title: fecul-B_ery-t30_r1_fc_r_v13

value: 5ug/ml Erythromycin for 30 minutes at 37˚C

value: fecul-B_ery-t30_r1  culture was grown anaerobically at 37˚C and diluted with fresh MCDA media at a 1:10 ratio  24 hours prior treatment. Erythromycin  (5µg/ml) for 30 minutes.

value: using PAN-Prokaryote Ribopool ( sitoolsbiotech REF dp-K024-000003)


title: NEU_DEL_NI_02

status: Public on Mar 24 2023

type: SRA

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

country: Denmark

institute: Technical University of Denmark

description: single cell RNA sequencing analysis of infected or bystander (noninfected) neutrophils during M. marinum infection

library_source: transcriptomic

data_processing:
Demultipexing and alignment of reads with CellRanger v2.1.1 for replicates 01 and v3.1.0 for replicates 02. Data is paired and pooled on 4 lanes.
Cells with very low counts of reads and genes (2-300) dependent on individual sample distribution, and mitonchondiral gene load > 10 % were discarded.
Contaminating cell types were removed from the merged replicates before merging all samples all done w. Seurat v3.
Genome_build: mm10 (replicates 01) and mm10-2.1.0 (replicates 02)
Supplementary_files_format_and_content: tsv.gz & mtx.gz

molecule: polyA RNA

organism: Mus musculus

source_name: Neutrophils

growth_protocol: Bacteria (WT and dRD1 M. marinum) were inoculated from frozen stocks and grown at 30°C in 7H9 culture medium until late log phase.

extract_protocol:
Two independent experiments were performed. For each experiment 14 to 15 tails (i.e. infected tissue) per group were collected, pooled and digested at two weeks post infection. Cell surface markers were stained with antibodies. Live infected neutrophils (CD45+Ly6G+CD11b+Wasabi+) or live uninfected neutrophils (CD45+Ly6G+CD11b+Wasabi-) were sorted by FACS in PBS supplemented with 1% BSA using a FACS ARIA Fusion (BD Biosciences).
Single cell RNA-sequencing libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics, PN-1000092) and Chromium Chip B Single Cell Kit (PN-1000074) with the Chromium Controller & Next GEM Accessory Kit (10x Genomics, PN-120223). Library quality control and quantification were performed using a KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems, KK4873) and the 2100 Bioanalyzer equipped with a High Sensitivity DNA kit (Agilent, 5067-4626).

treatment_protocol: C57Bl/6JRj female 8 weeks old mice were infected via tail vein injections with 5 x 10^7 bacteria per mouse, in a total volume of 200 µL.

tag: infection

value: Not Infected

tag: genotype

value: dRD1 M. marinum M-strain

tag: strain


title: NEU_DEL_INF_02

value: Infected


title: fecul-B_ctr_r1_fc_r_v13

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Adapter and quality trimming with the bbduk program of the BBTools suite, with options {qtrim=r, ktrim=r, hdist=3, hdist2=2, K=20, mink=14, trimq=16, minlen=30, maq=16}, using BBTools default adapter set and polyG or polyA sequences for short reads.
Deduplication of reads with both identical unique molecular identifier (UMI) and insert sequence using the dedupe program of the BBTools suite with its default parameters.
UMI sequences found in the first eight bases of each read were extracted using UMI-tools (version 1) with default options (using --bc-pattern NNNNNNNN).
Alignment was performed with the bbmap program of the BBTools suite, with the {32bit=t -da -eoom k=11 strictmaxindel=10 intronlen=0 t=16 trd=t minid=0.94 nzo=t} parameters. Alignment files were sorted and indexed with SAMtools.
Deduplication based on UMIs was then performed with UMI-tools (version 1) with options { --soft-clip-threshold 1 --edit-distance 2 --method unique}.
In selected samples, a dual undex strategy was used (sequencing runs v17). In brief, in addition of the Illumina indexes with dedicated reads used in HT-5Pseq, an additional index sequence is added before the UMI sequence. This is introduced during the ssRNA ligation space using anoligo with the following structure Illumina compatible-CCCCCC-NNNNNNNN. Please see dual_index_demultiplexing.txt for details on demultiplexing strategy for those samples.
Bedgraphs for read 5' positions for forward (fwd) and reverse (rev) strands were generated with BEDTools genomecov program with options {-bg -strand [+/-] -5}.
Assembly: The genome used for alignment is indicated in the processed file names with the G-xxxx patterns.  Those correspond to the NCBI accessions and builds indicated in the Supplementary file.
Assembly: Reference indiced for individual bacterial species and custom mixtures were built with the bbmap program of the BBTools suite, with default options (and k=10).
Supplementary files format and content: Processed files are bedgraphs containing read 5' counts on reverse (_rev) and forward (_fwd) strands of genomes indicated with _G-xxxx pattern. The genomes corresponding to each pattern are described in the genome build entry above.

molecule: total RNA

organism: human feces metagenome

growth_protocol: Bacteria were grown according to their requirements. Overnight Cultures were diluted to OD600 0.05-0.07, growth was continued and cells were harvested in log-phase by centrifugation. Resulting pellet was shock-frozen in Dry ice/Ethanol bath and stored for RNA analysis

extract_protocol:
Microbial cell pellets were resuspended in equal volume of LET (25 mM Tris pH 8.0, 100 mM LiCl, 20 mM EDTA) and water saturated Phenol pH 6.6 (Thermo Fisher),  lysed with acid washed glass beads (Sigma-Aldrich) and vortexing for three minutes in MultiMixer. Lysates were supplemented  with equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water, l two-minute vortexing followed by centrifugation. Resulting aqueous phase was purified in two steps using phenol-chloroform isoamyl alcohol (25:24:1) followed by chloroform. After centrifugation, the clean aqueous phase was precipitated with sodium acetate-ethanol.
Standard and random fragmented 5PSeq libraries were generated as described in PMID: 26046441 with minor modifications using 150-9000ng total RNA as an input. To prepare random fragmented samples (negative controls), ribosomal RNA was depleted from DNA-free RNA and subsequent fragmented by incubating five minutes at 80 ̊C in fragmentation buffer (40mM Tris Acetate pH 8.1, 100mM KOAc and 30mM MgOAc). Reaction was purified using 2 volumes of RNACleanXP beads (Beckman Coulter) as recommended by the manufacturer. Free 5’OH sites were re-phosphorylated using 5 Units of T4 Polynucleotide kinase (PNK, NEB) and incubated at 37 ̊C for 60 minutes as recommended by the manufacturer. Re-phosphorylated fragmented RNA was purified using Phenol:Chloroform: Isoamyl Alcohol (24:25:1), followed by sodium acetate-ethanol precipitation. From this step forward, procedures for random fragmented and standard 5PSeq library preparation merge. RNA was Ligated to either rP5_RND or rP5_RNA oligo (specified in characteristics protocol).    containing unique molecular identifiers). Ribosomal RNA was depleted using Ribozero rRNA removal kit (Illumina) suitable for Bacteria and Yeast. rRNA depleted sample was purified using 1.8V of Ampure beads (Abcam), fragmented using heat (80˚C) for 5 min in 5x Fragmentation Buffer (200mM Tris Acetate pH 8.1,500mM KOAc,150mM MgOAc) and reverse transcribed using random hexamers to prime. Resulting cDNA was bound to streptavidin beads (M-280), subjected to enzymatic reactions of DNA end repair, fill-in of adenine to 5’ protruding ends of DNA fragments using Klenow Fragment (NEB). Common adaptor (P7-MPX) was ligated and 5PSeq Libraries were amplified by PCR (15- 17 cycles). Purified samples were quantified using Qubit (Thermo Fisher), library size was estimated from bioanalyzer traces. 5PSeq Libraries were pooled by mixing equal amounts of each sample, following enrichment of fragments of the length between 300-500nt.   HT-5PSeq Libraries were generated as recently described (bioRxiv 2020.06.22.165134; doi: https://doi.org/10.1101/2020.06.22.165134). In brief, DNA-free RNA was ligated with RNA oligos containing unique molecular identifiers. Ligated RNA was reverse transcribed priming with oligos containing a random hexamer and an Illumina compatible region. RNA was eliminated by addition of NaOH. Ribosomal RNA was depleted by adding in-house rRNA DNA oligo depletion mixes (table 2) to the cDNA and performing a duplex-specific nuclease (DSN, Evrogen) treatment. rRNA depleted cDNA was PCR amplified (15-17 cycles). Depletion of ribosomal RNA with Ribozero Illumina (for bacteria and yeast) was done after the single-stranded RNA ligation step. Ribosomal depleted RNA was purified and reverse transcribed using the same oligos as stated above, and then amplified by PCR. Libraries were quantified by fluorescence (Qubit, Thermo Fisher), size estimated using an Agilent Bioanalyzer and sequence using a NextSeq500 Illumina sequencer.
other: 5PSeq that captures  transcripts with free 5' phospahte (without cap)

treatment_protocol: As for Chloramphenicol (CAM) treatment, Bacterial cells were incubated with Chloramphenicol (100µg/ml final) for 5 minutes at 37˚C with aeration and harvested at 4˚C on ice supplemented with Chloramphenicol (~100µg/ml final).   Mupirocin (MUP) was added to bacterial culture at a final concentration of 65µg/ml and incubated for 10 minutes at 37˚C with aeration.   Cultures for stationary growth phase samples were inoculated with single colony and harvested at indicated times post-inoculation.   Salt stress samples were generated as described in PMID: 28290514 with minor modifications Salt stress was initiated by mixing equal volumes of bacterial growth culture and 2M NaCl (~5.8% NaCl). Bacterial cells were exposed to salt stress for 10 minutes at room temperature and harvested by centrifugation.   Cultures for stationary growth phase samples were inoculated with single colony and harvested at indicated times post-inoculation.   Heat shock experiments were setup the following. Lactobacillus plantarum (ATCC 8014) growth culture was harvested by centrifugation and heat shock was induced by resuspending cell pellet in prewarmed broth media following 15-minute incubation at 60˚C.   To generate low nutrient samples, actively growing Lactobacillus plantarum (ATCC 8014) culture was harvested by centrifugation. Low nutrient stress was induced for 15 minutes beginning with excessive washing of the cell pellet with Low nutrient media (0.5x LB broth), followed by centrifugation. Washed cell pellet was resuspended in 0.5x LB broth, incubated at 37˚C for the remaining time.   Polyribosome fractions were generated as described in PMID: 27146487 with minor modifications. For short, exponentially grown bacterial cells were harvested by centrifugation (5 minutes) at 4˚C on ice supplemented with 100µg/ml Chloramphenicol. Lysis was done in 1xTN buffer (50mM TRIS/HCl pH 7.4,150mM NaCl, 1mM DTT, 100μg/ml CAM and Complete EDTA Free Protease inhibitor tablet) using glass beads and of vortexing (2minutes) followed by resting of sample on ice (5 minutes).  Vortexing/resting cycle was repeated two more times. Lysate was cleared by centrifugation at 1500g for 5 minutes at 4˚C. Resulting supernatant was loaded on to a 15-50% sucrose gradient with a 80% cushion and sedimentation was accomplished by ultracentrifugation for 90 minutes at 36,000rpm. Fractions were collected and A254 value was monitored. Subsequently, RNA was extracted from sucrose fractions by adding equal volumes of phenol/chloroform isoamyl alcohol pH 4.5 (25:24:1) and nuclease free water followed by 2-minute vortexing and centrifugation. Aqueous phase was further cleaned up by the addition of Chloroform, vortexing and centrifugation. Resulting aqueous phase was sodium acetate-ethanol precipitated.

tag: treatment

value: Untreated

tag: culture conditions

value: fecul-B_ctr_r1 culture was grown anaerobically at 37˚C and diluted with fresh MCDA media at a 1:10 ratio  24 hours prior harvesting.

tag: library protocol

tag: ribosomal rna depletion strategy


title: fecul-B_dox-t05_r1_fc_r_v13

value: 5ug/ml Doxycyclin for 5 minutes at 37˚C

value: fecul-B_dox-t05_r1 culture was grown anaerobically at 37˚C and diluted with fresh MCDA media at a 1:10 ratio  24 hours prior treatment. Doxycyclin  (5µg/ml) for 5 minutes.


title: afin_cam_r2_s_o_v15

organism: Alistipes finegoldii

source_name: Liquid culture of Alistipes finegoldii (DSM 17242)

value: 100ug/ml Chloramphenicol for 10 minutes at 37˚C

value: afin_cam_r2  was anaerobically cultured in GAM Broth (HyServe)  at 37˚C and split 24 hours prior treatments and Chloramphenicol was added to culture for 10 minutes.

value: in-house Bacterial rRNA Depletion MIX for Cultures , oVP670


title: NEU_WT_NI_02

value: Wild-type M. marinum M-strain


title: fecul-B_cam-t30_r1_fc_r_v13

value: 80ug/ml Chloramphenicol for 30 minutes at 37˚C

value: fecul-B_cam-t30_r1 culture was grown anaerobically at 37˚C and diluted with fresh MCDA media at a 1:10 ratio  24 hours prior treatment. Chloramphenicol (80µg/ml) for 30 minutes.


title: fecul-B_cam-t05_r1_fc_r_v13

value: 80ug/ml Chloramphenicol for 5 minutes at 37˚C

value: fecul-B_cam-t05_r1 culture was grown anaerobically at 37˚C and diluted with fresh MCDA media at a 1:10 ratio  24 hours prior treatment. Chloramphenicol (80µg/ml) for 5 minutes.


title: 02_SKM1-DMSO_BRD4

city: North Chicago

first: Josh

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

country: USA

institute: AbbVie Inc.

library_source: genomic

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the human genome (hg19) using the BWA algorithm
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated from BedGraph to BigWig. Scores represent peak density.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: SKM-1 cells were grown in 10%FBS RPMI 1640

extract_protocol:
Lysates were clarified from sonicated, fixed cell pellets and protein-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

treatment_protocol: Cells were treated with indicated inhibitors 6 hrs or DMSO as vehicle control

tag: chip antibody

tag: cell line

value: SKM-1 adult acute myeloid leukemia cell line

tag: agent

value: DMSO 6 hrs


title: 01_SKM1-DMSO_H3K27Ac


title: afin_cam_r1_s_o_v15

value: afin_cam_r1 was anaerobically cultured in GAM Broth (HyServe)  at 37˚C and split 24 hours prior treatments and Chloramphenicol was added to culture for 10 minutes.


title: RNA-seq siNT mESC Replicate 2

city: Boston

first: Claudia

middle: A

last: Mimoso

state: MA

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

description:
211012_mm10_mESC_RNAseq_DepthNorm_sorted_NT_N4_F.bedGraph
211012_mm10_mESC_RNAseq_DepthNorm_sorted_NT_N4_R.bedGraph

data_processing:
Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 120bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
Reads were first mapped to the dm6 version of the Drosophila genome using STAR 2.7.31. Reads not mapping to the spike genome were then used for alignment to mm10/hg38 using parameters --quantMode TranscriptomeSAM GeneCounts --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Duplicates were also removed using STAR.
Stranded coverage bedGraph files were generated from deduplicated BAM files using STAR.  For siRNA control and RRP40 KD conditions, bedGraphs were depth normalized using normalize_bedGraph
BedGraph files were converted to the bigWig format, and merged bedGraphs for each experimental condition were generated using bigWigMerge (UCSC tools).
Assembly: mm10 (mESC); hg38 (HEK293T)
Supplementary files format and content: bedGraph

source_name: F121-9 wt mESCs

growth_protocol: mESCs were cultured on gelatin in KnockOut DMEM (ThermoFisher, 10829018), supplemented with 15% KO serum replacement (ThermoFisher, 10828028), 1X penicillin-streptomycin (MP, TMS-005-C), 1X non-essential amino acids (MP, TMS-001-C), 1% b-ME (MP, ES-007-E), 1X GlutaMAX (ThermoFisher, 35050061), 1000 U/ml LIF (Cell Guidance Systems, GFM200), 1 µM MEK inhibitor (Stemgent, PD0325901), and 3 µM GSK3 inhibitor (Stemgent, CHIR99021) mESCs were fed daily and passaged every two days. HEK293Ts were cultured in DMEM (VWR, 45000-312) with 10% FBS (Thermo, 1600044). mESCs and HEK293Ts were cultured at 37°C with 5% CO2.

extract_protocol:
RNA was extracted in Trizol and purified.
Libraries were generated with the llumina TruSeq Stranded Total RNA kit using standard protocols.

treatment_protocol: See individual samples.

value: F121-9 wt mESCs

tag: cell type

value: Mouse embryonic stem cells

value: WT

value: Non-targeting siRNA control


title: kdrl:GFP+, mrc1a.125:GFP+ 72 hpf, rep2

status: Public on Mar 23 2023

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: Any cells from whole embryos that were GFP + and mCherry +

library_source: transcriptomic single cell

data_processing:
the inDrops single-cell RNA-seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation.
Assembly: GRCz11
Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode

organism: Danio rerio

source_name: kdrl:GFP, mrc1a.125:GFP transgenic zebrafish embryos (wild-type)

growth_protocol: Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized, filtered, and sorted using FACS into PBS, collecting at least 25,000 cells.

extract_protocol:
Approximately 3,000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method (Zilionis et al., 2017). Libraries were prepared for sequencing as previously described.
Libraries were prepared as previously described (Zilionis et al., 2017) and sequenced on an Illumina Hiseq 2500
Single cell RNA-seq (inDrops)

treatment_protocol: No treatments

tag: tissue

value: embryos

value: wild-type


title: Whole_tail, 72 hpf

description: All cells from embryonic tail tissues

source_name: transgenic zebrafish embryos (wild-type)

growth_protocol: Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension, tail tissues were then homogenized, filtered, and viable cells sorted using live-dead staining FACS into PBS, collecting at least 25,000 cells.

extract_protocol:
Approximately 5,000 cells were encapsulated using the inDrops method (Zilionis et al., 2017). Libraries were prepared for sequencing as previously described.
Libraries were prepared as previously described (Zilionis et al., 2017) and sequenced on an Illumina Hiseq 2500
Single cell RNA-seq (inDrops)

tag: developmental stage

value: 72 hpf


title: kdrl:GFP+, mrc1a.125:GFP+ 72 hpf, rep1


title: kdrl:GFP+, adult kidney

description: Any cells from adult kidneys that were GFP +

source_name: kdrl:GFP transgenic zebrafish adult kidney (wild-type)

growth_protocol: Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer.  Adult kidneys were dissected then homogenized, filtered, and sorted using FACS into PBS, collecting at least 25,000 cells.

extract_protocol:
Approximately 2,000-3,000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method (Zilionis et al., 2017). Libraries were prepared for sequencing as previously described.
Libraries were prepared as previously described (Zilionis et al., 2017) and sequenced on an Illumina Hiseq 2500
Single cell RNA-seq (inDrops)

value: adult

value: kidney


title: kdrl:mCherry+, adult kidney, rep2

description: Any cells from adult kidneys that were mCherry +

source_name: kdrl:mCherry transgenic zebrafish adult kidney (wild-type)


title: kdrl:mCherry+, adult kidney, rep1


title: WS_E_7_1

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

data_processing:
The sequencing was performed at BGI-Shenzhen using BGISEQ-500. The sequencing data was filtered using SOAPnuke (v1.5.2) software.
The processed FASTQ files were mapped to the human transcriptome and genome using HISAT2 (v2.0.4).
The genome version was GRCh38, with annotations from Bowtie2 (v2.2.5).
Expression level of the gene was calculated by RSEM (v1.2.12) software.
The set of differentially expressed genes identified from pairwise comparisons was identified using DEseq2 (v1.4.5) package (BGI, Wuhan, China). The number of reads per kilobase per million reads (RPKM) method was used to calculate the modification levels of unique genes. Significantly differentially expressed genes were defined as ones with at least 0.3 FPKM level of expression in at least one of the conditions and a q-value less than 0.05 by Bonferroni test. KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed genes was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test.
Assembly: NCBI: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: neural stem cells

growth_protocol: The cells were cultured in StemPro NSC SFM (ThermoFisher Scientific, cat. No. A1050901) and kept in a 37°C incubator with a humidified.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Kit (QIAGEN, 74104) following manufacturer’s instructions. Samples were sent to BGI, Wu Han, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 24M reads of 50bp per sample
Library preparation was conducted at BGI, Shenzhen, China, following the guide of the standard protocol.
Library preparation (BGISEQ-500RS High-throughput sequencing kit, PE50, V3.0, MGI Tech Co, Ltd, Shenzhen, China), hybridization and sequencing were performed according to the manufacturer's standard procedure provided by BGI (BGI-Shenzhen).

treatment_protocol: All iNSCs lines were seeded into Geltrex coated 24 well plates in NSC medium containing 0.1 mg/ml Sodium Pyruvate and 0.05 mg/ml uridine at a density of approximately 100,000 cells per well and the day was recorded as day -1 (D-1). At day 0 (D0), DNA was extracted from one well of each plate using the QIAGEN DNeasy Blood and Tissue Kit (QIAGEN, cat. no. 69504) in accordance with manufacturers protocol. The medium was then changed into NSC medium containing 50 ng/ml EtBr and supplemented with 0.1 mg/ml SP and 0.05 mg/ml uridine. The cells were kept in medium with EtBr for 7 days, with a medium change every two days. After 7 days, the EtBr medium was removed, the cells were washed with 2 ml DPBS without Calcium and Magnesium (DPBS-/-) and NSC medium supplemented with only SP and uridine was added. The cells were kept in this medium for 14 days (until D21), with changes of medium every two days. DNA was extracted from one well of each plate every day from D0 to D21 using QIAamp DNA Mini Kit (Qiange, cat. no. 51304) and stored at -20°C. For each cell line/clone, untreated control plates were studied in parallel, and DNA extracted every 4 days (D0, D4, D8, D12, D16 and D20).

value: iPSC-derived neural stem cells

value: POLG mutate (homozygous for c.2243G>C; p.W748S)


title: WS_E_7_2


title: WS_E_7_3


title: WS_E_21_3


title: NEU_WT_INF_02

value: Infected

value: Wild-type M. marinum M-strain


title: WS_E_21_1


title: WS_C_7_2


title: WS_C_0_3


title: WS_C_0_1


title: WS_C_21_3


title: WS_C_7_3


title: WS_C_21_1


title: WS_C_21_2


title: WS_E_21_2


title: CT_FE_7_2

value: wild type


title: CT_FE_21_1


title: CT_FC_7_2


title: CT_FE_21_2


title: CT_FC_7_3


title: CT_FE_7_1


title: CT_FC_21_3


title: CT_FE_21_3


title: CT_FC_21_2


title: CT_FC_21_1


title: CT_AE_7_2


title: CT_AE_7_3


title: CT_FC_0_2


title: CT_FC_0_1


title: CT_FC_0_3


title: WS_C_7_1


title: WS_C_0_2


title: CT_AE_21_3


title: CT_AE_7_1


title: CT_FE_7_3


title: CT_AE_21_1


title: CT_AC_7_3


title: CT_AC_21_3


title: CT_AE_21_2


title: CT_FC_7_1


title: CT_AC_21_1


title: CT_AC_7_1


title: CT_AC_7_2


title: CT_AC_21_2


title: CT_AC_0_3


title: CT_AC_0_1


title: CP_E_7_3

value: POLG mutate (heterozygous c.1399G>A/c.2243G>C; p.A467T/W748S)


title: CP_E_7_2


title: CP_E_21_3


title: CP_C_7_3


title: CP_E_21_1


title: CP_C_7_1


title: CT_AC_0_2


title: CP_C_21_2


title: CP_C_21_1


title: CP_C_7_2


title: CP_C_0_3


title: CP_C_0_2


title: CP_E_21_2


title: CP_E_7_1


title: CP_C_0_1


title: OCT-4A+1

type: RNA

city: Guangzhou

first: hong

last: hong

address: No.56, Lingyuan West Road

country: China

institute: Hospital of Stomatology,,Sun Yat-sen University

description: Gene expression in human dental pulp stem cells in OCT4A- overexpressing group

hyb_protocol: The labeled lnRNAs and mRNAs were hybridized onto the Arraystar Human LncRNA Microarray V3 (Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: A series of data processing including quantile normalization were performed using the R software limma package. Differentially expressed lncRNAs and mRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

label_protocol: Total RNA from each sample was treated with Rnase R to enrich lncRNA and mRNA. The enriched lncRNA  and mRNAwas then amplified and transcribed into fluorescent lncRNA and mRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol

growth_protocol: hDPSCs were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Rockford, USA) with 20% fetal bovine serum (FBS; Gibco, Australia), and incubated at 37 ℃ in 5% CO2. Cells from passages 3 to 5 were used in the following experiments.

extract_protocol: The extraction of total RNA from  OCT4A-overexpressing and vector hDPSCs using the Trizol reagent (Invitrogen, USA) following the manufacturer's recommendations.RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were labeled, purified and amplified. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner.

treatment_protocol: For OCT4A overexpression, the coding domain sequence region of the OCT4A gene was amplified and cloned into a replication-deficient lentivector (GenePharma, China) carrying a green fluorescent protein (GFP) reporter gene.hDPSCs  were transfected with OCT4A- overexpressing vector or empyt vector.

value: human dental pulp stem cells

value: dental pulp

tag: age

value: 18y to 25y


title: Control-3 [NC]

description: Gene expression in human dental pulp stem cells in vector group

value: control


title: OCT-4A+2

source_name: human dental pulp stem cells in OCT4A- overexpressing group


title: Control-1

source_name: human dental pulp stem cells in vector group


title: OCT-4A+3


title: R5-2

city: Hefei

first: Longlong

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

department: School of Agronomy

institute: Anhui Agricultural University

data_processing:
Paired-end reads were pre-processed by fastp (0.22.0).
High-quality reads were mapped to the L. japonicus v3.0 genome (http://www.kazusa.or.jp/lotus/) using HISAT2 v.2.0.543 with default parameters.
Aligned reads were assigned to annotated genomic features by FeatureCounts program from Rsubread package (1.32.4) to generate reads count matrices, and FPKM (fragments per kilobase of transcript per million mapped reads) values representing the expression level were calculated.
Transcripts with low reads count across all samples were filtered out.
Genome_build: MG-20 V3.0
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM values for every gene and every sample

organism: Lotus japonicus

source_name: Root nodule

extract_protocol:
Total RNA was extracted using a TransZol Plant kit (TransGen Biotech, China) based on the manufacturer’s protocol.
RNA libraries were prepared using a NEB Next Ultra II RNA Library Prep Kit (New England Biolabs).

value: Root nodule

value: Removal of 10 mM KNO3 for 5 days


title: R5-3


title: CP_C_21_3


title: Control-2


title: JU1088 strain; PAR1 treatment; rep 3

city: Atlanta

first: Avery

middle: Davis

last: Bell

state: GA

address: North Avenue

department: School of Biological Sciences

institute: Georgia Institute of Technology

description:
library fragment length information provided to Salmon - fldMean: 335.8493047; fldSD: 78.93783888
AP01-58

data_processing:
Basecalling, fastq generation, and de-multiplexing were performed in Illumina BaseSpace v5.3.7, September 2019, via bcl2fastq v2.2.0
Illumina TruSeq adapters were trimmed from RNA-seq reads using Trimmomatic v0.3.9, parameters: ILLUMINACLIP:TruSeq3-SE.fa:1:30:12
Strain-specific transcriptomes were generated by patching strains’ SNPs and INDELs from CeNDR’s (elegansvariation.org) 20210121 release onto the N2 reference genome release ws276 using g2gtools v0.1.31 (installed via conda v4.7.12, Python v2.7.16) followed by transcriptome extraction. CeNDR’s isotype-representative strain was used for any strain that was not an isotype representative (here, EG4349’s genome was used for strain EG4348). For each non-reference strain, first, INDELs were chained onto the reference genome using g2gtools vcf2chain and SNPs were patched onto the reference genome FASTA using g2gtools patch. Next, INDELs were chained onto the SNP-patched genome using g2gtools transform and strain-specific GTFs were created from this updated genome FASTA via g2gtools convert. Strain-specific transcriptomes were generated from these strain-specific genome FASTAs and GTFs using gffread v0.12.7
Strain-specific transcriptome indexes were generated with Salmon v1.4.0 command salmon index, parameters: -k 31 --keepDuplicates (all others default; no decoys used)
RNA quantification was performed via pseudo-alignment to strain-specific transcriptomes with Salmon v1.3.0 command salmon quant with parameters -l SR --dumpEq --rangeFactorizationBins 4 --seqBias, and library-specific --fldMean and --fldSD
Transcript-level abundances were converted to gene-level abundances with tximport v1.20.0 (in R v4.1.0) tximport function, parameter type = "salmon" after including 0 abundance for any transcripts not included in a wild isolate but included in the ws276 reference GTF
Gene-level abundances were normalized using DESeq2 v1.32.0 (in R v4.1.0) deseq() function with default parameters prior to differential expression analysis. This normalization and downstream differential expression analysis were only performed for genes with >10 reads summed across samples after tximport
Genome_build: ws276 (wormbase)
Supplementary_files_format_and_content: Tab-delimited text files with abundances for each transcript as output by salmon, one per sample (*_quant.sf.gz). One row per transcript. Columns (see Salmon documentation for even further detail): Name (transcript ID), Length (transcript length), Effective Length (sample-specific effective length of transcript computed by salmon), TPM (transcripts per kilobase million abundance estimate using sample-specific effective length), NumReads (estimated number of reads assigned to this transcript).
Supplementary_files_format_and_content: Matrix file (tab-delimited text) with normalized gene abundances (deseq2_normalized_counts.txt.gz) for each sample (column) and gene included in differential expression analysis (row; gene names are row names). Derived using the counts() function in DESeq2 v1.32.0 with parameter normalized = T. All genes with >10 reads (summed across samples, counts from tximport, see above) prior to this normalization are included, n = 18589. These are the counts used by DESeq2 for differential expression analysis.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Worms were cultured following standard protocol (Stiernagle, 2006 and described here), though we added 1.25% agarose to plates used to maintain non-N2 wild isolates, to avoid burrowing. Worms were maintained at 20°C without starving for at least three generations before initiating an experiment, with the exception of QX1211, which was maintained at 18°C to avoid induction of the mortal germline phenotype. Worms used for RNA-seq were grown during RNAi or control treatment as described in ‘Treatment protocol’.

extract_protocol:
All samples were collected and processed simultaneously and in triplicate, starting with replicate plates of worms. The following protocol follows (He, 2011). Worms stored at -80°C in TRIzol (Invitrogen #15596026) were thawed and then freeze-thawed 6 times by freezing via submersion in liquid nitrogen, heat at 37°C on a heating block, then vortexing for 10 seconds and placed on ice. 200 uL Trizol was added and samples were incubated for 5 minutes at room temperature. 140 uL chloroform was added and samples were shaken at 1450 rpm for 1 minute, followed by a 2 minute incubation at room temperature. These samples were spun at 12,000g for 15 minutes at 4°C. The top aqueous phase was removed to a new tube and used downstream. One volume of 70% ethanol was added to this aqueous phase and then samples were vortex mixed and quickly spun down. 500 uL of this mixture was transferred to RNeasy columns (Qiagen #74104) and RNA extracted following Qiagen’s instructions. RNA was eluted in 50uL RNAse-free water.
Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #7760) following the manufacturer’s instructions. 500ng of fresh RNA was used as input for cDNA generation with this kit with 10 cycles of PCR. Libraries quality checked using an Agilent 2100 Bioanalyzer. BluePippin (Sage Science) was used to size-select fragments size 210-650bp in the pooled library using a 2% agarose gel.

treatment_protocol: RNAi was induced by feeding and experiments were carried out on plates, at 20°C, based on methods previously described (Ahringer, 2006; Kamath et al., 2001). To target endogenous germline-expressed genes, we fed worms HT115 E. coli bacteria that had been transformed with the pL4440-derived par-1 (H39E23.1) or pos-1 (F52E1.1). The par-1 and pos-1 vectors were obtained from the Ahringer feeding library (Kamath & Ahringer, 2003). We used E. coli carrying the empty pL4440 vector as a negative control. Bacteria were streaked from frozen stocks onto LB agar plates with carbenicillin (25 ug/mL) and tetracycline (12.5 mg/mL); liquid cultures were inoculated with 5-10 colonies from <1 week old plates, into LB broth with carbenicillin (50 ug/mL) and tetracycline (12.5 mg/mL) and incubated for 16-18hrs shaking at 37°C, then amplified in a 1:200 dilution with carbenicillin (50 ug/mL) for 6hrs. Seeded plates were incubated in the dark at room temperature and used no earlier than 44hrs and no later than 78hrs. Experimental worms were bleach synchronized, allowed to grow for three days, then bleach synchronized on non-RNAi plates. The following day L1 larvae were transferred to RNAi plates and exposed to RNAi for two days, at which point day 1 adult hermaphrodites were harvested and stored in Trizol at -80°C after 2 minutes vortexing until RNA extraction.

value: whole animal

value: day 1 adult

tag: Sex

value: hermaphrodite


title: R4-3

value: Removal of 10 mM KNO3 for 4 days


title: R3-3

value: Removal of 10 mM KNO3 for 3 days


title: JU1088 strain; POS1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 336.8548057; fldSD: 79.65817187
AP01-59


title: R5-1


title: JU1088 strain; CTR treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 337.581877; fldSD: 80.32567008
AP01-57

value: CTR


title: FE3WH8

city: new haven

first: Yuping

last: Zhou

state: CT

address: 310 cedar street

department: OB/GYN

institute: Yale

hyb_protocol: Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 with Autoloader.

data_processing:
The data were analyzed with Expression Console using the following paramaters:
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-version = 1.4.1.46

label: biotin

source_name: hippocampus

label_protocol: High quality total RNA is used as starting material to obtain labeled cRNA. In the first step, single stranded cDNA is synthesized by reverse transcription using the poly (A) RNA present in the starting total RNA sample. Single stranded cDNA is then converted into double stranded cDNA and purified using the Affymetrix Cleanup Module. An in vitro transcription (IVT) reaction is then carried out overnight in the presence of biotinylated

growth_protocol: CD-1 mice were obtained from Charles River Laboratories (Wilmington, MA, USA). Animals were housed in a 12 hr day/night cycle. All experiments were conducted in accordance with Yale University Animal Care Committee Guidelines. Eight-week-old CD-1 female mice were bred to male mice of the same strain and examined every 12 hours until the presence of a vaginal plug was detected.

extract_protocol: The tissue intended for mRNA analysis was placed in 1 mL TRIzol per 100 mg tissue (Invitrogen, Carlsbad, CA, USA). Tissue was homogenized on ice, and total RNA was isolated using methodology described by the manufacturer.

treatment_protocol: Detection of a vaginal plug was considered day 0.5 of pregnancy.  Pregnant CD-1 mice were then housed individually and continuously treated with E3 (50µl of 0.46mg/ml in DMSO to approximate human exposure) or vehicle control (DMSO) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation for 7 days.We began each experiment by treating pregnant mice with E3, and ended by analyzing their offspring.

tag: stain

tag: gender

value: Female


title: ME3WC2

source_name: frontal cortexes

value: Male


title: JU1088 strain; CTR treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 329.477644; fldSD: 81.71050293
AP01-54


title: FE3WC4


title: MCTWH5


title: FCTWH7


title: MCTWC1


title: ME3WH6


title: FCTWC3


title: R3-1


title: JU1088 strain; POS1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 333.1474758; fldSD: 80.97535084
AP01-53


title: JU1088 strain; POS1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 336.5696; fldSD: 80.66246
AP01-56


title: R4-2


title: R3-2


title: JU1088 strain; PAR1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 335.1512472; fldSD: 78.58912554
AP01-55


title: EG4348 strain; CTR treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 334.7651304; fldSD: 78.18478265
AP01-47


title: R1-3

value: Removal of 10 mM KNO3 for 1 day


title: JU1088 strain; PAR1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 333.0226228; fldSD: 82.14809599
AP01-52


title: JU1088 strain; CTR treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 340.9248912; fldSD: 81.18814924
AP01-51


title: R2-2

value: Removal of 10 mM KNO3 for 2 days


title: R2-3


title: EG4348 strain; POS1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 335.6158995; fldSD: 77.33614119
AP01-49


title: R4-1


title: EG4348 strain; PAR1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 332.2526745; fldSD: 78.29568333
AP01-48


title: R2-1


title: R1-2


title: R1-1


title: EG4348 strain; POS1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 338.6271407; fldSD: 82.21438163
AP01-46


title: T6-3

value: Treatment with 10 mM KNO3 for 6 days


title: EG4348 strain; PAR1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 343.8666402; fldSD: 79.93930412
AP01-42


title: T6-1


title: EG4348 strain; PAR1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 339.7637757; fldSD: 84.32243969
AP01-45


title: T6-2


title: EG4348 strain; CTR treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 334.173604; fldSD: 80.33975192
AP01-44


title: EG4348 strain; POS1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 335.1864515; fldSD: 79.56640993
AP01-43


title: EG4348 strain; CTR treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 336.967328; fldSD: 79.53931155
AP01-41


title: lin5.4w.b2

city: changsha

first: FENG

middle: zhan

last: Gao

state: hunan

address: no

department: College of Biology

institute: Hunan university

data_processing:
The image data measured by the high-throughput sequencer are converted into   sequence data (reads) by CASAVA base recognition
Raw data (raw reads) of fastq   format were firstly processed through in-house perl scripts
Data mapping to the reference genome of  medicago (https://plants.ensembl.org/Medicago_truncatula/Info/Index).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Medicago truncatula

source_name: lin-5 4wpi

growth_protocol: Medicago incubated with S. meliloti Rm1021 nifH::GUS for 2 week or 4week

extract_protocol:
Total  RNA was isolated isolated using RNAiso Plus (Takara Japen)
Total RNA was used as input material for the RNA sample preparations. For   prokaryotic samples, mRNA was purified from total RNA by using probes to remove   rRNA. Fragmentation was carried out using divalent cations under elevated   temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was   synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then   use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to   replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA.   Remaining overhangs were converted into blunt ends via exonuclease/polymerase   activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop   structure were ligated to prepare for hybridization. Then USER Enzyme was used to   degrade the second strand of cDNA containing U, In order to select cDNA fragments   of preferentially 370~420 bp in length, the library fragments were purified with   AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the   PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: Collecting nodule using liquid nitrogen

value: nodule

value: 4 wpi


title: lin5.2w.b2

source_name: lin-5 2wpi

value: 2 wpi


title: lin5.4w.b1


title: lin5.2w.b1


title: T5-3

value: Treatment with 10 mM KNO3 for 5 days


title: lin5.4w.b3


title: lin5.2w.b3


title: T5-1

value: Root nodule


title: T5-2


title: CB4856 strain; PAR1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 336.5696; fldSD: 80.66246
AP01-38


title: T4-3

value: Treatment with 10 mM KNO3 for 4 days


title: ChIP-seq_PolII_JLAT_shPAF1_JQ1_HIV

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ChIP-seq: low-quality bases were removed using Trimmomatic v0.33, with parameters TRAILING:30 MINLEN:20. Reads were aligned with bowtie v1.1.2 with parameters -m 1 -v 2, to human GRCh38 genome assembly with Ensembl gene annotation GRCh38 release 78. J-LAT 5a8 cells were aligned to the concatenated hg38/HIV-1 genome, using the same parameters as for the human samples. After alignment, HIV-1 reads were filtered out and normalized by the mapped read counts. Bigwig files were generated using an in-house R script utilizing bam2bw function, with a parameter to extend reads length -extLen=150 and scaled to reads-per-million (rpm).
RNA-seq:low-quality bases were removed using Trimmomatic v0.33, with parameters TRAILING:30 MINLEN:20. Reads were aligned to human GRCh38 genome assembly with Ensembl gene annotation GRCh38 release 78 using TopHat2 v2.1.0 (Kim et al., 2013), with parameters --no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --max-multihits 20. Reads with non-primary alignment and low mapping quality were discarded. Reads were quantified using HTSeq v0.6.1.
PRO-seq: Low-quality bases and adapters from 30 ends of reads were removed using cutadapt 1.14 requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with option --very-sensitive, to a concatenated genome comprised of human hg38 (sample) and fly dm6 (spike-in) assemblies. The 5’ ends of aligned reads with MAPQ 30 were processed using bedtools genomecov v2.25.0 with paremeters -strand, -bg, and -5 to calculate coverage of 5’ ends. Read counts were normalized with total reads aligned to the spike-in genome (dm6), final bigwig files were scaled 10 to reads-per-million (rpm).
Assembly: hg38
Supplementary files format and content: bigWig files contain strand-specific, spike-in normalized PRO-seq signal.

source_name: peripheral blood

growth_protocol: DLD1 and HCT116 cells were maintained in DMEM supplemented with 10% FBS. J-LAT 5a8, 11.1, and 6.3 were cultured in RPMI-1640 supplemented with 5 mM HEPES, 50 μg/mL P/S, 5 mM sodium pyruvate, and 10% FBS. Cells were cultured at 37°C in humidified incubator with 5% CO2. For RNA interference, cells were infected with a lentivirus containing shRNA against PAF1 using 8 μg/ml polybrene for 24hrs followed by 2 μg/ml puromycin for 2 days.

extract_protocol:
Extraction of total RNA was performed using RNeasy Mini kit (Qiagen, Cat# 74106). Briefly, 1million of DLD1_PAF1_AID cells were plated in a 6-well plate 24 hrs prior to treatment with 20μM iPAF1C versus DMSO or 500 μM auxin versus non-treated cells.
ChIP-seq: ChIP-seq was performed according to a previously published protocol (Lee et al., 2006). For RNA Pol II, and PAF1 ChIP-seq, the chromatin was sonicated using Covaris E220 for 4 min using the following sonication conditions: 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Successively, pulldown of chromatin was carried out overnight at 4°C using the specific antibodies (Rpb1 NTD (D8L4Y) rabbit mAb for RNA Pol II and PAF1 (D9G9X) Rabbit mAb). DNA libraries were prepared by the HTP Library Preparation Kit for Illumina (KAPA). RNA-seq: Extraction of total RNA was performed using RNeasy Mini kit (Qiagen, Cat# 74106). Briefly, 1million of DLD1_PAF1_AID cells were plated in a 6-well plate 24 hrs prior to treatment with 20μM iPAF1C versus DMSO or 500 μM auxin versus non-treated cells. For performing RNA-seq polyadenylated RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490L). This isolated poly(A)+ RNA was used to prepare libraries using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Cat# E7760L). PRO-seq: PRO-seq was performed according to the previously published protocol with minor modifications (Mahat et al., 2016a). Reverse transcription was performed with SuperScript III (ThermoFisher, Cat#18080044). cDNA was amplified using Phusion Hot Start II DNA polymerase (ThermoFisher, Cat#F549). DNA Libraries were purified using Beckman Coulter AMpure XP (Fisher Scientific, Cat#NC9959336).

treatment_protocol:
ChIP-seq: HCT116 and DLD1 cells were treated with 20μM of iPAF1C or DMSO as a control. Knocking down PAF1 was achieved by transducing cells with a lenti-viral vector expressing shRNA against PAF1.
RNA-seq: 1million of DLD1_PAF1_AID cells were plated in a 6-well plate 24 hrs prior to treatment with 20μM iPAF1C versus DMSO or 500 μM auxin versus non-treated cells.
Heat shock of mammalian cells was performed using ∼70%–80% confluent DLD1 cells by 15 adding pre-heated (42°C) conditioned media collected from identically growing cells (Mahat et al., 2016b). The heat shock cells were incubated at 42°C for 1.5 hour.
J-Lat 5a8, 11.1, and 6.3 cell lines were plated in 96-well flat bottom plates at a density of 150,000 cells/250 μL supplemented RPMI. Cells were DMSO-treated or treated with iPAF1C (12.5 μM), JQ1 (1μM), PHA (0.5 μg/mL), and PMA (1 nM) for 48 hours.

value: peripheral blood

value: J-LAT 5a8

value: T lymphoblast

value: clone 5a8, PAF1 knockdown

value: Rpb1 NTD (D8L4Y)


title: T4-2


title: HUVEC_Control_2

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

country: Germany

institute: University Medical Center Freiburg

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11. The resulting .bcl files were converted into .fastq files with the bcl2fastq v2.18 software.
STAR aligner (Galaxy Version 2.7.5b) for mapping using standard settings
Merging BAM Files of Flow Cell 1 and 2
featureCounts (Galaxy Version 1.6.4) for generating count matrix using standard settings
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with counts generated by featureCounts and corresponding Ensembl Stable IDs

source_name: Human umbilical vein endothelial cells

growth_protocol: 150000 HUVECs (Cat#: C2519A, Lonza Group) were seeded on 6-well plates and incubated overnight

extract_protocol:
Qiazol (Cat#: 79306, Qiagen) and RNeasy Micro Kit (Cat#: 74004, Qiagen) was used for RNA extraction
Librarys were generated by Illumina TruSeq Stranded mRNA Sample Preparation Guide (Cat#: 20020594, Illumina)

treatment_protocol: Cells were stimulated for 24h by cytokines. The following concentrations were used: VEGF (25 ng/mL), OSM+VEGF (100 ng/mL + 25 ng/mL),  CNTF+CNTFR+VEGF (100 ng/mL + 200 ng/mL + 25 ng/mL)

value: Human umbilical vein endothelial cells

value: Endothelial basal medium for 24h


title: HUVEC_Control_1


title: CB4856 strain; POS1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 341.9360284; fldSD: 85.04329013
AP01-36

value: whole animal

value: day 1 adult

value: hermaphrodite


title: ChIP-seq_PolII_JLAT_iPAF1C_JQ1_HIV

value: clone 5a8


title: T4-1


title: CB4856 strain; PAR1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 345.1451383; fldSD: 86.78560956
AP01-35


title: ChIP-seq_PolII_JLAT_DMSO_HIV

value: DMSO


title: CB4856 strain; POS1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 341.0188695; fldSD: 81.48208643
AP01-39


title: PRO-seq_DLD1_shPAF1

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ChIP-seq: low-quality bases were removed using Trimmomatic v0.33, with parameters TRAILING:30 MINLEN:20. Reads were aligned with bowtie v1.1.2 with parameters -m 1 -v 2, to human GRCh38 genome assembly with Ensembl gene annotation GRCh38 release 78. J-LAT 5a8 cells were aligned to the concatenated hg38/HIV-1 genome, using the same parameters as for the human samples. After alignment, HIV-1 reads were filtered out and normalized by the mapped read counts. Bigwig files were generated using an in-house R script utilizing bam2bw function, with a parameter to extend reads length -extLen=150 and scaled to reads-per-million (rpm).
RNA-seq:low-quality bases were removed using Trimmomatic v0.33, with parameters TRAILING:30 MINLEN:20. Reads were aligned to human GRCh38 genome assembly with Ensembl gene annotation GRCh38 release 78 using TopHat2 v2.1.0 (Kim et al., 2013), with parameters --no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --max-multihits 20. Reads with non-primary alignment and low mapping quality were discarded. Reads were quantified using HTSeq v0.6.1.
PRO-seq: Low-quality bases and adapters from 30 ends of reads were removed using cutadapt 1.14 requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with option --very-sensitive, to a concatenated genome comprised of human hg38 (sample) and fly dm6 (spike-in) assemblies. The 5’ ends of aligned reads with MAPQ 30 were processed using bedtools genomecov v2.25.0 with paremeters -strand, -bg, and -5 to calculate coverage of 5’ ends. Read counts were normalized with total reads aligned to the spike-in genome (dm6), final bigwig files were scaled 10 to reads-per-million (rpm).
Assembly: hg38
Supplementary files format and content: bigWig files contain strand-specific, spike-in normalized PRO-seq signal.
Library strategy: PRO-seq

source_name: colon

value: colon

value: colorectal adenocarcinoma

value: PAF1 knockdown

value: untreated


title: PRO-seq_DLD1_shPAF1_HS

value: heat shock


title: PRO-seq_DLD1_DMSO_HS

value: WT

value: DMSO, heat shock


title: PRO-seq_DLD1_DMSO


title: T3-2

value: Root nodule

value: Treatment with 10 mM KNO3 for 3 days


title: T3-3


title: HUVEC_Control_3


title: PRO-seq_DLD1_iPAF1C

value: iPAF1C 20uM


title: CB4856 strain; POS1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 336.4674188; fldSD: 79.64037349
AP01-33


title: PRO-seq_DLD1_iPAF1C_HS

value: iPAF1C 20uM, heat shock


title: CB4856 strain; PAR1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 343.3264259; fldSD: 80.99733294
AP01-32


title: CB4856 strain; CTR treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 334.9674506; fldSD: 80.33031336
AP01-37

value: CTR


title: Cardiomyocytes, REV48-5

city: Leiden

first: Sebastiaan

middle: Johannes

last: van Kampen

address: Sylviusweg 62

country: Netherlands

institute: LUMC

data_processing:
STAR_2.4.2a mapping to reference genome
read count analysis HTSeq 0.6.1
Genome_build: hg38
Supplementary_files_format_and_content: raw read counts in matrix table, normalized abundance measurements

source_name: Cardiomyocytes

growth_protocol: hiPSCs were maintained in Essential 8 medium and grown till 80-90% confluency (Day 0). Next, medium was aspirated and the cells were washed once with dPBS (GIBCO, 14190094). Subsequently, cells were fed with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES (GIBCO, 72400-021) supplemented with 0.5 mg/mL human recombinant (Sigma-Aldrich, A9731), 0.2 mg/mL L-Ascorbic Acid 2-Phosphate (Sigma-Aldrich, A8960), and 4 µM CHIR99021 (Sigma-Aldrich, 361559). After 2 days (Day 2), medium was aspirated and cells were washed once with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES, followed by addition of RPMI-1640-Medium-GlutaMAX™Supplement-HEPES supplemented with 0.5 mg/mL human recombinant (Sigma-Aldrich, A9731), 0.2 mg/mL L-Ascorbic Acid 2-Phosphate , and 5 µM IWP2 (Sigma-Aldrich, 681671). On day 4 and day 6, cells were refreshed with RPMI-1640-Medium-GlutaMAX™Supplement-HEPES supplemented with 0.5 mg/mL human recombinant and 0.2 mg/mL L-Ascorbic Acid 2-Phosphate. From day 8 onwards, cells were maintained in RPMI-1640-Medium-GlutaMAX™-Supplement-HEPES supplemented with B-27™Supplement (50x)-serum free (GIBCO, 17504001). Spontaneous beating cardiomyocytes could be observed between day 8 and day 10. hiPSC-derived cardiomyocytes were subsequently dissociated for downstream applications with TrypLE™ Select Enzyme (10x)-no phenol red (GIBCO, A1217703) for a maximum of 20 minutes at 37oC. Cardiomyocytes were seeded at a density of 100,000 cells/cm2 in Geltrex-coated wells.

extract_protocol:
Qiagen RNeasy mini kit (74104)
Truseq RNA stranded polyA

value: hiPSC-derived cardiomyocytes

value: PKP2 WT/WT

value: 30 days post-differentiation


title: T3-1


title: Cardiomyocytes, REV48-2


title: ChIP-seq_PolII_JLAT_JQ1_HIV

value: peripheral blood

value: J-LAT 5a8

value: T lymphoblast

value: clone 5a8

value: Rpb1 NTD (D8L4Y)


title: CB4856 strain; CTR treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 333.7996814; fldSD: 77.05473985
AP01-31

value: whole animal

value: day 1 adult

value: hermaphrodite


title: T2-3

value: Treatment with 10 mM KNO3 for 2 days


title: QX1211 strain; POS1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 331.3130791; fldSD: 79.78396619
AP01-29


title: Cardiomyocytes, REV48-1


title: Cardiomyocytes, delC-4

value: PKP2 c.2013delC/WT


title: Cardiomyocytes, delC-3


title: CB4856 strain; CTR treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 336.694977; fldSD: 81.01442445
AP01-34


title: T2-1

value: Root nodule


title: QX1211 strain; PAR1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 337.4964168; fldSD: 83.1164373
AP01-28


title: Cardiomyocytes, delC-5


title: Cardiomyocytes, delC-2


title: T1-3

value: Treatment with 10 mM KNO3 for 1 day


title: QX1211 strain; CTR treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 340.8441748; fldSD: 87.72707645
AP01-27


title: Cardiomyocytes, REV48-3


title: 72h Treg TLA_R3

city: Amsterdam

first: PETROS

last: DIMITRIADIS

email: p.dimitriadis@nki.nl, d.rao@nki.nl

state: Noord-Holland

address: Plesmanlaan 121

institute: NETHERLANDS CANCER INSTITUTE - NKI

data_processing:
The samples were mapped with STAR (v2.7.3a) to mouse reference genome Mus_musulus.GRCm39.105 using default settings.
 The read counts were computed with HTseq-count (v0.12.4) and were analyzed with DESeq2 (v1.30.1)

source_name: cells from mouse spleen

growth_protocol: purified CD4 T cells were stimulated in low glucose RPMI media (containing 0.5mM D-Glucose, 10% heat inactivated FBS, 1% penicillin-Streptomycin, 50IU/ml recombinant mouse IL-2 and 50uM 2-mercaptoethanol)

extract_protocol:
Total RNA was isolated from cell pellets, using the RNeasy Mini Kit (Qiagen), including an on-column DNase digestion (Qiagen), according to manufacturer's instructions
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.,) according to the manufacturer's instructions.
The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent), diluted and pooled equimolar into a multiplex sequencing pool. The libraries were sequenced with 65 base single reads on a HiSeq2500 using V4 chemistry (Illumina Inc.,).

treatment_protocol: cells were stimulated with anti-mouse CD3 (1.25ug/ml), anti-mouse CD28 (2.5ug/ml) ± TGF-beta (3ng/ml) ± lactic acid (10mM)

value: cells from mouse spleen

value: sorted CD4+ FoxP3RFP+ cells

value: Treg

value: with TGFb

tag: time point

tag: lactic acid

tag: replicate

tag: source mouse_gender

value: female


title: T1-2

tag: treatment

tag: genotype


title: QX1211 strain; POS1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 340.9487314; fldSD: 81.48757082
AP01-26

tag: strain


title: QX1211 strain; PAR1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 352.0827867; fldSD: 79.45070262
AP01-25


title: T1-1


title: 72h Treg TLA_R2


title: 72h Tcon T_R3

value: sorted CD4+ FoxP3RFP- cells

value: Tcon


title: QX1211 strain; CTR treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 336.6310538; fldSD: 79.07468978
AP01-24

value: CTR


title: 72h Treg T_R2


title: S.solfataricus.P2.ChIP-exo.CreN7.replicate1

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

country: United Kingdom

institute: University College London

description:
NovaSeq SP Reagent Kit v1.5_50x50 bp Sequencing
19862X3

data_processing:
Paired-end reads were mapped using Bowtie v1.1.2 with parameters -v 2 -m 1 --fr allowing only for uniquely mapped  read pairs to be included
Bam files with alignments were filtered for first read in proper pairs (samtools view -f 66 -b)
Read 5'-end coverage was calculated using bedtools genomecov with bedgraph output
Bedgraph files were converted to bigwig format using ucsc-bedgaphToBigwig
Assembly: NC_002754.1
Supplementary files format and content: Bigwig files with raw 5'-end coverage

organism: Saccharolobus solfataricus P2

source_name: microbial cells

growth_protocol: S. solfataricus P2 was grown in Brock medium supplemented with 0.2% glucose, 0.1% tryptone, and 20 µg/ml uracil at 75 °C in Erlenmeyer shake flasks at 150 rpm

value: WT

tag: chip antibody

value: microbial cells


title: QX1211 strain; POS1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 340.3614689; fldSD: 79.96870405
AP01-23

value: whole animal


title: T0-3

value: Root nodules at 4 weeks post-inoculation (Control with no treatment)


title: T2-2


title: 72h Tcon TLA_R2

tag: cell line


title: 72h Tcon T_R2


title: 72h Tcon SLA_R2

value: no TGFb


title: T0-2


title: 72h Tcon S_R2


title: 72h Treg TLA_R1

value: male


title: 72h Treg T_R3


title: T0-1


title: QX1211 strain; PAR1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 340.9428014; fldSD: 81.45366151
AP01-22

value: day 1 adult

value: hermaphrodite


title: QX1211 strain; CTR treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 336.5696; fldSD: 80.66246
AP01-21


title: 72h Treg T_R1


title: NAC-OE-3

value: Root nodule

tag: Stage

value: Root nodules at 3 weeks post-inoculation

value: NAC-OE line in MG-20 background


title: 72h Tcon TLA_R1

value: cells from mouse spleen

tag: cell type


title: 72h Tcon TLA_R3

tag: tissue

value: with TGFb


title: 72h Tcon SLA_R3

value: female


title: N2 strain; PAR1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 334.3227136; fldSD: 82.20689934
AP01-18


title: 72h Tcon SLA_R1

value: sorted CD4+ FoxP3RFP- cells


title: NAC-OE-2


title: N2 strain; POS1 treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 336.450836; fldSD: 83.0159905
AP01-19


title: NAC-OE-1


title: 24h Tcon TLA_R3

value: Tcon


title: 72h Tcon T_R1


title: 24h Tcon T_R3


title: GUS-OE-3

value: GUS-OE line in MG-20 background


title: N2 strain; CTR treatment; rep 3

description:
library fragment length information provided to Salmon - fldMean: 339.944246; fldSD: 82.01863117
AP01-17

value: CTR


title: 72h Tcon S_R1


title: N2 strain; POS1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 334.4183668; fldSD: 80.30734131
AP01-16


title: 24h Tcon SLA_R3


title: 24h Tcon S_R3


title: 24h Tcon TLA_R2


title: GUS-OE-2


title: 24h Tcon T_R2


title: N2 strain; PAR1 treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 336.8576307; fldSD: 80.39158107
AP01-15


title: 24h Tcon S_R2


title: 24h Tcon TLA_R1


title: GUS-OE-1


title: NAC094-2

data_processing:
Reads were mapped to the L. japonicus genome v3.0 using BOWTIE2.
DAP-seq peaks were screened with MACS2 using default parameters (q-value < 0.05).
Localization of DAP-seq peaks upstream or downstream of the transcription start site within 1 kb were analyzed using Homer based on the General Feature Format files.
NAC094-targeted genes were identified by the closest gene to the NAC094-binding site using BEDTools.
Genome_build: MG-20 V3.0
Supplementary_files_format_and_content: BigWig is a file format for display of dense, continuous data in a genome browser track.

source_name: Mature leaves

extract_protocol:
Genomic DNA was extracted from mature leaves of MG-20 plants using a MICH DNA Clean Beads (Bluescape Hebei Biotech, China).
Libraries were constructed using the MICH TLX DNA-Seq Kit (Bluescape Hebei Biotech) according to the manufacturer’s instructions.
DAP-seq

value: Mature leaves


title: N2 strain; POS1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 334.701452; fldSD: 78.2208377
AP01-13

value: whole animal


title: NAC094-input


title: 24h Tcon SLA_R1


title: N2 strain; CTR treatment; rep 2

description:
library fragment length information provided to Salmon - fldMean: 333.4038468; fldSD: 81.15360179
AP01-14


title: 24h Tcon T_R1


title: 24h Tcon S_R1


title: NAC094-1


title: N2 strain; PAR1 treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 332.1172699; fldSD: 79.39541798
AP01-12


title: N2 strain; CTR treatment; rep 1

description:
library fragment length information provided to Salmon - fldMean: 330.991107; fldSD: 78.82838132
AP01-11


title: BALF_during_remission

city: Beijing

first: Longxiang

last: Su

state: Beijing

address: 1 Shuaifu Yuan

department: Department of Critical Care Medicine

institute: Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science

description: 10x Genomics

data_processing:
The Cell Ranger software was utilized to perform alignment, filtering, barcode counting, and Unique Molecular Identifier (UMI) counting in order to create a feature-barcode matrix (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bronchoalveolar lavage fluid (BALF)

extract_protocol:
Once the patient was sedated and received analgesia, 10ml of 0.9% saline was injected into either the middle lobe of the right lung or the upper lobe of the left lung to obtain BALF. The BALF was passed through a 70μm nylon cell strainer (ThermoFisher Scientific, 22-363-548) to remove clumps and debris. The cells were then centrifuged at 300 g for 5 min at 4℃(LICHEN, LC-LX-LR55C), and the supernatant was discarded. The cells were re-suspended in PBS (Bioss, C7033) containing 0.04% BSA (Solarbio, s9020) and counted using a Countstar Rigel S2 instrument (Shanghai Ruiyu Biotechnology). We adjusted the cell suspension concentration to 300-600 living cells per microlite.
Single-cell capturing and downstream library construction were performed using the Chromium Next GEM Single Cell 3'GEM Kit v3.1 (10x Genomics), following the manufacturer's protocol. In brief, a total of 70 μL of Master Mix and Cell Suspension (containing 6,000 cells), 50 μL of barcoded gel beads, and 45 μL of partitioning oil were loaded onto Chromium Chip K to generate single-cell gel bead-in-emulsion (GEM). Immediately following GEM generation, the gel beads were dissolved, and primers were released. The polyadenylated mRNA was reversetranscribed into cDNA. Full-length cDNA, along with cell barcode identifiers, was PCRamplified, and sequencing libraries were prepared and normalized.

value: bronchoalveolar lavage fluid (BALF)

tag: patient diagnosis

value: neutrophilic asthma

value: during remission


title: colorectal adenomas from patient 22-02078

city: Jiaxing

first: Wu

address: No 118, Rd Jiahang Avenue

institute: Jiaxing University

data_processing:
Adapters were trimmed off with the Trimmomatic program (v.0.36), and PCR duplicates were removed by homemade scripts. The poly(N) tails at the 3′ end were further clipped with the Cutadapt program (v.1.15).
After filtering, the paired reads were first aligned to 45S pre-rRNA, and the remaining reads were mapped to the human reference. After filtering, the paired reads were first aligned to 45S pre-rRNA, and the remaining reads were mapped to the human reference genome (assembly version: hg19) using the STAR software (v.020201).
We next extracted the gapped reads from the normally mapped reads and further discarded the reads resulting from RNA splicing. The chiastically mapped reads and remaining gapped reads constituted the set of chimeric reads representing useful data for determining RNA structures and RNA–RNA interactions
Message-Digest Algorithm 5
Assembly: hg19
Supplementary files format and content: text files include the information of two RNA-RNA interaction
Library strategy: RIC-seq

source_name: colorectal adenomas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Construction of the RIC-seq library for sequencing includes crosslinking,  permeabilization, MNase digestion, pCp–biotin labelling, proximity  ligation, RNA purification, DNase I treatment, RNA fragmentation,  pCp-biotin selection and strand-specific library preparation.

tag: disease state

value: colon cancer

value: colorectal adenomas

tag: individual


title: cancerous tissues  from patient 22-02078

source_name: cancerous tissues

value: cancerous tissues


title: BALF_before_remission

description: 10x Genomics

value: before remission


title: DC95_GM_CSF_FL_DMSO

data_processing:
The samples were mapped with STAR (v2.7.3a) to mouse reference genome Mus_musulus.GRCm39.105 using default settings.
The read counts were computed with HTseq-count (v0.12.4) and were analyzed with DESeq2 (v1.30.1)

source_name: bone marrow derived

growth_protocol: For the generation of granulocyte-macrophage colony stimulating factor (GM-CSF) DCs, BM cells were cultured in the presence of GM-CSF. 2 x 106 BM cells were plated in a 100mm sterile Petri dishes (SarsTedt) in the presence of DC culture media (10 mL) supplemented with 20 ng/ml GM-CSF (Immunotools). After three days, DC culture media (10 mL) containing 20 ng/ml GM-CSF was added. On day 6, half of the medium was refreshed with new DC culture media containing 20 ng/ml GM-CSF. GM-CSF DCs were used on day 9 for subsequent experiments, unless stated otherwise. GM-CSF + FMS-Like Tyrosine Kinase 3 Ligand (FLT3L) DCs were generated from BM cells, 10-15 x 106 cells were plated in 100mm sterile Petri dishes in the presence of DC culture media (10 mL) supplemented with 20 ng/ml GM-CSF and 200 ng/ml FLT3L (Fisher Scientific). After six days, DC culture media (10 mL) was added. On day 9, cells were harvested and 3 x 106 cells were replated in DC culture media (10 mL) supplemented with 20 ng/ml GM-CSF and 200 ng/ml FLT3L. GM-CSF + FLT3L DCs were used on day 16 for subsequent experiments.

extract_protocol:
GM-CSF DCs on day 8 of the differentiation protocol and GM-CSF + FLT3L DCs on day 16 were harvested. In addition, GM-CSF DCs or GM-CSF + FLT3L DCs were treated with AZD5582 or the same volume of DMSO for 24 hours. DCs were harvested, washed and cell pellets were snap-frozen. RNA isolation and sequencing was performed by CeGaT. Briefly, total RNA was isolated using RNeasy Mini Kit (Qiagen). Quantity of RNA was measured by Qubit (Thermo Fisher) and quality profile was made using the Fragment analyzer (Agilent). Total RNA samples having RIN>8 were subjected to library generation. The library was prepared using TruSeq Stranded mRNA kit (Illumina) according to manual and analyzed using the Fragment analyzer. The libraries were sequenced on NovaSeq6000 (Illumina Inc.).
Total RNA samples having RIN>8 were subjected to library generation. The library was prepared using TruSeq Stranded mRNA kit (Illumina) according to manual and analyzed using the Fragment analyzer.

treatment_protocol: Bone marrow (BM) cells were harvested by flushing the femurs and tibia from both hind legs of Cas9-EGFP or WT C57BL/6JRj mice. Erythrocyte-lysed BM cells were directly used for BMDC differentiation (44) and cultured in DC culture media, containing RPMI 1640 (Thermo Fisher), 10% heat-inactivated FBS, 1% P/S, 2 mM L-glutamine (Thermo Fisher), 10 mM HEPES buffer (Thermo Fisher), 1 mM sodium-pyruvate (Thermo Fisher), 1% MEM non-essential amino acids (Thermo Fisher) and 50 μM β-mercaptoethanol (Merck).

value: bone marrow derived

value: FL

value: bone marrow derived dendritic cell

value: No

tag: dose (um)

tag: dmso

value: Yes

tag: timepoint


title: cancerous tissues  from patient 22-01707


title: ShortTerm_L13234withLifweek8

city: San Francisco

first: Li

state: CA

address: 35 medical center way RMB-932E

department: Regeneration Medicine

institute: University of California - San Francisco

description: 10x Genomics 3' v2

data_processing:
The demultiplexing, barcoded processing, and  gene counting and aggregation were made using the Cell Ranger software v2.0.0
We identified cell-types of control and LIF-treated organoid samples using Louvain-Jaccard clustering. These normalized datasets were piped into Seurat v.3, in which cells with fewer than 500 genes per cell or more than 10% of reads aligning to mitochondrial genes were discarded. Clustering was performed using the Seurat package, with a few modifications. Principal component analysis was performed using FastPCA, and significant principal components were identified. In the space of these significant principal components, the k = 10 nearest neighbors were identified as per the RANN R package. The distances between these neighbors were weighted by their Jaccard distance, and Louvain clustering was performed using the igraph R package. If any clusters contained only one cell, the process was repeated with k = 11 and upwards until no clusters contained only one cell. Cluster markers and UMAP plots were generated with Seurat package default parameters.
Cell type annotations of clusters were performed based on marker genes
Assembly: GRCh38
Supplementary files format and content: Long-term.rds contains the Seurat object of long-term treatment experimental groups. The file contains raw count matrix as well as metadata of individual samples/cells.
Supplementary files format and content: Short-term.rds contains the Seurat object of short-term treatment experimental groups. The file contains raw count matrix as well as metadata of individual samples/cells.

source_name: human iPSC line 13234

growth_protocol: Cortical organoids are differentiated using a regionalized forebrain differentiation protocol 56,58. Stem cell lines were dissociated to single cells using accutase. After dissociation, cells were reconstituted in neural induction media maintaining a density of 10,000 cells per well of 96-well V-bottom ultra-low adhesion plates. Neural induction media is GMEM-based and includes 20% Knockout Serum Replacer (KSR), 1X non-essential amino acids, 0.11mg/mL Sodium Pyruvate, 1X Penicillin-Streptomycin, 0.1mM Beta Mercaptoethanol, 5uM SB431542 and 3uM IWR1-endo. Cells were treated with 20uM Rock inhibitor Y-27632 for the first 6 days. After 18 days, organoids were transferred to 6-well low adhesion plates and moved to an orbital shaker rotating at 90 RPM and transitioned into a DMEM/F12-based media containing 1X Glutamax, 1X N2, 1X CD Lipid Concentrate and 1X Penicillin-Streptomycin. After 35 days, organoids were moved into DMEM/F12-based media containing 10% FBS, 5ug/mL Heparin, 1X N2, 1X CD Lipid Concentrate and 0.5% Matrigel. At 70 days media was additionally supplemented with 1X B27 and Matrigel concentration increased to 1%. Throughout culture duration organoids were fed every other day.

extract_protocol:
Organoids were dissociated with a Papain dissociation kit (Worthington) for 45 minutes, spun down at 300g for 5mins, resuspended in PBS+0.5%BSA, filtered and counted while verifying single cell dissociation.
Single-cell capture from live cells was performed following the 10× v2 Chromium manufacturer’s instructions for both primary and organoid samples. 10,000 cells were targeted for capture and 12 cycles of amplification for each of the cDNA amplification and library amplification were performed. Libraries were sequenced as per manufacturer recommendation on a NovaSeq S2 flow cell.

treatment_protocol: For LIF treatment, recombinant LIF protein (10ng/ml, Millipore) was mixed into the media.

value: human iPSC line 13234

value: cortical organoids derived from iPSC line 13234

tag: group

value: short term

value: week 8

value: LIF


title: DC95_GM_CSF_FL_d16


title: tissues distal to cancer from patient 22-02078

source_name: tissues distal to cancer

value: tissues distal to cancer


title: ShortTerm_L13234withLifweek15

description: 10x Genomics 3' v2

value: week 15


title: DC94_GM_CSF_FL_005


title: colorectal adenomas from patient 22-01707


title: DC94_GM_CSF_FL_DMSO


title: MCF7 Suspension, technical replicate 3 (M7S_H012)

city: Silver Spring

first: Julianne

middle: D

last: Twomey

state: MD

address: 10903 New Hampshire Ave. Building 71-2260

department: CDER/OPQ/OBP

institute: Food and Drug Administration

description: Gene expression of MCF7 cells after 7 days of suspension culture

hyb_protocol: Phalanx Method

scan_protocol: Scanning is performed at Phalanx Biotech using internal protocols.

data_processing: The scanned images were analyzed with Agilent Extended Dynamic Range.

source_name: MCF7 Breast Cancer Cell Line (ATCC HTB-22), suspension, 7 days

label_protocol: Cy-dye coupling to aa-dUTP is used with internally validated thresholds for labeling efficiency measured with NanoDrop.

growth_protocol: Cells were cultured at 37°C/ 5% CO2 for seven days in either a monolayer tissue culture treated polystyrene plate or a Corning Ultra-Low Attachment plate prior to harvest.

extract_protocol: RNA was extracted using an RNeasy kit (Qiagen) following the manufacturer's recommendations. RNA quality was assessed using a Nanodrop ND-1000. Pass criteria of absorbance ratios of A260/A280 ≥ 1.8 and A260/A230 ≥ 1.5 were used for RNA quality control. RNA integrity number (RIN) pass criteria of > 6 was used to determine the acceptable RNA integrity. Gene expression fold changes were calculated by the Rosetta Resolver 7.2, with an error model adjusted by the Amersham Pairwise Ratio Builder.

value: 7 days of suspension culture


title: 24h Tcon SLA_R2

value: cells from mouse spleen

value: sorted CD4+ FoxP3RFP- cells

value: Tcon

value: no TGFb

tag: time point

tag: lactic acid

tag: replicate

value: female


title: MCF7 Suspension, technical replicate 1 (M7S_H010)

tag: treatment


title: Leukemia cells KK1 replicate3

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: RhoH expression consequences in KK1 cells, replicate3

hyb_protocol: Agilent-014850 Whole Human Genome Microarray 44K were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

source_name: RhoH vector in KK1 cells

label_protocol: Using manufacturer's instructions

growth_protocol: The characteristics of the cell line KK1 are described by Cellosaurus accession CVCL_X908. The establishment and growth conditions of KK1 are described by Yamada et al (1991) Leukemia Research, 15, 619-625.

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: The KK1 cell line was stably transfected with either the empty plasmid vector pMEP4 or this same vector expressing human RhoH (pMEP-RhoH). The construction of these plasmids is described by Galiègue-Zouitina et al (2008) Cancer Research, 68, 4531-4540. The plasmids pMEP4 and pMEP-RhoH were linearized by digestion with the restriction enzyme ClaI and then transfected by electroporation into KK1 cells. Pools of KK1 cells that contained the transfected plasmids stably integrated within their genome were selected and maintained by treatment with 340 mg/mL of hygromycin.

value: adult T-cell leukemia/lymphoma cell

tag: transfection

value: RhoH vector

source_name: empty vector in KK1 cells

value: empty vector


title: MCF7 Suspension, technical replicate 2 (M7S_H011)


title: DC95_GM_CSF_FL_005

value: bone marrow derived

value: FL

value: bone marrow derived dendritic cell

tag: genotype

value: Yes

value: No


title: tissues distal to cancer from patient 22-01707

value: colon cancer


title: colorectal adenomas from patient 22-406

value: colorectal adenomas

value: patient 22-406


title: DC94_GM_CSF_FL_d16

tag: cell line


title: DC91_GM_CSF_FL_005


title: cancerous tissues  from patient 22-406

value: cancerous tissues


title: ShortTerm_L13234withLifweek10

description: 10x Genomics 3' v2

value: human iPSC line 13234

value: cortical organoids derived from iPSC line 13234

value: short term

tag: Stage

value: week 10

value: LIF


title: ShortTerm_L13234controlweek8

description: 10x Genomics 3' v2

tag: cell type

value: week 8

value: control


title: Leukemia cells KK1 replicate1

description: RhoH expression consequences in KK1 cells, replicate1

value: adult T-cell leukemia/lymphoma cell

value: RhoH vector

value: empty vector


title: MCF7 Monolayer, technical replicate 2 (M7M_H008)

description: Gene expression of MCF7 cells after 7 days of monolayer culture

source_name: MCF7 Breast Cancer Cell Line (ATCC HTB-22), monolayer, 7 days

value: 7 days of monolayer culture


title: Irradiated Parotid - donor 39 [s39_PAR_IR]

first: Alejandro

last: Martinez Chibly

state: CALIFORNIA

address: 330A Guerrero Street

institute: Genentech

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCh38.v25human genome using STAR v2.5.2a in  single-pass mode with the following parameters:  --outFilterMultimapNmax 10 –outFilterType BySJout --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 21 --alignIntronMax 0 --alignMatesGapMax 0  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: hg38
Supplementary files format and content: Raw counts expression matrix.
Supplementary files format and content: Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: TMM-normalized Counts Per Million expression matrix.

source_name: Parotid Gland

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on a HiSeq2500 sequencer (Illumina).

tag: tissue

value: Parotid Gland

value: Irradiated


title: ShortTerm_H1withLifweek8

description: 10x Genomics 3' v2

source_name: human ESC line H1

value: human ESC line H1

value: cortical organoids derived from ESC line H1


title: ShortTerm_L13234controlweek10

description: 10x Genomics 3' v2


title: MCF7 Monolayer, technical replicate 3 (M7M_H009)


title: MCF7 Monolayer, technical replicate 1 (M7M_H007)


title: Leukemia cells KK1 replicate2

description: RhoH expression consequences in KK1 cells, replicate2


title: Irradiated Parotid - donor 37 [s37_PAR_IR]


title: tissues distal to cancer from patient 22-406

value: colon cancer

value: tissues distal to cancer

value: patient 22-406


title: DC105_3_GM_CSF_1

value: bone marrow derived

value: GM

value: bone marrow derived dendritic cell

value: Yes

value: No


title: DC105_3_GM_CSF_0.1


title: DC105_3_GM_CSF_05


title: Irradiated Parotid - donor 38 [s38_PAR_IR]


title: Irradiated Parotid - donor 35 [s35_PAR_IR]


title: DC105_3_GM_CSF_t0


title: DC105_3_GM_CSF_DMSO


title: ShortTerm_H1controlweek8

description: 10x Genomics 3' v2

value: short term

value: week 8

value: control


title: ShortTerm_H1controlweek15

description: 10x Genomics 3' v2

value: week 15


title: DC105_2_GM_CSF_1


title: ShortTerm_H1withLifweek15

description: 10x Genomics 3' v2

value: LIF


title: DC105_2_GM_CSF_05


title: Irradiated SMG - donor 30 [s30_SMG_IR]

source_name: Submandibular Gland

value: Submandibular Gland


title: MDA-MB-231 Suspension, technical replicate 3 (M231S_H006)

description: Gene expression of MB-231 cells after 7 days of suspension culture

source_name: MDA-MB-231 Breast Cancer Cell Line (ATCC HTB-26), suspension, 7 days

value: 7 days of suspension culture


title: MDA-MB-231 Suspension, technical replicate 1 (M231S_H004)


title: ShortTerm_L13234controlweek15

description: 10x Genomics 3' v2

value: human iPSC line 13234

value: cortical organoids derived from iPSC line 13234


title: ShortTerm_H1withLifweek10

description: 10x Genomics 3' v2

value: human ESC line H1

value: cortical organoids derived from ESC line H1

value: week 10


title: Irradiated SMG - donor 31 [s31_SMG_IR]

value: Irradiated


title: MDA-MB-231 Monolayer, technical replicate 3 (M231M_H003)

description: Gene expression of MB-231 cells after 7 days of monolayer culture

source_name: MDA-MB-231 Breast Cancer Cell Line (ATCC HTB-26), monolayer, 7 days

value: 7 days of monolayer culture


title: MDA-MB-231 Monolayer, technical replicate 2 (M231M_H002)


title: MDA-MB-231 Suspension, technical replicate 2 (M231S_H005)


title: DC105_2_GM_CSF_0.1

value: bone marrow derived

value: GM

value: bone marrow derived dendritic cell


title: MDA-MB-231 Monolayer, technical replicate 1 (M231M_H001)


title: Irradiated SMG - donor 27 [s27_SMG_IR]


title: NCTC_24hpi_2

city: DURHAM

first: ANKIT

last: GUPTA

address: TW 111 ALEXANDER DRIVE

department: RDBL

institute: NIEHS

description: Direct RNA-seq as method described by nanopore

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

source_name: NCTC cells

growth_protocol: Mouse NCTC clone 1469 cell line (derivative of NCTC 721, ATCC, Cat# CCL-9.1) were cultured n DMEM (Life Technologies) media supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), 10% Fetal Bovine Serum (FBS; Gemini Bio- Products), L-glutamine (Invitrogen), and 1x MEM non-essential amino acids (MilliporeSigma).  The NCTC cells were cultured at 37ºC and in 5% CO2.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Cat. No. 74104, Qiagen)
5 µg of total RNA isolated from mouse hepatitis virus-infected NCTC cells was used for each sample. Poly (A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) and libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.

treatment_protocol: NCTC cells were infected with MHV for 24 hours

value: NCTC

value: Wild-type

value: Infected with mouse hepatitis virus

tag: viral strain

value: MHV-S (ATCC_VR-766)

tag: duration

value: 24 hours


title: DC105_2_GM_CSF_DMSO

value: No

value: Yes


title: Control Parotid - donor 25 [s25_PAR]

value: Parotid Gland

value: Control


title: Control Parotid - donor 26 [s26_PAR]


title: NCTC_24hpi_1


title: DC105_2_GM_CSF_t0


title: DC91_GM_CSF_FL_DMSO

value: FL


title: DC105_1_GM_CSF_1


title: LongTerm_L13234withLifweek15

description: 10x Genomics 3' v2

value: human iPSC line 13234

value: cortical organoids derived from iPSC line 13234

value: long term

value: week 15

value: LIF


title: LongTerm_L13234controlweek8

description: 10x Genomics 3' v2

value: week 8

value: control


title: LongTerm_L13234withLifweek10

description: 10x Genomics 3' v2

value: week 10


title: LongTerm_L13234withLifweek8

description: 10x Genomics 3' v2


title: 17-CL1_shTUT47_48hpi_2

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Differential gene expression analysis was performed using DESeq2.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

source_name: 17-CL1 cells

growth_protocol: Mouse 17-CL1 cells were cultured in DMEM (Life Technologies) media supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), L-glutamine (Invitrogen), and Sodium pyruvate (Invitrogen). The 17-CL1 cells were cultured at 37ºC and in 5% CO2.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (Cat. No. 74104, Qiagen)
5 µg of total RNA from 17-CL1 shCTL and shTUT4/7 knowckdown cells were used for each sample. Poly (A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) and libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.

treatment_protocol: Cells were infected with 10 M.O.I. of MHV for different timepoints

value: 48 hours


title: ShortTerm_H1controlweek10

description: 10x Genomics 3' v2

value: human ESC line H1

value: cortical organoids derived from ESC line H1

value: short term


title: 17-CL1_shTUT47_48hpi_3

value: Infected with mouse hepatitis virus

value: MHV-S (ATCC_VR-766)


title: DC105_1_GM_CSF_05

value: bone marrow derived

value: GM

value: bone marrow derived dendritic cell

value: Yes

value: No


title: LongTerm_L13234controlweek10

description: 10x Genomics 3' v2

value: human iPSC line 13234

value: cortical organoids derived from iPSC line 13234

value: long term


title: Leukemia cells KK1 replicate4

description: RhoH expression consequences in KK1 cells, replicate4

value: adult T-cell leukemia/lymphoma cell

value: empty vector

value: RhoH vector


title: Irradiated SMG - donor 21 [s21_SMG_IR]

value: Submandibular Gland

value: Irradiated


title: LongTerm_H1withLifweek8

description: 10x Genomics 3' v2

value: human ESC line H1

value: cortical organoids derived from ESC line H1

value: week 8

value: LIF


title: Control SMG - donor 23 [s23_SMG]

value: Control


title: Irradiated Parotid - donor 22 [s22_PAR_IR]

value: Parotid Gland


title: DC105_1_GM_CSF_01

value: bone marrow derived

value: GM

value: bone marrow derived dendritic cell


title: DC105_1_GM_CSF_DMSO

value: No

value: Yes


title: 17-CL1_shTUT47_48hpi_1

value: Infected with mouse hepatitis virus

value: MHV-S (ATCC_VR-766)

value: 48 hours


title: 17-CL1_shCTL_48hpi_3

value: shCTL


title: Control SMG - donor 17 [s17_SMG]

value: Submandibular Gland


title: 17-CL1_shCTL_48hpi_2


title: Control Parotid - donor 16  [s16_PAR]


title: 17-CL1_shCTL_48hpi_1


title: LongTerm_H1withLifweek10

description: 10x Genomics 3' v2

value: long term

value: week 10


title: LongTerm_H1withLifweek15

description: 10x Genomics 3' v2

value: human ESC line H1

value: cortical organoids derived from ESC line H1

value: week 15


title: LongTerm_L13234controlweek15

description: 10x Genomics 3' v2

value: human iPSC line 13234

value: cortical organoids derived from iPSC line 13234

value: control


title: LongTerm_H1controlweek8

description: 10x Genomics 3' v2

value: week 8


title: Ep400 knockout clone 3

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

description:
raw_counts.tsv
normalized_counts_Ep400.csv

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014).
Quality trimming of the reads has not been performed.
Trimmed raw reads were aligned to mm10 using STAR (version 2.7.3) (Dobin et al. 2013).
Normalized counts have been calculated with DESeq2 (version 1.36.0) (Love et al. 2014) in R (version 4.2.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the number of aligned fragments for each gene; 1st column: ENSEMBL gene id, 2nd: column gene name, column 3-12: samples
Supplementary files format and content: comma-separated values (CSV) file of normalized read counts for WT and knockout samples

growth_protocol: O9-1 cells were maintained at 37°C under 5% CO2 on 1/100 Matrigel coated dishes in preconditioned O9-1 medium (Nguyen et al. 2018).

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
Library preparation kit: TruSeq Stranded mRNA (Illumina)

value: murine cranial neural crest

value: Ep400 knockout


title: Control SMG - donor 14 [s14_SMG]

value: Control


title: 17-CL1_shTUT47_24hpi_2

value: Infected with mouse hepatitis virus

value: 24 hours


title: 17-CL1_shTUT47_24hpi_3

value: MHV-S (ATCC_VR-766)


title: LongTerm_H1controlweek15

description: 10x Genomics 3' v2


title: Control SMG - donor 15 [s15_SMG]


title: Ep400 knockout clone 2


title: Control SMG - donor 12 [s12_SMG]


title: Control Parotid - donor 20 [s20_PAR]

value: Parotid Gland


title: DC91_GM_CSF_FL_d16

value: bone marrow derived

value: FL

value: bone marrow derived dendritic cell

value: No


title: Ep400 knockout clone 1


title: 17-CL1_shTUT47_24hpi_1


title: human_moDC_D3_AZD

data_processing:
The samples were mapped with STAR (v2.7.3a) to mouse reference genome Homo_sapiens.GRCh38.dna.primary_assembly using default settings.
 The read counts were computed with HTseq-count (v0.12.4) and were analyzed with DESeq2 (v1.30.1)

source_name: monocyte derived dendritic cells

growth_protocol: Human moDCs were generated from healthy donor buffy coats, as described by Ali et al. (48). In brief, buffy coats from healthy donors were obtained from Sanquin Amsterdam. Next, peripheral blood mononuclear cells (PBMCs) were isolated through Ficoll (Fisher Scientific) gradient separation and cells were stored at -80 °C. After thawing, monocytes were isolated with positive bead labeling using CD14 MicroBeads (Miltenyi Biotec) following manufacturer’s instructions. Isolated CD14+ cells were resuspended at 1 x 106 cells/ml in DC medium (GMP DC medium (CellGenix®) supplemented with 1% human serum (Sigma-Aldrich) and 1% P/S) with the addition of 50 IU/ml human recombinant IL-4 (Peprotech) and 800 IU/ml human recombinant GM-CSF (Peprotech) in a six-well plate (Corning). After 48 hours, DC medium with 200 IU/ml IL-4 and 3200 IU/ml GM-CSF was added and incubated for an additional 24 hours at 37 °C. The next day, DC medium was added with 50 IU/ml IL-4 and 800 IU/ml GM-CSF, in the presence of 0.5 μM AZD5582 or corresponding volume of control. After 24 hours, adherend DCs were dislodged from the plate and used for sequencing.

extract_protocol: Total RNA samples having RIN>8 were subjected to library generation. The library was prepared using TruSeq Stranded mRNA kit (Illumina) according to manual and analyzed using the Fragment analyzer.

value: monocyte derived dendritic cells

value: human moDC

value: Yes

tag: dose


title: 17-CL1_shCTL_24hpi_3

value: shCTL


title: Control SMG - donor 9 [s09_SMG]

value: Submandibular Gland


title: LongTerm_H1controlweek10

description: 10x Genomics 3' v2

value: human ESC line H1

value: cortical organoids derived from ESC line H1

value: long term

value: week 10

value: control


title: Kat5 knockout clone 3

description:
raw_counts.tsv
normalized_counts_Kat5.csv

value: murine cranial neural crest

value: Kat5 knockout


title: Control Parotid - donor 8  [s08_PAR]

value: Parotid Gland

value: Control


title: human_moDC_D3_DMSO


title: DC105_1_GM_CSF_t0

value: bone marrow derived

value: GM

tag: dose (um)


title: 17-CL1_shCTL_24hpi_2

value: Infected with mouse hepatitis virus

value: MHV-S (ATCC_VR-766)

value: 24 hours


title: Kat5 knockout clone 2


title: human_moDC_D3_t=0

value: monocyte derived dendritic cells

value: human moDC

value: No