-T7-R4


title: MEDA17-P-T7-R3


title: MEDA17-C-T7-R5


title: MEDA17-P-T7-R2


title: MEDA17-C-T7-R2


title: MEDA17-C-T7-R3


title: MEDA17-C-T7-R1


title: MEDA17-C-T7-R4


title: MEDA17-P-T5-R6

value: 5 days post treatment


title: MEDA17-P-T5-R5


title: MEDA17-P-T5-R3


title: NLS pulldown Rep2

first: Rasim

address: 6 Davis Drive

institute: ScitoVation

data_processing:
Library strategy: RNA pull-down
The raw reads were mapped to the human genome using STAR 2.7.4a (PMID: 23104886), and the uniquely-mapped reads were counted using the featurecounts package (PMID:  24227677).
For splicing analysis, the data was processed using vast-tools v2.5.1 (PMID: 28855263).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt file containing gene counts from APEX pulldown and pre-pulldown input samples, as well as polyA and rRNA-depleted SRSF7 pulldown samples

extract_protocol:
After the second wash with 2X quench buffer in the APEX labeling protocol, the cells were harvested by scraping them down in 2X quench buffer including 4 uL Ribolock RNase inhibitor (Thermo Fisher).  The cells were centrifuged for 5 minutes at 200xg at 4 oC.  Next, after aspirating the quench buffer, cells were lysed and processed using the RNeasy plus mini kit (Qiagen) following the manufacture protocol with minor modifications, including adding ß-mercaptoethanol to the RLT lysis buffer, washing with the RWT Buffer (Qiagen #1067933) instead of RW1 buffer, and application of the on-column DNaseI digestion (Qiagen #79256). The RNA was eluted in RNase-free water and quantified using Nanodrop. Same amounts of RNA were aliquoted before the streptavidin pull down of the RNA for downstream applications.  To enrich for biotinylated RNAs, Dynabeads™ MyOne™ Streptavidin C1 magnetic beads (Thermo Fisher) were used with 10 μl of beads per 25 μg of RNA. The beads were washed 3 times in B&W buffer (5 mM Tris-HCl, pH = 7.5, 0.5 mM EDTA, 1 M NaCl, 0.1% TWEEN 20 (Sigma Aldrich)), followed by 2 times in Solution A (0.1 M NaOH and 0.05 M NaCl), and 1 time in Solution B (0.1 M NaCl). Beads were then incubated with purified RNA (25-50ug) in 0.05M NaCl at 4oC for 2 hours with gentle agitations. Following the incubation step, beads were washed 3 times with B&W buffer, followed by the elution of RNA from the beads by adding the TRI Reagent (Sigma-Aldrich T9424) on the beads and extracting according to the manufacturer’s protocol.
The libraries were prepared by using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® with ribosome-depleted and polyA+ selected RNA

value: FLAG-APEX2 tagged

value: Flp-in HEK293

tag: molecule subtype

value: ribosome-depleted RNA


title: MEDA17-P-T5-R1


title: MEDA17-P-T7-R5


title: MEDA17-C-T5-R5


title: MEDA17-C-T5-R4


title: MEDA17-C-T5-R3


title: HOTTIP-KO-DRIP-seq

value: peripheral blood

value: Human-derived acute myeloid leukemia cells

value: MOLM13 leukemia cells

value: Gene fusion KMT2A-MLLT3 (MLL-MLLT3; MLL-AF9)

value: HOTTIP-KO

tag: chip antibody

value: Anti-DNA-RNA Hybrid [S9.6] Antibody, Kerafast, Cat# ENH001


title: MEDA17-C-T5-R2

value: Five seedlings


title: MEDA17-C-T7-R6

value: Biological replicate 6


title: MEDA17-C-T5-R1


title: MEDA17-C-T5-R6


title: MEDA17-P-T3-R3

value: P. oligandrum

value: 3 days post treatment

value: Biological replicate 3


title: MEDA17-P-T3-R2

value: Biological replicate 2


title: MEDA17-P-T3-R6


title: MEDA17-P-T3-R5

value: Biological replicate 5


title: MEDA17-P-T3-R4

value: Biological replicate 4


title: MEDA17-C-T3-R6

value: A17 (Control)


title: MEDA17-C-T3-R5


title: MEDA17-C-T3-R4


title: MEDA17-C-T3-R3


title: MEDA17-P-T5-R4

value: 5 days post treatment


title: MEDA17-C-T3-R1

value: Biological replicate 1


title: MEDA17-C-T3-R2


title: MEDA17-P-T5-R2


title: MEDA17-P-T3-R1


title: NE_VB_M2

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

description:
scRNA
NE_VB_M2

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v3.1.0 with default settings
Reads were aligned to mm10 reference genome using Cell Ranger v3.1.0 with --expect-cells=5000
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with raw gene counts for all genes and samples

source_name: Whole Lung

extract_protocol:
Cells were sorted from lung single-cell digests after 24 hours of treatment
scRNA-seq libraries were generated in BU DOM Single Cell sequencing core facility and sequenced by BU Microarray and Sequencing Resource Core Facility according to 10x Genomics protocol

treatment_protocol: Mice were intratracheally treated with IgG saline, IgG E. coli, or anti-LIF E. coli for 24 hours

value: Lung

value: IgG E. coli

value: Pooled cells from sorted lung single-cell suspensions

tag: gender

value: Female

tag: age

value: 9 weeks


title: NE_VB_M1

description:
scRNA
NE_VB_M1

value: IgG saline


title: E. coli + Control IgG 6 h 3

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from lung epithelial cells of animal treated for 6h with intratracheal instillate of E. coli and control IgG antibody.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene10stmmentrezgcdf R package (version 17.0.0).

source_name: lung epithelial cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Life Technologies). RNA was further purified using the the Qiagen RNEasy kit with the optional DNAse treatment.

treatment_protocol: Mice received intratracheal instillations of vehicle (PBS) or Escherichia coli (10^6 CFU). Control IgG or anti-LIF specific IgG was included in the instillate.

tag: infection

value: E. coli

tag: antibody

value: Control IgG


title: E. coli + anti-LIF 6 h 1

description: Gene expression data from lung epithelial cells of animal treated for 6h with intratracheal instillate of E. coli and anti-LIF antibody.

value: anti-LIF


title: PBS + Control IgG 2

description: Gene expression data from lung epithelial cells of animal treated for 24h with intratracheal instillate of PBS and control IgG antibody.

value: PBS


title: E. coli + anti-LIF 6 h 2


title: vehicle only primed paw 3

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
adapter trimming using cutadapt v1.18
alignment to GRCm38 genome using STAR v2.6.1c
determination of raw counts using subread (v1.6.1) featureCounts
differential expression analysis using DESeq2 v1.24.0
Genome_build: GRCm38.93
Supplementary_files_format_and_content: tab-separated text containing rlog-normalized count data

source_name: collagenase-digested mouse paw

growth_protocol: Mice were housed in cages that were maintained in a room with temperature 22 ± 1°C and relative humidity 50–60% on a 12h light/dark cycle. Water and food were provided ad libitum. Fibroblast cell suspensions were prepared by gently rocking dissected and skin-flayed paws for 1 hour at 37°C in DMEM containing 2 mg/ml collagenase type IV (Worthington Biochemicals, LS004188). Cells derived from 2 to 3 paws were pooled and cells were then grown in DMEM (Gibco) supplemented with 10% heat-inactivated calf serum, (glucose (4.5 g/L), L-glutamine 2 mM), penicillin and streptomycin (1% each) antibiotics, and 1% fungizone (Amphotericin B, Sigma Aldrich). Medium was changed twice a week. Cells were cultured for 5 passages before harvesting.

extract_protocol:
RNA was extracted using RNAeasy kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) from 1 µg of RNA according to the manufacturer's instructions.

treatment_protocol: Left paw was injected with MSU crystals on day 0 and then again on day 9; right paw was injected with MSU crystals only on day 9. RNA was extracted on day 18 from both paws. I-BET-treated mice (in vivo) received 20mg/kg I-BET per day i.p., starting 1 day before the first MSU injection; control mice (vehicle only) received i.p. injections without I-BET. In vitro-treated cells were subjected to 1µM I-BET for 24h before harvesting.

value: BALB/c

tag: msu priming

value: primed

tag: ibet treatment

value: vehicle only

value: synovial fibroblasts


title: in vitro-treated primed paw 3

value: treated in vitro


title: PBS + Control IgG 6 h 2

description: Gene expression data from lung epithelial cells of animal treated for 6h with intratracheal instillate of PBS and control IgG antibody.


title: in vivo-treated primed paw 2

value: treated in vivo


title: in vivo-treated primed paw 3


title: in vivo-treated primed paw 1


title: E. coli + anti-LIF 6 h 3


title: vehicle only primed paw 2


title: E. coli + Control IgG 6 h 2


title: E. coli + Control IgG 3

description: Gene expression data from lung epithelial cells of animal treated for 24h with intratracheal instillate of E. coli and control IgG antibody.


title: PBS + Control IgG 3


title: PBS + Control IgG 6 h 3


title: E. coli + Control IgG 2


title: PBS + Control IgG 6 h 1


title: E. coli + Control IgG 1


title: NE_VB_M5

description:
scRNA
NE_VB_M5

tag: treatment

value: anti-LIF E. coli

tag: cell type


title: in vitro-treated primed paw 1


title: vehicle only primed paw 1


title: in vitro-treated primed paw 2


title: E. coli + Control IgG 6 h 1


title: E. coli + anti-LIF 1

description: Gene expression data from lung epithelial cells of animal treated for 24h with intratracheal instillate of E. coli and anti-LIF antibody.


title: PBS + Control IgG 1


title: E. coli + anti-LIF 3


title: vehicle only non-primed paw 3

value: non-primed


title: vehicle only non-primed paw 2


title: E. coli + anti-LIF 2


title: 14089X8 ISRCL3 6hr

city: Salt Lake City

first: Jinze

last: Li

state: UT

address: 15 North Medical Drive #1100

department: Pathology

institute: UNIVERSITY OF UTAH

data_processing:
Libraries were sequenced with Illumina HiSeq 50 Cycle Single-Read Sequencing version 4.
Sequenced reads were aligned to the mouse genome from Ensembl release 87 using STAR and assigned to genes using featureCounts
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCount output files combined into a single raw count matrix

source_name: Bone marrow

growth_protocol: Bone marrow was isolated from the femurs and tibias of B6, ISRCL4 and ISRCL3 mice. BMDMs were prepared by culturing bone marrow in petri dish for 7 days in L929 cell-conditioned media as a source of M-CSF until fully confluence.

extract_protocol:
TRIzol reagent and Zymo Research Direct-zol RNA MiniPrep kit
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold

treatment_protocol: Harvested BMDMs were replated in 24-well dishes at a density of 600,000 per milliliter in media containing 1% nutridoma. Cultures were then treated with B. burgdorferi for 0hr, 3hr or 6hr.

value: Bone marrow-derived macrophages

value: Borrelia burgdorferi 6hrs


title: 14089X9 ISRCL3 6hr


title: vehicle only non-primed paw 1


title: 14089X7 ISRCL3 6hr


title: 14089X2 ISRCL3 0hr


title: 14089X1 ISRCL3 0hr


title: 14089X4 ISRCL3 3hr

value: Borrelia burgdorferi 3hrs


title: 13886X24 ISRCL4 6hr

description: 13886X24_161222_D00294_0281_ACA7NLANXX_6


title: 14089X6 ISRCL3 3hr


title: 14089X3 ISRCL3 0hr


title: 13886X23 ISRCL4 6hr

description: 13886X23_161222_D00294_0281_ACA7NLANXX_6


title: 13886X22 ISRCL4 6hr

description: 13886X22_161222_D00294_0281_ACA7NLANXX_6


title: 14089X5 ISRCL3 3hr


title: 13886X17 ISRCL4 3hr

description: 13886X17_161222_D00294_0281_ACA7NLANXX_6


title: 13886X18 ISRCL4 3hr

description: 13886X18_161222_D00294_0281_ACA7NLANXX_6


title: 13886X19 ISRCL4 3hr

description: 13886X19_161222_D00294_0281_ACA7NLANXX_6


title: 13886X15 ISRCL4 0hr

description: 13886X15_161222_D00294_0281_ACA7NLANXX_6


title: 13886X16 ISRCL4 0hr

description: 13886X16_161222_D00294_0281_ACA7NLANXX_6


title: 13886X14 ISRCL4 0hr

description: 13886X14_161222_D00294_0281_ACA7NLANXX_6


title: 13886X20 ISRCL4 3hr

description: 13886X20_161222_D00294_0281_ACA7NLANXX_6


title: 13886X21 ISRCL4 6hr

description: 13886X21_161222_D00294_0281_ACA7NLANXX_6


title: 13886X13 ISRCL4 0hr

description: 13886X13_161222_D00294_0281_ACA7NLANXX_6


title: 13886X12 B6 6hr

description: 13886X12_161222_D00294_0281_ACA7NLANXX_5


title: 13886X10 B6 6hr

description: 13886X10_161222_D00294_0281_ACA7NLANXX_5


title: 13886X9 B6 6hr


title: 13886X8 B6 3hr


title: 13886X11 B6 6hr

description: 13886X11_161222_D00294_0281_ACA7NLANXX_5


title: 13886X7 B6 3hr


title: 13886X6 B6 3hr


title: 13886X5 B6 3hr


title: 13886X3 B6 0hr


title: 13886X1 B6 0hr


title: 13886X4 B6 0hr


title: 13886X2 B6 0hr


title: BCM4154adds132

city: Vitry-sur-Seine

first: Emmanuel

last: Spanakis

address: 1 Imp. des Ateliers

department: Oncology

institute: Sanofi

description:
K-975 (Kirin) batch CLC.CNA22.185.1 100mg/kg p.o 10mL/Kg EtOH/Solutol/injectable glucose pH3 (12.5/12.5/75%)
BCM4154add_K975_processed.txt

data_processing:
STAR aligner
Cufflink
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: Malignant pleural mesothelioma

growth_protocol: In vivo pharmacodynamic studies of the Kyowa Kirin K-975 (Tokyo, Japan) compound were performed in SCID mice inoculated subcutaneously into the right flank with 3 × 106 NCI-H226 cells. Mice bearing around 300 mm3 subcutaneous NCI-H226 tumors were randomly assigned to groups of 5 mice/group.

extract_protocol:
Fresh tumors were preserved in RNAlater and frozen at -200°C. Copurification of miRNA and total RNA was performed using a miRNeasy Mini Kit (QIAGEN, 217004). The RNA concentration and purity were evaluated with an ND-1000 spectrophotometer (NanoDrop, Thermo Fisher Scientific, Wilmington, DE, USA). Quality metrics were the RNA Integrity Number (RIN) and DV200 value (% of RNA fragments with a length ≥200nt). 100 ng total RNA per sample was used as input material for the library preparation.
100 ng total RNA per sample was used as input material for the library preparation. The libraries were prepared with the KAPA RNA HyperPrep Kit (Kapa Biosystems, KK8541) and KAPA Target Enrichment using the Kapa HyperCap V3.0 kit for Illumina following the manufacturer’s recommendations.

treatment_protocol: Mice were treated with either vehicle or K-975 compound at 30, 100, and 200 mg/kg single administration. Tumor perpendicular diameters were measured twice a week with a caliper, and tumor volume (V) was calculated according to the following equation: V (mm3) = (d2 (mm2) x D (mm))/2, where d is the smallest, and D the largest perpendicular tumor diameters.

value: cell line in SCID mouse

tag: compound

value: K-975 (Kirin)


title: BCM4154adds133


title: BCM4154adds126

description:
K-975 (Kirin) batch CLC.CNA22.185.1 200mg/kg p.o 20mL/Kg EtOH/Solutol/injectable glucose pH3 (12.5/12.5/75%)
BCM4154add_K975_processed.txt


title: BCM4154adds131


title: BCM4154adds139

description:
K-975 (Kirin) batch CLC.CNA22.185.1 30mg/kg p.o 10mL/Kg EtOH/Solutol/injectable glucose pH3 (12.5/12.5/75%)
BCM4154add_K975_processed.txt


title: BCM4154adds138


title: BCM4154adds134


title: BCM4154adds136


title: BCM4154adds129


title: BCM4154adds127


title: BCM4154adds135


title: BCM4154adds130


title: BCM4154adds120

description:
Control 24h
BCM4154add_K975_processed.txt


title: BCM4154adds118


title: BCM4154adds122

description:
Vehicle K-975 (Kirin) 20mL/kg p.o EtOH/Solutol/injectable glucose pH3 (12.5/12.5/75%)
BCM4154add_K975_processed.txt

value: Vehicle


title: BCM4154adds119


title: BCM4154adds125


title: BCM4154adds124


title: BCM4154adds100


title: BCM4154adds117


title: BCM4154adds116


title: BCM4154adds099


title: BCM4154adds137


title: BCM4154adds128


title: BCM4154adds140


title: BCM4154adds097


title: BCM4154adds098


title: BCM4154adds096


title: BCM4154adds123


title: BCM4154adds095


title: BCM4154adds093


title: BCM4154adds082


title: BCM4154adds081


title: BCM4154adds090


title: BCM4154adds087


title: BCM4154adds088


title: BCM4154adds084


title: BCM4154adds083


title: BCM4154adds064


title: BCM4154adds094


title: BCM4154adds091


title: BCM4154adds062


title: BCM4154adds059


title: BCM4154adds065


title: BCM4154adds063


title: BCM4154adds061


title: BCM4154adds089


title: BCM4154adds057


title: BCM4154adds092


title: BCM4154adds056


title: BCM4154adds051


title: BCM4154adds052


title: BCM4154adds055


title: BCM4154adds058


title: BCM4154adds054


title: BCM4154adds086


title: BCM4154adds085


title: BCM4154adds049


title: BCM4154adds060


title: BCM4154adds048


title: BCM4154adds047


title: BCM4154adds045

description:
Control 3h-6h
BCM4154add_K975_processed.txt


title: BCM4154adds044


title: BCM4154adds041


title: BCM4154adds042


title: BCM4154adds043


title: BCM4154adds025


title: BCM4154adds023


title: BCM4154adds021


title: BCM4154adds053


title: BCM4154adds018


title: BCM4154adds022


title: BCM4154adds019


title: BCM4154adds050


title: BCM4154adds013


title: BCM4154adds015


title: BCM4154adds012


title: BCM4154adds016


title: BCM4154adds014


title: BCM4154adds011


title: BCM4154adds020


title: BCM4154adds009

description:
Vehicle Kirin 20mL/kg p.o EtOH/Solutol/injectable glucose pH3 (12.5/12.5/75%)
BCM4154add_K975_processed.txt


title: BCM4154adds008


title: BCM4154adds007


title: BCM4154adds024


title: BCM4154adds046


title: BCM4154adds006


title: BCM4154adds005

description:
Control 1h
BCM4154add_K975_processed.txt


title: BCM4154adds017


title: BCM4154adds001


title: BCM4154adds004


title: BCM4154adds002


title: BCM3487s075

description:
Doxycycline till end (D0-D34)
BCM3487s075
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt

growth_protocol: In a pharmacodynamic study, human malignant mesothelioma MSTO-211H cells transfected with a doxycycline-dependent dn-TEAD2 construct were inoculated subcutaneously in 5 mice per group at a 3 × 106 cells dose mixed with Matrigel. The control groups received glucose plus doxycycline supplementation or glucose alone for the entire duration of the experiment (34 days). In a third group, implanted tumors were allowed to growth up to 300 mm3 under glucose supplementation for 19 days and were, then, treated with glucose plus doxycycline supplement until the end of the experiment (day 34). Despite a significant initial inhibition of growth by doxycycline, all tumors attained similar growth rates by day 26. Tumor perpendicular diameters were measured twice a week with a caliper, and tumor volume (V) was calculated according to the following equation: V (mm3) = (d2 (mm2) x D (mm))/2, where d is the smallest, and D the largest perpendicular tumor diameters.

treatment_protocol: Doxycycline (0.5mg/ml) and glucose (5%) were supplemented with drinking water.

value: dn-TEAD2 transfected cell line in SCID mouse

value: glucose + doxyxycline

value: MSTO-211H [TEAD2-dn]


title: BCM4154adds003


title: BCM3487s074

description:
Doxycycline till end (D0-D34)
BCM3487s074
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s073

description:
Doxycycline till end (D0-D34)
BCM3487s073
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s071

description:
Doxycycline till end (D0-D34)
BCM3487s071
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s072

description:
Doxycycline till end (D0-D34)
BCM3487s072
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s070

description:
Glucose 5% till ~300mm3 (D0-D19) then Doxycycline till end (D19-D34)
BCM3487s070
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM4154adds010


title: BCM3487s066

description:
Glucose 5% till ~300mm3 (D0-D19) then Doxycycline till end (D19-D34)
BCM3487s066
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s064

description:
Glucose 5% till end (D0-D34)
BCM3487s064
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt

value: glucose


title: BCM3487s063

description:
Glucose 5% till end (D0-D34)
BCM3487s063
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s069

description:
Glucose 5% till ~300mm3 (D0-D19) then Doxycycline till end (D19-D34)
BCM3487s069
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s062

description:
Glucose 5% till end (D0-D34)
BCM3487s062
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s061

description:
Glucose 5% till end (D0-D34)
BCM3487s061
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s067

description:
Glucose 5% till ~300mm3 (D0-D19) then Doxycycline till end (D19-D34)
BCM3487s067
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s065

description:
Glucose 5% till end (D0-D34)
BCM3487s065
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s068

description:
Glucose 5% till ~300mm3 (D0-D19) then Doxycycline till end (D19-D34)
BCM3487s068
BCM3487 AN1698 MSTO211H dnTEAD end processed.txt


title: BCM3487s015

description:
5% glucose till ~300mm3 then + doxyxycline for 96h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s015

growth_protocol: In a pharmacodynamic study, human malignant mesothelioma MSTO-211H cells transfected with a doxycycline-dependent dn-TEAD2 construct were inoculated subcutaneously at a 3 × 106 cells dose mixed with Matrigel. Implanted tumors were allowed to growth up to 300 mm3 under glucose supplementation and were sampled just before doxycycline supplementation (time 0, n=5), or after 24 (n=5), 96 (n=5), or 216 (n=4) hours of doxycycline supplementation (time points 1 to 3, respectively). Tumor perpendicular diameters were measured twice a week with a caliper, and tumor volume (V) was calculated according to the following equation: V (mm3) = (d2 (mm2) x D (mm))/2, where d is the smallest, and D the largest perpendicular tumor diameters.

extract_protocol:
Fresh tumors were preserved in RNAlater and frozen at -200°C. Copurification of miRNA and total RNA was performed using a miRNeasy Mini Kit (QIAGEN, 217004). The RNA concentration and purity were evaluated with an ND-1000 spectrophotometer (NanoDrop, Thermo Fisher Scientific, Wilmington, DE, USA). Quality metrics were the RNA Integrity Number (RIN) and DV200 value (% of RNA fragments with a length ≥200nt). 100 ng total RNA per sample was used as input material for the library preparation.
100 ng total RNA per sample was used as input material for the library preparation. The libraries were prepared with the KAPA RNA HyperPrep Kit (Kapa Biosystems, KK8541) and KAPA Target Enrichment using the Kapa HyperCap V3.0 kit for Illumina following the manufacturer’s recommendations.
Paired-end sequencing of the libraries was performed using the NextSeq 500 platform (Illumina, Inc., San Diego, CA).

treatment_protocol: Mice were divided into groups. Each group received drinking water supplemented with either doxycycline (0.5mg/ml) and 5% glucose or with 5% glucose only.


title: BCM3487s014

description:
5% glucose till ~300mm3 then + doxyxycline for 96h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s014


title: BCM3487s019

description:
5% glucose till ~300mm3 then + doxyxycline for 216h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s019


title: BCM3487s016

description:
5% glucose till ~300mm3 then + doxyxycline for 216h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s016


title: BCM3487s017

description:
5% glucose till ~300mm3 then + doxyxycline for 216h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s017


title: BCM3487s013

description:
5% glucose till ~300mm3 then + doxyxycline for 96h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s013


title: BCM3487s011

description:
5% glucose till ~300mm3 then + doxyxycline for 96h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s011


title: BCM3487s010

description:
5% glucose till ~300mm3 then + doxyxycline for 24h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s010


title: BCM3487s007

description:
5% glucose till ~300mm3 then + doxyxycline for 24h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s007


title: BCM3487s009

description:
5% glucose till ~300mm3 then + doxyxycline for 24h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s009


title: BCM3487s012

description:
5% glucose till ~300mm3 then + doxyxycline for 96h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s012


title: BCM3487s005

description:
5% glucose till ~300mm3 and sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s005


title: BCM3487s004

description:
5% glucose till ~300mm3 and sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s004


title: BCM3487s006

description:
5% glucose till ~300mm3 then + doxyxycline for 24h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s006


title: BCM3487s002

description:
5% glucose till ~300mm3 and sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s002


title: BCM3487s018

description:
5% glucose till ~300mm3 then + doxyxycline for 216h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s018


title: BCM3487s003

description:
5% glucose till ~300mm3 and sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s003


title: PN_121B donor 3 [Bulk RNA-seq]

city: Huddinge

first: Jenny

last: Mjösberg

state: Stockholm

address: Alfred Nobels allé 8

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

description: Gene_Raw_Count_Bulk_RNA-seq_in_vitro.txt

data_processing:
Pair-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh37.87 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.5.3)
Smart-seq2 single cell data downstream analysis were perfored using R package Seurat v3.2.3.
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.5.3) with Ensembl Known Gene models (version GRCh37.87) as reference annotations

source_name: human mucosal tissues

extract_protocol:
Tonsillar mononuclear cells (MNCs) were extracted by cutting the tonsil tissue into small pieces and rinsing with PBS (Sigma), followed by LymphoprepTM gradient centrifugation.
For bulk RNA-seq, the Takara kit SMART-seq v4 Ultra Low Input RNA was used, following the manufacturer’s instructions with slight modifications according to our sample requirements. We sorted 1000 cells  of the desired subsets following protocol’s recommendations). Subsequently, we modified the protocol by immediately adding to the mix 2 µL of 3´SMART-seq CDS Primer II A (12uM), described in the next step of the official protocol, and samples were frozen overnight at -80°C to ensure better lysis of the cells. The next day, samples were immediately incubated for 3 min at 72°C prior to the reverse transcription described in the SMART-seq v4 Ultra Low Input RNA, avoiding RNA degradation and obtaining better amplifications and quality of the final cDNA. No further modifications were applied to the subsequent protocol and validation was made using the Agilent 2100 Bioanalyser. Library preparation was performed using the Illumina Nextera DNA library Preparation kit with cDNA tagmentation (Illumina) and pooling dual-indexed libraries for dual-indexed sequencing (Nextera XT Index Kit, Illumina). Samples were sequenced on a NextSeq2000 sequencer (Illumina).

tag: diagnosis

value: Tonsil

tag: endoscopic inflammation status

tag: sampling location

value: human mucosal tissues


title: PN_231B donor 4 [Bulk RNA-seq]


title: PP_121B donor 3 [Bulk RNA-seq]


title: PN_121B donor 4 [Bulk RNA-seq]


title: PP_231B donor 4 [Bulk RNA-seq]


title: PP_121B donor 4 [Bulk RNA-seq]


title: PN_231B donor 1 [Bulk RNA-seq]


title: PN_231B donor 2 [Bulk RNA-seq]


title: PP_121B donor 1 [Bulk RNA-seq]


title: PP_231B donor 3 [Bulk RNA-seq]


title: PP_231B donor 2 [Bulk RNA-seq]


title: PP_121B donor 2 [Bulk RNA-seq]


title: P16_GI1_P009 [scRNA-seq]

description:
#1 Inflamed
Gene_Raw_Count_Single_Cell_RNA-seq_Smart-seq2.txt

source_name: large intestine

extract_protocol:
Non-inflamed biopsies from the large intestine were obtained from three tumor- screening patients and inflamed biopsies from the large intestine were obtained from three Crohn’s disease patients. Briefly, eight punch-biopsies per patients were collected and transported in wash buffer, consisting of Hank’s Balanced Salt Solution (HBSS) supplemented with antibiotics, fungizone and HEPES. Samples were processed within 1 h of biopsy retrieval. Wash buffer was removed and biopsies were enzymatically digested while stirring. The filtered cell suspension was washed by centrifugation and the total cell pellet was used for staining with fluorescence-labeled antibodies for FACS.
Samples were prepared using the SMART-Seq2 platform according to manufacturer’s instructions.

value: Crohn's disease

value: inflamed

value: large intestine

tag: age (y)


title: PP_231B donor 1 [Bulk RNA-seq]


title: P17_GI1_P009 [scRNA-seq]


title: PN_121B donor 2 [Bulk RNA-seq]


title: PN_121B donor 1 [Bulk RNA-seq]


title: P21_GI1_P009 [scRNA-seq]


title: P14_GI1_P009 [scRNA-seq]


title: P20_GI1_P009 [scRNA-seq]


title: BCM3487s001

description:
5% glucose till ~300mm3 and sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s001

tag: cell line

tag: time point


title: O20_GI1_P009 [scRNA-seq]


title: P19_GI1_P009 [scRNA-seq]


title: P18_GI1_P009 [scRNA-seq]


title: O21_GI1_P009 [scRNA-seq]


title: O19_GI1_P009 [scRNA-seq]


title: O18_GI1_P009 [scRNA-seq]


title: PN_231B donor 3 [Bulk RNA-seq]


title: O14_GI1_P009 [scRNA-seq]


title: N16_GI1_P009 [scRNA-seq]


title: N13_GI1_P009 [scRNA-seq]


title: O13_GI1_P009 [scRNA-seq]


title: O15_GI1_P009 [scRNA-seq]


title: N18_GI1_P009 [scRNA-seq]


title: N17_GI1_P009 [scRNA-seq]


title: N23_GI1_P009 [scRNA-seq]


title: M22_GI1_P009 [scRNA-seq]


title: N21_GI1_P009 [scRNA-seq]


title: BCM3487s008

description:
5% glucose till ~300mm3 then + doxyxycline for 24h before sampling
BCM3487_AN1497_MSTO211H_TEADdn_processed.txt
BCM3487s008


title: M23_GI1_P009 [scRNA-seq]


title: N24_GI1_P009 [scRNA-seq]


title: M21_GI1_P009 [scRNA-seq]


title: M18_GI1_P009 [scRNA-seq]


title: L13_GI1_P009 [scRNA-seq]


title: M13_GI1_P009 [scRNA-seq]


title: L16_GI1_P009 [scRNA-seq]


title: L14_GI1_P009 [scRNA-seq]


title: L17_GI1_P009 [scRNA-seq]


title: M14_GI1_P009 [scRNA-seq]


title: O16_GI1_P009 [scRNA-seq]


title: L18_GI1_P009 [scRNA-seq]


title: L21_GI1_P009 [scRNA-seq]


title: L23_GI1_P009 [scRNA-seq]


title: L24_GI1_P009 [scRNA-seq]


title: N19_GI1_P009 [scRNA-seq]


title: M24_GI1_P009 [scRNA-seq]


title: K23_GI1_P009 [scRNA-seq]


title: K22_GI1_P009 [scRNA-seq]


title: M19_GI1_P009 [scRNA-seq]


title: K18_GI1_P009 [scRNA-seq]


title: K24_GI1_P009 [scRNA-seq]


title: K20_GI1_P009 [scRNA-seq]


title: K19_GI1_P009 [scRNA-seq]


title: K17_GI1_P009 [scRNA-seq]


title: K13_GI1_P009 [scRNA-seq]


title: K15_GI1_P009 [scRNA-seq]


title: K16_GI1_P009 [scRNA-seq]


title: K14_GI1_P009 [scRNA-seq]


title: L19_GI1_P009 [scRNA-seq]


title: J19_GI1_P009 [scRNA-seq]


title: I21_GI1_P009 [scRNA-seq]


title: I23_GI1_P009 [scRNA-seq]


title: I22_GI1_P009 [scRNA-seq]


title: J20_GI1_P009 [scRNA-seq]


title: J16_GI1_P009 [scRNA-seq]


title: J15_GI1_P009 [scRNA-seq]


title: J14_GI1_P009 [scRNA-seq]


title: I19_GI1_P009 [scRNA-seq]


title: J18_GI1_P009 [scRNA-seq]


title: I20_GI1_P009 [scRNA-seq]


title: I18_GI1_P009 [scRNA-seq]


title: I17_GI1_P009 [scRNA-seq]


title: M15_GI1_P009 [scRNA-seq]


title: I13_GI1_P009 [scRNA-seq]


title: I15_GI1_P009 [scRNA-seq]


title: J13_GI1_P009 [scRNA-seq]


title: I16_GI1_P009 [scRNA-seq]


title: H18_GI1_P009 [scRNA-seq]


title: H16_GI1_P009 [scRNA-seq]


title: H15_GI1_P009 [scRNA-seq]


title: H17_GI1_P009 [scRNA-seq]


title: H20_GI1_P009 [scRNA-seq]


title: H22_GI1_P009 [scRNA-seq]


title: H23_GI1_P009 [scRNA-seq]


title: H19_GI1_P009 [scRNA-seq]


title: G24_GI1_P009 [scRNA-seq]


title: H24_GI1_P009 [scRNA-seq]


title: G23_GI1_P009 [scRNA-seq]


title: G21_GI1_P009 [scRNA-seq]


title: G19_GI1_P009 [scRNA-seq]


title: G13_GI1_P009 [scRNA-seq]


title: F13_GI1_P009 [scRNA-seq]


title: G15_GI1_P009 [scRNA-seq]


title: G14_GI1_P009 [scRNA-seq]


title: G16_GI1_P009 [scRNA-seq]


title: G22_GI1_P009 [scRNA-seq]


title: F15_GI1_P009 [scRNA-seq]


title: F16_GI1_P009 [scRNA-seq]


title: F17_GI1_P009 [scRNA-seq]


title: F19_GI1_P009 [scRNA-seq]


title: F20_GI1_P009 [scRNA-seq]


title: F24_GI1_P009 [scRNA-seq]


title: E24_GI1_P009 [scRNA-seq]


title: E23_GI1_P009 [scRNA-seq]


title: E20_GI1_P009 [scRNA-seq]


title: E21_GI1_P009 [scRNA-seq]


title: E16_GI1_P009 [scRNA-seq]


title: E19_GI1_P009 [scRNA-seq]


title: E15_GI1_P009 [scRNA-seq]


title: E14_GI1_P009 [scRNA-seq]


title: E13_GI1_P009 [scRNA-seq]


title: G17_GI1_P009 [scRNA-seq]


title: G20_GI1_P009 [scRNA-seq]


title: F14_GI1_P009 [scRNA-seq]


title: D13_GI1_P009 [scRNA-seq]


title: D14_GI1_P009 [scRNA-seq]


title: D16_GI1_P009 [scRNA-seq]


title: D15_GI1_P009 [scRNA-seq]


title: H13_GI1_P009 [scRNA-seq]


title: D17_GI1_P009 [scRNA-seq]


title: D18_GI1_P009 [scRNA-seq]


title: D20_GI1_P009 [scRNA-seq]


title: D19_GI1_P009 [scRNA-seq]


title: D22_GI1_P009 [scRNA-seq]


title: D24_GI1_P009 [scRNA-seq]


title: C23_GI1_P009 [scRNA-seq]


title: D23_GI1_P009 [scRNA-seq]


title: C22_GI1_P009 [scRNA-seq]


title: C21_GI1_P009 [scRNA-seq]


title: C20_GI1_P009 [scRNA-seq]


title: E17_GI1_P009 [scRNA-seq]


title: E18_GI1_P009 [scRNA-seq]


title: C18_GI1_P009 [scRNA-seq]


title: C19_GI1_P009 [scRNA-seq]


title: D21_GI1_P009 [scRNA-seq]


title: B17_GI1_P009 [scRNA-seq]


title: C16_GI1_P009 [scRNA-seq]


title: B15_GI1_P009 [scRNA-seq]


title: B19_GI1_P009 [scRNA-seq]


title: B16_GI1_P009 [scRNA-seq]


title: B22_GI1_P009 [scRNA-seq]


title: A23_GI1_P009 [scRNA-seq]


title: B21_GI1_P009 [scRNA-seq]


title: C17_GI1_P009 [scRNA-seq]


title: B20_GI1_P009 [scRNA-seq]


title: A19_GI1_P009 [scRNA-seq]


title: A22_GI1_P009 [scRNA-seq]


title: A17_GI1_P009 [scRNA-seq]


title: A16_GI1_P009 [scRNA-seq]


title: A20_GI1_P009 [scRNA-seq]


title: A14_GI1_P009 [scRNA-seq]


title: A15_GI1_P009 [scRNA-seq]


title: A13_GI1_P009 [scRNA-seq]


title: P13_GI1_P006 [scRNA-seq]


title: P14_GI1_P006 [scRNA-seq]