title: 191227_Lec_L5Ba_IgG1


title: Histone_3_K27_acetylation, DIPG4, DMSO, radiation, replicate 2

status: Public on Apr 12 2024

type: SRA

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

country: USA

institute: University of Colorado, Denver - Anschutz Medical Campus

library_source: genomic

data_processing:
The quality of fastq files was accessed using FastQC (v.0.11.8), FastQ Screen (v.0.13.0) and MultiQC (v.1.8).
The Illumina adapters and low quality reads were filtered using BBDuk with the parameters for paired-end reads.
The ATAC-seq reads were aligned to the hg38 genome assembly using bowtie2 (v.2.3.4.3).
Samtools (v. 1.11) was used to select the mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates tool (v.2.21.1).
Bedtools genomecov (v.2.27.1) was used to create bedgraph files from the bam files.
Bigwig files were created using deepTools bamCoverage (v.3.2.1) and visualized using IGV (v.2.8.2).
Peaks were called using MACS2 (v2.1.2) using ENCODE recommendations.
IDR (v.2. 0.3) was used to identify the reproducible peaks between the replicates.
Further processing of the peak data was performed in R, using in particular the following tools: valR  (v.0.6.4), and DiffBind (v.3.6.2).
Metagene plots and heatmaps were generated using ngs.plot (v.2.61).
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: DIPG4 cell lines were cultured in 50% Neurobasal-A medium (Invitrogen), 50% DMEM/F12(Invitrogen) supplemented with 1 mM sodium pyruvate (Gibco), 10mM HEPES Buffer Solution, 1mM MEM Non-Essencial Amino Acids, GlutaMAX-I Supplement. 1× penicillin/streptomycin solution, 1x B-27 Supplement Minus Vitamin A, H-EGF, H-FGF basic 154, H-PDGFAA, H-PGF -BBa and Heparin Solution 0.25%. Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
Cells were crosslinked with 1% formaldehyde added to the growth media for 10 min, followed by quenching with 0.125M glycine for 5 min. Cells were washed twice with cold PBS, collected in ice-cold PBS by scraping, pelleted, and resuspended in cell lysis buffer (5mM PIPES, pH 8.0; 85mM KCl; 0.5% NP-40). Following incubation on ice for 10 min, a nuclear-enriched fraction was collected by centrifugation for 5 min at 2500 xg at 4 C. Pellet was resuspended in ChIP lysis buffer (50mM Tris-HCl, pH 8.0; 10mM EDTA; 1% SDS) containing COmplete EDTA free protease inhibitors (Sigma) and quantified with BCA. 2ug/ul of lysates were sonicated with a Bioruptor Plus (Diagenode) for 20 cycles (30 seconds ON and 30 seconds OFF). The size of the sonicated DNA fragments was checked on an 1X TAE 1% agarose gel electrophoresis and ranged between 250 to 500 bp. After removing the debris via centrifugation, chromatin extracts were collected.   For immunoprecipitation, chromatin extracts were diluted with Chip Dilution Buffer (16.7mM Tris-HCl, pH8.1, 1.2Mm EDTA, 167mM NaCl, 0.01%SDS and 1.1% Triton x100) incubated with primary antibodies anti-K27Ac (#39133, Active Motif) overnight at 4 C.  After incubation with the primary antibody, 20 uL of pre-washed magnetic beads (Magna ChIP Protein A+G Magnetic Beads, Millipore Sigma) were added to each sample for 2 hours at 4 C. Using a magnetic rack, the immunoprecipitates were washed successively with 1 ml of low salt buffer (20 mM Tris-HCl [pH 8.0], 150 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), high salt buffer (20 mM Tris-HCl [pH 8.0], 500 mM NaCl, 0.1% SDS, 1% triton X-100, 2 mM EDTA), LiCl washing buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 1.0% NP40, 1.0% deoxycholate, 1 mM EDTA) and twice with TE buffer. The DNA-protein complexes were eluted with 300 µl of IP elution buffer (1% SDS, 0.1 M NaHCO3). The cross-links were reversed by adding NaCl (a final concentration 0.2 M) into the eluents and incubating them at 65  C overnight. The DNA was recovered by proteinase K and RNase A digestion, followed by phenol/chloroform extraction and ethanol precipitation. Pellets were resuspended in 25 ul of RNase and DNase free water, and ChIP-DNA was quantified using the Qubit dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific), followed by library preparation.
The NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #E7645S) with Dual Index Primers (NEB #E7600) were used to library preparation for ChIP-seq.    NEBNext End Prep  1x TE was added to the DNA to get final volume of 50 ul and mixed with 3 ul of NEBNext Ultra II End Prep Enzyme Mix and 7 ul of NEBNext Ultra II End Prep Reaction Buffer. This was placed in a thermocycler with heated lid set to 75 C and run for 30 minutes at 20 C, 60 minutes at 50 C, then held at 4 C.  Adaptor Ligation  The adaptor ligation reaction was performed with 60 ul of Prep Reaction Mixture, 2.5 ul of NEBNext Adaptor for Illumina diluted following the manufacture recommendations, 30 ul of NEBNext Ultra Ligation Master Mix, and 1 ul of NEBNext Ligation Enhancer, incubated at 20 C for 15 min with heated lid off. 3 ul of USER Enzyme was then added to the reaction and incubated at 37 C for 15 min with heated led set to 47 C.  Cleanup of Adaptor-Ligated DNA without size selection  1.1x of AMPure XP Beads were added to the Adaptor Ligation reaction, and samples were incubated for 5 min at room temperature. Tubes were placed on a magnetic stand for 5 min to separate beads from supernatant, then supernatant was removed and beads were washed 2 times with 200 ul of 80% freshly prepared ethanol. Beads were air dried for up 5 min while tubes were on magnet with lid open. DNA was eluted from the beads by adding 17 ul of 0.1XTE buffer.   PCR Enrichment of Adaptor-ligated DNA  To 15 ul of the Adaptor Ligated DNA fragments was added 25 ul of NEBNext Ultra Q5 Master Mix, 5 ul of Index primer i7 and 5 ul Universal PCR Primer i5, and PCR amplification was performed following the cycling conditions: 98 C for 45s, 98 C 15s and 60 C 10s for 16 cycles, 72 C for 1 min, and hold at 4 C. Followed by a clean up of the PCR reaction using AMPure XP Beads.   The DNA was quantified using Qubit, and the quality and size of libraries were checked at the Bioanalyzer prior to sequencing.

treatment_protocol: Cells were treated with DMSO or 40nM AZD4573. After 2 hrs, cells were irradiated at 6 Gy and collected after an additional 4 hrs.

tag: cell line

tag: cell type

value: Diffuse intrinsic pontine glioma

tag: treatment

value: DMSO and 6 Gy radiation

tag: chip antibody

value: H3K27Ac_histone H3_acetyl K27; Abcam Cat. #ab4729


title: shNT_IN_H3K27ac_1

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

data_processing:
ChIP-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
ChIP-seq data processing included sequencing reads filtering based on quality and adapter sequences removal using Trim_galore (https://github.com/FelixKrueger/TrimGalore) with the default options.
The resulting fastq files were aligned to the human reference genome (hg19) using bowtie2 (Langmead& Salzberg, 2012) with the following parameters:” -N 1 -L 25 -X 500 --no-mixed --no-discordant”; the rest of the options were set to the default. Duplicated reads were removed from the bam files using MarkDuplicates software (http://broadinstitute. github.io/picard/).
H3K3me3 and H3K27ac ChIP-seq peak calling was done with Macs2 (q-value < 0.01). DeepTools software (https://deeptools.readthedocs.io/en/develop/) was used to generate BigWig files (“bamCoverage” function) and produce ChIP-seq heatmaps (“computeMatrix” and “plotHeatmap” functions).
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: The GSCs were cultured in human neural stem cell Maintenance Media (Millipore), 1% Penicillin-Streptomycin (PS) supplemented with EGF and FGF (20 ng/ml each) to maintain stemness.

extract_protocol:
GSC cells were cross-linked with 1% formaldehyde for 10 min at room temperature. The cells were lysed using SDS Lysis buffer for ChIP (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8). The lysate was then sonicated for 25 cycles at 30% amplitude (15 s ON and 45 s OFF). The sonicated samples were then diluted in ChIP dilution buffer (0.01% SDS, 1% Triton-X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8, 167 mM NaCl) and used for the immunoprecipitation with anti-H3K4me3 (Abcam, Ab8580), or H3K27ac (Abcam, Ab4729) beads. After an over-night incubation with antibody, the bound DNA was washed sequentially with low salt wash buffer (0.1% SDS, 1% Triton X 100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% NP40, 1%deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8) and TE wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA) to remove non-specific sequences and eluted in the elution buffer (84 mg NaHCO3, 1 ml 10% SDS, 9 ml H2O). Then the samples were reverse cross-linked using NaCl at 65°C overnight. The eluted DNA was purified and used for library preparation.  Briefly, end repair with NEBNext End Repair enzyme (NEB, E6050) and clean-up with 2.4x volume AMPure XP beads (Beckman Coulter, A63880). A-tailing with Klenow Fragment (3'?5' exo-, NEB, M0212) and purified with 2.4x volume AMPure XP beads. Adapter ligation reactions contained annealed universal adapter and T4 rapid ligase (NEB, B0202) and clean-up with 1.8x volume AMPure XP beads. Chromatin was amplified using KAPA Real-time Library Amplification Kit (KAPABIOSYSTEMS, KK2701) with universal primer and barcoded primer. Amplified chromatin was purified with QIAquick Gel Extraction Kit (Qiagen).
Library preparation was performed as previously described as described in Bowman et al. BMC Genomics 2013. Briefly, end repair with NEBNext End Repair enzyme (NEB, E6050) and clean-up with 2.4x volume AMPure XP beads (Beckman Coulter, A63880). A-tailing with Klenow Fragment (NEB, M0212) and purified with 2.4x volume AMPure XP beads. Adapter ligation reactions contained annealed universal adapter and T4 rapid ligase (NEB, B0202) and clean-up with 1.8x volume AMPure XP beads. Chromatin was amplified using KAPA Real-time Library Amplification Kit (KAPABIOSYSTEMS, KK2701) with universal primer and barcoded primer. Amplified chromatin was purified with QIAquick Gel Extraction Kit (Qiagen) and sequenced paired-end with Illumina NextSeq 500.

treatment_protocol: ChIP-seq from glioblastoma stem cell specimens (TS-576) following treatment with either non-targeting RNA (shNT), targeting RNA sh515 or targeting RNA sh516.

value: Glioblastoma patient derived cancer stem cell

tag: genotype

value: wild type

value: non-targeting RNA (shNT)


title: 25_ENDO5_t1_MB_NK

city: Huddinge

first: Dan

last: Sun

address: Alfred Nobels allé 8

department: MedH

country: Sweden

institute: Karolinska Institutet

description: Longitudinal ind1 t1

library_source: transcriptomic

data_processing:
Adaptor and quality trimming (-q 30) of RNAseq data was performed using Trim Galore! 0.6.1.
Processed RNA-seq reads were then aligned to the human genome (GRCh38 build) using HISAT2 2.2.1 (Kim et al., 2019), and non-uniquely and non-paired alignments were filtered out by the 'view’ command of SAMTools 1.12 (-f 2 -q 60).
Non-uniquely and non-paired alignments were filtered out by the 'view’ command of SAMTools 1.12 (-f 2 -q 60).
StringTie 2.1.4 was used to count the number of reads per gene per sample, and DESeq2 was used to normalize counts across libraries.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values

molecule: polyA RNA

source_name: Menstrual blood

extract_protocol:
PB CD56dim and MB uNK cells as well as PB CD8+ TEM and MB CD8+ TRM cells were pre-gated on alive CD45+CD14-CD15-CD19- cells and sorted directly into 300 ul of RLT plus buffer (QIAGEN) in a sterile ribonuclease- and DNase-free 1.5 ml Eppendorf tube and frozen on dry ice immediately after sorting. RNA was isolated with the RNeasy Plus Micro Kit (QIAGEN).
Extracted RNA was quality tested with a Bioanalyzer Pico kit (Agilent), before cDNA was generated with the Smart-seq v4 (Clontech). Next, indexed cDNA libraries were normalized, combined, and pool-sequenced on the Illumina NextSeq 550 for a 75-cycle v2.5 sequencing generating 150–base pair paired-end reads.

tag: tissue

value: Menstrual blood

value: uNK

tag: sample type

value: longitudinal

tag: cmv

value: pos


title: shNT_H3K27ac_IP2


title: mESC Srrm2 KD 72h Replicate 3

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

data_processing:
Expression levels from RNA-seq profiles were pseudo-aligned using Kallisto v0.46.1 (Bray et al., 2016, Nat. Biot. 34, p.525).
Assembly: mm10 (M24)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Mus musculus

growth_protocol: mESCs E14tg2a.4 were grown as previously described (Ferrai et al. 2017 Mol. Syst. Biol. 13, p. 946) on 0.1% v/v gelatin-coated flasks in GMEM medium with LIF and additional supplements. Prior to collection of material for experiments, cells were grown for 24h or 72h in serum-free ESGRO medium supplemented with LIF.

extract_protocol:
Total RNA  from three replicates of each condition was isolated with TRIzol (Invitrogen) and DNA was degraded with TURBO DNase (Invitrogen), according to the manufacturer’s protocol.
RNA spike-ins (Invitrogen) were added to each purified RNA sample. PolyA RNA-seq libraries were produced from 1 ug of RNA using the TruSeq® Stranded mRNA Library Prep kit (Illumina), according to the manufacturer's instructions. The libraries were paired-end sequenced using the NovaSeq 6000 system at 100-bp length, according to the manufacturer's protocol.

treatment_protocol: mESC were transfected using OptiMEM (Invitrogen), Lipofectamine RNAiMAX (Invitrogen) and 50 nM synthetic siRNA duplexes (Eurogentec) targeting either Srrm2 or firefly luciferase (GL2), which was used as a control. RNA interference was done according to the manufacturer’s instructions. Cells were harvested at 24h or re-transfected with the same siRNA duplexes and transfection reagents and harvested 72h after seeding.

value: mouse embryonic stem cells

value: Srrm2 knockdown

tag: Sex

value: male


title: Histone_3_K27_acetylation, DIPG4, DMSO, radiation, replicate 1


title: mESC Srrm2 KD 24h Replicate 3


title: 32_ENDO5_t1_PB_CD8T

description: Longitudinal ind1 t1

source_name: Peripheral blood

value: Peripheral blood

value: CD8+ Tem


title: shNT_IN_H3K27ac_2


title: 24_MZ05_B_PB_CD8T

description: Twin pair3 ind2

value: twin


title: mESC Srrm2 KD 72h Replicate 2


title: mESC Control 72h Replicate 2

value: Gl2 knockdown


title: shNT_H3K27ac_IP1


title: Histone_3_K27_acetylation, DIPG4, DMSO, replicate 2

value: Diffuse intrinsic pontine glioma

value: DMSO


title: sh516_IN_H3K27ac_2

value: METTL8 targeting RNA (sh516)


title: mESC Control 72h Replicate 1


title: MDA-MB-453, Scrambled, Sample ID 1, rep1

city: Turku

first: Teemu

middle: Daniel

last: Laajala

address: Turun yliopisto

department: Department of Mathematics and Statistics

country: Finland

institute: University of Turku

data_processing:
Reads were called using the manufacturer's bcl2fastq2 base calling software.
Reads were then aligned the reference genome (hg38) using R-package Rsubread (v2.0.0) function align, with the reference genome along with annotations downloaded from Illumina iGenomes web site.
Reads were then associated with known genes and the number of reads associated with each gene was counted using the Rsubreads package v2.0.0, with non-default parameters for isPairedEnd="yes" and strandSpecific=2.
Gene-wise read counts were normalised using the TMM normalization method of the edgeR R/Bioconductor package with log(x+1) transformation for downstream applications.
The data processing pipeline was run using default parameters when possible.
Assembly: hg38
Supplementary files format and content: Tab-separated gene-wise expression (rows) per samples (columns) normalized using TMM.

molecule: total RNA

growth_protocol: MDA-MB-453 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Illumina TruSeq Stranded Total mRNA kit
RNA was harvested using the NucleoSpin RNA purification kit (Macherey‐Nagel). 300 ng of total RNA was used for the construction of sequencing libraries.
TruSeq® Stranded mRNA Sample Preparation, Illumina

value: HER2+ breast cancer cell line

value: WT


title: Histone_3_K27_acetylation, DIPG4, DMSO, replicate 1

value: H3K27Ac_histone H3_acetyl K27; Abcam Cat. #ab4729


title: mESC Control 24h Replicate 3


title: mESC Srrm2 KD 24h Replicate 2


title: 23_MZ05_B_PB_NK

description: Twin pair3 ind2

value: CD56dim NK


title: 22_MZ05_A_PB_CD8T

description: Twin pair3 ind1


title: mESC Srrm2 KD 24h Replicate 1


title: sh516_IN_H3K27ac_1

value: Glioblastoma patient derived cancer stem cell

value: wild type


title: 21_MZ05_A_PB_NK

description: Twin pair3 ind1

value: pos


title: mESC Control 24h Replicate 2

value: mouse embryonic stem cells


title: IgG, DIPG4, AZD4573_with_radiation, replicate 2

data_processing:
The quality of fastq files was accessed using FastQC (v.0.11.8), FastQ Screen (v.0.13.0) and MultiQC (v.1.8).
The Illumina adapters and low quality reads were filtered using BBDuk with the parameters for paired-end reads.
The ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 (v.2.3.4.3).
Samtools (v. 1.11) was used to select the mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates tool (v.2.21.1).
Bedtools genomecov (v.2.27.1) was used to create bedgraph files from the bam files.
Bigwig files were created using deepTools bamCoverage (v.3.2.1) and visualized using IGV (v.2.8.2).
Peaks were called using MACS2 (v2.1.2) using ENCODE recommendations.
IDR (v.2. 0.3) was used to identify the reproducible peaks between the replicates.
Further processing of the peak data was performed in R, using in particular the following tools: valR  (v.0.6.4), and DiffBind (v.3.6.2).
Metagene plots and heatmaps were generated using ngs.plot (v.2.61).
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT & RUN

growth_protocol: DIPG4 cell lines were cultured in 50% Neurobasal-A medium (Invitrogen), 50% DMEM/F12(Invitrogen). supplemented with, 1 mM sodium pyruvate (Gibco), 10 mM HEPES Buffer Solution, 1 mM MEM Non-Essencial Amino Acids, GlutaMAX-I Supplement. 1× penicillin/streptomycin solution, 1x B-27 Supplement Minus Vitamin A, H-EGF, H-FGF basic 154, H-PDGFAA, H-PGF -BBa and Heparin Solution 0.25%. Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
Beads were prepared using 10 ul/sample of CUTANA Concavalin A Conjugated Paramagnetic Beads (EpiCypher, SKU:21-1401). Beads were transferred to a 1.5 ml tube and placed in a magnetic separation rack. Supernatant was removed and beads were washed 2 times with 100 ul/sample of cold Bead Activation Buffer (20 mM HEPES pH7.9, 10 mM Kcl, 1 mM CaCl2, 1 mM MnCl2). Beads were then resuspended in 10 ul/sample of cold Bead Activation Buffer and aliquot 10 ul/sample of activated bead slurry into 8-strip tube and kept on ice.   Cells were collected using 0.05% trypsin and washed with 100 ul/sample of Wash Buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete EDTA-free Protease Inhibitor (1187358001)) at room temperature and centrifuged at RT, 600 g for 3min, for a total of two washes. Cells were resuspended in 100 ul/sample RT Wash Buffer and then aliquot of 100ul washed cells to each 8-strip tube containing 10 ul of activated beads and mixed by pipetting. Cells were incubated with bead slurry for 10 min at RT. Tube strip was placed on a magnetic separation rack until slurry clears and the supernatant was removed. 50 ul of cold Antibody Buffer was added to each sample and mixed by pipetting; 1 ul of antibody IgG (Rabbit IgG Negative Control, EpiCypher, 13-0042K), PolI (Rpb1 CTD (4H8), Cell Signaling, #2629S), and pPolI (pRpb1 CTD (S2), Cell Signaling, #13499S), was added to each sample, mixed and incubated on a nutator overnight at 4oC. Tube was placed on a magnet until slurry clears and the supernatant was removed. While beads were on magnet, 250 ul of cold Digitonin Buffer was added directly onto beads of each sample and then pipet to remove supernatant, for a total of 2-washes. 50 ul of cold Digitonin Buffer was added to each sample and mixed. 2.5 ul of CUTANA pAG-MNase (20Xstock) was added to each sample, mixed and incubated for 10min at RT. Tube was placed on a magnet and supernatant was removed. Beads were washed 2 times with cold Digitonin Buffer. Supernatant and 50 ul of cold Digitonin Buffer was added to each sample and mixed. Tubes were placed on ice and 1 ul of 100 mM CaCl2 was added to each sample, mixed, and then incubated on nutator 2 hrs at 4oC. 33 ul/sample of Stop buffer, to stop the MNase activity by chelating Ca++ ions, containing 0.5 ng/sample of E.coli Spike-in DNA, was added to the samples, mixed by pipetting  and incubated for 10 min at 37oC in a thermocycler. Tubes were placed on a magnet stand until slurry cleared and the supernatant was transferred to a 1.5ml tube. Finally, the DNA was purified using CUTANA DNA Purification Kit (EpiCypher, 14-0050) according to the manufactory instructions and 1ul of DNA was used to be quantified using Qubit and library preparation.
The NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #E7645S) with Dual Index Primers (NEB #E7600) were used to library preparation for ChiPseq and Cut and Run samples sequencing.    For the NEBNext end prep, 1x TE was added to the DNA to get final volume of 50 ul and mixed with 3ul of NEBNext Ultra II End Prep Enzyme Mix and 7ul of NEBNext Ultra II End Prep Reaction Buffer, placed in thermocycler with heated lid set to 75oC and run the program 30 minutes at 20oC, 60 minutes at 50oC and hold at 4oC.  The adaptor ligation reaction was performed with 60u l of Prep Reaction Mixture, 2.5ul of NEBNext Adaptor for Illumina diluted following the manufacture recommendations, 30 ul of NEBNext Ultra Ligation Master Mix and 1ul of NEBNext Ligation Enhancer, incubated at 20oC for 15 min with heated lid off. 3 ul of USER Enzyme was added to the reaction and incubated at 37oC for 15 min with heated led set to 47oC. For the cleanup of the adaptor-ligated DNA without size selection, 1.1x of AMPure XP Beads were added to the Adaptor Ligation reaction and samples were incubated for 5min at room temperature. Tubes were placed on a magnetic stand to separate beads from supernatant, after 5 min, supernatant was removed, and beads were washed 2 times with 200ul of 80% freshy prepared ethanol. Beads were air dried for up 5 min while tubes were on magnet with lid open. DNA was eluted from the beads by adding 17 ul of 0.1XTE buffer.   For the PCR enrichment of adaptor-ligated DNA step, to 15 ul of the Adaptor Ligated DNA fragments was added 25ul of NEBNext Ultra Q5 Master Mix, 5 ul of Index primer i7 and 5ul Universal PCR Primer i5, and PCR amplification was performed following the cycling conditions: 98oC for 45s, 98oC 15s and 60oC 10s for 16 cycles, 72oC for 1 min and hold at 4oC. Followed by a Clean Up of the PCR reaction using AMPure XP Beads.   The DNA was quantified using Qubit and the quality and size of libraries were checked with the Bioanalyzer and sent for sequencing at the Genomics Shared Resource (sequencing core) of CU Anschutz Medical Campus.

treatment_protocol: Cells were treated with DMSO or 40 nM AZD. After 2 hrs, cells were irradiated at 6 Gy and collected after 4 hrs.

value: AZD4573 (40 nM) and 6 Gy radiation

value: IgG Negative Control; EpiCypher Cat. #13-0042


title: sh516_H3K27ac_IP2


title: mESC Control 72h Replicate 3

value: male


title: IgG, DIPG4, AZD4573_with_radiation, replicate 1


title: 20_MZ05_B_MB_CD8T

description: Twin pair3 ind2

value: Menstrual blood

value: CD8+ Trm


title: mESC Control 24h Replicate 1

value: Gl2 knockdown


title: 19_MZ05_B_MB_NK

description: Twin pair3 ind2

value: uNK

value: twin


title: sh516_H3K27ac_IP1

value: METTL8 targeting RNA (sh516)


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, AZD4573_with_radiation, replicate 2

value: Diffuse intrinsic pontine glioma

value: Phospho RNA Polymerase II phosphorylated at Ser2_P-Rpb1 CTD (S2); Cell Signaling Cat. #13499S


title: sh515_IN_H3K27ac_2

value: METTL8 targeting RNA (sh515)


title: sh515_IN_H3K27ac_1


title: 18_MZ05_A_MB_CD8T

description: Twin pair3 ind1


title: mESC Srrm2 hKO Replicate 1

library_source: transcriptomic single cell

data_processing:
The four 10X Genomics scRNA-seq libraries were simultaneously mapped to the mouse genome (mm10) using the cellranger count function from 10X Genomics Cellranger software (version cellranger-6.1.2) with default parameters, except -expect-cells 10000 (total number of cells targeted per experiment).
The four libraries were aggregated on one unique count matrix using cellranger aggr function from 10X Genomics Cellranger software (version cellranger-6.1.2) with default parameters.
Assembly: mm10 (M24)
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Total RNA from two replicates of WT and Srrm2 heterozygous knockout cells was isolated with TRIzol (Invitrogen) and DNA was degraded with TURBO DNase (Invitrogen), according to the manufacturer’s protocol.
Cells were loaded on a 40 µm Flowmi™ Tip Strainer to remove cell debris and clumps into a suspension of 10^6 cells/ml in PBS + 0.04% BSA. Single-cell mRNA-seq libraries were prepared with the Chromium Single Cell 3' v3 chemistry Kit (10x Genomics), according to the manufacturer’s instructions. Briefly, a droplet emulsion was generated in a microfluidic chip followed by barcoded cDNA generation inside these droplets. Purified and amplified cDNA was then subjected to library preparation, and sequenced on a NovaSeq 6000 instrument (Illumina).

treatment_protocol: mESC E14tg2a.4 wild-type and mESC E14tg2a.4 with a derived heterozygous truncation in the Srrm2 gene (SIGTR ES cell line CG0630, RRID:MMRRC_028099-UCD) were generated by the Sanger Institute Gene Trap Resource (SIGTR), Cambridge, UK, and obtained from the Mutant Mouse Resource Center (MMRRC) at University of California at Davis, an NIH-funded strain repository.

value: Srrm2 gene-trap SIGTR ES cell line CG0630, RRID:MMRRC_028099-UCD


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, AZD4573_with_radiation, replicate 1


title: 17_MZ05_A_MB_NK

description: Twin pair3 ind1


title: IgG, DIPG4, DMSO_with_radiation, replicate 2

value: DMSO and 6 Gy radiation


title: 14_MZ12_A_PB_CD8T

description: Twin pair2 ind1

value: Peripheral blood

value: CD8+ Tem

value: neg


title: shNT_IN_H3K4me3_1

value: Glioblastoma patient derived cancer stem cell

value: wild type

value: non-targeting RNA (shNT)


title: 13_MZ12_A_PB_NK

description: Twin pair2 ind1

value: CD56dim NK


title: 16_MZ12_B_PB_CD8T

description: Twin pair2 ind2


title: MSC, siRNA control, replicate3, ATAC-seq

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina, Chapel Hill

description:
siRNA_CTL_rep3
ATACseq.counts.txt

data_processing:
ATAC: PEPATAC v0.9.15 with default parameters
Assembly: mm10
Supplementary files format and content: bam file - alignment file in standard sam/bam format
Supplementary files format and content: counts.txt - count of reads assigned to each gene (RNAseq) or accessible chromatin region (ATAC-seq)

source_name: mesynchymal stem cells

extract_protocol:
DNA was prepared from 50,000 MSC cells using an ATAC-seq protocol (Omni-ATAC).
ATAC DNA was prepared from 50,000 MSC cells using an ATAC-seq protocol (Omni-ATAC) and primers with transposase from llumina Kit (cat# 20034197).

tag: strain

value: male

value: mesynchymal stem cells

value: siRNA mock


title: sh515_H3K27ac_IP2


title: IgG, DIPG4, DMSO_with_radiation, replicate 1

value: IgG Negative Control; EpiCypher Cat. #13-0042


title: 15_MZ12_B_PB_NK

description: Twin pair2 ind2

value: twin


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, DMSO_with_radiation, replicate 3

value: Diffuse intrinsic pontine glioma


title: 12_MZ12_B_MB_CD8T

description: Twin pair2 ind2

value: Menstrual blood

value: CD8+ Trm


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, AZD4573_with_radiation, replicate 3

value: AZD4573 (40 nM) and 6 Gy radiation

value: Phospho RNA Polymerase II phosphorylated at Ser2_P-Rpb1 CTD (S2); Cell Signaling Cat. #13499S


title: MSC, siRNA Arp4 plus CK666, replicate3, ATAC-seq

description:
siRNA_Arp4_CK666_rep3
ATACseq.counts.txt

value: siRNA Arp4, CK666


title: shNT_IN_H3K4me3_2


title: shNT_H3K4me3_IP_2


title: mESC Srrm2 hKO Replicate 2

value: mouse embryonic stem cells

value: Srrm2 gene-trap SIGTR ES cell line CG0630, RRID:MMRRC_028099-UCD


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, DMSO_with_radiation, replicate 1

value: DMSO and 6 Gy radiation


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, DMSO_with_radiation, replicate 2


title: MSC, siRNA Arp4 plus CK666, replicate2, ATAC-seq

description:
siRNA_Arp4_CK666_rep2
ATACseq.counts.txt


title: MSC, siRNA control, replicate1, ATAC-seq

description:
siRNA_CTL_rep1
ATACseq.counts.txt


title: sh515_H3K27ac_IP1

value: Glioblastoma patient derived cancer stem cell

value: wild type

value: METTL8 targeting RNA (sh515)


title: IgG, DIPG4, DMSO, replicate 1

value: DMSO


title: 11_MZ12_B_MB_NK

description: Twin pair2 ind2

value: uNK

value: neg


title: shNT_H3K4me3_IP_1

value: non-targeting RNA (shNT)


title: mESC WT Replicate 1

value: Wild-type

value: male


title: sh516_IN_H3K4me3_2

value: METTL8 targeting RNA (sh516)


title: mESC WT Replicate 2


title: IgG, DIPG4, DMSO, replicate 2

value: Diffuse intrinsic pontine glioma

value: IgG Negative Control; EpiCypher Cat. #13-0042


title: 10_MZ12_A_MB_CD8T

description: Twin pair2 ind1

value: Menstrual blood

value: CD8+ Trm

value: twin


title: MSC, siRNA Arp4 plus CK666, replicate1, ATAC-seq

description:
siRNA_Arp4_CK666_rep1
ATACseq.counts.txt

value: mesynchymal stem cells

value: siRNA Arp4, CK666


title: MSC, siRNA Arp4, replicate3, ATAC-seq

description:
siRNA_Arp4_rep3
ATACseq.counts.txt

value: siRNA Arp4


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, DMSO, replicate 3

value: Phospho RNA Polymerase II phosphorylated at Ser2_P-Rpb1 CTD (S2); Cell Signaling Cat. #13499S


title: MSC, siRNA control, replicate2, ATAC-seq

description:
siRNA_CTL_rep2
ATACseq.counts.txt

value: siRNA mock


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, DMSO, replicate 2

value: DMSO


title: 9_MZ12_A_MB_NK

description: Twin pair2 ind1

value: uNK


title: 8_MZ10_B_PB_CD8T

description: Twin pair1 ind2

value: Peripheral blood

value: CD8+ Tem

value: pos


title: sh516_IN_H3K4me3_1

value: Glioblastoma patient derived cancer stem cell

value: wild type


title: sh516_H3K4me3_IP_1

value: METTL8 targeting RNA (sh516)


title: sh516_H3K4me3_IP_2


title: 7_MZ10_B_PB_NK

description: Twin pair1 ind2

value: CD56dim NK


title: phosphorylated_RNA_Polymerase_ II_Ser2, DIPG4, DMSO, replicate 1

value: Diffuse intrinsic pontine glioma


title: MSC, siRNA Arp4, replicate2, ATAC-seq

description:
siRNA_Arp4_rep2
ATACseq.counts.txt

value: male


title: 6_MZ10_A_PB_CD8T

description: Twin pair1 ind1

value: twin

value: neg


title: sh515_IN_H3K4me3_2

value: METTL8 targeting RNA (sh515)


title: MSC, siRNA Arp4, replicate1, ATAC-seq

description:
siRNA_Arp4_rep1
ATACseq.counts.txt

value: mesynchymal stem cells

value: siRNA Arp4


title: sh515_IN_H3K4me3_1


title: MSC, control, replicate3, ATAC-seq

description:
CTL_rep3
ATACseq.counts.txt


title: ATAC-seq, DIPG4, AZD4573, radiation, replicate 2

extract_protocol:
100,000 cells were spun down at 500 xg for 5min at 4 C. The pellet was washed once with 500 ul of cold 1x PBS and spun down again at 500 xg for 5min at 4 C. Pellet was resuspended in 450 ul of cold hypotonic buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2) and immediately added 50 ul of 1% IGEPAL CA-630 (0.1% final), inverting to mix. Cells were incubated on ice for 15 min before spinning down at 500 xg for 10 min at 4 C. Pellet was set on ice, and the transposition reaction was performed following the ATAC-seq Kit instructions (Cell Biologics, Cat No. CB6936). Pelleted cells were resuspended in 50 ul of transposition reaction mix (25 ul 2X Reaction Buffer, 2.5ul Transposome, 22.5ul Nuclease free water) and incubated at 37 C for 1 hour. DNA was purified using Qiagen MinElute kit (Qiagen, #28004) and eluted in 15 ul of Elution Buffer, followed by library generation to amplify transposed DNA fragments.
10 ul of transposed DNA, 10 ul of nuclease free water, 2.5 ul of Ad1.noMX (Oligo 1), 2.5 ul Ad2._Barcode (Oligo 2) and 25 ul of High Fidelity 2x PCR Master Mix was run on a thermocycler using the following cycle: 98 C 30 sec, (98 C 10 sec, 63 C 30 sec, 72 C 1 min) x 10 times and held at 4 C.  For double-sided bead purification (to remove primer dimers and large >1,000 bp fragments), each PCR sample was transferred to a 1.5 ml tube and 0.5X volume (25ul) of AMPure XP beads was added, mixed by pipetting 10 times before incubation at room temperature for 10 min. Tubes were placed in a magnetic rack for 5 min, and the supernatant was transferred to a new tube. 1.3X of the original volume (65ul) of AMPure XP beads was added, mixed by pipetting 10x, and incubated at room temperature for 10 min. Tubes were placed in a magnetic rack for 5 min, supernatant was discarded, and beads were washed with 200 ul 80% EtOH. EtOH was removed, and tubes were left on magnetic rack with cap open for 10 min or until the pellet was totally dry. Beads were resuspended in 20 ul of nuclease-free water and mixed thoroughly, and then tubes were placed in the magnetic rack for 5 min before the supernatant was transferred to a new tube.

value: AZD4573 (40 nM) and 6 Gy radiation


title: MSC, control, replicate2, ATAC-seq

description:
CTL_rep2
ATACseq.counts.txt


title: ATAC-seq, DIPG4, AZD4573, radiation, replicate 1


title: 5_MZ10_A_PB_NK

description: Twin pair1 ind1


title: ATAC-seq, DIPG4, DMSO, radiation, replicate 2

value: DMSO and 6 Gy radiation


title: MSC, control, replicate1, ATAC-seq

description:
CTL_rep1
ATACseq.counts.txt


title: 4_MZ10_B_MB_CD8T

description: Twin pair1 ind2

value: Menstrual blood

value: CD8+ Trm


title: ATAC-seq, DIPG4, DMSO, radiation, replicate 1


title: MSC, CytoD, replicate3, ATAC-seq

description:
CytoD_rep3
ATACseq.counts.txt

value: CytoD


title: sh515_H3K4me3_IP_1


title: 3_MZ10_B_MB_NK

description: Twin pair1 ind2

value: uNK

value: pos


title: ATAC-seq, DIPG4, DMSO, replicate 2

value: DMSO


title: MSC, CytoD, replicate2, ATAC-seq

description:
CytoD_rep2
ATACseq.counts.txt


title: 1_MZ10_A_MB_NK

description: Twin pair1 ind1


title: 2_MZ10_A_MB_CD8T

description: Twin pair1 ind1


title: ATAC-seq, DIPG4, DMSO, replicate 1


title: N87_NC_3

city: Tianjin

first: Cai

middle: feng

last: lin

state: China

address: Tianjin Medical University Cancer Institute and Hospital

country: China

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In 1 this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routinesfor determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: NCI-N87 cells cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) (HyClone, South Logan, UT, USA), penicillin (100 U/ml), and   streptomycin (100 U/ml) at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
Cells were washed twice with pre-chilled PBS, and then total RNAs were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NCI-N87 cells were transfected with PLVX-IRES-Puro-EGLN3 or empty vector (PLVX-IRES-Puro) respectively for 24 hours,then added puro screening for 7days

value: gastric cancer cells

value: control

value: treated with PLVX-IRES-Puro-empty vector for 1 days,puro screening for 7days

tag: time

value: Day 7


title: MSC, CK666, replicate3, ATAC-seq

description:
CK666_rep3
ATACseq.counts.txt

value: male


title: 56_ENDO14_t2_PB_CD8T

description: Longitudinal ind3 t2

data_processing:
Adaptor and quality trimming (-q 30) of RNAseq data was performed using Trim Galore! 0.6.1.
Processed ATACseq reads were aligned to the GRCh38 genome using Bowtie 2.3.5.1 with -X 2000 --no-mixed --no-discordant options (Langmead and Salzberg, 2012).
Unpaired alignment or reads with low mapping quality were filtered out by SAMTools view (-f 2 -q 40), and duplicated reads were discarded by SAMTools markup (-l 150 -r).
To ensure fair comparisons across samples, we randomly subsampled reads of a sample to the lowest number of reads of that group (four groups: MB T, PB T, MB NK, and PB NK).
ATACseq peaks were then called from subsampled reads using MACS 2.2.6 (Zhang et al., 2008) with ‘-g hs -f BAMPE -q 0.01 --shift -100 --extsize 200 -B --nomodel --keep-dup all’ options. We calculated the fraction of reads in called peak regions (i.e. FRiP score) and discarded any samples with scores lower than 0.1.
Assembly: GRCh38
Supplementary files format and content: merged_peaks.bed: BED file
Supplementary files format and content: rawCounts_merged_peaks.csv: Comma-separated values

extract_protocol:
PB CD56dim and MB uNK cells as well as PB CD8+ TEM and MB CD8+ TRM cells were pre-gated on alive CD45+CD14-CD15-CD19- cells and sorted directly into 300 ul of RLT plus buffer (QIAGEN) in a sterile ribonuclease- and DNase-free 1.5 ml Eppendorf tube and frozen on dry ice immediately after sorting. The ATACseq protocol was adapted from the previously published work (Buenrostro et al., 2013 and Corces et al., 2016). Between 1000 and 5000 cells for each of the cell subsets from MB and PB were sorted into 22.5 ml of cold lysis buffer containing 12.5 ml of 2x TD buffer reagent (Illumina), 0.5 ml of 1% Digitonin (Promega) and 9.5 ml of nuclease-free water (NEB). After sorting, cells were spun in a centrifuge at 500g for 5 minutes at 4°C. Then, 2.5 ml of TDE1 Tagment DNA Enzyme (Illumina) was added to each reaction, and the pellet was resuspended thoroughly by pipetting up and down for at least 15 times to lyse the cells. Immediately after the lysis, nuclei were spun again, and the transposition reaction was carried out by incubating the samples at 37°C for 30 minutes. At the end of it, the transposition reaction was stopped by adding 300 ml of ERC buffer from MinElute Reaction Cleanup Kit (Qiagen), after which the sample was purified using the MinElute Reaction Cleanup Kit, as per manufacturer’s instructions.
The resulting libraries were amplified using 2x NEB Next High-Fidelity PCR Master Mix and 1.25 mM of Nextera PCR forward and reverse primers. The PCR program used was as follows: 72°C for 5 minutes, 98°C for 30 seconds, and 13 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute (Buenrostro et al., 2013). Amplified libraries were cleaned up and size-selected through double-sided size selection (0.5x - 1.2x ratio) using Mag-Bind TotalPure NGS beads (Omega Bio-tek). The final libraries were eluted in 15 ml EB buffer (Qiagen), quantified using 2100 Bioanalyzer (Agilent) and Qubit 4 (Invitrogen), and subsequently pooled for sequencing.

value: Peripheral blood

value: CD8+ Tem

value: longitudinal


title: healthy human airway epithelial cells, IL-13 treatment for 7 days

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were aligned to human genome assembly GRCh38. Filtering, barcode counting, and UMI counting were performed with 10x CellRanger software.
Assembly: GRCh38
Supplementary files format and content: HDF5 format file containing counts for each gene (row) and cell barcode (column)

source_name: lung

growth_protocol: DMEM/F12 media with Ultroser G was replaced every two days.

extract_protocol:
Cultured cells were rinsed in PBS -/- and lifted in TrypLE for 45 min at 37C. Cells were centrifuged for 5 min at 200xrcf, supernatent was removed, and cells were resuspended in Phenol red-free DMEM:F12 with 0.04% non-acetylated BSA and counted.
10x Genomics Chromium Single Cell 3’ Reagent Kits v2 system

treatment_protocol: Air-liquid interface cultures of primary airway epithelia from 1 de-identified human donor with no known disease were exposed to apical and basolateral IL13 or vehicle at a concentration of 20ng/mL for up to 21 days.

value: lung

value: healthy human airway epithelial cells


title: MSC, CytoD, replicate1, ATAC-seq

description:
CytoD_rep1
ATACseq.counts.txt

value: mesynchymal stem cells


title: N87_NC_2

institute: Tianjin Medical University Cancer Institute and Hospital


title: healthy human airway epithelial cells, IL-13 treatment for 2 days


title: healthy human airway epithelial cells, no IL-13 treatment


title: MSC, CK666, replicate2, ATAC-seq

description:
CK666_rep2
ATACseq.counts.txt


title: N87_NC_1


title: 55_ENDO14_t2_PB_NK

description: Longitudinal ind3 t2

value: CD56dim NK


title: HeLa_siTIME_R120_ThyRel_2_nm

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

data_processing:
100-bp single end reads were aligned to the reference human genome Human GRCh37/hg19 using bwa v.0.7.17, retaining only the reads with the highest quality score.
CSV processed files have been generated as described in the section "Sequence alignment and calculation of sigma values" of Methods published in https://doi.org/10.1038/nature25507
bigWig files: Uniquely mapped reads and deduplicated.
Assembly: Human GRCh37/hg19

source_name: Human cell line

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS , 1% penicillin/streptomycin and 1% glutamine.

extract_protocol:
After fixation, the cells were permeabilized with 0.2% Triton-X in PBS and EdU was coupled to a cleavable biotin-azide linker (Azide-PEG(3+3)-S-S-biotin) using the Click-it Kit. Purification of genomic DNA was then performed by phenol-chloroform extraction and ethanol precipitation and subjected to EdU-labelled DNA isolation.
Purified EdU-labeled DNA was used for library preparation with TrueSeq ChIP Library Preparation Kit (Illumina) and high-throughput 100-bp single-end sequencing was performed on Illumina Hi-Seq 4000 sequencer.

treatment_protocol: To deplete TIMELESS or TIPIN expression, cells were transfected with siRNAs against TIMELESS or TIPIN. To synchronise cells in the G1-S transition, a thymidine block for 18hrs was performed. Cells were then released in S phase for 120min, in the presence of 25μΜ EdU for the last 30min. Cells were then collected and fixed with 90% methanol overnight.

value: Human cell line

value: HeLa

value: Human cervical cancer

value: siRNA


title: 54_ENDO14_t1_PB_CD8T

description: Longitudinal ind3 t1

value: pos


title: HeLa_siTIPI_R120_ThyRel_2_nm


title: sh515_H3K4me3_IP_2

value: Glioblastoma patient derived cancer stem cell

value: wild type

value: METTL8 targeting RNA (sh515)


title: healthy human airway epithelial cells, IL-13 treatment for 21 days


title: MSC, CK666, replicate1, ATAC-seq

description:
CK666_rep1
ATACseq.counts.txt


title: 53_ENDO14_t1_PB_NK

description: Longitudinal ind3 t1


title: 50_ENDO14_t2_MB_CD8T

description: Longitudinal ind3 t2

value: Menstrual blood

value: CD8+ Trm


title: MSC, siRNA control, replicate2, RNA-seq

description:
siRNA_CTL_rep2
RNAseq.counts.txt

data_processing:
RNA: Paired-end reads were aligned to the GRCm38 (mm10) genome assembly and quantified with Salmon v1.2.1 using default parameters and with version vM25 of the GENCODE gene annotations.
Assembly: mm10
Supplementary files format and content: bam file - alignment file in standard sam/bam format
Supplementary files format and content: counts.txt - count of reads assigned to each gene (RNAseq) or accessible chromatin region (ATAC-seq)

extract_protocol:
Total RNA was isolated with the RNeasy plus mini kit (Qiagen; Germantown, MD).
RNA-seq was performed by NovaGene using their Standard RNA-seq service which is unstranded.

value: male

value: siRNA mock


title: HeLa_siCTRL_R120_ThyRel_2_nm


title: N87_EGLN3_2

value: gastric cancer cells

value: EGLN3 overexpression

value: treated with PLVX-IRES-Puro-EGLN3 for 1 days,puro screening for 7days

value: Day 7


title: MSC, siRNA control, replicate3, RNA-seq

description:
siRNA_CTL_rep3
RNAseq.counts.txt

value: mesynchymal stem cells


title: N87_EGLN3_3

value: treated with PLVX-IRES-Puro-EGLN3 for 5 days,puro screening for 7days


title: HeLa_siCTRL_R120_ThyRel_1_nm

value: Human cell line

value: HeLa


title: sgRNA_Hoxb8FL_pDC

city: New York

first: Ioanna

last: Tiniakou

state: NY

address: 435 E 30th St

institute: NYU Langone

description: pDC

data_processing:
Reads were counted by first searching for the CACCG sequence in the primary read file that appears in the vector 5’ to all sgRNA inserts. The next 20 nts are the sgRNA insert.
The 20nt sgRNA sequence reads were then mapped to a reference file of all possible sgRNAs present in the library.
Assembly: mm10
Supplementary files format and content: csv; raw counts

source_name: bone marrow-derived

growth_protocol: Hoxb8-FL cells were maintained in RPMI supplemented with 10% FCS, 10% supernatant from the Flt3L-producing B16 cell line, and 10 μM β-estradiol  in humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Genomic DNA was extracted using the QIAamp Blood Maxi/Midi kit (QIAGEN) according to the manufacturer’s instructions
As described in depositor's Sequencing protocol for the mouse CRISPR knockout pooled library (Brie) by addgene #73633

treatment_protocol: In order to achieve a representation of ~400 cells per sgRNA in the library post-selection, 110 million undifferentiated Hoxb8-FL-Cas9 cells were distributed to 6-well plates with 5x105 cells per well. Cells were spinoculated with the pre-determined amount of virus and 5 μg/mL puromycin was added 48 h later. Transduced cells were maintained in puromycin throughout the screen and were split every two days to prevent overconfluence. Samples of 50 million cells were obtained 5 days post selection (progenitors_0) and 11 days post selection on the day of differentiation induction (progenitors). A bulk sample of 100 million differentiated cells (DC) was obtained at the end of differentiation and prior to sorting. Hoxb8-FL-derived DCs were sorted as follows: CD11c+ CD11b+ B220- for cDC2s (4.6 million) and CD11c+ CD11b- B220+ for pDCs (3 million). Sample cell pellets were stored at -80oC until genomic DNA (gDNA) isolation.

value: bone marrow-derived

value: hematopoietic cell

value: WT

tag: developmental stage

value: 18 days post selection; sorted pDC


title: N87_EGLN3_1


title: 49_ENDO14_t2_MB_NK

description: Longitudinal ind3 t2

value: uNK

value: longitudinal

value: pos


title: Pool52_Stromal_BCR

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Samples in Pool 44, Pool 51 and Pool 52 paired from the same patients
S54.zip

data_processing:
Illumina bcl2fastq was used to convert raw bcl files to fastq format
Fastq files were processed using 10x Genomics Cellranger software
Genome_build: hg38
Supplementary_files_format_and_content: compressed raw UMI counts matrices from Cellranger outputs for mRNA and antibody libraries.

source_name: Colonic tissue

extract_protocol:
Matched Cells from biopsies (Tissue) and Peripheral Blood (Blood) were defrosted. Tissue was processed to yield high viability single cells, enriched for Epithelial or Stromal/Immune fractions and then tissue and blood pools were tagged with CITE-seq and hashing antibodies, pooled and loaded on to the 10X platform for single-cell RNA sequencing
Pooled tagged samples were loaded onto the 10X sc-RNA seq platform, with GEM generation and RNA RT, followed by generation of Gene expression (GEX), Antibody tagged oligo (ADT - with CITE-seq proteins and hashing information - '#1' = Hashtag#1 antibody, '#2' = Hashtag#2 antibody, etc) and T-cell receptor (TCR) and B-cell receptor (BCR) library amplification and indexing, as per protocol CG000186 (Rev A). Details of hashing & cite-seq antibodies in methods.

tag: chemistry

value: 5' chemistry

value: Colon

tag: sample

tag: hashtag

tag: disease

tag: immunotherapy

value: GI4738(Monotherapy), GI2935(Monotherapy), GI4680(Dual Therapy), GI3128(Monotherapy), PRISE 13(Monotherapy)

tag: age

tag: mixed gender


title: MSC, siRNA control, replicate1, RNA-seq

description:
siRNA_CTL_rep1
RNAseq.counts.txt

value: male

tag: cell type

tag: treatment

value: siRNA mock


title: MSC, siRNA Arp4 plus CK666, replicate3, RNA-seq

description:
siRNA_Arp4_CK666_rep3
RNAseq.counts.txt

value: siRNA Arp4, CK666


title: 46_ENDO14_t1_MB_CD8T

description: Longitudinal ind3 t1

value: Menstrual blood

value: CD8+ Trm


title: sgRNA_Hoxb8FL_cDC

tag: cell line

tag: genotype

value: 18 days post selection; sorted cDC2


title: Pool52_Stromal_TCR

description:
Samples in Pool 44, Pool 51 and Pool 52 paired from the same patients
S53.zip

tag: tissue


title: sgRNA_Hoxb8FL_DC

description: DC

value: 18 days post selection; DC


title: 44_MB056_t2_PB_CD8T

description: Longitudinal ind2 t2

value: Peripheral blood

value: CD8+ Tem

tag: sample type

tag: cmv


title: 47_ENDO14_t1_MB_NK

description: Longitudinal ind3 t1


title: MSC, siRNA Arp4 plus CK666, replicate2, RNA-seq

description:
siRNA_Arp4_CK666_rep2
RNAseq.counts.txt

tag: strain

tag: Sex

value: mesynchymal stem cells


title: sgRNA_Hoxb8FL_progenitors

description: progenitors

value: bone marrow-derived

value: hematopoietic cell

value: WT

tag: developmental stage

value: 11 days post selection; progenitors


title: MSC, siRNA Arp4 plus CK666, replicate1, RNA-seq

description:
siRNA_Arp4_CK666_rep1
RNAseq.counts.txt


title: MSC, siRNA Arp4, replicate3, RNA-seq

description:
siRNA_Arp4_rep3
RNAseq.counts.txt

value: siRNA Arp4


title: Pool44_PBMC_BCR

description:
Samples in Pool 44, Pool 51 and Pool 52 paired from the same patients
S48.zip

tag: chemistry

value: 5' chemistry

value: PBMC


title: 42_MB056_t1_PB_CD8T

description: Longitudinal ind2 t1

value: longitudinal

value: pos


title: MSC, siRNA Arp4, replicate2, RNA-seq

description:
siRNA_Arp4_rep2
RNAseq.counts.txt

value: male


title: ATAC_Hoxb8FL_pDC_2_S4

data_processing:
All the ATAC-Seq reads were mapped using bowtie2
BAM to bedgraph performed using bedtools and bedgraph to bigwig performed using bedGraphToBigWig v4
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
Hoxb8-FL cells were sorted as described in the manuscript. Cells were washed with PBS and immediately processed as previously described (Buenostro et al, 2015, PMC4374986).
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hoxb8-FL cells were induced to differentiate into DCs by washing and replating in RPMI supplemented with 10% charcoal-stripped FCS and 10% Flt3L supernatant.

value: day7 post differentiation; dendritic cell


title: sgRNA_Hoxb8FL_progenitors0

value: 5 days post selection; progenitors


title: 41_MB056_t1_PB_NK

description: Longitudinal ind2 t1

value: CD56dim NK


title: Pool43_PBMC_BCR

description:
Samples in Pool 37, Pool 38 and Pool 43 paired from the same patients
S46.zip

tag: sample

value: GI3052(CC_I), PRISE5(CC_I) GI4069(CC_I), PRISE 4(CC_NI), GI4448(CC_NI)

value: GI3052(Monotherapy), PRISE 5(Monotherapy) GI4069(Dual Therapy), PRISE 4(Monotherapy), GI4448(Monotherapy)


title: Pool58_Stromal_BCR

description:
Samples in Pool 57 and Pool 58 paired from the same patients
S60.zip

value: Colon

tag: hashtag

value: TIP 309(Infectious colitis), TIP 299(Microscopic colitis), GI 4379(UC_I), GI 4449(CC_I), GI 4051(CC_I)

value: TIP 309 (N/A), TIP 299(N/A), GI 4379(N/A), GI 4449 (Monotherapy), GI 4051(Dual Therapy)


title: ATAC_Hoxb8FL_cDC_2_S3

value: bone marrow-derived

value: hematopoietic cell


title: MSC, siRNA Arp4, replicate1, RNA-seq

description:
siRNA_Arp4_rep1
RNAseq.counts.txt

value: mesynchymal stem cells


title: 40_MB056_t2_MB_CD8T

description: Longitudinal ind2 t2

value: Menstrual blood

value: CD8+ Trm


title: MSC, control, replicate3, RNA-seq

description:
CTL_rep3
RNAseq.counts.txt


title: Pool44_PBMC_TCR

description:
Samples in Pool 44, Pool 51 and Pool 52 paired from the same patients
S47.zip

value: 5' chemistry

value: PBMC

tag: disease

value: GI4738(Monotherapy), GI2935(Monotherapy), GI4680(Dual Therapy), GI3128(Monotherapy), PRISE 13(Monotherapy)


title: 39_MB056_t2_MB_NK

description: Longitudinal ind2 t2

value: uNK

value: longitudinal

value: pos


title: ATAC_Hoxb8FL_day4_2_S2

value: WT

value: day4 post differentiation


title: MSC, control, replicate2, RNA-seq

description:
CTL_rep2
RNAseq.counts.txt

value: male


title: Pool58_Stromal_TCR

description:
Samples in Pool 57 and Pool 58 paired from the same patients
S59.zip

value: Colon

tag: immunotherapy


title: Pool43_PBMC_TCR

description:
Samples in Pool 37, Pool 38 and Pool 43 paired from the same patients
S45.zip

value: GI3052(CC_I), PRISE5(CC_I) GI4069(CC_I), PRISE 4(CC_NI), GI4448(CC_NI)

value: GI3052(Monotherapy), PRISE 5(Monotherapy) GI4069(Dual Therapy), PRISE 4(Monotherapy), GI4448(Monotherapy)

tag: age


title: ATAC_Hoxb8FL_day0_2_S1

value: bone marrow-derived

value: day0; progenitor


title: Pool38_Stromal_BCR

description:
Samples in Pool 37, Pool 38 and Pool 43 paired from the same patients
S40.zip

tag: mixed gender


title: MSC, control, replicate1, RNA-seq

description:
CTL_rep1
RNAseq.counts.txt

tag: cell type

value: mesynchymal stem cells


title: Pool38_Stromal_TCR

description:
Samples in Pool 37, Pool 38 and Pool 43 paired from the same patients
S39.zip


title: 43_MB056_t2_PB_NK

description: Longitudinal ind2 t2

value: Peripheral blood

value: CD56dim NK


title: 37_MB056_t1_MB_NK

description: Longitudinal ind2 t1

value: Menstrual blood


title: 38_MB056_t1_MB_CD8T

description: Longitudinal ind2 t1

value: CD8+ Trm


title: MSC, CytoD, replicate3, RNA-seq

description:
CytoD_rep3
RNAseq.counts.txt

tag: treatment

value: CytoD


title: ATAC_Hoxb8FL_pDC_1_S4

tag: cell line

value: hematopoietic cell

value: day7 post differentiation; dendritic cell


title: 36_ENDO5_t2_PB_CD8T

description: Longitudinal ind1 t2

value: CD8+ Tem

value: longitudinal

value: pos


title: ATAC_Hoxb8FL_day4_1_S3

tag: genotype

value: WT

value: day4 post differentiation


title: MSC, CytoD, replicate2, RNA-seq

description:
CytoD_rep2
RNAseq.counts.txt

value: male


title: Pool32_Stromal_TCR

description:
Samples in Pool 31 and Pool 32 paired from the same patients
S33.zip

value: 5' chemistry

tag: tissue

value: Colon

value: TIP332(N/A), IBD3778(N/A), GI4442(Dual Therapy) GI3662(Dual Therapy)


title: Pool32_Stromal_BCR

description:
Samples in Pool 31 and Pool 32 paired from the same patients
S34.zip


title: ATAC_Hoxb8FL_day0_1_S1

value: bone marrow-derived

value: day0; progenitor


title: 35_ENDO5_t2_PB_NK

description: Longitudinal ind1 t2

value: Peripheral blood

value: CD56dim NK

tag: sample type


title: MSC, CytoD, replicate1, RNA-seq

description:
CytoD_rep1
RNAseq.counts.txt

value: mesynchymal stem cells


title: Pool21_PBMC_BCR

description:
Samples in Pool 21, Pool 22 and Pool 23 paired from the same patients
S25.zip

value: PBMC

value: TIP200(N/A), GI4381 (N/A), GI4158 (Dual Therapy), PRISE11 (Dual Therapy)


title: 32_ENDO5_t1_PB_CD8T

description: Longitudinal ind1 t1

tag: cmv


title: MSC, CK666, replicate3, RNA-seq

description:
CK666_rep3
RNAseq.counts.txt

tag: strain


title: Pool21_PBMC_TCR

description:
Samples in Pool 21, Pool 22 and Pool 23 paired from the same patients
S24.zip


title: 31_ENDO5_t1_PB_NK

description: Longitudinal ind1 t1


title: MSC, CK666, replicate1, RNA-seq

description:
CK666_rep1
RNAseq.counts.txt

tag: Sex


title: Para9150 polymyxin B replicate 2 [Barseq9]

city: Palo Alto

first: Benjamin

last: Wang

state: CA

address: 299 Campus Drive

institute: Stanford

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: Barseq9_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq9_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq9_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq9_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

organism: Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150

source_name: ATCC 9150

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B).

extract_protocol:
DNA was extracted using a Qiagen gDNA kit using standard procedures.
Purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.

treatment_protocol: Each library was grown in stresses (either LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B) overnight for 16 hours.

value: ATCC 9150

value: Bacterial Tn library

value: 0.75 ug/mL polymyxin B


title: MSC, CK666, replicate2, RNA-seq

description:
CK666_rep2
RNAseq.counts.txt


title: Para9150 cotrimoxazole replicate 2 [Barseq9]

value: 0.125 ug/mL cotrimoxazole


title: 30_ENDO5_t2_MB_CD8T

description: Longitudinal ind1 t2

value: Menstrual blood

value: CD8+ Trm

value: longitudinal

value: pos


title: Pool23_Stromal_BCR

description:
Samples in Pool 21, Pool 22 and Pool 23 paired from the same patients
S27.zip

value: 5' chemistry

value: Colon


title: WT liver, normal diet, biol rep 3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Liver tissue from WT C57BL/6 mice was collected after feeding with normal diet for 21 days.

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC mouse genome build mm9) using HISAT2 (v2.1.0) default settings. The aligned BAM files sorted (SAMTools) and then processed using FeatureCounts (v1.5.0) to obtain the counts per gene
gene count measurements were obtained using FeatureCounts
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format generated by FeatureCounts. Seven (7) columns are: Geneid; Chr; Start; End; Strand; Length; bamFileName

extract_protocol:
RNA was extracted by Triazol and Qiagen RNeasy Plus Mini kit. RNA quality was determined by BioAnalyzer and RIN > 4. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq library preparation by following the NEB stranded mRNA sample preparation guide

treatment_protocol: At 4 weeks old, mice were fed either standard chow diet or ketogenic diet (90% fat, 9.7% protein, 0.3% carb) for 21 days.

value: liver

value: normal diet (control)


title: Para9150 rifampicin replicate 2 [Barseq9]

value: 4 ug/mL rifampicin


title: Para9150 gentamycin replicate 2 [Barseq9]

value: 1 ug/mL gentamycin


title: WT liver, normal diet, biol rep 2


title: 29_ENDO5_t2_MB_NK

description: Longitudinal ind1 t2

value: uNK


title: Pool11_PBMC_BCR

description:
Samples in Pool 11, Pool 12 and Pool 13 paired from the same patients
S15.zip

value: PBMC

value: TIP246(N/A), IBD3350(N/A), GI3152(Dual Therapy), PRISE12(Dual Therapy)


title: Pool23_Stromal_TCR

description:
Samples in Pool 21, Pool 22 and Pool 23 paired from the same patients
S26.zip

value: TIP200(N/A), GI4381 (N/A), GI4158 (Dual Therapy), PRISE11 (Dual Therapy)


title: 25_ENDO5_t1_MB_NK

description: Longitudinal ind1 t1


title: Para9150 LB replicate 2 [Barseq9]

value: ATCC 9150

value: Bacterial Tn library

value: LB


title: Para time 0 replicate 2 [Barseq9]

description: time0 is used as reference for other samples


title: Pool13_Stromal_BCR

description:
Samples in Pool 11, Pool 12 and Pool 13 paired from the same patients
S17.zip


title: ATAC_Hoxb8FL_cDC_1_S2

value: bone marrow-derived

value: hematopoietic cell

value: WT

tag: developmental stage

value: day7 post differentiation; dendritic cell


title: WT kidney, normal diet, biol rep 3

description: Kidney tissue from WT C57BL/6 mice was collected after feeding with normal diet for 21 days.

value: kidney


title: WT liver, normal diet, biol rep 1


title: Pool13_Stromal_TCR

description:
Samples in Pool 11, Pool 12 and Pool 13 paired from the same patients
S16.zip

tag: chemistry

value: 5' chemistry

value: Colon


title: Para9150 polymyxin B replicate 1 [Barseq9]

value: 0.75 ug/mL polymyxin B


title: 23_MZ05_B_PB_NK

description: Twin pair3 ind2

value: Peripheral blood

value: CD56dim NK

value: twin

value: pos


title: WT kidney, normal diet, biol rep 2

value: normal diet (control)


title: Para9150 rifampicin replicate 1 [Barseq9]

value: 4 ug/mL rifampicin


title: 26_ENDO5_t1_MB_CD8T

description: Longitudinal ind1 t1

value: Menstrual blood

value: CD8+ Trm

value: longitudinal


title: WT kidney, normal diet, biol rep 1


title: Para9150 cotrimoxazole replicate 1 [Barseq9]

value: ATCC 9150

value: Bacterial Tn library

value: 0.125 ug/mL cotrimoxazole


title: Pool13_Stromal_GEX

description:
Samples in Pool 11, Pool 12 and Pool 13 paired from the same patients
STR_CD45_S13.zip

tag: sample

value: TIP246(N/A), IBD3350(N/A), GI3152(Dual Therapy), PRISE12(Dual Therapy)


title: WT heart, normal diet, biol rep 3

description: Heart tissue from WT C57BL/6 mice was collected after feeding with normal diet for 21 days.

value: heart


title: 21_MZ05_A_PB_NK

description: Twin pair3 ind1


title: Pool23_Stromal_ADT

description:
Samples in Pool 21, Pool 22 and Pool 23 paired from the same patients
STR_CD45_S23.zip

value: 5' chemistry

tag: hashtag

value: TIP200(N/A), GI4381 (N/A), GI4158 (Dual Therapy), PRISE11 (Dual Therapy)


title: Pool11_PBMC_TCR

description:
Samples in Pool 11, Pool 12 and Pool 13 paired from the same patients
S14.zip

value: PBMC

tag: disease


title: 20_MZ05_B_MB_CD8T

description: Twin pair3 ind2


title: 19_MZ05_B_MB_NK

description: Twin pair3 ind2

value: uNK


title: Para time 0 replicate 1 [Barseq9]


title: WT heart, normal diet, biol rep 1


title: Pool23_Stromal_GEX

value: Colon

tag: immunotherapy


title: Pool32_Stromal_ADT

description:
Samples in Pool 31 and Pool 32 paired from the same patients
STR_CD45_S32.zip

value: TIP332(N/A), IBD3778(N/A), GI4442(Dual Therapy) GI3662(Dual Therapy)

tag: age


title: WT heart, normal diet, biol rep 2


title: Para9150 LB replicate 1 [Barseq9]

value: LB


title: Para9150 gentamycin replicate 1 [Barseq9]

value: 1 ug/mL gentamycin


title: 24_MZ05_B_PB_CD8T

description: Twin pair3 ind2

value: Peripheral blood

value: CD8+ Tem

value: twin

value: pos


title: WT liver, 21 days keto, biol rep 3

description: Liver tissue from WT C57BL/6 mice was collected after feeding with ketogenic diet for 21 days.

value: liver

value: ketogenic diet, 21 days


title: WT liver, 21 days keto, biol rep 2


title: 22_MZ05_A_PB_CD8T

description: Twin pair3 ind1


title: Para9150 THP-1 infection replicate 2 [Barseq13]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness. Data was analyzed using DEseq2 analysis, as has previously been done with macrophage Tn library papers and Salmonella.
Assembly: ASM754v1 for Ty2, ASM1188v1 for Para9150.
Supplementary files format and content: Barseq13_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq13_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then used to infect THP-1 human macrophages at an MOI of 100. Infections were allowed to proceed for 1 hour, then cells were treated with media+high gentamycin (100 ug/mL) for 1 hour to kill extracellular bacteria. Media was then changed to low gentamycin (10 ug/mL) for the duration of the infection, which proceeded for 18 hours.

extract_protocol:
DNA was extracted using the epicentre masterpure dna extraction kit, which was applied to macrophages lysed with 2% saponin after the duration of the 18 hour infection.
Purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.

treatment_protocol: Macrophages were infected with Ty2 and para9150 libraries for 18 hours after changing the media to high gentamycin (10 ug/mL).

value: ATCC 9150

value: Bacterial Tn library


title: 17_MZ05_A_MB_NK

description: Twin pair3 ind1

value: Menstrual blood


title: 16_MZ12_B_PB_CD8T

description: Twin pair2 ind2

value: neg


title: Pool38_Stromal_ADT

description:
Samples in Pool 37, Pool 38 and Pool 43 paired from the same patients
STR_CD45_S38.zip

value: 5' chemistry

value: GI3052(CC_I), PRISE5(CC_I) GI4069(CC_I), PRISE 4(CC_NI), GI4448(CC_NI)

value: GI3052(Monotherapy), PRISE 5(Monotherapy) GI4069(Dual Therapy), PRISE 4(Monotherapy), GI4448(Monotherapy)

tag: mixed gender


title: Pool32_Stromal_GEX

value: Colon


title: WT liver, 21 days keto, biol rep 1


title: 18_MZ05_A_MB_CD8T

description: Twin pair3 ind1

tag: cell type

value: CD8+ Trm


title: 15_MZ12_B_PB_NK

description: Twin pair2 ind2

value: CD56dim NK


title: Pool38_Stromal_GEX


title: Para time 0 replicate 2 [Barseq13]

tag: treatment


title: Pool13_Stromal_ADT

value: TIP246(N/A), IBD3350(N/A), GI3152(Dual Therapy), PRISE12(Dual Therapy)


title: Para time 0 replicate 1 [Barseq13]


title: WT kidney, 21 days keto, biol rep 3

description: Kidney tissue from WT C57BL/6 mice was collected after feeding with ketogenic diet for 21 days.

value: kidney


title: Pool52_Stromal_ADT

description:
Samples in Pool 44, Pool 51 and Pool 52 paired from the same patients
STR_CD45_S52.zip

value: GI4738(Monotherapy), GI2935(Monotherapy), GI4680(Dual Therapy), GI3128(Monotherapy), PRISE 13(Monotherapy)


title: WT kidney, 21 days keto, biol rep 2


title: Para protamine [Barseq6]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: barseq6_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: barseq6_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: barseq6_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: barseq6_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either anaerobic LB, GMM, zinc overload, Nmedia, protamine- the second set of samples).

treatment_protocol: Each library was grown in stresses (anaerobic LB, GMM, zinc overload, Nmedia, protamine- the second set of samples) overnight for 16 hours.

value: 2.3 ug/mL protamine


title: 14_MZ12_A_PB_CD8T

description: Twin pair2 ind1

value: Peripheral blood

value: CD8+ Tem

value: twin


title: Pool52_Stromal_GEX


title: WT kidney, 21 days keto, biol rep 1

value: ketogenic diet, 21 days


title: Para9150 THP-1 infection replicate 1 [Barseq13]

value: ATCC 9150

value: Bacterial Tn library


title: Pool58_Stromal_ADT

description:
Samples in Pool 57 and Pool 58 paired from the same patients
STR_CD45_S58.zip

value: TIP 309(Infectious colitis), TIP 299(Microscopic colitis), GI 4379(UC_I), GI 4449(CC_I), GI 4051(CC_I)

value: TIP 309 (N/A), TIP 299(N/A), GI 4379(N/A), GI 4449 (Monotherapy), GI 4051(Dual Therapy)


title: 13_MZ12_A_PB_NK

description: Twin pair2 ind1

value: neg


title: 12_MZ12_B_MB_CD8T

description: Twin pair2 ind2

value: Menstrual blood


title: Pool58_Stromal_GEX

value: 5' chemistry

value: Colon


title: WT heart, 21 days keto, biol rep 3

description: Heart tissue from WT C57BL/6 mice was collected after feeding with ketogenic diet for 21 days.

value: heart


title: WT heart, 21 days keto, biol rep 2


title: Para zinc  [Barseq6]

value: 500 uM zinc


title: 11_MZ12_B_MB_NK

description: Twin pair2 ind2

value: uNK


title: Pool22_EPI_ADT

description:
Samples in Pool 21, Pool 22 and Pool 23 paired from the same patients
Epi_S22.zip

value: TIP200(N/A), GI4381 (N/A), GI4158 (Dual Therapy), PRISE11 (Dual Therapy)


title: Para time0, rep 2  [Barseq6]


title: para GMM  [Barseq6]

value: GMM


title: Pool22_EPI_GEX


title: 10_MZ12_A_MB_CD8T

description: Twin pair2 ind1

value: CD8+ Trm


title: 9_MZ12_A_MB_NK

description: Twin pair2 ind1


title: C57_MAZ51-TREATING CD45 POSTIVE VA

city: Hangzhou

first: Qingbo

last: Xu

address: 79 Qingchun Road

department: Department of Cardiology

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

description: 10x Genomics

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.1.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Assembly: mm10
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: Vascular allografts

extract_protocol:
Mice were euthanized and perfused with PBS and vascular allografts were harvested and placed in a petri dish containing DMEM with 10% fetal bovine serum (FBS) on ice. Perivascular adipose tissues and connective tissues were carefully removed. After collecting all grafts, to obtain single cell suspensions, arteries were washed with PBS for three times, cut into fine pieces and incubated with 1 mg/ml papain digesting solution [1 mg/ml papain (Sigma, P4762), 0.5 mg/ml 1,4-Dithioerythritol (Sigma, D8255), 0.156 mg/ml Taurine (Sigma, T8691), 0.25 mg/ml bovine serum albumin in PBS]. The digestion was performed at 37 ℃ water bath with reciprocal shaking. Detached cells in the supernatant were collected and suspended in DMEM with 10% FBS. Vascular allografts were then incubated with fresh digestion solutions every 10 min. After 3-4 digestions, the remaining tissues were incubated with 1 mg/ml papain digesting solution and 2 mg/ml collagenase I (Gibco, 17018029) and 1 mg/ml dispase II (Sigma, D4693) in Hank’s balanced salt solution containing calcium and magnesium. Detached cells were collected and fresh digestion solutions were added until the tissues dissolved completely. All digested cells from one sample were pooled together at the end of the digestion process. After sufficient digestion, cells were filtered through a 40-μm cell strainer, and the collected cells were centrifuged 8 min at 500 g speed at 4 ℃. Subsequently, cell pellet was suspended in PBS and stained with LIVE/DEAD ™ Fixable Near-IR Dead Cell Stain Kit, Hoechst 33342 and CD45 (BD Pharmingen™, 553079) for 30 mins on ice. After PBS washing, cells were resuspended in PBS and single nucleated live cells (Hoechst+ & Dead Cell Stain- & CD45+/-) were sorted into PBS with 0.04% BSA using a Flow Cytometer. Samples were subjected to scRNA-seq. A ChromiumTM Single Cell 3' Reagent Kit v2 or V3 chemistry (10x Genomics) was used and a standard protocol was followed. The library was generated and sequenced on a Novaseq6000 PE150 platform (Illumina) with paired-end 150 bp sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Vascular allografts

value: CD45 postive

value: wild type

value: 10-12 weeks old

value: MAZ51 treating for 4 weeks


title: WT heart, 21 days keto, biol rep 1

value: ketogenic diet, 21 days


title: Pool31_EPI_ADT

description:
Samples in Pool 31 and Pool 32 paired from the same patients
Epi_S31.zip

value: TIP332(N/A), IBD3778(N/A), GI3662(Dual Therapy)


title: 8_MZ10_B_PB_CD8T

description: Twin pair1 ind2

value: Peripheral blood

value: CD8+ Tem

value: twin

value: pos


title: Para anaerobic LB  [Barseq6]

value: ATCC 9150

value: Bacterial Tn library

value: anaerobic LB


title: Pool31_EPI_GEX

value: 5' chemistry

value: Colon


title: Para time 0  [Barseq6]

description: time0 is used as reference for other samples


title: 7_MZ10_B_PB_NK

description: Twin pair1 ind2

value: CD56dim NK


title: C57_CD45 NEGATIVE VA_2

description: 10x Genomics

value: Vascular allografts

value: CD45 negative


title: Para9150 protamine [Barseq5]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: barseq5_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: barseq5_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: barseq5_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: barseq5_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either anaerobic LB, GMM, zinc, Nmedia, protamine).

treatment_protocol: Each library was grown in stresses (anaerobic LB, GMM, zinc, Nmedia, protamine) overnight for 16 hours.

value: 2.3 ug/mL protamine


title: C57_CD45 NEGATIVE VA_3

description: 10x Genomics

value: wild type

value: 10-12 weeks old


title: Pool37_EPI_ADT

description:
Samples in Pool 37, Pool 38 and Pool 43 paired from the same patients
Epi_S37.zip

value: GI3052(Monotherapy), GI4069(Dual Therapy), PRISE 4(Monotherapy), GI4448(Monotherapy)


title: Para Nmedia [Barseq6]

value: Nmedia


title: 6_MZ10_A_PB_CD8T

description: Twin pair1 ind1

value: Peripheral blood

value: neg


title: C57_CD45 NEGATIVE VA_1

description: 10x Genomics


title: Pool37_EPI_GEX


title: Para9150 Nmedia [Barseq5]


title: Para9150 zinc [Barseq5]

value: 500 uM zinc


title: Pool51_EPI_ADT

description:
Samples in Pool 44, Pool 51 and Pool 52 paired from the same patients
Epi_S51.zip

value: GI4738(Monotherapy), GI2935(Monotherapy), GI4680(Dual Therapy), GI3128(Monotherapy), PRISE 13(Monotherapy)


title: 4_MZ10_B_MB_CD8T

description: Twin pair1 ind2

value: Menstrual blood

value: CD8+ Trm

value: twin

value: pos


title: RNA_Hoxb8FL_cDC_3_S14

data_processing:
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and ATAC-Seq reads were mapped using bowtie2
RNA-Seq read counting performed using HT-seq
BAM to bedgraph performed using bedtools and bedgraph to bigwig performed using bedGraphToBigWig v4
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
Hoxb8-FL cells were sorted as described in the manuscript and RNA was isolated using RNeasy mini kit (QIAGEN) and QIAshredder homogenizer (QIAGEN) according to the manufacturer’s instructions. 1 ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard Illumina protocols and Low input Clontech SMART-Seq HT with Nxt HT following manufacturer's protocols.

value: bone marrow-derived

tag: cell line

value: hematopoietic cell

value: WT

value: day7 post differentiation; dendritic cell


title: Pool51_EPI_GEX

value: 5' chemistry

value: Colon


title: 3_MZ10_B_MB_NK

description: Twin pair1 ind2

value: uNK


title: Para9150 GMM [Barseq5]

value: ATCC 9150

tag: genotype

value: Bacterial Tn library

value: GMM


title: Para9150 anaerobic LB [Barseq5]

tag: tissue

value: LB


title: Pool57_EPI_ADT

description:
Samples in Pool 57 and Pool 58 paired from the same patients
They had quality issues and we excluded them from the analysis and therefore there is no matched processed data for them, however wanted to upload the raw data for completeness regardless.

value: TIP 309(Infectious colitis), TIP 299(Microscopic colitis), GI 4379(UC_I), GI 4449(CC_I), GI 4051(CC_I)

value: TIP 309 (N/A), TIP 299(N/A), GI 4379(N/A), GI 4449 (Monotherapy), GI 4051(Dual Therapy)


title: 2_MZ10_A_MB_CD8T

description: Twin pair1 ind1

value: Menstrual blood

tag: sample type

value: neg


title: RNA_Hoxb8FL_day2_3_S12

value: day2 post differentiation


title: RNA_Hoxb8FL_day0_3_S11

value: day0; progenitor


title: 1_MZ10_A_MB_NK

description: Twin pair1 ind1

value: twin

tag: cmv


title: Pool21_PBMC_ADT

description:
Samples in Pool 21, Pool 22 and Pool 23 paired from the same patients
PBMC_S21.zip

value: PBMC

value: TIP200(N/A), GI4381 (N/A), GI4158 (Dual Therapy), PRISE11 (Dual Therapy)


title: RNA_Hoxb8FL_pDC_2_S10

value: bone marrow-derived

value: hematopoietic cell

value: WT

value: day7 post differentiation; dendritic cell


title: mv Para Nitric oxide replicate 2 [Barseq4]

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: barseq4_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: barseq4_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: barseq4_para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: barseq4_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either InSPI2 stress, H2O2, nitric oxide, sodium hypochlorite).

treatment_protocol: Each library was grown in stresses (either InSPI2 stress, H2O2, nitric oxide, sodium hypochlorite) overnight for 16 hours.

value: ATCC 9150

value: 250 uM spermine NONOate


title: Pool57_EPI_GEX

value: 5' chemistry

value: Colon


title: GD4_input

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
*library strategy: MeRIP-Seq
Clean reads were mapped to mouse genome (UCSC mm10) by using HISAT v2.2.1
Peaks were called uing MACS v3.0.0a7 with the significance cut-off q-value <=0.05
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: mixed

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB).

treatment_protocol: Female mice aged 6-8 weeks were mated with fertile males to induce pregnancy. The appearance of the vaginal plug was designated as gestation day (GD) 1. Pregnant females were sacrificed on GD4.

tag: ip antibody

tag: time

value: gestational day 4

value: mixed

value: wild-type


title: Pool21_PBMC_GEX


title: 5_MZ10_A_PB_NK

description: Twin pair1 ind1

value: Peripheral blood

value: CD56dim NK

value: neg


title: mv para H2O2 replicate 2 [Barseq4]

value: Bacterial Tn library


title: RNA_Hoxb8FL_cDC_2_S9

tag: developmental stage


title: RNA_Hoxb8FL_pDC_3_S15


title: Mettl14_dd

data_processing:
Clean reads were mapped to mouse genome (UCSC mm10) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: whole uterus

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

value: whole uterus

value: d/d


title: RNA_Hoxb8FL_day4_2_S8

value: bone marrow-derived

value: day4 post differentiation


title: mv Para InSPI2 replicate 2 [Barseq4]


title: Pool44_PBMC_GEX

description:
Samples in Pool 44, Pool 51 and Pool 52 paired from the same patients
PBMC_S44.zip

tag: chemistry

value: PBMC

value: GI4738(Monotherapy), GI2935(Monotherapy), GI4680(Dual Therapy), GI3128(Monotherapy), PRISE 13(Monotherapy)


title: RNA_Hoxb8FL_day4_3_S13

value: hematopoietic cell

value: WT


title: RNA_Hoxb8FL_day2_2_S7

value: day2 post differentiation


title: Mettl14_ff

value: f/f


title: Pool43_PBMC_ADT

description:
Samples in Pool 37, Pool 38 and Pool 43 paired from the same patients
PBMC_S43.zip

value: 5' chemistry

tag: sample

value: GI3052(CC_I), PRISE5(CC_I) GI4069(CC_I), PRISE 4(CC_NI), GI4448(CC_NI)

value: GI3052(Monotherapy), PRISE 5(Monotherapy) GI4069(Dual Therapy), PRISE 4(Monotherapy), GI4448(Monotherapy)


title: mv Para time 0 replicate 2 [Barseq4]

value: ATCC 9150


title: mv Para sodium hypochlorite replicate 1 [Barseq4]

value: 8 ug/mL sodium hypochlorite


title: Pool43_PBMC_GEX

tag: hashtag


title: mv Para sodium hypochlorite replicate 2 [Barseq4]


title: Para9150 time0 [Barseq5]

value: LB


title: RNA_Hoxb8FL_pDC_1_S5

value: day7 post differentiation; dendritic cell


title: mv Para Nitric oxide replicate 1 [Barseq4]

value: Bacterial Tn library

value: 250 uM spermine NONOate


title: GI3060 (SB)

extract_protocol:
Fresh or Frozen colonic biopsies from UC_I, UC_NI, CC_I, CC_NI and HC were digested to yield high viability single cells, which were put through flow-cytometry (FACS) sorting to enrich for CD45+ immune cells, before loading on to the 10X platform for single-cell RNA sequencing
Samples were loaded onto the 10X sc-RNA seq platform, with GEM generation and RNA RT, followed by generation of Gene expression (GEX) libraries, as per protocol CG000183, Rev A

value: Colon

tag: disease

value: Checkpoint inhibitor-induced colitis

value: Monotherapy

tag: inflammation

value: Not inflamed

tag: fresh/frozen

value: Frozen

tag: gender

value: Male

value: 3' chemistry


title: mv para H2O2 replicate 1 [Barseq4]


title: GI3126 (SC)

tag: immunotherapy

value: Inflamed

tag: age


title: Pool12_EPI_GEX

description:
Samples in Pool 11, Pool 12 and Pool 13 paired from the same patients
Epi_S12.zip

value: 5' chemistry

tag: mixed gender


title: GI3031 (SA)


title: GD4_IP

value: anti-m6a (Synaptic Systems, #202003)

value: gestational day 4

tag: cell type

value: mixed

tag: genotype

value: wild-type


title: mv Para InSPI2 replicate 1 [Barseq4]

tag: tissue

value: ATCC 9150

tag: treatment


title: RNA_Hoxb8FL_day4_1_S3

value: bone marrow-derived

tag: cell line

value: hematopoietic cell

value: WT

value: day4 post differentiation


title: Pool44_PBMC_ADT

value: PBMC

value: GI4738(Monotherapy), GI2935(Monotherapy), GI4680(Dual Therapy), GI3128(Monotherapy), PRISE 13(Monotherapy)


title: Pool11_PBMC_ADT

description:
Samples in Pool 11, Pool 12 and Pool 13 paired from the same patients
They had quality issues and we excluded them from the analysis and therefore there is no matched processed data for them, however wanted to upload the raw data for completeness regardless.

value: TIP246(N/A), IBD3350(N/A), GI3152(Dual Therapy), PRISE12(Dual Therapy)


title: RNA_Hoxb8FL_day2_1_S2

value: day2 post differentiation


title: Pool11_PBMC_GEX


title: mv Para time 0 replicate 1 [Barseq4]

value: Bacterial Tn library


title: TIP 517

data_processing:
Illumina bcl2fastq was used to convert raw bcl files to fastq format
Fastq files were processed using 10x Genomics Spaceranger (version 1.0) software
Genome_build: hg38
Supplementary_files_format_and_content: Spaceranger outputs - raw feature barcode matrix in mtx format, gene list in tab delimited format, spot barcodes in tab delimited format, spatial transcriptomics slide H&E image in jpeg format, spot position to image pixel coordinates.

source_name: Colon tissue

extract_protocol: Adult colonic samples were freshly frozen in OCT blocks and then 4uM sections placed onto an oligo-covered array with subsequent H&E, imaging, sample permeabilization, RNA RT and amplification as per protocol for the 10x visium spatial platform (10x CG000239 Rev D)

value: Healthy Control

tag: section cut

value: Biopsy

value: Colon

tag: activity

value: Not inflamed

value: Female


title: RNA_Hoxb8FL_day0_1_S1

tag: developmental stage

value: day0; progenitor


title: GI3236 (SD)

value: Checkpoint inhibitor-induced colitis

value: Monotherapy

value: Frozen

value: Male

tag: chemistry

value: 3' chemistry


title: GI 3667 (#1)

value: Checkpoint inhibitor induced colitis

value: Inflamed


title: RNA_Hoxb8FL_day0_2_S6

value: bone marrow-derived

value: hematopoietic cell

value: WT


title: Pool3_Stromal_BCR

description:
Samples in Pool 1, Pool 2 and Pool 3 paired from the same patients
S7.zip

value: 5' chemistry

tag: sample

tag: hashtag

value: TIP278 (N/A), IBD3947 (N/A), GI4059 (Dual Therapy)


title: GI 6274

tag: disease

value: Biopsy


title: Pool12_EPI_ADT

value: Colon


title: RNA_Hoxb8FL_cDC_1_S4

value: day7 post differentiation; dendritic cell


title: Para cipro rep 2 [Barseq3]

description:
IT035
barseq3_para9150_processed.csv

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150
Supplementary files format and content: Barseq3_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq3_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq3_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq3_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either LB, ceftriaxone, ciprofloxacin, azithromycin).

treatment_protocol: Each library was grown in stresses (bLB, ceftriaxone, ciprofloxacin, azithromycin) overnight for 16 hours.

value: ATCC 9150

value: Bacterial Tn library

value: 0.0125 ug/mL ciprofloxacin


title: BB4652

value: Ulcerative Colitis


title: BT474, Resistant, Month 9, rep3

data_processing:
Reads were called using the manufacturer's bcl2fastq2 base calling software.
Reads were then aligned the reference genome (hg38) using Star version 2.5.2b, with the reference genome along with annotations downloaded from Illumina iGenomes web site.
Reads were then associated with known genes and the number of reads associated with each gene was counted using the subreads-package v1.5.1.
Gene-wise read counts were normalised using the TMM normalization method of the edgeR R/Bioconductor package with log(x+1) transformation for downstream applications.
The data processing pipeline was run using default parameters when possible.
Assembly: hg38
Supplementary files format and content: Tab-separated gene-wise expression (rows) per samples (columns) normalized using TMM.

growth_protocol: BT474 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the NucleoSpin RNA purification kit (Macherey‐Nagel). 300 ng of total RNA was used for the construction of sequencing libraries.
TruSeq® Stranded mRNA Sample Preparation, Illumina

treatment_protocol: The cells were treated with 1 uM of lapatinib every 3 days for 9 months

value: HER2+ breast cancer cell line

value: Lapatinib, 1 uM

tag: time

value: Month 9


title: Pool1_PBMC_BCR

description:
Samples in Pool 1, Pool 2 and Pool 3 paired from the same patients
S5.zip

value: PBMC

value: TIP278 (N/A), IBD3947 (N/A), GI4059 (Dual Therapy), PRISE1 (Dual Therapy)


title: GI 4980

value: Inflamed

tag: gender

value: Female


title: Pool3_Stromal_TCR

description:
Samples in Pool 1, Pool 2 and Pool 3 paired from the same patients
S6.zip

tag: immunotherapy


title: sgRNA_Hoxb8FL_pDNA

description: pDNA

organism: unidentified plasmid

source_name: library-carrying plasmid DNA

value: library-carrying plasmid DNA


title: Para LB, rep 2 [Barseq3]

description:
IT027
barseq3_para9150_processed.csv

value: LB


title: BT474, Resistant, Month 9, rep2

value: WT


title: Pool1_PBMC_TCR

description:
Samples in Pool 1, Pool 2 and Pool 3 paired from the same patients
S4.zip

value: 5' chemistry

tag: age


title: GI 6658

value: Biopsy

value: Colon

value: Male


title: BT474, Resistant, Month 9, rep1


title: Para LB time 0, rep 2 [Barseq3]

description:
time0 is used as reference for other samples
barseq3_para9150_processed.csv

value: ATCC 9150

value: Bacterial Tn library


title: GI 6925

value: Healthy Control

value: Not inflamed


title: BT474, DTEP, Month 6, rep3

value: HER2+ breast cancer cell line

value: Lapatinib, 1 uM

value: Month 6


title: Para cef, rep 2 [Barseq3]

description:
IT031
barseq3_para9150_processed.csv

value: 0.03 ug/mL ceftriaxone


title: Pool3_Stromal_ADT

description:
Samples in Pool 1, Pool 2 and Pool 3 paired from the same patients
STR_CD45_S3.zip

value: TIP278 (N/A), IBD3947 (N/A), GI4059 (Dual Therapy)

tag: mixed gender


title: Para azithro rep 2 [Barseq3]

description:
IT039
barseq3_para9150_processed.csv

value: 5 ug/mL azithromycin


title: GI 6278

value: Checkpoint inhibitor induced colitis

value: Inflamed

value: Dual therapy


title: Pool2_EPI_ADT

description:
Samples in Pool 1, Pool 2 and Pool 3 paired from the same patients
Epi_S2.zip

value: 5' chemistry


title: BT474, DTEP, Month 6, rep2

tag: cell type

value: WT


title: Para cipro rep 1 [Barseq3]

description:
IT015
barseq3_para9150_processed.csv

tag: genotype

value: 0.0125 ug/mL ciprofloxacin


title: Pool1_PBMC_ADT

description:
Samples in Pool 1, Pool 2 and Pool 3 paired from the same patients
PBMC_S1.zip

tag: tissue

value: PBMC

value: TIP278 (N/A), IBD3947 (N/A), GI4059 (Dual Therapy), PRISE1 (Dual Therapy)


title: BT474, DTEP, Month 6, rep1

tag: treatment


title: Para cef, rep 1 [Barseq3]

description:
IT011
barseq3_para9150_processed.csv

value: ATCC 9150

value: Bacterial Tn library


title: Pool3_Stromal_GEX

value: Colon


title: BT474, DTP, Day 9, rep3

tag: cell line

value: HER2+ breast cancer cell line

value: Day 9


title: GI 6967_B8

value: Ulcerative Colitis

tag: section cut

value: Resection

value: Female


title: PRISE 23

value: Biopsy

tag: activity

value: Monotherapy

value: Male


title: Pool2_EPI_GEX

value: TIP278 (N/A), IBD3947 (N/A), GI4059 (Dual Therapy),


title: BT474, DTP, Day 9, rep2

value: Lapatinib, 1 uM


title: Para 42 degrees replicate 2

description:
IT039
barseq2_Para9150_processed.csv

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: Barseq2_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq2_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq2_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq2_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either bile stress, iron limitation, osmotic pressure, heat shock).

treatment_protocol: Each library was grown in stresses (bile stress, iron limitation, osmotic pressure, heat shock) overnight for 16 hours.

value: 42 degrees


title: BT474, DTP, Day 9, rep1

value: WT


title: Para LB time 0, rep 1 [Barseq3]


title: PRISE 14

value: Checkpoint inhibitor induced colitis

value: Inflamed


title: BT474, Control, Day 0, rep3

value: Day 0


title: Para azithro rep 1 [Barseq3]

description:
IT019
barseq3_para9150_processed.csv

value: ATCC 9150

value: Bacterial Tn library

value: 5 ug/mL azithromycin


title: GI3409

value: Colon

value: Healthy control

tag: inflammation

value: Not inflamed

tag: fresh/frozen

value: Fresh

value: 3' chemistry


title: Para naCl replicate 2

description:
IT035
barseq2_Para9150_processed.csv

value: 0.4 M NaCl


title: para iron replicate 2

description:
IT031
barseq2_Para9150_processed.csv

value: 0.2 mM 2-2' bipyridyl


title: GI3410

value: Female

tag: chemistry


title: GI Biobank Corona Recovery 15 (GI 6264)

value: Ulcerative Colitis

value: Biopsy


title: GI 6967_B9

value: Resection


title: BT474, Control, Day 0, rep1

value: HER2+ breast cancer cell line

value: WT

value: Lapatinib, 1 uM


title: PRISE 31

value: Checkpoint inhibitor induced colitis

value: Inflamed

value: Dual therapy

value: Male


title: Para bile replicate 2

description:
IT027
barseq2_Para9150_processed.csv

value: ATCC 9150

value: Bacterial Tn library

value: 4% bile


title: IBD2218_I

value: Colon

value: Ulcerative colitis

value: Fresh

value: 3' chemistry


title: GI Biobank Corona Recovery 17 (GI 6266)

value: Ulcerative Colitis


title: Pool 22 Antibody: Sorted CD3_ADT_Blood_Pool19_Repeat 2

description: Pool 16 (Tissue) paired samples with Pool 19 (Blood) and Pool 22 (Blood)

source_name: T-cells

extract_protocol:
Matched Colonic biopsy (Tissue) and Peripheral Blood (Blood) samples from Healthy controls, patients with inflamed Ulcerative Colitis (UC_I) and Checkpoint inhibitor-induced colitis (CC_I) were defrosted. Tissue was digested to yield high viability single cells, and then tissue and blood were put through flow-cytometry (FACS) sorting to enrich for T cells, before loading on to the 10X platform for single-cell RNA sequencing
Samples were loaded onto the 10X sc-RNA seq platform, with GEM generation and RNA RT, followed by generation of Gene expression (GEX), Antibody tagged oligo (ADT - with CITE-seq proteins and hashing information) and T-cell receptor (TCR) library amplification and indexing, as per protocol CG000208, Rev F

value: Blood

value: T-cells

tag: samples

tag: immunotherapy regimen

value: TIP376(Female), IBD 1464 (Male), TIP489 (Male)

tag: hashtag

value: TIP376 (Hashtag#1), IBD 1464 (Hashtag#2), TIP489 (Hashtag#3)

value: 5' Chemistry