title: d14_mid_untreated_Sample_5513-JL-S2-C_GTCCTTCG-CTGTGCAT

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2800 Plymouth Rd.

department: Biomedical Engineering

institute: University of Michigan

description: Visium 10X Genomics

data_processing:
10X Genomics Space Ranger pipeline and 10X Genomics Cell Ranger pipeline
Assembly: CanFam3.1 v97 genome
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Visium Spatial-seq

organism: Canis lupus familiaris

extract_protocol:
For single-nuclear RNA sequencing, samples were collected from biopsy samples of untreated canine skeletal muscle tissues at  0, 7, and 14 days post volumetric muscle loss (VML) injury. Canine tissues from animals at 0, 7, and 14 days post VML were collected for spatial gene expression profiling. Samples wereflash-frozen, OCT embedded, muscle tissue. Canine tissues were collected in different wound locations (mid or edge) in treated samples. There were a total of 4 replicates for untreated samples, 3 untreated samples at 7 days post injury, 3 untreated samples, and 4 ECM-treated samples at 14 days post injury.
Libraries were constructed according to the manufacturer's instructions for 10X Genomics Visium Spatial gene expression slides and 10X Genomics Single Cell 3' (v3)

value: Skeletal Muscle

value: Untreated


title: patient12

status: Public on Jun 01 2024

type: SRA

city: Atlanta

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

country: USA

institute: Emory University

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s019_PNA42D1_MONO_TA_A1

library_source: transcriptomic

data_processing:
Fastp was used to perform quality control and adapter trimming and the results were filtered by quality. HISAT2 (Version: 2.2.1) was used to map RNA sequencing reads prior to building the index using the human reference genome GRCh38. We then used indices to map our sequential reads to the human genome. We applied featureCounts (Version: 2.0.2) to generate a matrix of row counts of each of the genes in all the samples. Genes were kept in the analysis that had at least 10 reads in at least half of the samples.
Assembly: GRCh38
Supplementary files format and content: txt counts

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
RNA was isolated from CD14+ monocytes using the Nucleospin RNA II kit with on-column genomic DNA digestion according to the manufacturer’s protocol (Takara, Mountain View, CA, USA)
cDNA was generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio), and the final RNA-seq library was generated using the Nextera XT kit (Illumina). RNA-seq libraries were sequenced on the Illumina NovaSeq 6000 with a sequencing depth of 30M PE100 reads per sample.

tag: tissue

value: blood

tag: cell line

value: primary human cell

tag: cell type

value: Monocyte

tag: time

tag: treatment

value: PARDS


title: patient11

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s018_PNA39D1_MONO_TA_A1


title: B16F10 cells, anti-PD-1+Eudoraea, MEL_93

city: Shanghai

first: Zhao

last: Zhang

state: SHANGHAI

address: 130 Dongan Rd

country: China

institute: FUDAN UNIVERSITY

data_processing:
Trimmed sequence reads were mapped to mm10 using Hisat2
Gene annotation using Stringtie
Differential expression analysis using DeSeq2
Assembly: mm10
Supplementary files format and content: FPKM (log2)

organism: Mus musculus

extract_protocol:
RNA was harvested using TRIzol Reagent(Ambion/Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
Library construction protocol RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Melanoma

tag: genotype

value: WT

value: Day 17


title: d14_mid_ecm_treated_Sample_6539-JL-S1-C_CAATCCCGAC-TACTACTCGG

description: Visium 10X Genomics

source_name: Skeletal Muscle

value: ECM treated


title: Animal_A12X028_W0_D1

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

data_processing:
Reads were aligned using STAR 2.7.10a
Assembly: Mmul-10
Supplementary files format and content: Reads per transcript, tab-delimited text

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
The blood Paxgene tubes were stored until all samples were collected. The whole blood samples were then subjected to RNA extraction using the Thermo Fisher “MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes.”
Sample QC was performed with Agilent 2100 bioanalyzer to identify samples with RIN > 7. Qualified RNA from each sample was processed with non-stranded mRNAseq library prep (with globin mRNA removal). In brief, mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. Globin mRNA was depleted using globin mRNA probes. mRNA molecules were fragmented into small pieces using a fragmentation reagent, and the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. They were then end-repaired, followed by A-tailing and adapter ligation reactions. The library was subsequently PCR enriched and purified by the Ampure XP bead size selection method. All libraries are quantified by Agilent Technologies 2100 bioanalyzer. The double-stranded PCR products were heat-denatured and circularized by the splint oligo sequence. The single-strand circle DNA (ssCir DNA) was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and paired-end 150-base reads were generated by sequencing using the sequencer G400.

value: PBMC

tag: animal

tag: week

tag: day

tag: group

tag: regimen


title: patient10

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s017_PNA37D1_MONO_TA_A1


title: B16F10 cells, anti-PD-1+Eudoraea, MEL_94


title: B16F10 cells, anti-PD-1+Eudoraea, MEL_91


title: Animal_A12X028_Baseline_D0

value: Baseline


title: Animal_A11L072_W12_D0


title: patient9

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s016_PNA35D1_MONO_TA_A1


title: d14_edge_untreated_Sample_5513-JL-S2-D_AATGTATC-TAAGCTCA

description: Visium 10X Genomics


title: d14_edge_untreated_Sample_6834-JL-S1-D-GEX_GCCTTCGG-AAATCGTT

description: Visium 10X Genomics


title: patient8

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s014_PNA31D1_MONO_TA_A1


title: B16F10 cells, anti-PD-1+Eudoraea, MEL_92


title: patient7

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s008_PNA17D1_TA_MONO_A1


title: d14_edge_ecm_treated_Sample_6833-JL-S1-D_AGAACTTA-AAAGGACT

description: Visium 10X Genomics


title: B16F10 cells, lgG + Eudoraea, MEL_83

value: lgG + Eudoraea


title: B16F10 cells, lgG + Eudoraea, MEL_82


title: Animal_A11L072_W9_D0


title: Animal_A11L072_W8_D1


title: d14_edge_ecm_treated_Sample_6539-JL-S1-D_CCCAGCTTCT-GTTTGGTGTC

description: Visium 10X Genomics


title: B16F10 cells, lgG + Eudoraea, MEL_81


title: d14_mid_ecm_treated_Sample_6833-JL-S1-C_CCGGAGGA-AACATCCG

description: Visium 10X Genomics


title: patient6

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s006_PNA9D1_TA_MONO_A1


title: Animal_A11L072_W8_D0


title: d7_mid_untreated_Sample_6834-JL-S1-C-GEX_TCCCAAGG-AAAGGTAG

description: Visium 10X Genomics


title: patient5

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s005_PNA7D1_TA_MONO_A1


title: Animal_A11L072_W4_D0


title: B16F10 cells, lgG + Eudoraea, MEL_80


title: patient4

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s004_PNA6D1_TA_MONO_A1


title: patient3

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s003_PNA5D1_TA_MONO_A1


title: d7_edge_untreated_Sample_5513-JL-S2-B_CCTGTCAG-GTTACGGG

description: Visium 10X Genomics


title: Animal_A11L072_W1_D0


title: B16F10 cells, anti-PD-1 + PBS, MEL_64

value: anti-PD-1 + PBS


title: Animal_A11L072_W0_D1


title: d0_untreated_Sample_6833-JL-S1-B_GTCCCATC-GTCACGTT

description: Visium 10X Genomics


title: B16F10 cells, anti-PD-1 + PBS, MEL_60


title: patient1

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s001_PNA1D1_TA_MONO_A1


title: Animal_A11L072_Baseline_D0


title: patient2

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s002_PNA3D1_TA_MONO_A1


title: d0_untreated_Sample_6833-JL-S1-A_TGTCCCAA-TGGACATC

description: Visium 10X Genomics


title: B16F10 cells, anti-PD-1 + PBS, MEL_58


title: B16F10 cells, lgG+PBS, MEL_56

value: lgG+PBS


title: Animal_A10N096_W12_D0


title: d0_untreated_Sample_6539-JL-S1-B_TCTACCATTT-GACTCTCCCG

description: Visium 10X Genomics


title: Animal_A10N096_W9_D0


title: THZ

city: Beijing

first: Jichang

last: Li

address: No. 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

library_source: genomic

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
ATAC-seq reads were aligned to the hg38 genome using BWA（0.7.13-r1126） . Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.2 with the significance cut-off q-value <=0.05
bigWig files were generated using the deeptools. Peak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: HUVECs

extract_protocol:
cells were harvested from cell culture and lysed in lysis buffer. The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 50 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃.
The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen).

value: HUVECs

value: human umbilical vein endothelial cells

value: wt

value: THz


title: CON

value: control


title: d0_untreated_Sample_6539-JL-S1-A_GTGGATCAAA-CAGGGTTGGC

description: Visium 10X Genomics

value: Skeletal Muscle

value: Untreated


title: B16F10 cells, lgG+PBS, MEL_55


title: Animal_A10N096_W8_D1


title: D15_PF_2

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
10X Genomics Space Ranger pipeline and 10X Genomics Cell Ranger pipeline
Assembly: CanFam3.1 v97 genome
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA


title: Animal_A10N096_W8_D0


title: HT-29 cells,TNF-a+4-HDHA,replicate3 [TH3]

city: Jinan

first: Yanqing

state: Shandong province

address: No. 44 Wenhua West Road，Lixia district,

department: Gastroenterology

institute: Shandong University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: Homo sapiens Ensembl v96
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

growth_protocol: HT-29 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5%CO2 at 37C

extract_protocol:
Total RNA was isolated and purified usingTRIzol reagent (Invitrogen, Carlsbad, CA, USA)following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Cell apoptosis was induced by treatment of 100ug/ml human recombinant TNF-a(peprotech) for 72h

value: human colorectal carcinoma cell line

value: 100ug/ml human recombinant TNF-a + 600nm 4-HDHA  added into culture medium for 72h to induce apoptosis


title: d7_mid_untreated_Sample_5513-JL-S2-A_CGCGCACT-AGAATACA

description: Visium 10X Genomics


title: Animal_A12X028_W1_D0


title: D7_PF_1

description: 10X Genomics


title: B16F10 cells, lgG+PBS, MEL_54

value: Melanoma

value: WT


title: B16F10 cells, anti-PD-1 + PBS, MEL_59

value: Day 17


title: HT-29 cells,TNF-a+4-HDHA,replicate2 [TH2]


title: HT-29 cells,TNF-a+4-HDHA,replicate1 [TH1]


title: Untreated_7912

description: 10X Genomics


title: B16F10 cells, lgG+PBS, MEL_52


title: Animal_A10N096_W4_D0

value: PBMC


title: HT-29 cells,TNF-a,replicate3 [T3]

value: 100ug/ml human recombinant TNF-a added into culture medium for 72h to induce apoptosis


title: Animal_A10N096_W0_D1


title: HEK293CDK7as_STARTseq_1-NM-PP1_30min_Rep2

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

country: Germany

institute: Max-Planck-Institute for Multidisciplinary Scienes

data_processing:
All sequencing data were demultiplexed with Illumina bcl2fastq demultiplexing software, provided the barcodes for each of the samples, and subsequently quality checked with FastQC (Babraham-Institute) (Andrews, 2010).
Start-seq: For all samples, paired-end 42 base reads were trimmed for adapters and then mapped to the merged human hg38 (GRCh38.p13) and Drosophila (BDGP6.28) genome assembly using STAR (v 2.6.0c) (Dobin et al., 2013) with default parameters. Samtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, where alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f 2) were selected. Total read counts mapping to the Drosophila genome were used to generate normalization factors to normalize the Start-seq data. Coverage tracks for further analysis were restricted to the nucleotides at the 5’- or 3’-end of the sequenced fragments.
Assembly: GRCh38
Supplementary files format and content: bigwig files

source_name: genome edited HEK293

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, 11960085) supplemented with 10% fetal bovine serum (Gibco, 10500–064) and 1 % GlutaMAX (Thermo Fisher Scientific, 35050087) in a humidified incubator at 37°C and 5% CO2. Cells were passaged every 2-3 days using 0.25% Trypsin-EDTA (Gibco, 25200056). Biological replicates were cultured separately. All cell lines were verified to be free of mycoplasma contamination with PlasmoTest Mycoplasma Detection Kit (InvivoGen).  Drosophila Schneider-2 (S2) cells, used for MNase-ChIP-seq and Start-seq spike-ins, were obtained from DSMZ (ATCC Cat# CRL-1963, RRID: CVCL_Z232) and cultured in Schneider's Drosophila-Medium (Gibco, 21720024) supplemented with 10% fetal bovine serum (Gibco, 10500–064) in a non-humidified incubator at 27°C, protected from light. Yeast S. cerevisiae cells (BY4741 strain), used for mNET-seq spike-ins, were obtained from Euroscarf (ACC-Y00000) and cultured in yeast medium (YP + 2% glucose) at 30°C until OD595 of 0.8 was reached.

extract_protocol:
Start-seq: Start-seq was performed as previously described (Nechaev et al. 2010) with minor changes. 3.5x10^7 CDK7as cells were treated for 30 min with 7.5 μM of 1-NM-PP1 or DMSO (solvent control). For spike-in normalization, 2.5 x10^7 Drosophila S2 cells were added to each sample. After the treatment, nuclei isolation was performed as described in the protocol for cellular fractionation (Conrad et al. 2017). All buffers were supplemented with 7.5 μM 1-NM-PP1 or respective amounts of DMSO, protease (Sigma-Aldrich, P8340), and phosphatase (Roche, 4906837001) inhibitors. RNA was extracted from the isolated nuclei using 5 ml of TRIzol reagent (Invitrogen, 15596026), precipitated with 100% ethanol and GlycoBlue coprecipitant (Invitrogen, AM9515) at -20°C for 30 minutes, then washed twice with 70% ethanol. The RNA pellets were air-dried and dissolved in 7 M urea. To size select 16-65 nt RNA, samples were resolved on 9% polyacrylamide gel containing 7 M urea. RNA of corresponding sizes was extracted from the gel and precipitated with 100% ethanol and GlycoBlue coprecipitant. After short RNA isolation, uncapped pRNAs were degraded using Terminator 5′ phosphate-dependent exonuclease (Biozym, 162370) at 30°C for 60 min. After the reaction, short RNA was cleaned up using 1.8x of AMPure RNAClean XP (Beckman Coulter, A63987) beads and 270 µl of isopropanol. Next uncapped pppRNAs and pRNAs were dephosphorylated using rSAP (NEB, M0371) at 37°C for 30 min. RNA was cleaned up using the AMPure RNAClean XP beads, and RNA was uncapped with Cap-Clip (Biozym, C-CC15011H) at 37°C for 60 min. RNA was cleaned up using the AMPure RNAClean XP beads.
Start-seq: 44 ng of RNA was used for library preparation with TruSeq Small RNA Library Prep Kit (RS-200-0048) according to the manufacturer’s instructions. Fragment sizes were analyzed with the Fragment Analyzer (HS NGS Fragment Kit).

treatment_protocol: Cells were treated for 15, 30, or 60 min with 7.5 μM of 1-NM-PP1 (Sigma-Aldrich, St. Louis, MO USA) or an equal DMSO (solvent control; Sigma-Aldrich, St. Louis, MO USA) volume.

value: genome edited HEK293

value: Human embryonic kidney

value: analog-sensitive CDK7

value: 30 min 1-NM-PP1

tag: method

value: Start-seq


title: HT-29 cells,TNF-a,replicate2 [T2]


title: Animal_A10N096_Baseline_D0

value: Baseline


title: pDC_TRIM33_1

first: Xiangyi

last: Shen

address: D303 Zhengyutong Medical Building, Tsinghua University

department: The Institute for Immunology, School of Medicine

institute: Tsinghua University

data_processing:
Raw reads in FASTQ format were filtered by Trimmomatic (v0.40) (ILLUMINACLIP:Adapter.fa:2:30:10, SLIDINGWINDOW:4:15, LEADING:3 TRAILING:3, MINLEN:36).
Clean reads were mapped to the GRCm38 (mm10) build by Bowtie2 (v2.2.5).
The reads coverage and sequencing depth were monitored by Samtools.
Signal track files in bigWig format were generated using the MACS2 (v2.2.7) pileup function. Fragment pileup per million reads was visualized for normalized comparison.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are in bigWig format for graphic display of genomic binding sites.

source_name: Plasmacytoid dendritic cell

extract_protocol:
Splenic cDC1s (CD11c+ SiglecH- MHC II+ CD24+ CD172a-), cDC2s (CD11c+ SiglecH- MHC II+ CD24- CD172a+) and bone marrow pDCs (CD11b- CD19- CD11c+ SiglecH+ PDCA-1+) of B16FL-treated mice were isolated by fluorescent activated cell sorting.  ChIP samples were prepared with the ChIP-IT® Express Enzymatic Shearing Kit (#53035, Active Motif) after cross-linking cells with 1 % formaldehyde at room temperature for 10 min and quenching with 0.125 M glycine. For each sample, chromatin from 5 × 10^6 sonicated and enzyme-sheared cells was incubated with 5 µg anti-TRIM33 antibody (#A301-059A, Bethyl Laboratories) at 4 ℃ overnight. Magna ChIP™ Protein A+G magnetic beads (#16-663, Millipore, Temecula, CA, USA) and MinElute PCR purification kit (#28004, Qiagen, Germantown, MD, USA) were used to retrieve immunoprecipitated DNA.
Annoroad Gene Technology (Beijing, China) constructed the sequencing libraries using standard Illumina protocols.

treatment_protocol: To acquire large numbers of primary DCs for ChIP-Seq sample preparation, 2 × 10^6 Flt3L-secreting B16F10 melanoma cells (B16FL) were injected subcutaneously to 6-week-old wildtype male C57BL/6 mice to boost DC numbers in vivo. Splenic cDCs and BM pDCs were sorted 2 weeks following inoculation.

tag: strain

value: Bone Marrow

tag: antibody

value: Rabbit anti-mouse/human TRIM33 polyclonal antibody (#A301-059A, Bethyl Laboratories)


title: HT-29 cells,TNF-a,replicate1 [T1]


title: HEK293CDK7as_STARTseq_DMSO_30min_Rep2

value: 30 min DMSO


title: cDC2_input

source_name: Type 2 conventional dendritic cell

extract_protocol:
Splenic cDC1s (CD11c+ SiglecH- MHC II+ CD24+ CD172a-), cDC2s (CD11c+ SiglecH- MHC II+ CD24- CD172a+) and bone marrow pDCs (CD11b- CD19- CD11c+ SiglecH+ PDCA-1+) of B16FL-treated mice were isolated by fluorescent activated cell sorting.  ChIP samples were prepared with the ChIP-IT® Express Enzymatic Shearing Kit (#53035, Active Motif) after cross-linking cells with 1 % formaldehyde at room temperature for 10 min and quenching with 0.125 M glycine. For each sample, chromatin from 5 × 10^6 sonicated and enzyme-sheared cells were incubated with 5 µg anti-TRIM33 antibody (#A301-059A, Bethyl Laboratories) at 4 ℃ overnight. Magna ChIP™ Protein A+G magnetic beads (#16-663, Millipore, Temecula, CA, USA) and MinElute PCR purification kit (#28004, Qiagen, Germantown, MD, USA) were used to retrieve immunoprecipitated DNA.
Annoroad Gene Technology (Beijing, China) constructed the sequencing libraries using standard Illumina protocols.

value: Spleen


title: HT-29 cells,control+4-HDHA,replicate3 [CH3]

value: human colorectal carcinoma cell line

value: 600nm 4-HDHA added into culture medium for 72h


title: cDC2_TRIM33_2


title: HEK293CDK7as_STARTseq_DMSO_30min_Rep1


title: Animal_A10L091_W9_D0


title: HT-29 cells,control+4-HDHA,replicate2 [CH2]


title: Animal_A10L091_W8_D1


title: cDC2_TRIM33_1


title: ATAC_SIRPG-Ex4-sg1-C8

city: Gainesville

first: Jeremy

middle: Robert Barker

last: Newman

state: FL

address: 2033 Mowry Road

department: Genetics Institute

institute: University of Florida

data_processing:
Sequencing reads were processed using the PEPATAC pipeline. Reads were trimmed using Skewer (version 0.2.2), and reads that mapped to mitochondrial or human repeat regions were removed. The remaining reads were mapped to the complete human genome version GRCh38.p13 using BWA-MEM.
PCR duplicates were removed using SAMBLASTER. Enzymatic cut sites were inferred from read alignments and peaks were called using MACS2.
Data quality was assessed using TSS enrichment plots, and plots of the fraction and cumulative fraction of reads in genomic features to evaluate enrichment of reads in genomic features
Consensus peaks were determined by identifying overlapping (1 bp) peaks between all clones and the overlapping peak with the highest score was used as the consensus peak coordinate. Peaks present in at least 2 clones with a score of ≥ 1 per million were retained
Consensus peak counts for each clone were calculated by multiplying individual peak counts for an overlapping peak by the percent overlap of the sample peak with the consensus peak
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text narrowPeak BED file for each clone (raw counts)
Supplementary files format and content: tab-delimited text narrowPeak BED file for each clone (normalized counts)
Supplementary files format and content: tab-delimited text BED file of counts for consensus peaks for each clone
Supplementary files format and content: wide-formatted tab-delimited text file of raw consensus peak counts as integer counts for all clones
Supplementary files format and content: wide-formatted tab-delimited text file of peak consensus counts as counts per million for all clones used in the final analysis
Supplementary files format and content: wide-formatted tab-delimited text file of peak consensus counts as log-transformed counts per million (voom) for all clones used in the final analysis
Supplementary files format and content: tab-delimited text file of TMM normalization factors used in the final analysis
Supplementary files format and content: tab-delimited text file of voom weights for each subject and peak

source_name: SIRPG clone 2

extract_protocol:
A total of 50,000 cells per clone were harvested and lysed in Base Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, pH 7.4) with 0.1% NP-40 (Sigma/Roche Cat# 11332473001), 0.1% Tween-20 (Sigma-Aldrich Cat# 11332465001) and 0.01% Digitonin (Promega Cat# G9441).
After pelleting the cells, transposition reaction was performed using Nextera DNA Library Prep Kit (Illumina, Cat# FC-121-1030) and amplification of transposed DNA fragments was performed using Nextera Index Kit (Illumina, Cat# FC-121-1011) following manufacture’s protocols. Sample purification was achieved by using Agencourt AMPure XP beads (Beckman Coulter, Cat# A63881). Sample yield was determined using Qubit High Sensitivity dsDNA (ThermoFisher, Cat# Q32851) and DNA integrity was assessed by D1000 High Sensitivity Tape Station (Agilent TapeStation system).

value: Jurkat cell

tag: crispr target

value: SIRPG exon 4

tag: guide rna

tag: crispr edit_(dna)

tag: crispr edit_(rna,_refseq)

tag: crispr edit_(rna,_ensembl)


title: Animal_A10L091_W8_D0

tag: tissue


title: ATAC_SIRPG-Ex4-sg1-C3

source_name: SIRPG clone 1

tag: cell line


title: cDC1_input

source_name: Type 1 conventional dendritic cell


title: HT-29 cells,control,replicate3 [C3]

tag: cell type

value: WT

tag: treatment

value: normal cell culture medium with 0.1%DMSO


title: ATAC_SIRPG-Ex4-sg1-C23

source_name: SIRPG clone 5


title: pDC_input


title: Animal_A10N096_W1_D0

value: PBMC

tag: animal


title: HEK293CDK7as_STARTseq_1-NM-PP1_30min_Rep1

value: genome edited HEK293

tag: genotype


title: pDC_TRIM33_2


title: Animal_A10L091_W4_D0

tag: week

tag: day


title: Animal_A10L091_W1_D0

tag: group

tag: regimen


title: cDC1_TRIM33_1

tag: strain


title: ATAC_SIRPG-Ex4-sg1-C14

source_name: SIRPG clone 4


title: ATAC_SIRPG-Ex4-sg1-C11

source_name: SIRPG clone 3


title: HT-29 cells,control,replicate2 [C2]


title: Animal_A10L091_W12_D0


title: Animal_A10L091_W0_D1


title: HT-29 cells,control,replicate1 [C1]


title: TRIM33_2

data_processing:
Raw reads in FASTQ format were processed through fastp (v0.19.11) to remove adapter-containing, poly-N containing, or low-quality reads in order to generate clean data.
Index of the reference genome (mm10) was built using BWA (v 0.7.12), and clean reads were aligned to the reference genome using BWA-MEM(v 0.7.12).
The bamCoverage tool (v2.2) of Deeptools was used to generate bigWig files.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are in bigWig format for graphic display of genomic binding sites.

source_name: Immortalized dendritic cells

growth_protocol: Mutu DC1940 cells were cultured in IMDM Modified (Hyclone, with HEPES) media supplemented with 10% FBS, 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco) and 50 µM β-Mercaptoethanol.

extract_protocol:
For each biological repeat, 2×10^7 cells were cross-linked with 1 % formaldehyde at room temperature for 10 min and quenched with 0.125 M glycine. Samples were further sonicated and enzyme-sheared  with the ChIP-IT® Express Enzymatic Shearing Kit (#53035, Active Motif). Chromatin from 5×10^6 cells was incubated with 5µg antibody or IgG at 4 ℃ overnight, followed by purification of IP product with the Magna ChIP™ Protein A+G magnetic beads (#16-663, Millipore) , de-crosslinking, and extraction with the MinElute PCR purification kit (#28004, Qiagen).
The libraries were constructed by Novogene Corporation (Beijing, China) using standard Illumina protocols

value: untreated

tag: chip antibody


title: A2780 cells, Pt-ttpy, 96h, biol rep 3

city: Chengdu

first: Kuang

middle: ke

last: li

state: Sichuan

address: No.17, Block 3, Southern Renmin Road

department: West China School of Pharmacy

institute: sichuang university

data_processing:
CLC Genomics workbench v 11.0.1
Sequence reads were trimmed for adaptor  sequence/low-quality sequence  using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were mapped to GRCh38_release95 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: GRCh38_release95
Supplementary files format and content: tab-dalimited txt file includes raw counts for each Sample

source_name: ovary

growth_protocol: A2780 Ovarian cancer cells were cultured in complete DMEM medium supplemented with 10% fetal bovine serum  and 100 U/ml penicillin + 100 ug/ml streptomycin in humidified atmosphere with 5%CO2 at 37℃.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The Cispt and Pt-ttpy were added to each group at their IC80 concentration for 96-hours treatment period.

value: ovary

value: Human ovarian carcinoma

value: 5.5 uM Pt-ttpy


title: HT-29 cells,control+4-HDHA,replicate1 [CH1]


title: Animal_A10L091_Baseline_D0

value: Baseline


title: ATAC_IKZF4-Ex3-sg1-C4

source_name: IKZF4 clone 3

tag: crispr target

value: IKZF4 exon 3


title: ATAC_IKZF4-Ex3-sg1-C22

source_name: IKZF4 clone 4

tag: guide rna


title: cDC1_TRIM33_2

tag: antibody

value: Rabbit anti-mouse/human TRIM33 polyclonal antibody (#A301-059A, Bethyl Laboratories)


title: A2780 cells, Pt-ttpy, 96h, biol rep 1


title: TRIM33_1


title: IgG_2

extract_protocol:
For each biological repeat, 2×10^7 cells were cross-linked with 1 % formaldehyde at room temperature for 10 min and quenched with 0.125 M glycine. Samples were further sonicated and enzyme-sheared  with the ChIP-IT® Express Enzymatic Shearing Kit (#53035, Active Motif). Chromatin from 5×10^6 cells were incubated with 5µg antibody or IgG at 4 ℃ overnight, followed by purification of IP product with the Magna ChIP™ Protein A+G magnetic beads (#16-663, Millipore) , de-crosslinking, and extraction with the MinElute PCR purification kit (#28004, Qiagen).
The libraries were constructed by Novogene Corporation (Beijing, China) using standard Illumina protocols

value: Normal Rabbit IgG (#2729, CST)


title: Animal_A10L018_W9_D0


title: ATAC_IKZF4-Ex2-sg1-C7

source_name: IKZF4 clone 1

value: IKZF4 exon 2

tag: crispr edit_(dna)

tag: crispr edit_(rna,_refseq)


title: Animal_A10L018_W12_D0

tag: tissue


title: ATAC_IKZF4-Ex3-sg1-C1

source_name: WT 4

tag: cell line

tag: crispr edit_(rna,_ensembl)


title: Animal_A10L018_W8_D1

source_name: PBMC

tag: treatment


title: Input_2


title: ATAC_IKZF4-Ex2-sg1-C29

source_name: IKZF4 clone 2


title: A2780 cells, Cispt, 96h, biol rep 2

tag: cell type

value: 0.6 uM Cispt


title: Input_1


title: Animal_A10L018_W4_D0

tag: animal


title: ATAC_IKZF4-Ex2-sg1-C10

source_name: WT 3


title: Animal_A10L018_W8_D0

tag: week


title: Lsym-TdTomato perioteum cells

city: 市辖区

first: zaiqi

last: xie

state: 徐汇区

address: 上海市徐汇区岳阳路320号

institute: chinese academy of science

data_processing:
We applied fastp with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve the clean data.
UMI-tools was applied for Single Cell Transcriptome Analysis to identify the cell barcode whitelist. The UMI-based clean data was mapped to mouse genome (mm10 Ensemble version 92) utilizing STAR mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of sample.
Cells contained over 200 expressed genes and mitochondria UMI rate below 20% passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (seurat 2.3.4) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
PCA was constructed based on the scaled data with top 2885 high variable genes and top 10 principals were used for tSNE construction and UMAP construction.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file with raw gene counts for every gene in every cluster

source_name: Periosteum

growth_protocol: Lysm-Cre;Rosa26 Tdtomato+ periosteal/cortical single cells after bone marrow cells were totally flushed and endosteal cells were removed via enzyme digestion.

extract_protocol:
The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin.
Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific).

treatment_protocol: Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell.

value: Periosteum

tag: age

value: post natal day 28

tag: genotype

value: Wild type


title: ATAC_IKZF1-Ex5-sg2-C9

source_name: IKZF1 clone 15

value: Jurkat cell

value: IKZF1 exon 6


title: A2780 cells, UT(DMSO), 96h, biol rep 3

value: WT

value: 0.5% DMSO


title: A2780 cells, Pt-ttpy, 96h, biol rep 2


title: A2780 cells, UT(DMSO), 96h, biol rep 2


title: Animal_A10L018_W0_D1

value: PBMC

tag: day

tag: group

tag: regimen


title: ATAC_IKZF1-Ex5-sg2-C5

source_name: IKZF1 clone 14

tag: crispr target


title: IgG_1

tag: strain

value: untreated

tag: chip antibody


title: A2780 cells, UT(DMSO), 96h, biol rep 1

value: ovary

value: Human ovarian carcinoma


title: A2780 cells, Cispt, 96h, biol rep 3


title: Wild-type sample WT3

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Raw sequence reads were mapped to the mouse genome mm10 using STAR aligner version 2.5.3
Reads mapped to each gene were counted using Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Hematopoietic stem cells

extract_protocol:
RNA sequencing of sorted hematopoeitic stem cells was performed by the Genomics Core of Weill Cornell Medicine
Standard Illumina protocols

value: Wild-type


title: ATAC_IKZF1-Ex5-sg2-C11

source_name: IKZF1 clone 16

tag: guide rna

tag: crispr edit_(dna)


title: Wild-type sample WT2


title: ATAC_IKZF1-Ex5-sg1-C4

source_name: WT 2

tag: crispr edit_(rna,_refseq)


title: Animal_A10L018_Baseline_D0

tag: tissue

value: Baseline


title: Emu-myc sample E3

value: Emu-myc


title: Animal_A10L002_W9_D0


title: ATAC_IKZF1-Ex5-sg1-C21

source_name: IKZF1 clone 13

tag: cell line

tag: crispr edit_(rna,_ensembl)


title: HT-29 cells,TNF-a+20umliproxstatin-1,replicate2

treatment_protocol: Cell apoptosis was induced by treatment of 100ug/ml human recombinant TNF-a(peprotech) for 3 days

tag: cell type

value: human colorectal carcinoma cell line

tag: treatment

value: 100ug/ml human recombinant TNF-a and 20um liproxstatin-1 added into culture medium for 72h to induce apoptosis


title: Emu-myc sample E2


title: HT-29 cells,TNF-a+20umliproxstatin-1,replicate1


title: ATAC_IKZF1-Ex5-sg1-C10

source_name: IKZF1 clone 12


title: A2780 cells, Cispt, 96h, biol rep 1

value: 0.6 uM Cispt


title: Emu-myc sample E1


title: Animal_A10L002_W8_D1

tag: animal

tag: week


title: Animal_A10L018_W1_D0


title: Emu-myc Casp1 -/- Casp11 -/- sample CE3

tag: genotype

value: Emu-myc Casp1 -/- Casp11 -/-


title: HT-29 cells,TNF-a+20umferrostatin-1,replicate2

value: 100ug/ml human recombinant TNF-a and 20umferrostatin-1 added into culture medium for 72h to induce apoptosis


title: Wild-type sample WT4


title: ATAC_IKZF1-Ex5-Ex3-sg1-C8

source_name: IKZF1 clone 21

value: IKZF1 exons 4 and 6


title: ATAC_IKZF1-Ex5-Ex3-sg1-C5

source_name: IKZF1 clone 20

value: Jurkat cell


title: Animal_A10L002_W8_D0

tag: day


title: HT-29 cells,TNF-a+20umferrostatin-1,replicate1

value: 100ug/ml human recombinant  TNF-a and 20umferrostatin-1 added into culture medium for 72h to induce apoptosis


title: Animal_A10L002_W12_D0

tag: group


title: ATAC_IKZF1-Ex5-Ex3-sg1-C4

source_name: IKZF1 clone 19


title: HT-29 cells,TNF-a,replicate1

value: WT

value: 100ug/ml human recombinant TNF-a added into culture medium for 72h to induce apoptosis


title: ATAC_IKZF1-Ex5-Ex3-sg1-C3

source_name: IKZF1 clone 18


title: HT-29 cells,TNF-a,replicate2


title: Emu-myc Casp1 -/- Casp11 -/- sample CE2


title: Animal_A10L002_W1_D0

value: PBMC

tag: regimen


title: Casp1 -/- Casp11 -/- sample C3


title: Animal_A10L002_W0_D1


title: Animal_A10L002_Baseline_D0


title: ATAC_IKZF1-Ex5-Ex3-sg1-C24

source_name: IKZF1 clone 25

tag: crispr target


title: HT-29 cells,TNF-a+20umferrostatin-1,replicate3


title: HT-29 cells,control+20umliproxstatin-1,replicate1

value: 20um liproxstatin-1 added into culture medium for 72h


title: Animal_11C044_W12_D0


title: HT-29 cells,control+20umliproxstatin-1,replicate2


title: Emu-myc Casp1 -/- Casp11 -/- sample CE1

tag: strain


title: ATAC_IKZF1-Ex5-Ex3-sg1-C21

source_name: IKZF1 clone 23


title: Casp1 -/- Casp11 -/- sample C2


title: Casp1 -/- Casp11 -/- sample C1


title: Animal_11C044_W9_D0

source_name: PBMC


title: HT-29 cells,control+20um ferrostatin-1,replicate2

value: 20umferrostatin-1 added into culture medium for 72h


title: ATAC_IKZF1-Ex5-Ex3-sg1-C23

source_name: IKZF1 clone 24


title: Animal_A10L002_W4_D0


title: Animal_11C044_W8_D1


title: ATAC_IKZF1-Ex5-Ex3-sg1-C13

source_name: IKZF1 clone 22


title: HT-29 cells,control+20um ferrostatin-1,replicate1


title: HT-29 cells,control,replicate3

value: normal cell culture medium with 0.1%DMSO


title: Animal_11C044_W8_D0


title: Animal_11C044_W4_D0


title: Multiseq embryoid body experiment for D4-D8 Multiseq1_S1_L001

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

institute: Johns Hopkins University

description:
Multiseq embryoid body experiment for D4-D8
multiseq.loom

data_processing:
10X CellRanger was used for the preprocessing of all the FASTQ files.
Genome_build: GRCm38

source_name: Embryoid body

extract_protocol:
Embryos were harvested from the uterus and dissected in cold dissecting buffer (Dulbecco’s phosphate buffered saline with 10% fetal bovine serum and antibiotics). Dissected tissues were dissociated in 0.125% collagenase type I (Sigma-Aldrich) and 1 U Dispase (Stemcell Technologies) at 37°C for 30 min. The samples were reduced to single cell suspension by tripsin digestion, washed with cold PBS, and passed through 40mm cell strainer.
Embryonic cells were lysed and single cell libraries prepared by following protocols provided by 10x Genomics. For the ESC differentiation experiment, we utilized the MULTI-seq sample barcoding and library preparation protocol from the McGinnis lab (McGinnis et al. 2019).

value: in vitro embryonic tissue


title: Multiseq embryoid body experiment for D4-D8 Multiseq1_S1_L002


title: ATAC_IKZF1-Ex3-sg2-C17

source_name: IKZF1 clone 11

value: IKZF1 exon 4


title: ATAC_IKZF1-Ex3-sg2-C14

source_name: IKZF1 clone 10


title: Animal_11C044_W1_D0


title: Multiseq embryoid body experiment for D4-D8 Multiseq2_S3_L001


title: HT-29 cells,control,replicate1


title: E6.5 embryo YT-E1_S4_L002

description:
E6.5 embryo
embryo_filtered.loom

source_name: E6.5 emrbyo

value: embryonic tissue


title: HT-29 cells,control,replicate2

value: human colorectal carcinoma cell line


title: ATAC_IKZF1-Ex3-sg1-C29

source_name: IKZF1 clone 9


title: HUVECs, Thz 3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38 ensemble v107
Supplementary files format and content: tab-delimited text file includes count and FPKM values for each Sample

source_name: HUVECs

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: HUVECs

value: human umbilical vein endothelial cells

value: wt

value: terahertz irradiation


title: E6.5 embryo YT-E1_S4_L001

description:
E6.5 embryo
embryo_filtered.loom


title: HUVECs, Thz 2


title: Animal_11C044_W0_D1


title: ATAC_IKZF1-Ex5-Ex3-sg1-C2

source_name: IKZF1 clone 17

value: IKZF1 exons 4 and 6


title: ATAC_IKZF1-Ex3-sg1-C23

source_name: IKZF1 clone 8

value: Jurkat cell


title: HUVECs, Thz 1


title: Animal_11C044_Baseline_D0

value: Baseline


title: Multiseq embryoid body experiment for D4-D8 Multiseq2_S3_L002


title: ATAC_IKZF1-Ex3-sg1-C22

source_name: IKZF1 clone 7


title: E8.25 embryo YT_3_S2_L001

description:
E8.25 embryo
embryo_filtered.loom

source_name: E8.25 embryo


title: ATAC_IKZF1-Ex3-sg1-C19

source_name: IKZF1 clone 6


title: HUVECs, Sham 3

value: control


title: HUVECs, Sham 2


title: E8.25 embryo YT_1_S1_L002

description:
E8.25 embryo
embryo_filtered.loom


title: ATAC_IKZF1-Ex3-sg1-C15

source_name: WT 1

value: WT


title: E8.25 embryo YT_1_S1_L001

description:
E8.25 embryo
embryo_filtered.loom


title: Biology Group 3, sample 6

city: Poitiers

first: Sebastien

last: Giraud

address: CHU de Poitiers

country: France

institute: IRMETIST UMR INSERM U1313, Université de Poitiers, CHU de Poitiers service de Biochimie

description:
E328
G3_vs_G1_pvalue0.05_fcall.csv

data_processing:
Sequence reads were trimmed for adaptator sequence/low quality sequence using Cutadapt v4.0 (with options -j 20 -n 5 -m 20).
Trimmed sequence reads were mapped to Sscrofa11.1 using star v2.7.5a (with options runThreadN 20, outFilterType BySJout, outFilterMultimapNmax 20, alignSJoverhangMin 8, alignSJDBoverhangMin 1, outFilterMismatchNoverReadLmax 0.04, outFilterScoreMinOverLread 0.5, outFilterMatchNminOverLread 0.5, outFilterMatchNmin 20, outFilterMismatchNmax 1, alignIntronMin 20, alignIntronMax 20000, alignMatesGapMax 2000, quantMode GeneCounts, outReadsUnmapped Fastx, outSAMtype BAM SortedByCoordinate, limitBAMsortRAM 6000000000, outBAMsortingBinsN 200)
Read count were performed using star v2.7.5a
Differentially expressed genes between groups were obtained using DESeq2
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited csv file includes raw counts for each sample
Supplementary files format and content: comma-delimited csv file includes differentially expressed genes between Biological group 3 and Biological Group 1

organism: Sus scrofa

source_name: Kidney

growth_protocol: We used kidney tissues from Dutch Landrace pigs (6 months to 1 year old)

extract_protocol:
RNA was extracted using the Nucleospin RNA plus kit (Macherey Nagel) and following manufacturer’s instruction. The RNA concentration was evaluated on NanoDrop (Thermo Fisher). The resulting RNA quality was determined using a Bioanalyzer Instrument (Agilent) and all samples had RNA integrity numbers above 8.1.
RNA sequencing libraries were prepared according to Illumina’s protocols using the Illumina Stranded mRNA Prep, Ligation kit (reference no. 20040534). Ten cycles of polymerase chain reaction (PCR) were applied to amplify the libraries. Library quality was assessed using a LabChip GXII Touch Instrument (PerkinElmer) and libraries were quantified by qPCR using the NEBNext Library Quant Kit (E7630), on the LightCycler 480 II Instrument (Roche).

treatment_protocol: Porcine kidneys (5-6/group) were collected after 32 min of warm ischemia and submitted to 24h of Hypothermic Machine Perfusion (HMP) followed by 5h Normothermic Machine Perfusion (NMP). Porcine kidneys of Group 1 were injected with PBS-1X during both HMP and NMP; Porcine kidneys of Group 2 were injected with Exosomes during HMP only; Porcine kidneys of Group 3 were injected with Exosomes during both HMP and NMP. At the end of NMP, kidneys were immediatly sampled and snap frozen in liquid nitrogen.

value: Kidney

tag: breed

value: Dutch Landrace

tag: Sex

value: Female

tag: age

value: 6 months to 1 year old

value: Wild Type

value: group 3


title: ATAC_IKZF1-Ex3-sg1-C11

source_name: IKZF1 clone 5

value: IKZF1 exon 4

tag: guide rna

tag: crispr edit_(dna)

tag: crispr edit_(rna,_refseq)


title: Biology Group 2, sample 6

tag: tissue

value: group 2


title: Biology Group 1, sample 5

description:
E327
G3_vs_G1_pvalue0.05_fcall.csv

value: group 1


title: IR_3

city: Chongqing

first: CHENGFANG

last: ZHOU

address: No. 30, Gaotanyan Street.

department: Department of Hematology, Southwest Hospital

institute: Army Medical University

data_processing:
NOT PROVIDED; REQUESTED
Assembly: hg38
Supplementary files format and content: tab-delimited text  file includes raw counts for each sample
Supplementary files format and content: tab-delimited text  file includes RPKM valuses for each sample

source_name: Bone marrow

growth_protocol: The isolated CD34-positive cells were cultured in a Stem Span medium with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using TRIzol™ LS Reagent(invitrogen).All the RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruePrepTM DNA Library Prep Kit V2 for Illumina® and TruePrepTM Index Kit V2/V3 for Illumina® (vazyme).

treatment_protocol: TheCD34+ cells were irradiated with 2Gy γ-rays or nonirradiated.

value: Bone marrow

tag: cell line

tag: time

value: after 2h of IR exposure


title: HUVECs, Sham 1

value: HUVECs

tag: cell type

value: human umbilical vein endothelial cells

value: wt

tag: treatment


title: E7.5 embryo YT_E7-5-2_S5_L002

description:
E7.5 embryo
embryo_filtered.loom

source_name: E7.5 embryo

value: embryonic tissue


title: SIRPG clone 2

data_processing:
Quality of sequencing data was assessed using GC content, and the percentage of adapter content, duplication rate, and homopolymer content in each sample using FASTQC
Duplicated sequence reads were removed using custom Python scripts. Distinct read pairs were aligned to transcript sequences with Bowtie and quantified using RSEM (default parameters)
Transcript counts expressed as TPM were upper-quartile normalized
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include transcript counts as TPM for each sample
Supplementary files format and content: tab-delimited text files include transcript counts as normalized TPM for each sample

source_name: Jurkat cell

extract_protocol:
RNA was isolated from selected clones using the RNeasy Plus Mini kit (Qiagen Cat# 74134). RNA yield was measured by fluorometric quantitation using Qubit RNA Broad Range kit (ThermoFisher Cat# Q10210) and RNA integrity and purity were determined by automated electrophoresis (Agilent TapeStation system)
RNA-seq libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs Cat# E7760) according to manufacturer protocol.

value: Jurkat cell

value: SIRPG exon 4

tag: crispr edit_(rna,_ensembl)


title: Biology Group 3, sample 5

description:
E326
G3_vs_G1_pvalue0.05_fcall.csv

value: Kidney

tag: genotype


title: SIRPG clone 1


title: E7.5 embryo YT_E7-5-2_S5_L001

description:
E7.5 embryo
embryo_filtered.loom


title: Biology Group 2, sample 5

value: Dutch Landrace

tag: group


title: IR_2


title: E8.25 embryo YT_3_S2_L002

description:
E8.25 embryo
embryo_filtered.loom


title: SIRPG clone 5


title: Biology Group 3, sample 4

description:
E324
G3_vs_G1_pvalue0.05_fcall.csv

value: Female


title: IR_1


title: E7.5 embryo YT_E7-5-1_S3_L002

description:
E7.5 embryo
embryo_filtered.loom


title: SIRPG clone 4


title: Biology Group 2, sample 4

value: 6 months to 1 year old


title: E7.5 embryo YT_E7-5-1_S3_L001

description:
E7.5 embryo
embryo_filtered.loom


title: Ctr_3


title: Biology Group 3, sample 3

description:
E322
G3_vs_G1_pvalue0.05_fcall.csv

value: Wild Type


title: SIRPG clone 3


title: ZD101, PE, biol rep 3

city: Chapel Hill

first: Robert

middle: Houston

last: Dowen

state: NC

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

description:
Column names listed in line one for each txt file
FC_gene_read_counts_tir-1_study.txt
DESeq2_norm_gene_counts_tir-1_study.txt
DESeq2_DEGs_ZD101_v_N2_tir-1_study.txt

data_processing:
The adapter-trimmed mRNA-Seq reads were mapped to the WS260 genome using the STAR aligner. The mapping was performed using a GTF obtained from Wormbase (c_elegans.PRJNA13758.WS260.canonical_geneset.gtf) with the parameter --outFilterIntronMotifs RemoveNoncanonical.
The gene-level read counts were calculated using the featureCounts algorithm of the subread package (Liao et al., Bioinformatics, 2014), using the following flags: -t exon -g gene_id -a c_elegans.PRJNA13758.WS260.canonical_geneset.gtf.
Differential expression was calculated relative to the N2 wild-type sample using the DESeq2 package using a 1% FDR cutoff (Love et al., 2014). Comparisons between individual mutants were also performed.
Assembly: WS260
Supplementary files format and content: FC_gene_read_counts_study_name.txt: A tab-delimited text file for each sub-study that includes gene level unnormalized read counts for each sample in matrix format generated using the featureCounts aligorithm.
Supplementary files format and content: DESeq2_norm_gene_counts_study_name.txt: A tab-delimited text file that for each sub-study includes gene level normalized read counts for each sample in matrix format generated using the DESeq2 aligorithm.
Supplementary files format and content: DESeq2_DEGs_sample1_v_sample2_study_name.txt: A tab-delimited text file that includes a list of differentially expressed genes, the log2 FC values, and the p values called by DESeq2 at a 1% FDR threshold for sample1 relative to sample2 for each sub-study.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole animals

growth_protocol: Wild-type and mutant C. elegans animals were synchronized at the L1 stage by egg prep and grown for ~72 hours at 20°C on 10cm NGM Agarose plates (5000 animals/plate) seeded with E. coli OP50 until they reached day 1 of adulthood. For RNAi experiments, synchronized animals were reared on E. coli HT115 bacteria expressing dsRNAs for ~72 hours at 20°C on 10cm NGM Agarose plates containing 5 mM isopropyl-β-D-thiogalactoside (IPTG) and 100 μg/ml ampicillin.

extract_protocol:
Animals were harvested in M9 buffer, washed three times, and flash frozen in liquid Nitrogen. Total RNA was isolated using Trizol.
mRNA-Seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation v2 kit. For the tra-1 and tir-1 studies, mRNA-Seq libraries were prepared by Novogene Inc.

value: tir-1(qd4) III

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50

tag: developmental stage

value: Day 1 adults

value: Whole animals

value: hermaphrodite


title: ZD101, PE, biol rep 2


title: IKZF4 clone 3

tag: crispr target

value: IKZF4 exon 3


title: Ctr_1

value: Bone marrow


title: Biology Group 2, sample 3

value: group 2


title: Biology Group 3, sample 2

description:
E286
G3_vs_G1_pvalue0.05_fcall.csv

value: group 3


title: ZD101, PE, biol rep 1

tag: strain


title: Biology Group 1, sample 4

description:
E285
G3_vs_G1_pvalue0.05_fcall.csv

tag: breed

value: group 1


title: DLS943, PE, biol rep 3

description:
Column names listed in line one for each txt file
FC_gene_read_counts_tir-1_study.txt
DESeq2_norm_gene_counts_tir-1_study.txt
DESeq2_DEGs_DLS943_v_N2_tir-1_study.txt

tag: Sex


title: HEK-293R, dCas9-VP64-FUS_gTetO_RNA-seq rep2

city: ShenZhen

first: Rui

last: Chen

state: GuangDong

address: Southern University of Science and Technology

data_processing:
For RNA-seq data analysis, clean reads were aligned to human reference genome (hg38) supplemented with GFP sequence by HISAT2. Aligned reads were inputted into featureCounts for counting the read number of coding genes and GFP. The genome annotation gtf file was obtained from Ensemble v105 and only coding genes and addition GFP annotation were used for count. The differential expression genes were identified using DEseq2.
Assembly: hg38 supplemented with GFP sequence
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: HEK-293T cells were cultured in DMEM medium with addition of 10% FBS and 1% PS at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using the TRIzol™ reagent (Invitrogen, #15596018).
Sequencing libraries were prepared using the Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit (Yeasen, #12309), with 2 μg of total RNA input.

value: Human embryonic kidney

value: TetO-GFP reporter

value: Transfected by dCas9-VP64-FUS fusion protein and TetO gRNA


title: Biology Group 1, sample 3

description:
E284
G3_vs_G1_pvalue0.05_fcall.csv

value: Kidney

value: Dutch Landrace

tag: age


title: DLS943, PE, biol rep 2


title: Biology Group 2, sample 2

value: Female

value: 6 months to 1 year old


title: IKZF4 clone 1

value: Jurkat cell

value: IKZF4 exon 2

tag: guide rna


title: HEK-293R, dCas9-VP64-FUS_gScramble_RNA-seq rep2

institute: Southern University of Science and Technology

value: Transfected by dCas9-VP64-FUS fusion protein and scrambled gRNA


title: DLS943, PE, biol rep 1

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50

value: Day 1 adults

value: Whole animals


title: HEK-293R, dCas9-VP64-FUS_gScramble_RNA-seq rep1


title: Biology Group 3, sample 1

description:
E262
G3_vs_G1_pvalue0.05_fcall.csv

value: Wild Type


title: Biology Group 2, sample 1

value: group 2


title: HEK-293T, HS2-HBG_treated_by_ABA

data_processing:
*library strategy: ChIA-PET
The obtained sequencing data from the in situ ChIA-PET experiment were subjected to data processing using the ChIA-PIPE software. Visualization of the data was performed using the BASIC Browser. Chromatin Contacts within the regions of interest were plotted as violin plots, with the corresponding pet counts being aggregated on the top. Statistical analysis was conducted using a binomial test to determine the significance, and the resulting p-value was shown.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes track loop for each sample
Supplementary files format and content: tab-delimited text file includes peak for each sample

extract_protocol:
Cells was fixed by 1% Formaldehyde and chromatin was sonicated after cell lysis, nuclei permeabilization, is situ digestion & ligation.
Sequencing libraries were constructed following the established in situ ChIA-PET protocol using 10 million input HEK 293 cells co-expressing both ABI1-mCherry-dCas9-VP64-FUS with gHS2 and PYL1-BFP-dCpf1-VP64-FUS with crRNAs before and after ABA treatment, employing an antibody specifically targeting mCherry

value: Stably expressing ABI-mCherry-dCas9-VP64-FUS and PYL-BFP-dCpf1-VP64-FUS

value: Transfected by HS2 and HBG gRNAs and treated by ABA


title: IKZF4 clone 2

tag: crispr edit_(dna)


title: DLS938, PE, biol rep 2

description:
Column names listed in line one for each txt file
FC_gene_read_counts_tir-1_study.txt
DESeq2_norm_gene_counts_tir-1_study.txt
DESeq2_DEGs_DLS938_v_N2_tir-1_study.txt

value: rict-1(mg360) II; tir-1(qd4) III

value: hermaphrodite


title: Ctr_2

value: Bone marrow


title: HEK-293R, dCas9-VP64-FUS_gTetO_RNA-seq rep1

value: Human embryonic kidney

value: TetO-GFP reporter

value: Transfected by dCas9-VP64-FUS fusion protein and TetO gRNA


title: IKZF1 clone 15

value: IKZF1 exon 6

tag: crispr edit_(rna,_refseq)


title: HEK-293T, HS2-HBG_without_ABA

value: Transfected by HS2 and HBG gRNAs and treated by DMSO


title: IKZF1 clone 14

value: Jurkat cell


title: WT 4

value: WT


title: IKZF4 clone 4

value: IKZF4 exon 3


title: Biology Group 1, sample 1

description:
E259
G3_vs_G1_pvalue0.05_fcall.csv

tag: tissue

value: Kidney

value: Dutch Landrace

value: Female

value: 6 months to 1 year old

value: group 1


title: N2, PE, biol rep 3

description:
Column names listed in line one for each txt file
FC_gene_read_counts_tir-1_study.txt
DESeq2_norm_gene_counts_tir-1_study.txt

value: wild-type

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50

value: Day 1 adults

value: Whole animals


title: HEK-293T, HS2-HBD_treated_by_ABA

tag: cell line

value: Human embryonic kidney

value: Stably expressing ABI-mCherry-dCas9-VP64-FUS and PYL-BFP-dCpf1-VP64-FUS

value: Transfected by HS2 and HBD gRNAs and treated by ABA


title: DLS938, PE, biol rep 1

value: rict-1(mg360) II; tir-1(qd4) III

value: hermaphrodite


title: WT 3

value: Jurkat cell


title: Biology Group 1, sample 2

description:
E260
G3_vs_G1_pvalue0.05_fcall.csv

value: Wild Type


title: N2, PE, biol rep 2


title: DLS938, PE, biol rep 3


title: Mou_SplT_R2

city: 昆明市

first: Lin

last: dongdong

state: 云南

address: 云南省昆明市五华区茭菱路

institute: Peking Union Medical College

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Deduplicated Reads were mapped to the reference genome of macaca mulatta and mus Musculus from Mmul_8.0.1 and GRCm38 respectively using STRA software (version 2.5.3a) with default parameters. Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with an FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
For lncRNA analysis, new lncRNAs were predicted. briefly, The mapped reads were spliced to obtain new transcripts by Stringtie(version 1.3.2). Then，new transcripts were fileted by four principle:1) Filter out the transcripts less than 200bp in length; 2) Filter out the transcripts containing less than 2 exons; 3) Include the transcripts containing at least 3 reads; 4) Remove known transcripts from the genome annotation file. Then, CPC2(version beta)、CPAT(version 1.2.4)、CNCI(version 2) and Pfam(version 27.0)were used to predict the coding potential of the selected transcripts. The transcripts predicted to be non-coding in all four softwares or database were referred to them as novel lncRNA.
The expression of novel lncRNA and genome annotated known lncRNA were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated. LncRNA differentially expressed between groups were identified using the edgeR package (version 3.12.1). P-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of lncRNA expression differences.
Assembly: Mmul_8.0; GRCm38

source_name: spleen

extract_protocol:
Total RNAs were extracted from （monkey and mouse’ organs including heart, liver, spleen, lung, kidney, brain) using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies，Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: spleen

value: CHIKV infection

tag: time


title: Bone marrow, myelofibrosis, Identifier: 1193, batch 2

city: Manchester

first: Naseer

middle: Jr

last: Basma

address: Cancer Research UK Manchester Institute, Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description:
10x Genomics
srt_main.rds.gz
srt_stromal.rds.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger), using  'mkfastq' (parameters:  jobmode=local, localcores=16, localmem=60, barcode-mismatches=1), then 'count' (parameters: transcriptome=GRCh38-2020-A)
The Seurat R toolkit (version 4.0.2 – 4.3.0) was used for QC of each sample separately: filters were applied to identify and discard poor-quality cells ( high mitochondrial gene percentage (<0.15), low number of detected genes (<400) or a high UMI count, which potentially represents multiplets (<30,000))
Counts were normalized, scaled and centred using the global-scaling normalization method “LogNormalize”.
Data from the different samples were integrated using canonical correlation analysis (CCA) (Butler et al., 2018) where sample-wise batch effects were observed. This was applied to the srt.stromal.rds file, but not the srt.main.rds file where no batch effects were observed.
Assembly: GRCh38-2020-A
Supplementary files format and content: Both processed datafiles are R Data Serialization (RDS) files, a common format for saving R objects. The processed data can be retrieved using the readRDS() function in R. Both files were compressed into gzip compression files. The corresponding R objects are Seurat objects, which are representations of single-cell expression data for R

source_name: Bone Marrow

growth_protocol: Trephine samples were kept at 4°C overnight in media culture (Minimum Essential Medium α upplemented with 2mM L-Glutamine, 50U/ml penicillin-streptomycin and 10% Fetal Bovine Serum ), and processed the following day

extract_protocol:
Samples were fragmented then twice subjected to collagenase Type II (1 mg/ml in HBSS) and placed in shaker at 37°C, spun at 200rpm. Cells post-fragmentation, and after each digestion round were pooled and filtered through a 70-µm filter.These cells were then immuno-stained and flow sorted for CD45- Glycophorin A+ (haematopoietic) cells and the CD45- CD71- Glycophorin A- (microenvironmental) cells.These cells were re-pooled at an appropriate fraction,   washed in 0.04% BSA/PBS and submitted for single-cell RNA seq library preparation.
The libraries were prepared using the Chromium Single Cell 3’ Reagent Kit using either v3.0 or v3.1 chemistry.

value: Bone Marrow

tag: cell type

value: Bone Marrow cells

tag: condition

value: MF


title: IKZF1 clone 13

value: IKZF1 exon 6

tag: crispr edit_(rna,_ensembl)


title: Bone marrow, myelofibrosis, Identifier: 1193, batch 1


title: Mou_SplT_R1

address: 云南省昆明市五华区茭菱路

tag: treatment


title: IKZF1 clone 12


title: MGH171, tra-1 RNAi, PE, biol rep 3

description:
Column names listed in line one for each txt file
FC_gene_read_counts_tra-1_study.txt
DESeq2_norm_gene_counts_tra-1_study.txt
DESeq2_DEGs_MGH171_tra-1_v_MGH171_L4440_tra-1_study.txt

tag: genotype

value: sid-1(qt9) V; alxIs9[Pvha-6::SID-1::SL2::GFP]; tra-1 RNAi


title: Mou_SplC_R3

address: 云南省昆明市五华区茭菱路

value: CHIKV control


title: Bone marrow, normal control, Identifier: 728

value: Healthy


title: IKZF1 clone 16


title: MGH171, tra-1 RNAi, PE, biol rep 2

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50

tag: developmental stage

value: Day 1 adults

value: Whole animals


title: IKZF1 clone 21

tag: crispr target

value: IKZF1 exons 4 and 6


title: Mou_SplC_R2

address: 云南省昆明市五华区茭菱路


title: MGH171, tra-1 RNAi, PE, biol rep 1

tag: strain


title: Bone marrow, MF post-Tx, Identifier: 668


title: IKZF1 clone 20


title: MGH171, control RNAi, PE, biol rep 3

description:
Column names listed in line one for each txt file
FC_gene_read_counts_tra-1_study.txt
DESeq2_norm_gene_counts_tra-1_study.txt

value: sid-1(qt9) V; alxIs9[Pvha-6::SID-1::SL2::GFP]; L4440 RNAi


title: Bone marrow, normal control, Identifier: 252


title: IKZF1 clone 19


title: Mou_SplC_R1

address: 云南省昆明市五华区茭菱路


title: Mou_SplT_R3

address: 云南省昆明市五华区茭菱路


title: HEK-293T, HS2-HBD_without_ABA

value: Human embryonic kidney

value: Stably expressing ABI-mCherry-dCas9-VP64-FUS and PYL-BFP-dCpf1-VP64-FUS

value: Transfected by HS2 and HBD gRNAs and treated by DMSO


title: WT 2

value: Jurkat cell

value: WT


title: Mou_LunT_R3

address: 云南省昆明市五华区茭菱路

source_name: lung

value: lung

value: CHIKV infection


title: IKZF1 clone 18


title: Mou_LunT_R2

address: 云南省昆明市五华区茭菱路


title: Bone marrow, MF post-Tx, Identifier:1184

value: Bone Marrow

value: Bone Marrow cells


title: IKZF1 clone 25


title: MGH171, control RNAi, PE, biol rep 1

value: hermaphrodite


title: Mou_LunT_R1

address: 云南省昆明市五华区茭菱路


title: IKZF1 clone 24


title: Mou_LunC_R3

address: 云南省昆明市五华区茭菱路

value: CHIKV control


title: Bone marrow, MF post-Tx, Identifier:1040

value: Healthy


title: IKZF1 clone 23


title: CL6_neg3_Bursa_S4, snRNAseq

city: Columbia

first: Wesley

middle: C

last: Warren

state: MO

address: 1201 Rollins St.

department: Animal Sciences

institute: University of Missouri

description:
10X Genomics
CL6_neg3_Bursa

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were done using Cell Ranger v7.0.1
Cell barcodes from the pseudobulk count matrix analysis output were used as input into pyDESeq2 v0.3.5
To cluster cells, we used the Scanpy platform v1.9.1 and a process based on best practices established in Luecken and Theis, 2019. Briefly, we filtered out nuclei expressing fewer than 200 or more than 2,000 genes, nuclei with total counts greater than 5,000, and nuclei with more than 3% of counts assigned to mitochondrial transcripts or 5% of counts assigned to ribosomal transcripts. We normalized and log-scaled the counts matrix, computed highly variable genes, and regressed out counts per nuclei. We performed principal component analysis (PCA) and then integrated across samples using Harmonypy v0.0.9 to create an adjusted PCA basis. We computed the 10-neighbor graph with the first 20 adjusted principal components clustering using the Leiden algorithm with resolution of 0.5, and visualized it in two dimensions with uniform manifold approximation and projection.
Supplementary files format and content: Tab-separated values files and matrix files

organism: Gallus gallus

source_name: Bursa

extract_protocol:
After euthanizing the birds, spleens and bursae were aseptically removed, and flash frozen in liquid nitrogen then stored at -80 until shipment. The nuclei isolation methods performed were as described in 10X Genomics Isolation of a Single Cell Suspension (10X Genomics). In brief, approximately 50 mg of tissue was homogenized using a glass Dounce homogenizer with ten repeated plunging movements, the homogenate was then filtered first on a 70-micron then a 40-micron cell strainer (Fischer Scientific, Waltham, MA). The nuclei were subsequently washed twice in wash buffer of PBS and 1% BSA. Nuclei were manually counted by staining with trypan blue and a hemocytometer. The nuclei suspension was resuspended in resuspension buffer to a targeted 3,000 nuclei/sample. Single nuclei capture and cDNA preparation were performed with the 10X Genomics Chromium Single Cell 3’ kit, version 2, and lipid encapsulation instrument (10X Genomics, Pleasanton, CA) according to the manufacturer’s recommendations. Pooled libraries were barcoded by sample and sequenced (2x 150 bp length) on an Illumina HiSeq 6000 instrument (Illumina, Inc., San Diego, CA) to achieve 50,000 reads per nuclei.
The individual tissue-specific sequenced Gel Bead-In Emulsion (GEM) libraries were each processed with the CellRanger v7.0.1 pipeline (10X Genomics), which performs demultiplexing, alignment, barcode processing, and sample aggregation to create a cellular barcode by genomic feature matrix. The chicken reference used for all single-nuclei read alignments was bGalGal1b or GRCg7b. First, we used the “cellranger mkgtf” command to filter out everything except protein-coding genes and long non-coding RNAs from the annotation, and then use the “cell ranger mkref” command to create the necessary indices. We aligned reads to this modified GRCg7b reference and generated count matrices for each sample individually using the command “cellranger count” with default options. Molecular barcodes that were most likely to be ambient signals and doublets were eliminated using the default settings of cellranger’s “remove-background” v.0.2.0 function, and cell counts were calculated using cellranger default parameters

value: Bursa

value: Female

value: Immune

value: Control (PBS)

value: 5 weeks


title: Mou_LunC_R2

address: 云南省昆明市五华区茭菱路


title: CL6_neg2_Bursa_S3, snRNAseq

description:
10X Genomics
CL6_neg2_Bursa


title: Bone marrow, myelofibrosis, Identifier:  656

value: MF


title: IKZF1 clone 17

value: IKZF1 exons 4 and 6


title: Bone marrow, normal control, Identifier: 892


title: CL6_neg1_Bursa_S6, snRNAseq

description:
10X Genomics
CL6_neg1_Bursa


title: Bone marrow, normal control, Identifier: 1039


title: Bone marrow, myelofibrosis, Identifier:  1131


title: IKZF1 clone 11

value: IKZF1 exon 4


title: IKZF1 clone 22

value: Jurkat cell


title: CL6_LPS3_Bursa_S12, snRNAseq

description:
10X Genomics
CL6_LPS3_Bursa

value: LPS


title: CL6_LPS2_Bursa_S10, snRNAseq

description:
10X Genomics
CL6_LPS2_Bursa


title: Mou_LivT_R3

address: 云南省昆明市五华区茭菱路

source_name: liver

value: liver


title: Mou_LunC_R1

address: 云南省昆明市五华区茭菱路

value: lung


title: Bone marrow, myelofibrosis, Identifier:  1110

value: Bone Marrow


title: Neg3_S1, snRNAseq

description:
10X Genomics
Neg3_spleen

source_name: Spleen

value: Spleen


title: Bone marrow, myelofibrosis, Identifier:  1043b

value: Bone Marrow cells


title: Mou_LivT_R2

address: 云南省昆明市五华区茭菱路

value: CHIKV infection


title: Bone marrow, MF post-Tx, Identifier: 698b

value: Healthy


title: Mou_LivT_R1

address: 云南省昆明市五华区茭菱路


title: MGH171, control RNAi, PE, biol rep 2

value: sid-1(qt9) V; alxIs9[Pvha-6::SID-1::SL2::GFP]; L4440 RNAi

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50

value: Day 1 adults

value: Whole animals

value: hermaphrodite


title: Neg2_S2, snRNAseq

description:
10X Genomics
Neg2_spleen

value: Female

value: Immune

value: Control (PBS)

value: 5 weeks


title: IKZF1 clone 9

value: Jurkat cell

value: IKZF1 exon 4


title: IKZF1 clone 8


title: Mou_LivC_R2

address: 云南省昆明市五华区茭菱路

value: liver

value: CHIKV control


title: Bone marrow, myelofibrosis, Identifier:  698a

value: Bone Marrow

value: MF


title: IKZF1 clone 10


title: Neg1_S3, snRNAseq

description:
10X Genomics
Neg1_spleen

value: Spleen


title: IKZF1 clone 7


title: Bone marrow, normal control, Identifier:845

value: Bone Marrow cells

value: Healthy


title: Bone marrow, normal control, Identifier: 951


title: Mou_LivC_R3

address: 云南省昆明市五华区茭菱路


title: Mou_LivC_R1

address: 云南省昆明市五华区茭菱路


title: LPS1_S5, snRNAseq

description:
10X Genomics
LPS1_spleen

value: LPS


title: LPS2_S4, snRNAseq

description:
10X Genomics
LPS2_spleen


title: IKZF1 clone 6


title: Bone marrow, myelofibrosis, Identifier:  1086


title: Mou_KidT_R3

address: 云南省昆明市五华区茭菱路

source_name: kidney

value: kidney

value: CHIKV infection


title: hypothalamus, 180 day, M6-4

city: Tai'an

first: Qing

address: Tai’an, Shandong Province, P.R. China

institute: College of Animal Science and Veterinary Medicine

data_processing:
Clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data
Index of the reference genome was built using hisat2-v2.0.5  and paired-end clean reads were mapped to the reference genome.
Stringtie-1.3.3b was used to count the read numbers mapped to each gene.
Assembly: ARS1.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Capra hircus

source_name: hypothalamus

extract_protocol:
RNA was harvested using Trizol reagent.
A total of 1 µg total RNA per sample was used as input material for the lncRNA library preparation. Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: hypothalamus


title: hypothalamus, 180 day, M6-5


title: WT 1

value: WT


title: Mou_KidT_R2

address: 云南省昆明市五华区茭菱路


title: Bone marrow, myelofibrosis, Identifier:  1045


title: Bone marrow, normal control, Identifier: 1079


title: hypothalamus, 180 day, M6-3


title: Mou_KidT_R1

address: 云南省昆明市五华区茭菱路


title: IKZF1 clone 5


title: Mou_KidC_R3

address: 云南省昆明市五华区茭菱路


title: hypothalamus, 180 day, M6-2


title: HEK293CDK7as_MNaseChIPseq_Input_Ser5P_SPT5_1-NM-PP1_30min_Rep3

data_processing:
All sequencing data were demultiplexed with Illumina bcl2fastq demultiplexing software, provided the barcodes for each of the samples, and subsequently quality checked with FastQC (Babraham-Institute) (Andrews, 2010).
TT-seq: For all samples, paired-end 75 base reads were mapped using STAR (v 2.6.1b) (Dobin et al., 2013) to the GRCh38.p13 genome assembly merged with synthetic RNA spike-in sequences (Schwalb et al., 2016; Żylicz et al., 2019) with a maximum 2% mismatches [mapping parameters: --outFilterMismatchNoverLmax 0.02 --outFilterMultimapScoreRange 0 --alignIntronMax 500000]. SAMtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f2) were selected.  A spike-in (RNA) normalization strategy was used essentially as described (Schwalb et al., 2016). This spike-in normalization allows for calculating sequencing depth σ_j, cross-contamination rate ϵ_j, and antisense bias ratio c_j. Sequencing depth σ_j allows to observe global shifts. The read counts (kij) for spike-ins were calculated using HTSeq (Anders et al., 2015).
mNET-seq: For all samples, paired-end 45 base reads were trimmed for adapters (-a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACT), and low-quality bases (< Q20) were removed with Cutadapt (v 1.9.1) (Martin, 2011). The reads were then mapped to the GRCh38.p13 genome assembly merged with the yeast genome version SacCer3 using STAR (v 2.5.2b) (Dobin et al., 2013) with a maximum of 2% mismatches [mapping parameters: --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.02 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 500000 ]. Samtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, where alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f 2) were selected.   Read counts (kij) for yeast genes for each condition j (control or CDK7as inhibited) were calculated using HTSeq (Anders et al., 2015). The counts data was used to generate normalization factors with DESeq2 (Love et al., 2014) to normalize the mNET-seq data.
MNase-seq: For all samples, paired-end 45 base reads were trimmed for low-quality bases, random matches, and for a minimum length [trimming parameters: -q 20,20 -O 12 -m 25] with Cutadapt (v 1.9.1) (Martin, 2011). Processed reads were then mapped to the GRCh38.p13 genome assembly using STAR (v 2.6.1b) (Dobin et al., 2013) with maximum 2 percent mismatches [mapping parameters: --outFilterMismatchNoverLmax 0.02 --outFilterMultimapScoreRange 0 --alignIntronMax 1]. Samtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, where alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f 2) were selected.
MNase-ChIP-seq: For all samples, paired-end 43 base reads were mapped using Bowtie 2 (v 2.3.4.1) (Langmead and Salzberg, 2012) to the merged human hg38 (GRCh38.p13) and Drosophila (BDGP6.28) genome assembly [mapping parameters: --no-discordant --no-mixed --very-sensitive]. SAMtools (v 1.3.1) (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped, and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. Duplicate fragments and fragments longer than 100 bp (70 bp for Pol II) were excluded from further analysis. MNase-ChIP-seq coverages were obtained from piled-up fragment midpoint counts for every genomic position. Pol II, Ser5P, and SPT5 coverages were normalized to the signal at untranscribed regions to allow for the detection of global changes. To this end, genome-wide coverage was calculated from all MNase-ChIP-seq fragment midpoints in consecutive 2 kbp bins throughout the non-transcribed human genome (i.e. excluding 32,789 transcribed units we annotated using GenoSTAN (Zacher et al., 2017) and everything annotated in GENCODE v31) and used to generate normalization factors with DESeq2 (Love et al., 2014). For all other factors, which exhibited a peak-like binding behavior, normalization factors were obtained from total human fragment counts. Bigwig files are for normalized (except Inputs), entire fragment coverages.
Assembly: GRCh38
Supplementary files format and content: bigwig files

source_name: genome edited HEK293

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, 11960085) supplemented with 10% fetal bovine serum (Gibco, 10500–064) and 1 % GlutaMAX (Thermo Fisher Scientific, 35050087) in a humidified incubator at 37°C and 5% CO2. Cells were passaged every 2-3 days using 0.25% Trypsin-EDTA (Gibco, 25200056). Biological replicates were cultured separately. All cell lines were verified to be free of mycoplasma contamination with PlasmoTest Mycoplasma Detection Kit (InvivoGen).   Drosophila Schneider-2 (S2) cells, used for MNase-ChIP-seq spike-ins, were obtained from DSMZ (ATCC Cat# CRL-1963, RRID: CVCL_Z232) and cultured in Schneider's Drosophila-Medium (Gibco, 21720024) supplemented with 10% fetal bovine serum (Gibco, 10500–064) in a non-humidified incubator at 27°C, protected from light.  Yeast S. cerevisiae cells (BY4741 strain), used for mNET-seq spike-ins, were obtained from Euroscarf (ACC-Y00000) and cultured in yeast medium (YP + 2% glucose) at 30°C until OD595 of 0.8 was reached.

extract_protocol:
TT-seq: Total RNA was extracted using TRIzol reagent (Invitrogen, 15596026), 4sU-labeled RNA was extracted according to Gressel at al., protocols.io, 2019.
mNET-seq: mNET-seq was performed as previously described (Caizzi et al. 2021; Gressel et al. 2017; Nojima et al. 2016; Schlackow et al. 2017) with minor changes. 50 mio CDK7as cells were treated for 15 or 30 min with 7.5 μM of 1-NM-PP1 or DMSO (solvent control). After the treatment, chromatin isolation was performed as described in the protocol for cellular fractionation (Conrad et al. 2017) using 25 mio cells per reaction. All buffers were supplemented with 7.5 μM 1-NM-PP1 or respective amounts of DMSO, protease (Sigma-Aldrich, P8340), and phosphatase (Roche, 4906837001) inhibitors. After the fractionation, the chromatin pellet was digested in 100 μl MNase digest buffer (1x MNase buffer, 1x BSA, 100 mM NaCl, 50 units/μl MNase (NEB, M0247S)) at 37°C and 1,400 rpm for 2 min. The digestion was stopped by adding 11 μl of 250 mM EGTA, and samples were centrifuged at 13,000 g for 5 min at 4°C. Supernatants were pooled together for each sample and 8-fold diluted with IP buffer (50 mM Tris HCl pH 7.4, 150 mM NaCl, 0.05% NP-40, 0.3% empigen (Sigma-Aldrich, 30326)). 15 μg of anti-Pol II CTD antibody (Diagenode, C15200004) conjugated with 125 μl of Dynabeads M-280 Sheep Anti-Mouse IgG (Invitrogen, 11201D) were added to each sample and incubated on a rotating wheel at 4°C and 12 rpm for 1 h. After IP, beads were washed seven times with 1 ml of IP buffer and once with 300 μl of PNKT buffer (1x T4 PNK buffer (NEB, M0236L), 0.1% Tween-20). After washes, 5’ RNA ends were phosphorylated with T4 Polynucleotide Kinase (PNK) (3' phosphatase minus; NEB, M0236L) at 800 rpm for 10 min at 37°C. Next, beads were washed once with IP buffer, and 0.5 ml of TRIzol reagent (Invitrogen, 15596026) was added to the beads. 2.5 ng of S. cerevisiae spike-ins were added to each sample in TRIzol. RNA spike-ins for mNET-seq were obtained from S. cerevisiae cells as previously described (Caizzi et al. 2021). RNA was extracted from beads, followed by RNA precipitation with 100% ethanol and GlycoBlue coprecipitant (Invitrogen, AM9515) at -80°C overnight. RNA pellets were washed twice with 70% ethanol, air-dried, and dissolved in 7 M urea. In order to size select 25-110 nt RNA, samples were resolved on 6% polyacrylamide gel containing 7 M urea. RNA of corresponding sizes was extracted from the gel and precipitated with 100% ethanol and GlycoBlue coprecipitant.
MNase-seq: 5 mio CDK7as cells were treated for 15 min with 7.5 μM of 1-NM-PP1 or DMSO (solvent control) and centrifuged at 500 g for 3 min at 4°C. Cell pellets were resuspended in 50 μl of Buffer I (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 10 % sucrose, 0.5 mM CaCl2) and incubated at 37°C for 2 min. Next, we added 500 μl of Buffer II (50 mM Tris-HCl pH 7.5, 50 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 10 % sucrose, 2 mM CaCl2) supplemented with 3,000 U of MNase (NEB, M0247S) and incubated at 37°C for 9 min. MNase digestion was quenched with 11 μl of EGTA (500 mM). 550 μl of SDS Lysis Buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) was added, and samples were incubated on ice for 10 min. Samples were then treated with 0.1 μg/μl RNAse A (Thermo Scientific, EN0531) for 1.5 h at 37°C and 0.05 μg/μl Proteinase K (Life Technologies, AM2546) for 4 h at 65°C. DNA was extracted with an equal volume of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich, P2069), followed by DNA precipitation with an equal volume of 100% ethanol and 200 mM NaCl for 2 h at -20°C. DNA pellets were washed twice with 1 ml of 70% ethanol, air-dried, and dissolved in water.
MNase-ChIP-seq: MNase-ChIP-seq was performed as previously described (Skene et al. 2015) with the following changes. 40 mio CDK7as cells were treated for 30 min with 7.5 μM of 1-NM-PP1 or DMSO (solvent control), following 8 min crosslinking with 1% formaldehyde (16% formaldehyde (w/v), methanol-free, Thermo Fisher Scientific, 28908). The crosslinking was quenched for 5 min with 125 mM glycine, and cells were washed with 10 ml PBS at room temperature. 2 ml of ice-cold PBS was added to plates for cell scraping. Scraped cells were transferred to falcons, washed twice with 5 ml ice-cold PBS, and centrifuged at 200 g for 5 min at 4°C. All buffers were supplemented with protease (Sigma-Aldrich, P8340) and phosphatase (Roche, 4906837001) inhibitors. Cell pellets were lysed with 5 ml of Farnham Lysis buffer (5 mM Pipes pH 8, 85 mM KCl, 0.5% NP-40) for 10 min on ice. Nuclei were pelleted by centrifugation at 1,700 g for 5 min at 4°C and washed with ice-cold PBS. Nuclei pellets were resuspended in 200 μl of 1% SDS Lysis buffer (50 mM Tris HCl pH 8.0, 10 mM EDTA, 1% SDS) and incubated for 10 min at room temperature to permeabilize nuclei. The reaction was quenched with 1.8 ml of IP buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100) supplemented with 5 mM CaCl2 and incubated for 2 min at 37°C before the addition of 16,000U of MNase (NEB, M0247S) for 20 min at 37°C. MNase digestion was quenched with 40 μl of EDTA (500 mM) and 20 μl EGTA (500 mM). 1 ml of sample was transferred to AFA milliTubes (Covaris, 520135) and sonicated with a Covaris S220 Focused-ultrasonicator with the following parameters: 5% duty cycle, 140 W peak incident power, 200 cycles per burst, 600 sec processing time, 6°C bath temperature, continuous degassing mode, water level 8. Sonicated samples were centrifuged at 10,000 g for 15 min at 4°C, and supernatants were snap-frozen in liquid nitrogen and stored at −80°C before use. For each IP, 30 μg of sample chromatin and 200 ng of Drosophila S2 MNase-digested crosslinked chromatin were diluted in IP buffer to obtain a final concentration of 0.05% SDS and a final volume of 1.6 ml. Pre-clearing was carried out by adding 20 μl of Dynabeads Protein G (Thermo Fisher Scientific, 10009D) diluted in IP buffer, and incubating for 30 min at 4°C on the rotation wheel. Pre-cleared samples were incubated with 10 μg of Pol II (RPB1, Diagenode, C15200004), 10 μg of Ser5P (phospho-CTD Ser-5 of RPB1, Merck Millipore, 04-1572), 8 μl of Mediator (MED26, Cell Signaling, 14950), 6 μg of TFIIB (Santa Cruz, sc-271736), 5 μg of TFIIE (TFIIE-α, abcam, ab28177), 6 μg of NELF (NELF-E, Bethyl Laboratories, A301-913A) or 6 μg of SPT5 (Proteintech, 16511-1-AP) together with 1 μg of Spike-in (Active Motif, 61686) antibodies at 4°C overnight. The next day samples were centrifuged at 16,000g for 2 min at 4°C and inputs were taken for each sample. Samples were incubated for 2 h at 4°C with Dynabeads Protein G. Beads were washed once with Buffer 1 (20 mM Tris HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), four times with Buffer 2 (20 mM Tris HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with Buffer 3 (10 mM Tris HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% sodium-deoxycholate), and three times with TE buffer (10 mM Tris HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). After the last wash, 200 μl of elution buffer (0.1 M NaHCO3, 160 mM NaCl, 1% SDS) was added to the beads, and samples were de-crosslinked overnight at 65°C. Next, samples were diluted with 200 μl of PBS and treated with 0.02 μg/μl RNAse A (Thermo Scientific, EN0531) for 1.5 h at 37°C and 0.2 μg/μl Proteinase K (Life Technologies, AM2546) for 2 h at 45°C. DNA was extracted with an equal volume (400 μl) of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich, P2069), followed by DNA precipitation with 100% ethanol and 200 mM NaCl for 1 h at -80°C. DNA pellets were washed twice with 70% ethanol, air-dried, and dissolved in water.
TT-seq: Libraries were prepared from 100 ng of RNA with the strand-specific Ovation Universal RNA-Seq library kit (NuGEN, 0343-32).
mNET-seq: 8.4 ng of RNA for replicate 1 and 12.3 ng of RNA for replicate 2 were used for library preparation with TruSeq Small RNA Library Prep Kit (RS-200-0048) according to the manufacturer’s instructions.
MNase-seq: Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s instructions.
MNase-ChiP-seq: Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s instructions with adjusted for short fragments end repair, 5’ phosphorylation, and dA-tailing thermocycler program (30 min at 20°C, 1 h at 50°C; the heated lit set to 60°C). After amplification, libraries were double-sided (1.0 – 1.6x) size-selected with Agencourt AMPure XP beads (Beckman Coulter, A63881).

value: genome edited HEK293

value: Human embryonic kidney

value: analog-sensitive CDK7

value: 30 min 1-NM-PP1

tag: immunoprecipitation antibody

tag: method

value: MNase-ChIP-seq


title: HEK293CDK7as_MNaseChIPseq_Input_Ser5P_SPT5_1-NM-PP1_30min_Rep2


title: U118-SPNS2, rep2

city: Guangzhou

first: Waiyip

last: Leung

state: Guangdong

address: Guangzhou Higher Education Mega Centre, Panyu District

institute: South China University of Technology

data_processing:
TrimGalore v0.6.9, Hisat2 v2.2.1, featureCounts v.0.3
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore.
Trimmed sequence reads were mapped to hg38 using Hisat2
Read count extraction and normalization were performed using featureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

growth_protocol: The cell lines U118MG were cultured at 37˚C, 5% CO2, and 10% fetal bovine serum in DMEM.

extract_protocol:
U118-SPNS2 and U118-NC were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For lentiviral vectors expressing SPNS2 and negative control (NC), the corresponding cDNAs were cloned into the pCDH-CMV-MCS-EF1-puro overexpression vector, then U118-MG were infected with lentivirus-mediated SPNS2 overexpression vector and negative control vector

value: glioma cell

value: SPNS2 overexpressed


title: hypothalamus, 180 day, M6-1


title: Mou_KidC_R2

address: 云南省昆明市五华区茭菱路

value: CHIKV control


title: HEK293CDK7as_MNaseChIPseq_Input_Ser5P_SPT5_1-NM-PP1_30min_Rep1


title: U118-SPNS2, rep1


title: Mou_KidC_R1

address: 云南省昆明市五华区茭菱路


title: hypothalamus, 120 day, M4-5


title: HEK293CDK7as_MNaseChIPseq_Input_Ser5P_SPT5_DMSO_30min_Rep3

value: 30 min DMSO


title: U118-NC, control, rep2

value: control


title: U118-NC, control, rep1


title: Mou_HeaT_R3

address: 云南省昆明市五华区茭菱路

source_name: heart

value: heart


title: HEK293CDK7as_MNaseChIPseq_Input_Ser5P_SPT5_DMSO_30min_Rep2


title: hypothalamus, 120 day, M4-4


title: Mou_HeaT_R2

address: 云南省昆明市五华区茭菱路


title: Bone marrow, myelofibrosis, Identifier: 1043a

value: Bone Marrow

value: Bone Marrow cells

value: MF


title: HEK293CDK7as_MNaseChIPseq_Input_Ser5P_SPT5_DMSO_30min_Rep1


title: Mou_HeaT_R1

address: 云南省昆明市五华区茭菱路

value: CHIKV infection