title: Suv420h2_sh24_2

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #1), replicate 2


title: MCF7, Day3, FulvPalbo, RNA

status: Public on Jun 29 2026

type: SRA

city: New York

first: Viviana

middle: I.

last: Risca

state: NY

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

country: USA

institute: The Rockefeller University

description:
Library name: MCF7_Day3_FulvPalbo
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: 009Day3FP_15_Aligned.sortedByName.out.bam

library_source: transcriptomic

data_processing:
For RNA samples sent to Novogene for sequencing, reads containing adapters, N > 10% (N represents the base cannot be determined) and low quality (Qscore<= 5) base were filtered out.  For RNA samples sent to Plasmidsaurus for sequencing, quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3.
Pseudoalignment and quantification of transcripts were performed with kallisto for LS8817 cells. Alignment and quantification of transcripts were performed with STAR v2.7.10a for MCF7 cells.
for LS8817 cells, kallisto counts were imported into R using tximport v1.14.2, and counts matrix normalized by sequencing depth was generated using was DESeq2 v1.26.0  for MCF7 cells, STAR counts were imported into R and counts matrix normalized by sequencing depth was generated using was DESeq2 v1.26.0
Assembly: hg38
Supplementary files format and content: files ending in kallisto_abundance.tsv is the abundance estimates of transcripts by kallisto
Supplementary files format and content: Files ending in ReadsPerGene.out.tab is the abundance counts of transcripts by STAR.
Supplementary files format and content: MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt is the counts of transcripts by STAR for all samples from the 21 day 100 nM palbociclib + 10 nM fulvestrant timecourse experiment

molecule: total RNA

organism: Homo sapiens

source_name: mammary gland

growth_protocol: LS8817 Cells were cultured in DMEM high glucose no glutamine (11960044, Gibco™), supplemented with 9% FBS (10082147, Gibco™), 1% of 100x GlutaMAX™ Supplement (35050061, Gibco™) and 1% of 10,000U/mL penicillin/streptomycin (15140122, Gibco™) and maintained at 37°C and 5% CO2.  Human MCF-7 cells (RRID:CVCL_0031) were cultured in in 75 cm2 flasks DMEM/F-12 (#Cat 10565018, Thermo Fisher Scientific) supplemented with GlutaMAX, 10% Fetal Bovine Serum (Cat# F4135, Sigma-Aldrich) and 1% Penicillin-Streptomycin at 37 °C and 5% CO2.

extract_protocol:
RNA extraction was done using the Quick-RNA Microprep Kit (Zymo Research, cat# R1050).
Total RNA from at least 2 biological replicates per condition was sent to Novogene for stranded library preparation and sequencing. cDNA libraries were made with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB cat# E7765). For MCF7 samples treated with  MCF7 cells were treated with 100 nM doxorubicin, 1 uM palbociclib or 100 nM palbociclib + 10 nM fulvestrant, samples were sent to PlasmidSaurus for forward-stranded library preparation. Plasmidsaurus'  RNA-seq service sequences polyadenylated (poly-A) eukaryotic transcripts using a 3′ end-counting approach to provide gene-level counts only, where a short stretch of RNA (~90nt) located within the last 300-400nt of the transcript is sequenced.

treatment_protocol: Cells were passaged at a 1:3 ratio one day before drug treatment and treated with drugs at the specified concentrations, with media changes every 2–3 days until harvest.

tag: tissue

value: mammary gland

tag: cell line

tag: cell type

value: epithelial

tag: genotype

value: WT

tag: treatment

value: day3 100nM palbociclib+10nM fulvestrant

tag: batch


title: Suv420h2_sh24_1

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #1), replicate 1

data_processing:
Following quality controls, raw sequencing reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3). Trimmed reads were next aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: Tab-delimited text file of raw read counts per gene/samples.

molecule: polyA RNA

organism: Mus musculus

source_name: Keratinocytes

growth_protocol: Mouse keratinocytes were grownin low-calcium Dulbecco’s modified Eagle medium supplemented with 10% FBS, 100 U ml−1 penicillin–streptomycin, HCE cocktail consisting of hydrocortisone 0.5 μg ml−1, insulin 5 μg ml−1 (Thermo Fisher), cholera enterotoxin 10−10 M (Sigma-Aldrich) and EGF 10 ng ml−1 (PeproTech) and cultured at 37 °C in a humidifiedatmosphere, with 8% CO2.

extract_protocol:
Mini bulk RNA-seq were performed as described before (Levra Levron C. et al., 2023) with some modifications. GFP+ mouse keratinocytes (expressing the shRNAs for Cbx3, Ehmt2, Kmt5c or a scramble shRNA) were sorted in 100 μl of lysis buffer (0.5% Triton X-100), in presence of RNase inhibitor. Then, a biotinylated Oligo(dT) was bound to Dynabeads MyOne Streptavidin T1 beads (ThermoFisher Scientific) and used to isolate mRNA from the cell lysate. Reverse transcription was perform on total RNA with SuperScript II Reverse Transcriptase (ThermoFisher Scientific) at 42°C x 50', for 10 cycles of [ 50°C x 2' 42°C x 2'], at 50° x 15 minutes  and at 70°C x 15'. The resulting cDNA was amplified with 25 cycles of PCR and libraries were prepared for sequencing with Illumina NexteraXT Illumina protocol (Illumina).
For extracted RNA, indexed cDNA libraries were obtained following the NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 and 1000 System.
Mini-bulk RNA-seq

value: Keratinocytes

tag: replicate

tag: condition

value: Suv420h2 KD

tag: shRNA

tag: shRNA type


title: MCF7, Day1, FulvPalbo, RNA

description:
Library name: MCF7_Day1_FulvPalbo
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: 001Day1FP_6_Aligned.sortedByName.out.bam

value: day1 100nM palbociclib+10nM fulvestrant


title: Scramble2_8

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #2, Ehmt2 ctrl), replicate 6

value: Scramble (Ctrl)

value: sh-Scramble


title: MCF7, Cycling, rep3, RNA

description:
Library name: MCF7_Cycling_rep3
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: 010Day21Cycling_1_Aligned.sortedByName.out.bam


title: Scramble2_6

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #2, Ehmt2 ctrl), replicate 5


title: MCF7, Cycling, rep2, RNA

description:
Library name: MCF7_Cycling_rep2
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: 002Day5Cycling_11_Aligned.sortedByName.out.bam


title: MCF7, Cycling, rep1, RNA

description:
Library name: MCF7_Cycling_rep1
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: 016Day1Cycling_3_Aligned.sortedByName.out.bam


title: MCF7, day18PalboandFulv, rep2, RNA

description:
Library name: MCF7_day18PalboandFulv_rep2
Counts were obtained from 2nd column in MCF7_HS_day18.PalboandFulv_rep2_21_ReadsPerGene.out.tab

value: day18 100nM palbociclib+10nM fulvestrant


title: Scramble2_3

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #2, Ehmt2 ctrl), replicate 2


title: MCF7, day18PalboandFulv, rep1, RNA

description:
Library name: MCF7_day18PalboandFulv_rep1
Counts were obtained from 2nd column in MCF7_HS_day18.PalboandFulv_rep1_20_ReadsPerGene.out.tab


title: Scramble2_2

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #2, Ehmt2 ctrl), replicate 1


title: MCF7, day21Palbo, rep3, RNA

description:
Library name: MCF7_day21Palbo_rep3
Counts were obtained from 2nd column in MCF7_HS_day21.Palbo_rep3_12_ReadsPerGene.out.tab

value: day21 1uM palbociclib


title: Scramble1_7

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #1, Cbx3, Suv420h2 ctrl), replicate 5


title: Scramble1_6

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #1, Cbx3, Suv420h2 ctrl), replicate 4


title: MCF7, day21Palbo, rep1, RNA

description:
Library name: MCF7_day21Palbo_rep1
Counts were obtained from 2nd column in MCF7_HS_day21.Palbo_rep1_9_ReadsPerGene.out.tab


title: Scramble1_5

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #1, Cbx3, Suv420h2 ctrl), replicate 3


title: MCF7, day21Palbo, rep2, RNA

description:
Library name: MCF7_day21Palbo_rep2
Counts were obtained from 2nd column in MCF7_HS_day21.Palbo_rep2_10_ReadsPerGene.out.tab


title: Scramble1_2

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #1, Cbx3, Suv420h2 ctrl), replicate 1


title: Scramble1_4

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #1, Cbx3, Suv420h2 ctrl), replicate 2


title: MCF7, day14Doxo, rep2, RNA

description:
Library name: MCF7_day14Doxo_rep2
Counts were obtained from 2nd column in MCF7_HS_day14.Doxo_rep2_7_ReadsPerGene.out.tab

value: 100 nM doxorubicin (48 h), harvested on day 14


title: MCF7, day14Doxo, rep1, RNA

description:
Library name: MCF7_day14Doxo_rep1
Counts were obtained from 2nd column in MCF7_HS_day14.Doxo_rep1_6_ReadsPerGene.out.tab


title: Ehmt2_sh2_8

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #2), replicate 5

value: Ehmt2 KD


title: Ehmt2_sh2_5

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #2), replicate 4


title: MCF7, PvsPFvsD, Cycling, rep3, RNA

description:
Library name: MCF7_PvsPFvsD_Cycling_rep3
Counts were obtained from 2nd column in MCF7_HS_Cycling_rep3_13_ReadsPerGene.out.tab


title: Ehmt2_sh2_3

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #2), replicate 2


title: Ehmt2_sh2_4

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #2), replicate 3


title: MCF7, PvsPFvsD, Cycling, rep1, RNA

description:
Library name: MCF7_PvsPFvsD_Cycling_rep1
Counts were obtained from 2nd column in MCF7_HS_Cycling_rep1_2_ReadsPerGene.out.tab


title: MCF7, PvsPFvsD, Cycling, rep2, RNA

description:
Library name: MCF7_PvsPFvsD_Cycling_rep2
Counts were obtained from 2nd column in MCF7_HS_Cycling_rep2_3_ReadsPerGene.out.tab


title: RNAseq HEK293 HEMK1 KO Repeat 2

city: Stuttgart

first: Albert

last: Jeltsch

address: Allmandring 31

department: Institute of Biochemistry and Technical Biochemistry

country: Germany

institute: University Stuttgart

description: Library name: KO Rep2

data_processing:
The Next Generation Sequencing data were received in FASTQ format and all further data processing steps were performed on the European Galaxy web platform (https://usegalaxy.eu). The quality of the reads was assessed using the FastQC tool followed by trimming of the Illumina adapters using the Trimmomatic tool with default settings {Bolger, 2014 #23}.
Reads were mapped on the human reference genome Hg38 using the gapped-read mapper RNA-Star under default settings.WTRep1 and KORep1 data were merged.
The obtained BAM files were used to generate count tables using the HTseq-count tool. Finally, differential gene expression was analyzed by DeSeq2, using the HTseq-count tables. DeSeq2 utilizes the median-of-ratios method for normalization.
Assembly: Hg38
Supplementary files format and content: HTseq-count and DESeq2 output

growth_protocol: HEK293 cells were cultured in DMEM high glucose media (Sigma-Aldrich) supplemented with 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich), 10 mM L-glutamate (Sigma-Aldrich) and 100 U/ml penicillin and 0.1 mg/ml streptomycin (Sigma-Aldrich). The cells were grown at 37°C and 5% CO2 and split every 2-3 days to keep confluency at 70-80%. For sub-culturing, the cells were washed with Dulbecco's Phosphate Buffered Saline without MgCl2 and CaCl2 (Sigma-Aldrich), immersed with Trypsin-EDTA solution (Sigma Aldrich) and incubated at 37°C for 5 min. Trypsinization was stopped by resuspension in respective media and cells were usually split in a 1:4–1:8 ratio.

extract_protocol:
For RNA isolation, 106 HEK293 wildtype or HEMK1 KO 1F8 cells were harvested by centrifugation at 300 rpm for 5 min. The total RNA was isolated using the QIAGEN RNeasy® Plus Mini Kit.
RNA libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB) according to the manufacturers protocol using 100 ng of total RNA per sample as input. Two biological replicates were processed. Sequencing libraries were prepared using the NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1).

treatment_protocol: HEMK1 KO cell lines were generated basically following the protocol described previously (Chandrasekaran TT, Choudalakis M, Brohm A, Weirich S, Kouroukli AG, Ammerpohl O, et al., Jeltsch A., 2024, Nucleic Acids Res 52: 13690-13705). Two different sgRNAs were adopted from Fang et al., 2022  and used to clone two Cas9-sgRNA plasmids (Fang Q, Kimura Y, Shimazu T, Suzuki T, Yamada A, Dohmae N, et al., Shinkai Y, 2022, Sci Rep 12: 4104). Both Cas9-sgRNA plasmids were pooled (150ng/µl) and used to transfect HEK293 cells at 70% confluency using FuGENE® HD Transfection Reagent (Promega). Two days after transfection, mCherry positive cells were single cell sorted using Sony cell sorter SH800S into 96 well plates containing DMEM supplemented with 20% FBS and single cells clones were expanded. For validation of individual knockout clones, genomic DNA was isolated using QIAamp DNA mini kit (QIAGEN), and PCR amplified with primers located approx. 500-600 bp away from the sgRNA target site. PCR products were then cloned into TOPO-TA vector (Invitrogen) and individual clones were Sanger sequenced.

value: HEMK1 KO


title: Ehmt2_sh2_2

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #2), replicate 1


title: RNAseq HEK293 HEMK1 KO Repeat 1

description: Library name: KO Rep1


title: RNAseq HEK293 WT Repeat 2

description: Library name: WT Rep2


title: Ehmt2_sh1_7

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #1), replicate 4


title: Ehmt2_sh1_6

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #1), replicate 3


title: Ehmt2_sh1_5

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #1), replicate 2


title: PRS CK STORM exosomes, Production batch 3 (miRNA)

status: Public on Jun 30 2026

city: Madrid

first: Daniel

last: Lapuente

address: Calle de Isabel Colbrand, 6, 4ª planta, Fuencarral-El Pardo

country: Spain

institute: Peaches Biotech

description: Library name: PRS_CK_STORM_Batch3

data_processing:
FastQC v0.11.9 was employed to evaluate raw read quality using default parameters.
Trim Galore! v0.6.10 was applied to remove adapter sequences, discard low-quality bases, and retain reads within the expected human microRNA length range.
UMI-tools v1.1.5 was used with the extract and dedup modules to remove PCR duplicates based on UMI sequences.
Deduplicated reads were aligned to the human reference genome (GRCh38) using miRDeep2 v2.0.1.2 with default settings.
Known human miRNA species were quantified via the quantifier.pl module of miRDeep2, using mature and hairpin reference sequences for Homo sapiens and Mus musculus obtained from miRBase release 22.1.
Assembly: GRCh38
Supplementary files format and content: The processed data file is a tab-delimited text (.txt) file containing raw read counts of known Homo sapiens miRNAs for each PRS CK STORM production batch. Each row corresponds to a mature miRNA species annotated with miRBase identifiers, and each column represents an individual sample.

source_name: Human primary M2 macrophages and adipose-derived stem cells (PRS CK STORM co-culture origin)

extract_protocol:
Total exosomal RNA was extracted from PRS CK STORM using the exoRNeasy Maxi Kit (QIAGEN), following the manufacturer’s instructions.
Small RNA libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN), incorporating UMIs during reverse transcription. Libraries were PCR-amplified (22 cycles), indexed, purified, quality-checked (TapeStation D1000), and pooled at equimolar concentrations based on insert size and qPCR quantification.

tag: production batch

value: Batch 3


title: H3K9me2_ab1220_Rods_Rep1

city: Berlin

first: Konrad

middle: Jakub

last: Chudzik

address: Hannoversche Str. 28

institute: MDC-BIMSB

description: Library name: H3K9me2_ab1220_Rods_Rep1

library_source: genomic

data_processing:
Sequencing adapters were trimmed using Trim Galore (v0.6.4) with the options --paired --nextera. Trimmed reads were aligned to the mouse genome (mm10) for rod cells or the human genome (hg38) for HeLa cells using Bowtie2 (v2.3.5.1) with --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 2000. Aligned reads were filtered for mapped, paired-end reads (MAPQ ≥ 20) using samtools (v1.10) with view -f 2 -q 20 and then sorted. ENCODE blacklisted regions were removed using bedtools (v2.29.2) with intersect -v.
Normalized coverage tracks (bigWig) were generated with deepTools2 (v3.4.1) using a bin size of 10 bp, read extension (-e), and CPM normalization, ignoring chrX and chrY. For merged tracks, FASTQ files were concatenated from biological replicates. To visualize enrichment relative to matched IgG controls, log2 ratio tracks were generated using deepTools bigwigCompare (v3.4.1). Analogous 20 kb binned subtraction bedGraphs were used as input for domain calling.
Domain calling was performed as previously described (Kefalopoulou et al., 2025) with minor changes in parameters. Specifically, 20 kb binned log2 matrices were binarized: bins above a signal threshold were considered positive (within domain) and below as negative. Adjacent segments separated by gaps ≤200 kb were merged, and regions smaller than 100 kb were removed. To evaluate biological replicate consistency, consensus domains were defined using bedtools intersect (v2.29.2). Consensus regions were used for all subsequent downstream analyses.
To characterize signal distribution across distinct chromatin environments, the genome was segmented into four categories based on the presence or absence of LMNB1 and ab1220 consensus domains: LMNB1+/ab1220+, LMNB1+/ab1220−, LMNB1−/ab1220+, and LMNB1−/ab1220−, using bedtools intersect and subtract (v2.29.2).
Assembly: mm10/hg38
Supplementary files format and content: bigWig (.bw): per-replicate CPM-normalized coverage tracks (10 bp bins, chrX/Y excluded), generated from blacklist-filtered alignments with deepTools2. Merged log2 ratio bigWigs (vs matched IgG, replicate-pooled) are provided as series-level supplementary files for visualization.
Supplementary files format and content: bedGraph (.bedgraph): per-replicate log2 ratio of signal vs matched IgG control, binned at 20 kb. Used as input for domain calling.
Supplementary files format and content: BED (.bed): per-replicate domain calls from the binarized 20 kb log2 bedGraphs (".bedgraph.bed"). Series-level supplementary BEDs include consensus domains per condition (intersection of biological replicates) and four genome-segmentation tracks (LMNB1+/ab1220+, LMNB1+/ab1220−, LMNB1−/ab1220+, LMNB1−/ab1220−)
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: retina

growth_protocol: All mice were housed in a centrally controlled environment with a 12 h light and 12 h dark cycle, temperature of 20-22.2°C, and humidity of 30–50%. All mice had access to food and water ad libitum. Bedding, food and water were routinely changed. All experiments involving animals were carried out following institutional guidelines as approved by LaGeSo Berlin and following the Directive 2010/63/EU of the European Parliament on the protection of animals used for scientific purposes. Biological replicates represent samples collected independently from different animals.  HeLa cells were cultured in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin at 37°C and 5% CO₂, and routinely tested for Mycoplasma contamination. Biological replicates represent HeLa cells grown independently from separate cryovials.

extract_protocol:
HeLa cells were collected using TrypLE (Gibco, 12604021) and following centrifugation (5 min, 300g, RT), resuspended in CUT&Tag wash buffer (20 mM HEPES pH 7.5 (Jena Bioscience, BU10675), 150 mM NaCl (Invitrogen, AM9760G), 0.5 mM spermidine (Sigma, S0266), 10 mM sodium butyrate (Sigma Aldrich, B5887), 1 mM PMSF (Thermo Scientific, 36978), Protease Inhibitor Cocktail (Roche, 04693132001)) and quantified using EVE automatic cell counter (NanoEntek). For sampling rod cells, retinas from 2-month-old NRL-GFP mice were dissociated using the Papain Dissociation System (Worthington, #130-094-802). Four retinas from two mice were used for one biological replicate. Briefly, retinas were dissociated in papain solution for 60 min at 37°C, while shaking at 700 rpm. Afterwards, retinas were triturated with a 1 ml micropipette and transferred to a new tube containing a mix of EBSS, DNase and albumin-ovomucoid inhibitor. Cell suspensions were triturated again with a glass Pasteur pipette ten times until tissue fragments were no longer visible. Finally, 250 µl of EBSS/albumin-ovomucoid inhibitor was added, and the single-cell suspension was cleared of cell clumps by filtration (pluriStrainer Mini 70 μm). FACS sorting of single cells was performed on the BD FACS Aria II or Aria III Cell Sorter System with sample and plate cooling at 4°C. Forward-side scatter gating was used to eliminate debris and identify intact cells, and GFP intensity was used to specifically isolate rod cells. Single cells were sorted into 15 ml falcons pre-coated with BSA and containing 5 ml of wash buffer for approximately 1 h. After sorting, rod cells were quantified using a haemocytometer. For each CUT&Tag reaction, 11 μl Concanavalin A beads (BioMag, 86057) were equilibrated twice with 100 μl and then concentrated in 11 μl of binding buffer (20 mM HEPES pH 7.5, 10 mM KCl (Invitrogen, AM9640G), 1 mM CaCl₂ (Merck, 102382), 1 mM MnCl₂ (Thermo, J63150.AD)). 100,000 cells were then bound to the beads by incubating for 10 min at RT with rotation. Beads were subsequently separated on a magnet and resuspended in 100 μl CUT&Tag Antibody buffer (Wash buffer with 0.05% Digitonin (Millipore, 30410) and 2 mM EDTA (Invitrogen, 15575-038)). Subsequently, 1 μl of primary antibody or IgG control was added and incubated on a rotator overnight (15 h) or for 48 h at 4°C. After magnetic separation, beads were resuspended in 100 μl of Dig-wash buffer containing 1 μl of matching secondary antibody (Abcam, ab46540 for mouse; Antibodies-online, ABIN101961 for rabbit) and incubated for 1 h at 4°C with rotation. Following three washes with CUT&Tag Dig-wash buffer (Wash buffer with 0.05% Digitonin), beads were resuspended in 100 μl CUT&Tag Dig-300 buffer (20 mM HEPES-KOH, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 10 mM Sodium butyrate, 1 mM PMSF) with a 1:250 dilution of homemade 3xFLAG-pA-Tn5 preloaded with Mosaic-end adapters. After incubation for 1 h at 4°C with rotation, beads were washed four times with Dig-300 buffer and resuspended in 50 μl Tagmentation buffer (Dig-300 buffer with 10 mM MgCl₂ (Invitrogen, AM9530G)). Homemade spike-in-AmpR was added to the tagmentation buffer at a final concentration of 33.6 fM (Li et al., 2021). Tagmentation was performed for 1 h at 37°C and subsequently stopped by adding 2.25 μl EDTA, 2.75 μl 10% SDS (Invitrogen, 15553-035) and 0.5 μl Proteinase K (Invitrogen, 25530049). DNA fragments were solubilized for 16 h at 55°C followed by 30 min at 70°C to inactivate residual Proteinase K. DNA fragments were finally purified and eluted with 25 μl of elution buffer (Zymo, D5205).
NGS libraries were generated by PCR amplifying the CUT&Tag DNA fragments with barcoded i5 and i7 primers (Buenrostro et al., 2015) as described previously (Gjaltema et al. 2022). Briefly, DNA fragments with Nextera barcoded HPLC grade primers were loaded with NEBNext HiFi 2x PCR Master Mix (New England BioLabs, M0541S) into a thermocycler for 5 min at 72 °C, 30 sec at 98 °C, 10 sec at 98 °C, 10 sec at 63 °C (14 Cycles for steps 3-4) and 1 min at 72°C. Following PCR, 1x volume of Ampure XP beads (Beckman Coulter) were mixed with the NGS libraries and incubated at RT for 10 minutes. After magnetic separation, the beads were washed three times on the magnet with 80% ethanol, and the libraries were eluted with Tris-HCL, pH 8.0 (Roth, 9090.3). The quality of the purified NGS libraries was assessed with the D5000 tapestation (Agilent Technologies).

value: retina

value: rod photoreceptors

tag: time

tag: chip antibody

value: H3K9me2 (ab1220, Abcam)

tag: strain background

tag: age

value: 8-10 weeks


title: Spatial Transcriptomics, Spleen, MPN, 9

city: Pessac

first: Bérénice

last: Dugué

address: 1 Av. Magellan

country: France

institute: INSERM

description: Library name: MPN9

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger (v2.0.0) pipeline.
Assembly: GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene Ids
Supplementary files format and content: matrix.mtx.gz : gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducial.jpg.gz : aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz : image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz : scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz : hi-res image of tissue
Supplementary files format and content: tissue_positions.csv.gz : list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Spleen

extract_protocol:
5 um sections were cut from FFPE blocks
Spatial transcriptome sequencing librairies were prepared with 10xGenomics Visium CytAssist Spatial Gene Expression Slides & Reagent kit according to manufacturer’s construction. Visium V4 Slides FFPE v2 were used.

value: Spleen


title: Ehmt2_sh1_4

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #1), replicate 1


title: Cbx3_sh33_8

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #2), replicate 5

value: Cbx3 KD


title: Spatial Transcriptomics, Spleen, MPN, 6

description: Library name: MPN6


title: Cbx3_sh12_8

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #1), replicate 5

value: Keratinocytes


title: Cbx3_sh12_7

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #1), replicate 4


title: Spatial Transcriptomics, Spleen, MPN, 2

description: Library name: MPN2


title: Spatial Transcriptomics, Spleen, MPN, 1

description: Library name: MPN1


title: Cbx3_sh12_3

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #1), replicate 3


title: Cbx3_sh12_2

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #1), replicate 2


title: Spatial Transcriptomics, Spleen, control, 3

description: Library name: CTRL3


title: Spatial Transcriptomics, Spleen, control, 2

description: Library name: CTRL2


title: Cbx3_sh12_1

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #1), replicate 1


title: Spatial Transcriptomics, Spleen, control, 1

description: Library name: CTRL1


title: s7_t3w_Neo_Rep2_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, 3 weeks of Neo selection, replicate 2, 5 PCR upstream nt

data_processing:
Following quality controls (performed with FastQC), sequencing reads were trimmed of the common portion of the vector and upstream PCR nucleotides using Cutadapt v2.6 (options: -e 0.2 -a TGCCTACTGCCTCGGACTTCAAGGGGCTAGAATTC -g TAGTGAAGCCACAGATGTA -m 22 -M 22 -n 2 --discard-untrimmed). The extracted hairpin seed sequences (22 nt) were aligned to the reference shRNA library using Bowtie v1.2.3 (options: -a --best --strata -v 2 -m 1 -S -q). Counts per hairpin were retrieved running Samtools (v1.9) idxstats utility on BAM files.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: Tab-delimited text files of raw read counts per hairpin / per sample.

extract_protocol:
30 millions of mouse keratinocytes were transduced with low efficiency (5%) in triplicate. 48 h after infection cells were treated with G418 antibiotic (30 mg ml−1) for 10 days. t=0 (day 11 after infection), t=2w and t=3w were collected in triplicate and stored for genomic DNA extraction (gDNA). Specifically, gDNA was isolated by two rounds of Phenol-Chloroform extraction.
DNA-sequencing libraries were generated by performing two consecutive PCR. For each sample, gDNA from 5-10 × 106 cells was used as template in three parallel PCR-1 reactions to amplify shRNA guide strands. The three PCR-1 products were mixed and purified using AMPure XP beads (Beckman Coulter). For PCR-2, the purified PCR-1 product of each replicate was used as a template in two parallel PCR reactions to be tagged with standard Illumina adapter (p7, p5). The two PCR-2 were combined, checked on 2% agarose gel and then quantified. 100 ng DNA of each sampled were pooled together and purified on 0.6% agarose gel (Minielute gel extraction kit, Qiagen). The final library was quantified on a Bioanalyzer (Agilent). DNA libraries were sequenced on an Illumina NextSeq 500 platform, according to manufacturer's guideline (Illumina).
shRNA-seq

tag: pcr upstream_nt

tag: selection

value: Neo

tag: experiment


title: SnRNAseq, Human Spleen (from samples CTRL1, CTRL2, MPN1, MPN2, MPN6, MPN7, MPN8, MPN9)

description: Library name: SnRNAseq Human Spleen

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger pipeline (10x Genomics) v8.0.0.
Assembly: GRCh38-2024-A
Supplementary files format and content: barcodes.tsv.gz : list of barcodes
Supplementary files format and content: features.tsv.gz : list of gene Ids
Supplementary files format and content: matrix.mtx.gz : gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: probe_set.csv : list of probes used in the FLEX assay

molecule: nuclear RNA

extract_protocol:
25 um sections were cut from FFPE blocks
25 µm-thick FFPE sections were processed following the snPATHOseq protocol, using the FLEX technology (10X Genomics) optimized for FFPE samples. Experiments were performed at the Lyon Cancer Genomics Platform (CRCL, France), targeting 8,000 nuclei per sample and 30,000 reads per nucleus.

tag: tissue


title: Treatment naïve EAC tissue 66

city: Ann Arbor

first: Laura

middle: A

last: Kresty

email: lkresty@umich.edu, Kresty.1@osu.edu

state: MI

address: 1500 E Medical Center Dr

department: Surgery

institute: University of Michigan

description: Library name: Sample 66

data_processing:
Qiagen CLC Genomics Workbench (20.0) was used to processing sequencing data.
After QC and joining reads from different lanes, sequencing files were mapped using hg38 human reference genome. Differential gene expression analysis was performed using the default parameters in CLC Genomics Workbench.
Assembly: hg38
Supplementary files format and content: An expression matrix (TPM) generated by CLC Genomics Workbench in csv format.

source_name: Esophageal

extract_protocol:
RNA was isolated using the Trizol reagnet. Fresh-frozen treatment-native esophageal adenocarcinoma tissue samples were used for RNA isolation.
Library was constructed using standard Illumina protocols.

value: Esophageal


title: s7_t2w_Neo_Rep3_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, 2 weeks of Neo selection, replicate 3, 5 PCR upstream nt

tag: cell type


title: Treatment naïve EAC tissue 65

description: Library name: Sample 65


title: s7_t2w_Neo_Rep2_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, 2 weeks of Neo selection, replicate 2, 5 PCR upstream nt


title: Spatial Transcriptomics, Spleen, MPN, 8

description: Library name: MPN8


title: Cbx3_sh33_3

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #2), replicate 2


title: Spatial Transcriptomics, Spleen, MPN, 5

description: Library name: MPN5


title: Cbx3_sh33_1

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #2), replicate 1


title: Spatial Transcriptomics, Spleen, MPN, 3

description: Library name: MPN3


title: Treatment naïve EAC tissue 64

description: Library name: Sample 64


title: s7_t2w_Neo_Rep1_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, 2 weeks of Neo selection, replicate 1, 5 PCR upstream nt


title: Treatment naïve EAC tissue 63

description: Library name: Sample 63


title: Treatment naïve EAC tissue 62

description: Library name: Sample 62


title: s7_t0_Rep3_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, time 0, replicate 3, 5 PCR upstream nt


title: s7_t0_Rep2_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, time 0, replicate 2, 5 PCR upstream nt


title: Treatment naïve EAC tissue 61

description: Library name: Sample 61


title: s7_t0_Rep1_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, time 0, replicate 1, 5 PCR upstream nt


title: Treatment naïve EAC tissue 60

description: Library name: Sample 60


title: s4_t3w_Neo_Rep3_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 3, 5 PCR upstream nt


title: s4_t3w_Neo_Rep3_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 3, 25 PCR upstream nt


title: Treatment naïve EAC tissue 59

description: Library name: Sample 59


title: Treatment naïve EAC tissue 58

description: Library name: Sample 58


title: s4_t3w_Neo_Rep3_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 3, 0 PCR upstream nt


title: Treatment naïve EAC tissue 67

description: Library name: Sample 67


title: s7_t3w_Neo_Rep3_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, 3 weeks of Neo selection, replicate 3, 5 PCR upstream nt


title: Treatment naïve EAC tissue 57

description: Library name: Sample 57


title: s7_t3w_Neo_Rep1_N5

description: shRNA-seq (viability screening 2) in mouse keratinocytes, 3 weeks of Neo selection, replicate 1, 5 PCR upstream nt


title: Treatment naïve EAC tissue 56

description: Library name: Sample 56


title: s4_t3w_Neo_Rep2_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 2, 5 PCR upstream nt


title: s4_t3w_Neo_Rep2_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 2, 25 PCR upstream nt


title: Treatment naïve EAC tissue 55

description: Library name: Sample 55


title: s4_t3w_Neo_Rep2_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 2, 0 PCR upstream nt


title: Treatment naïve EAC tissue 54

description: Library name: Sample 54


title: s4_t3w_Neo_Rep1_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 1, 5 PCR upstream nt


title: Treatment naïve EAC tissue 53

description: Library name: Sample 53


title: s4_t3w_Neo_Rep1_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 1, 25 PCR upstream nt


title: Treatment naïve EAC tissue 52

description: Library name: Sample 52


title: Treatment naïve EAC tissue 51

description: Library name: Sample 51


title: s4_t3w_Neo_Rep1_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 3 weeks of Neo selection, replicate 1, 0 PCR upstream nt


title: s4_t2w_Neo_Rep3_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 3, 5 PCR upstream nt


title: Treatment naïve EAC tissue 50

description: Library name: Sample 50


title: s4_t2w_Neo_Rep3_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 3, 25 PCR upstream nt


title: Treatment naïve EAC tissue 49

description: Library name: Sample 49


title: s4_t2w_Neo_Rep3_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 3, 0 PCR upstream nt


title: Treatment naïve EAC tissue 48

description: Library name: Sample 48


title: s4_t2w_Neo_Rep2_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 2, 5 PCR upstream nt


title: Treatment naïve EAC tissue 46

description: Library name: Sample 46


title: Stingfl/fl Cdh5-Cre- mouse liver scRNA-seq, biological replicate 3

city: Xi'an

first: Lin

last: Wang

state: Shaanxi

address: West Changle Road 169

country: China

institute: Xijing Hospital, Air Force Medical University

description:
Library name: N4415-3H
10X Genomics Chromium 3' scRNA-seq of mouse liver tissue.

data_processing:
Raw reads were processed using Cell Ranger v7.1.0 to align reads to the mm10 (Ensembl version 100) reference genome and generate feature-barcode matrices.
Downsampling analysis was performed according to mapped barcoded reads per cell. Cells with over 300 expressed genes and mitochondria UMI rate below 20% were retained.
Seurat v4.1.1 was used for normalization, scaling, PCA, UMAP, and graph-based clustering. Marker genes were identified using Wilcoxon rank-sum test.
Assembly: mm10 (Ensembl version 100)
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz per sample.

source_name: liver

growth_protocol: Mice were maintained under specific pathogen-free conditions. Stingfl/fl Cdh5-Cre+ and Stingfl/fl Cdh5-Cre- mice were generated and maintained on a normal chow diet until 8 weeks of age.

extract_protocol:
Liver tissues were dissociated into single-cell suspensions. Cells were washed, filtered, and resuspended in PBS with 0.04% BSA for 10X Genomics library construction.
Single-cell RNA-seq libraries were prepared using the 10X Genomics Chromium 3' reagent kit according to the manufacturer's protocol. Briefly, single cells were partitioned into gel beads in emulsion (GEMs) for reverse transcription. Barcoded cDNA was amplified, fragmented, end-repaired, A-tailed, and ligated with adapters for sequencing.

treatment_protocol: Mice were fed a western diet combined with CCl4 administration (WD-CCl4) for 12 weeks to induce MASH.

value: liver

value: liver sinusoidal endothelial cells

tag: genotype

value: Stingfl/fl Cdh5-Cre-

value: WD-CCl4 for 12 weeks


title: Treatment naïve EAC tissue 47

description: Library name: Sample 47


title: s4_t2w_Neo_Rep2_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 2, 25 PCR upstream nt


title: Treatment naïve EAC tissue 45

description: Library name: Sample 45


title: Stingfl/fl Cdh5-Cre- mouse liver scRNA-seq, biological replicate 2

description:
Library name: N4415-3F
10X Genomics Chromium 3' scRNA-seq of mouse liver tissue.

tag: treatment


title: Treatment naïve EAC tissue 44

description: Library name: Sample 44


title: s4_t2w_Neo_Rep2_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 2, 0 PCR upstream nt


title: Treatment naïve EAC tissue 43

description: Library name: Sample 43


title: Stingfl/fl Cdh5-Cre- mouse liver scRNA-seq, biological replicate 1

description:
Library name: N4415-3D
10X Genomics Chromium 3' scRNA-seq of mouse liver tissue.


title: s4_t2w_Neo_Rep1_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 1, 5 PCR upstream nt


title: Treatment naïve EAC tissue 42

description: Library name: Sample 42


title: Stingfl/fl Cdh5-Cre+ mouse liver scRNA-seq, biological replicate 3

description:
Library name: N4415-3J
10X Genomics Chromium 3' scRNA-seq of mouse liver tissue.

value: Stingfl/fl Cdh5-Cre+


title: Treatment naïve EAC tissue 41

description: Library name: Sample 41


title: Native cells at P0, 0 h, replicate 1

city: Guangzhou

first: Jiangfan

last: Cao

address: Xiaoguwei Street

institute: South China University of Technology

description:
Library name: Native I-1
Native, without cryosilicification

data_processing:
Raw FASTQ data were quality controlled using FastQC and filtered using Cutadapt to remove adapters and low-quality reads (Q<20, length <75 bp).
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2.
Gene expression was quantified using Cufflinks/Cuffdiff to obtain read counts and FPKM values.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Gene count matrices are provided in CSV format for P0 and P1-P3 samples
Supplementary files format and content: FPKM expression matrices are also provided in CSV format for the same samples, with identical structure

source_name: cervical cancer

growth_protocol: HeLa cells were cultured in standard DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA quality was assessed by agarose gel electrophoresis and RNA integrity number (RIN).
RNA sequencing libraries were prepared using standard Illumina TruSeq RNA library preparation kits following the manufacturer's protocol, including mRNA enrichment, fragmentation, cDNA synthesis, end repair, adaptor ligation, and PCR amplification.

treatment_protocol: Cells were subjected to cryosilicification treatment using Si20 or Si30 conditions. Native cells without cryosilicification treatment were used as controls. Samples were collected at early response stage (P0, 0 h and 6 h) and after passaging (P1–P3).

value: cervical cancer

tag: cell line

value: Hela

value: epithelial-like cervical cancer cell

value: No cryosilicification

tag: passage

tag: batch


title: MCF7, Day21, FulvPalbo, RNA

description:
Library name: MCF7_Day21_FulvPalbo
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt:

value: mammary gland

value: epithelial

value: WT

value: day21 100nM palbociclib+10nM fulvestrant


title: Treatment naïve EAC tissue 40

description: Library name: Sample 40


title: s4_t2w_Neo_Rep1_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 1, 25 PCR upstream nt

tag: replicate


title: Treatment naïve EAC tissue 39

description: Library name: Sample 39


title: Stingfl/fl Cdh5-Cre+ mouse liver scRNA-seq, biological replicate 2

description:
Library name: N4415-3C
10X Genomics Chromium 3' scRNA-seq of mouse liver tissue.


title: Treatment naïve EAC tissue 38

description: Library name: Sample 38


title: Suv420h2_sh24_6

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #1), replicate 3

tag: condition

value: Suv420h2 KD

tag: shRNA

tag: shRNA type


title: Treatment naïve EAC tissue 37

description: Library name: Sample 37


title: Stingfl/fl Cdh5-Cre+ mouse liver scRNA-seq, biological replicate 1

description:
Library name: N4415-3B
10X Genomics Chromium 3' scRNA-seq of mouse liver tissue.


title: s4_t2w_Neo_Rep1_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, 2 weeks of Neo selection, replicate 1, 0 PCR upstream nt

value: Keratinocytes

tag: time


title: Treatment naïve EAC tissue 36

description: Library name: Sample 36


title: s4_t0_Rep3_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 3, 5 PCR upstream nt


title: Scramble2_4

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #2, Ehmt2 ctrl), replicate 3

value: Scramble (Ctrl)

value: sh-Scramble


title: Treatment naïve EAC tissue 35

description: Library name: Sample 35

value: Esophageal


title: Treatment naïve EAC tissue 34

description: Library name: Sample 34


title: Scramble2_5

description: Mini-bulk RNA-seq of control mouse keratinocytes, infected with sh-scramble (scrambe #2, Ehmt2 ctrl), replicate 4


title: Second replicate of HNF1B ChIP-seq from kidney

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: Library name: WT_HNF1_chip_2

data_processing:
Sequencing reads were aligned to the Mus musculus GRCm39 genome (Ensembl release 111) using Bowtie2 v2.5. The aligned chromatin fragments were converted to BED files using bamToBed (Bedtools v2.31), read into R as GRanges objects, converted to coverage and exported in bigWig format for visualization. Peak calling was performed using HOMER v4.11 with default parameters to identify enriched regions. Only peaks that overlapped with the BMAL1 binding regions defined in (beytebiere, menet 2019,) were considered for downstream analyses of BMAL1, PROX1 and HNF1B ChIP-MS experiments.
Assembly: GRCm39
Supplementary files format and content: bigWig files of ChipSeq coverage
Supplementary files format and content: bed files of Peaks called

source_name: Kidney

extract_protocol:
Mouse tissues were dissected and washed with ice-cold PBS and immediately transferred into liquid nitrogen and kept at -80C. For ChIP-Seq, samples were crosslinked with 1% formaldehyde for 10 minutes. After quenching, chromatin was sheared using Bioruptor.
Library preparation is performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China) using MGIEasy Universal DNA Library Prep Set (MGI-Shenzhen, China). Firstly, A certain amount of purified ChIPed DNA sample is taken and converted into blunt-end DNA through end repair reaction. Then an adenosine is added to the 3′ ends of the end repaired DNA through A-tailing reaction. Later, library adaptors are connected through adaptor ligation process, Finally, the library products are amplified through PCR reaction and subjected to quality control.

value: Kidney

tag: chip antibody

value: HNF1B Antibody (NovusBio, #NBP1-89680)


title: s4_t0_Rep3_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 3, 25 PCR upstream nt


title: Treatment naïve EAC tissue 33

description: Library name: Sample 33


title: s4_t0_Rep3_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 3, 0 PCR upstream nt


title: Treatment naïve EAC tissue 32

description: Library name: Sample 32


title: First replicate of HNF1B ChIP-seq from kidney

description: Library name: WT_HNF1_chip_1


title: Treatment naïve EAC tissue 31

description: Library name: Sample 31


title: Second replicate of BMAL1 ChIP-seq from kidney

description: Library name: WT_Bmal1_chip_2

value: BMAL1 Antibody (CellSignaling, D2L7G - #14020)


title: Treatment naïve EAC tissue 30

description: Library name: Sample 30


title: Treatment naïve EAC tissue 29

description: Library name: Sample 29


title: s4_t0_Rep2_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 2, 5 PCR upstream nt


title: First replicate of BMAL1 ChIP-seq from kidney

description: Library name: WT_Bmal1_chip_1


title: MCF7, day14Doxo, rep3, RNA

description:
Library name: MCF7_day14Doxo_rep3
Counts were obtained from 2nd column in MCF7_HS_day14.Doxo_rep3_8_ReadsPerGene.out.tab

value: 100 nM doxorubicin (48 h), harvested on day 14


title: Treatment naïve EAC tissue 28

description: Library name: Sample 28


title: Treatment naïve EAC tissue 27

description: Library name: Sample 27


title: s4_t0_Rep2_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 2, 25 PCR upstream nt


title: PROX1 ChIP-seq from liver

description: Library name: D_Prox

source_name: Liver

value: Liver

value: PROX1 Antibody (ProteinTech, #11067-2-AP)


title: Treatment naïve EAC tissue 26

description: Library name: Sample 26


title: MCF7, PvsPFvsD, Cycling, rep4, RNA

description:
Library name: MCF7_PvsPFvsD_Cycling_rep4
Counts were obtained from 2nd column in MCF7_HS_Cycling_rep4_14_ReadsPerGene.out.tab


title: s4_t0_Rep2_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 2, 0 PCR upstream nt


title: Second replicate of BMAL1 ChIP-seq from liver

description: Library name: C_Bmal1


title: Treatment naïve EAC tissue 25

description: Library name: Sample 25


title: Treatment naïve EAC tissue 24

description: Library name: Sample 24


title: s4_t0_Rep1_N5

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 1, 5 PCR upstream nt


title: First replicate of BMAL1 ChIP-seq from liver

description: Library name: B_Bmal1


title: Ehmt2_sh1_8

description: Mini-bulk RNA-seq of Ehmt2-silenced mouse keratinocytes, infected with sh-Ehmt2 (KD sh #1), replicate 5

value: Ehmt2 KD


title: Treatment naïve EAC tissue 23

description: Library name: Sample 23


title: Treatment naïve EAC tissue 22

description: Library name: Sample 22


title: RNAseq HEK293 WT Repeat 1

description: Library name: WT Rep1


title: s4_t0_Rep1_N25

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 1, 25 PCR upstream nt


title: Treatment naïve EAC tissue 20

description: Library name: Sample 20


title: Treatment naïve EAC tissue 19

description: Library name: Sample 19


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 5 biological replicate 4

city: Vancouver

first: Luis

middle: M.

last: Silva

state: British Columbia

address: 2212 Main Mall

department: Department of Zoology

country: Canada

institute: The University of British Columbia

description:
Library name: L54
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 5, biological replicate 4; column name in processed expression matrix: L54

data_processing:
Demultiplexing was performed with bcl2fastq2 v2.20.
Adapters and low-quality bases were removed with Cutadapt, reads shorter than 40 nt were discarded, and reads mapping to rRNA were removed with fastq_screen. Filtered reads were aligned to a concatenated Anopheles gambiae and Vavraia culicis reference using STAR. Gene-level counts were obtained with htseq-count.
Assembly: Anopheles gambiae assembly GCA_943734735.2 and Vavraia culicis floridensis assembly GCA_000192795.1
Supplementary files format and content: File_S9_data1.txt: tab-delimited processed host gene expression matrix for all 48 samples, with gene identifiers, sample expression values and gene annotation columns.

organism: Anopheles gambiae

source_name: whole adult female mosquito

growth_protocol: Anopheles gambiae Kisumu larvae were reared under standard insectary conditions at 26 ± 1 °C, 70 ± 5% relative humidity and a 12 h light:12 h dark cycle. Freshly hatched larvae were reared at 50 larvae in 80 ml distilled water and fed daily with fish food. Adult females were maintained with constant access to 6% sucrose solution.

extract_protocol:
Total RNA was extracted from independent pools of 10 adult females using the Qiagen RNeasy Universal Plus kit. Adults were homogenized in QIAzol reagent with stainless steel beads, genomic DNA was removed according to the manufacturer protocol, and RNA was eluted in nuclease-free water.
RNA quality was assessed on an Agilent Fragment Analyzer. Libraries were prepared from 250 ng total RNA per sample using the Illumina Stranded mRNA Prep kit with unique dual indices and sequenced as 150 bp single-end reads on an Illumina NovaSeq 6000 platform.

treatment_protocol: On day 2 of larval development, mosquitoes were exposed to 10,000 Vavraia culicis spores per larva from the relevant parasite lineage. Treatments were uninfected controls, an unselected reference parasite lineage, five early-selected parasite lineages and five late-selected parasite lineages. Adult females were sampled on day 10 of adulthood, when infections were chronic and sporulating.

value: whole adult female mosquito

value: Kisumu


title: s4_t0_Rep1_N0

description: shRNA-seq (viability screening 1) in mouse keratinocytes, time 0, replicate 1, 0 PCR upstream nt


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 5 biological replicate 3

description:
Library name: L53
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 5, biological replicate 3; column name in processed expression matrix: L53


title: Treatment naïve EAC tissue 21

description: Library name: Sample 21


title: Treatment naïve EAC tissue 18

description: Library name: Sample 18


title: ChIPseq_Cbx3_shscramble_1_input_Rep2

description: Input DNA in sh-scramble-1 (Cbx3 ctrl) replicate 2

data_processing:
Following quality controls (performed with FastQC v0.11.2), paired-end sequencing reads were aligned to the mouse reference genome (mm10/GRCm38) using Bowtie v2.3.5.1 [Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).]. Duplicated alignments (identified by Picard MarkDuplicates, https://broadinstitute.github.io/picard) and low-quality alignments/multi-mapping reads were excluded using SAMtools v1.6 [Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)]. Immunoprecipitation and corresponding control (Input DNA) datasets were treated identically. Peak calling was performed for each IP against its matched Input DNA using MACS v2.1.4 [Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).] (command: callpeak -g mm --nomodel -f BAMPE -q 0.05). Input-normalized ChIP-seq fold-enrichment signal tracks were obtained using MACS v2.1.4 [Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).] (command: callpeak -g mm --nomodel -f BAMPE -q 0.05 --SPMR -B and bdgcmp -m FE).  For Cbx3 ChIP-seq, braod peak calling was performed using epic2 [Endre Bakken Stovner, Pål Sætrom, epic2 efficiently finds diffuse domains in ChIP-seq data, Bioinformatics, Volume 35, Issue 21, November 2019] (command: --genome mm10 --false-discovery-rate-cutoff 0.05 --guess-bampe).
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig files of input-normalized signal tracks.
Supplementary files format and content: NarrowPeak files of called peaks.

extract_protocol:
ChIP was performed on mouse keratinocytes cross-linked in 1% formaldehyde  for 15 minutes at RT. After blocking the cross-link with 0.125 M glycine for 5 minutes and washing with PBS containing protease  inhibitors, the pellets were resuspended in Lysis buffer (5mM HEPES pH7.9, 85mM KCl, 0.5 NP-40) incubated on ice for 10 min and centrifuged 200 × g for 5 min at 4°C. Chromatin was sonicated to achieve fragment lengths of approximately 0.2-0.5 kb and then subjected to Immunoprecipitation using H3K27ac, Cbx3, Suv420h2 and Ehmt2 antibodies and Protein G Dynabeads in immunoprecipitation buffer (56.25mM HEPES pH7.9, 157.2mM NaCl, 1mM EDTA, 1.125% Triton X-100, 0.1% Na-deoxycholate). After washes with LiCl Wash buffer (100 mM Tris pH 8.0, 100 mM Tris pH 8.0, 1% NP-40, 1% Na-deoxycholate) and with TE Buffer (10 mM Tris, 1 mM EDTA) the material was resuspend in Elution buffer (1 % SDS, 0.1 M NahCo3 Sodium hydrogen carbonate ) to be reverse crosslinked overnight at 65 °C O/N, treated with proteinase K and RNase A and purified by kit QiaQuick PCR Purification Kit.
Starting from 10 ng of ChIP eluted sample, the library was produced for the genome wide analysis following the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® (E 6240L NEB) manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 500 and 1000 platforms.

treatment_protocol: H3K27ac ChIP-seq were performed in Cbx3, Suv420h2 and Ehmt2 knockdown (KD) and control (scramble shRNA) mouse keratinocytes. Cbx3 ChIP-seq was performed on wild type mouse keratynocites.

value: Input


title: Treatment naïve EAC tissue 16

description: Library name: Sample 16


title: Cbx3_sh33_7

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #2), replicate 4

value: Cbx3 KD


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 5 biological replicate 2

description:
Library name: L52
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 5, biological replicate 2; column name in processed expression matrix: L52


title: Treatment naïve EAC tissue 17

description: Library name: Sample 17


title: Treatment naïve EAC tissue 15

description: Library name: Sample 15


title: ChIPseq_Cbx3_shscramble_1_input_Rep1

description: Input DNA in sh-scramble-1 (Cbx3 ctrl) replicate 1


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 5 biological replicate 1

description:
Library name: L51
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 5, biological replicate 1; column name in processed expression matrix: L51


title: Spatial Transcriptomics, Spleen, MPN, 7

description: Library name: MPN7

value: Spleen


title: Treatment naïve EAC tissue 14

description: Library name: Sample 14


title: Cbx3_sh33_6

description: Mini-bulk RNA-seq of Cbx3-silenced mouse keratinocytes, infected with sh-Cbx3 (KD sh #2), replicate 3


title: Spatial Transcriptomics, Spleen, MPN, 4

description: Library name: MPN4


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 4 biological replicate 4

description:
Library name: L44
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 4, biological replicate 4; column name in processed expression matrix: L44


title: ChIPseq_Cbx3_shscramble_1_Ac_Rep2

description: H3K27ac IP in sh-scramble-1 (Cbx3 ctrl) replicate 2


title: Treatment naïve EAC tissue 12

description: Library name: Sample 12


title: ChIPseq_Cbx3_shscramble_1_Ac_Rep1

description: H3K27ac IP in sh-scramble-1 (Cbx3 ctrl) replicate 1


title: Treatment naïve EAC tissue 10

description: Library name: Sample 10


title: ChIPseq_Cbx3_sh33_1_input_Rep2

description: Input DNA in sh-Cbx3 (KD sh #2) replicate 2


title: Treatment naïve EAC tissue 9

description: Library name: Sample 9


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 4 biological replicate 2

description:
Library name: L42
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 4, biological replicate 2; column name in processed expression matrix: L42


title: Treatment naïve EAC tissue 8

description: Library name: Sample 8


title: Treatment naïve EAC tissue 11

description: Library name: Sample 11


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 4 biological replicate 3

description:
Library name: L43
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 4, biological replicate 3; column name in processed expression matrix: L43


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 4 biological replicate 1

description:
Library name: L41
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 4, biological replicate 1; column name in processed expression matrix: L41


title: Treatment naïve EAC tissue 6

description: Library name: Sample 6


title: Treatment naïve EAC tissue 7

description: Library name: Sample 7


title: ChIPseq_Cbx3_sh33_1_Ac_Rep2

description: H3K27ac IP in sh-Cbx3 (KD sh #2) replicate 2


title: Treatment naïve EAC tissue 5

description: Library name: Sample 5


title: Treatment naïve EAC tissue 4

description: Library name: Sample 4


title: Treatment naïve EAC tissue 2

description: Library name: Sample 2


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 3 biological replicate 3

description:
Library name: L33
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 3, biological replicate 3; column name in processed expression matrix: L33


title: ChIPseq_Cbx3_sh12_1_input_Rep2

description: Input DNA in sh-Cbx3 (KD sh #1) replicate 2


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 3 biological replicate 2

description:
Library name: L32
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 3, biological replicate 2; column name in processed expression matrix: L32


title: HT29,Tryptophan depletion,sample2

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

description: Library name: 7000_12_HT29_Wdepl_2_ATGTTGCCAC-TAGAAGCCAT_S12

data_processing:
Fastq files were aligned using STAR (STAR-2.7.10a/) to the human GRCh38 genome. Aligned reads on exons of protein-coding genes were then counted using htseq-count (version 2.0.5) and gencode hg38 reference annotation. DESeq2 was used for normalization and differential expression analysis
Assembly: hg38
Supplementary files format and content: Tab separated.txt file of htseq-count readcounts normalized with DESeq2 for W depletion versus control. Wdepl_normalized_counts.txt
Supplementary files format and content: Tab separated.txt file of htseq-count readcounts normalized with DESeq2 for H depletion versus control. Hdepl_normalized_counts.txt

source_name: colon

growth_protocol: HT29 cells were treated for 48 hours with either control medium, histidine-depleted medium, or tryptophan-depleted medium. Cells were subsequently harvested in RLT buffer (Qiagen).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (74106, Qiagen), including an on column DNase digestion (79254, Qiagen),  according to the manufactures instructions.  Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using “Agilent RNA 6000 Nano” (G2938-90034, Agilent Technologies).
Total RNA samples having RIN>8 were subjected to library generation using the TruSeq stranded mRNA library preparation kit, according to the manufacturer's instructions (Document # 1000000040498 v00 , Illumina) with incorporation of xGen UDI-UMI adapters (Integrated DNA Technologies, Inc., Coralville). The stranded mRNA libraries were analyzed on a 2100 Bioanalyzer instrument following the manufacturer’s protocol “Agilent DNA 7500 kit” (G2938-90025, Agilent Technologies), diluted to 10nM and pooled equimolar into multiplex sequencing pools for paired end sequencing on the NovaSeq 6000 Illumina sequencing instrument. Paired-end sequencing was performed using 150 cycles for Read 1, 19 cycles for Read i7, 10 cycles for Read i5 and 150 cycles for Read 2, using the NovaSeq6000 Reagent Kit v1.5 (300 cycles) (20028400, Illumina). On average 40 M paired reads per sample were generated.

value: colon

value: colon adenocarcinoma

value: WT

value: Tryptophan depletion


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 3 biological replicate 1

description:
Library name: L31
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 3, biological replicate 1; column name in processed expression matrix: L31


title: HT29,Histidine depletion,sample2

description: Library name: 7000_10_HT29_Hdepl_2_CATCAGGCGT-CGTGTTACCG_S10

treatment_protocol: HT29 cells were treated for 48 hours with either control medium, histidine-depleted medium, or tryptophan-depleted medium.

value: Histidine depletion


title: ChIPseq_Cbx3_sh12_1_Ac_Rep2

description: H3K27ac IP in sh-Cbx3 (KD sh #1) replicate 2

value: Keratinocytes


title: HT29,Histidine depletion,sample1

description: Library name: 7000_9_HT29_Hdepl_1_TTGTGATCCT-ATGAAGGCAT_S9


title: HT29,Tryptophan depletion,sample1

description: Library name: 7000_11_HT29_Wdepl_1_AACCTGATCT-ATTCCGTCCG_S11


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 2 biological replicate 4

description:
Library name: L24
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 2, biological replicate 4; column name in processed expression matrix: L24


title: HT29,untreated,sample2

description: Library name: 7000_8_HT29_untreated_2_CGTACTTAGA-CCGATGTTCA_S8

value: Untreated


title: ChIPseq_Cbx3_sh12_1_Ac_Rep1

description: H3K27ac IP in sh-Cbx3 (KD sh #1) replicate 1


title: HT29,untreated,sample1

description: Library name: 7000_7_HT29_untreated_1_GAAGATCGAC-AGTGACCACG_S1


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 2 biological replicate 3

description:
Library name: L23
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 2, biological replicate 3; column name in processed expression matrix: L23


title: ROI 127, Patient 21, Lymph node, NMPR

city: Beijing

first: Rongzhen

last: Li

state: 北京Beijing

address: Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China

institute: Peking Union Medical College

description: Library name: ROI 127

data_processing:
The raw FASTQ files were run through GeoMx NGS pipelines to acquire digital count conversions and initial data files for further analysis.
The initial data were further processed using quality control (QC) and normalization. RNA data were normalized using Total Count normalization with a scaling factor set at 10,210.
Assembly: mm10
Supplementary files format and content: csv file include normalized count data

source_name: Non-small cell lung cancer, Lymph node

extract_protocol:
Formalin-fixed and paraffin-embedded (FFPE) tissues were used to construct tissue microarrays (TMAs). Cores (2.0 mm in diameter) were punched from each FFPE block and arrayed across two recipient TMA blocks. Five-μm-thick TMA sections were deparaffinized and rehydrated, and regions of interest (ROIs) were selected based on immunofluorescence morphology markers.
RNA extraction was performed using the NanoString GeoMx Digital Spatial Profiler according to the manufacturer’s protocol. Briefly, TMA sections were processed and regions of interest (ROIs) were selected based on immunofluorescence morphology markers. Each ROI was sequentially decoupled from the oligonucleotides using ultraviolet (UV) light. UV-cleavable oligos coupled with individual genes were cleaved and collected from all ROIs using a digital mirror device-guided UV illumination. The resultant oligos were amplified by polymerase chain reaction (PCR) amplified (Bio-Rad Laboratories, Hercules, CA, USA) using GeoMx Seq Code primers for downstream library construction.

treatment_protocol: Interventions included pembrolizumab at a fixed dose of 200 mg combined with carboplatin (area under the curve 5) or cisplatin 75mg/m2, pemetrexed at 500 mg/m2 for nonsquamous cell carcinoma, and paclitaxel at 175 mg/m2 or nab-paclitaxel at 260 mg/m2 for squamous cell carcinoma. Surgery was performed after at least two cycles of neoadjuvant therapy. All patients received adjuvant pembrolizumab for up to one year after surgery. To ensure that all patients received four cycles of perioperative chemotherapy, adjuvant chemotherapy was given to patients who had not received adequate neoadjuvant therapy. The surgical approaches were chosen by the surgeon.

value: Non-small cell lung cancer, Lymph node


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 2 biological replicate 2

description:
Library name: L22
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 2, biological replicate 2; column name in processed expression matrix: L22


title: ROI 126, Patient 21, Lymph node, NMPR

description: Library name: ROI 126


title: ROI 125, Patient 21, Lymph node, NMPR

description: Library name: ROI 125


title: Root,2,5-D,24hours,rep1

city: Saijo

first: Theint

last: Thida

state: 広島県

address: 2081-1, Joy Seven, room no. 213

department: Hiroshima University

country: Japan

institute: Hiroshima University

description:
Library name: Sample7
Root_Proceed_Data.txt

data_processing:
HISAT2 v2.0.4
Assembly: GCF_000001735.4
Supplementary files format and content: txt files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: 100 µM of 2,5-dimethylpyrazine volatile and sterilized water (control) applied to the paper disc.  After 14 days of co-cultivation in the I-plate, shoots and roots from plants were harvested.

extract_protocol:
RNA was harvested using RNA Extraction Kit Mini. 100 ng of total RNA was used for the construction of sequencing libraries.
DNBSEQ Fast RNA Library Prep Set is paired with DNBSEQ UDB Primers Adapter Kit for library construction.

treatment_protocol: Arabidopsis plants were treated with 100 µM of 2,5-D, along with a control group treated with water,  for 24 hours

tag: ecotype

value: Root


title: ROI 124, Patient 22, Lymph node, NMPR

description: Library name: ROI 124


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 2 biological replicate 1

description:
Library name: L21
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 2, biological replicate 1; column name in processed expression matrix: L21


title: ROI 123, Patient 22, Lymph node, NMPR

description: Library name: ROI 123


title: ROI 122, Patient 22, Lymph node, NMPR

description: Library name: ROI 122


title: Root,Control,24hours,rep1

description:
Library name: Sample5
Root_Proceed_Data.txt

value: Water


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 1 biological replicate 4

description:
Library name: L14
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 1, biological replicate 4; column name in processed expression matrix: L14


title: ROI 119, Patient 22, Primary tumor bed, NMPR

description: Library name: ROI 119

source_name: Non-small cell lung cancer, Primary tumor bed


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 1 biological replicate 2

description:
Library name: L12
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 1, biological replicate 2; column name in processed expression matrix: L12


title: ROI 116, Patient 21, Primary tumor bed, NMPR

description: Library name: ROI 116

value: Non-small cell lung cancer, Primary tumor bed


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 1 biological replicate 1

description:
Library name: L11
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 1, biological replicate 1; column name in processed expression matrix: L11


title: Shoot,2,5-D,24hours,rep1

description:
Library name: Sample3
Shoot_Proceed_Data.txt

source_name: Shoot

value: Shoot


title: Shoot,Control,24hours,rep2

description:
Library name: Sample2
Shoot_Proceed_Data.txt


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 5 biological replicate 4

description:
Library name: E54
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 5, biological replicate 4; column name in processed expression matrix: E54

value: whole adult female mosquito


title: ROI 113, Patient 20, Lymph node, NMPR

description: Library name: ROI 113


title: Ly6Clow monocyte, d7 Hpb, Biol rep 2

city: Manchester

first: Kelly

last: Wemyss

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description:
Library name: Sample 8
P10-d7Hpb-2

data_processing:
Raw fastq files were trimmed with Trimmomatic (v0.36), aligned to the mouse GENCODE genome (GRCm38.p5) using STAR (v2.5.3).
Reads were then sorted, compressed and unaligned reads removed using Samtools (v0.1.18).
Filtered reads were then normalised and compared, respectively, using the Cuffnorm and Cuffdiff functions of Cufflinks (v2.2.1).
Assembly: mouse GENCODE genome (GRCm38.p5)
Supplementary files format and content: csv file contains FPKM values for each sample

source_name: Blood

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen)
cDNA libraries were generated using the SMART-Seq V3 Ultra Low Input RNA Kit (Clontech)

value: Blood

value: Ly6Clow Monocyte

value: Wild-type

value: day 7 p.i. Hpb


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 5 biological replicate 2

description:
Library name: E52
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 5, biological replicate 2; column name in processed expression matrix: E52

value: Kisumu


title: Root,Control,24hours,rep2

description:
Library name: Sample6
Root_Proceed_Data.txt


title: ROI 121, Patient 22, Primary tumor bed, NMPR

description: Library name: ROI 121


title: Ly6Clow monocyte, d7 Hpb, Biol rep 1

description:
Library name: Sample 7
P10-d7Hpb-1


title: ROI 115, Patient 20, Lymph node, NMPR

description: Library name: ROI 115


title: ROI 114, Patient 20, Lymph node, NMPR

description: Library name: ROI 114


title: ROI 108, Patient 19, Lymph node, NMPR

description: Library name: ROI 108


title: Shoot,Control,24hours,rep1

description:
Library name: Sample1
Shoot_Proceed_Data.txt


title: ROI 112, Patient 20, Primary tumor bed, NMPR

description: Library name: ROI 112


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 5 biological replicate 1

description:
Library name: E51
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 5, biological replicate 1; column name in processed expression matrix: E51


title: ROI 111, Patient 20, Primary tumor bed, NMPR

description: Library name: ROI 111


title: ROI 107, Patient 19, Lymph node, NMPR

description: Library name: ROI 107


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 4 biological replicate 4

description:
Library name: E44
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 4, biological replicate 4; column name in processed expression matrix: E44


title: ROI 110, Patient 20, Primary tumor bed, NMPR

description: Library name: ROI 110


title: ROI 105, Patient 19, Primary tumor bed, NMPR

description: Library name: ROI 105


title: Ly6Clow monocyte, Naïve, Biol rep 1

description:
Library name: Sample 5
P10-Naive-1

value: Naïve


title: ROI 104, Patient 19, Primary tumor bed, NMPR

description: Library name: ROI 104


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 4 biological replicate 3

description:
Library name: E43
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 4, biological replicate 3; column name in processed expression matrix: E43


title: ROI 102, Patient 18, Lymph node, NMPR

description: Library name: ROI 102


title: ROI 103, Patient 18, Lymph node, NMPR

description: Library name: ROI 103


title: Ly6Chi monocyte, d7 Hpb, Biol rep 2

description:
Library name: Sample 4
P9-d7Hpb-2

value: Ly6Chi Monocyte


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 4 biological replicate 2

description:
Library name: E42
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 4, biological replicate 2; column name in processed expression matrix: E42


title: ROI 101, Patient 18, Lymph node, NMPR

description: Library name: ROI 101


title: Ly6Chi monocyte, d7 Hpb, Biol rep 1

description:
Library name: Sample 3
P9-d7Hpb-1


title: ROI 109, Patient 19, Lymph node, NMPR

description: Library name: ROI 109


title: ROI 100, Patient 18, Primary tumor bed, NMPR

description: Library name: ROI 100


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 4 biological replicate 1

description:
Library name: E41
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 4, biological replicate 1; column name in processed expression matrix: E41


title: ROI 99, Patient 18, Primary tumor bed, NMPR

description: Library name: ROI 99


title: Ly6Chi monocyte, Naïve, Biol rep 2

description:
Library name: Sample 2
P9-Naive-2


title: ROI 98, Patient 18, Primary tumor bed, NMPR

description: Library name: ROI 98


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 3 biological replicate 4

description:
Library name: E34
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 3, biological replicate 4; column name in processed expression matrix: E34


title: ROI 97, Patient 17, Lymph node, NMPR

description: Library name: ROI 97


title: Ly6Chi monocyte, Naïve, Biol rep 1

description:
Library name: Sample 1
P9-Naive-1


title: ROI 96, Patient 17, Lymph node, NMPR

description: Library name: ROI 96


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 3 biological replicate 3

description:
Library name: E33
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 3, biological replicate 3; column name in processed expression matrix: E33


title: ROI 95, Patient 17, Lymph node, NMPR

description: Library name: ROI 95


title: Granuloma at 90 days_3

city: Stony Brook

first: Maurizio

last: Del Poeta

address: 150 Life Science Building

department: Molecular Genetics and Microbiology

institute: Stony Brook University

description:
Library name: G90_3
10X Genomics

data_processing:
Initial identification of cell types was performed using Over Representation Analysis 60 using canonical marker lists from previous studies in lung or established databases. Subsetting and re-clustering was performed to enhance identification of different cell types. At this stage a few small clusters that expressed markers from two or more cell types were eliminated. Based on this initial analysis, a hierarchical ontology of cell types was constructed (Supplementary Table S1). Use of a hierarchical approach reduces the possibility of misclassification by relying on multiple choice points in the classification tree before assignment of cell type. A total of several distinct cell types were identified in this analysis although not all cell types were found in every experimental condition.
Assembly: Mouse mm10
Supplementary files format and content: Mus musculus
Supplementary files format and content: Count matrices (barcodes.tsv,features.tsv and matrix.mtx)

source_name: Lung

extract_protocol:
Lung granulomas and/or lung tissue were rapidly dissected and immediately homogenized. Large granulomas were cut into smaller pieces on ice in the buffer using spring scissors before dounce homogenization. The homogenates were filtered (40 µm Flowmi filters, Bel-Art) and pelleted by centrifugation at 500 g for 5 minutes at 4C. The nuclei pellets were resuspended in homogenization buffer with 25% iodixanol (OptiPrep™ Density Gradient Medium, Millipore Sigma), and single nuclei were purified on an iodixanol gradient (25%-30%-40%) by centrifugation at 2,200 g for 20 minutes at 4C without brake. A 120µl aliquot containing nuclei was taken at the interface between the 30% and the 40% iodixanol layers. Nuclei concentrations were determined using a Countess 2FL and Trypan Blue staining. The nuclei suspensions were used directly for single-nucleus capture in the 10x Genomics Chromium iX. Single nuclei RNA-sequencing was performed using a Chromium Next GEM Single Cell 5' Reagent Kit, v2 on a Chromium iX, according to the manufacturer’s instructions. Briefly, single nuclei suspensions, gel beads, and partitioning oil were loaded onto a Chromium NextGEM K Chip, for a target recovery of up to 10,000 nuclei per sample. The chip was loaded into a Chromium iX (10X Genomics) and single nuclei were captured in Gel Bead-In-Emulsions (GEMs).
Reverse transcription was performed in a PCR cycler, and the cDNA was collected using Recovery Agent (10X Genomics), purified with DynaBeads MyOne Silane beads (10X Genomics), amplified with PCR for 13 cycles, and further purified with SPRISelect reagent (Beckman Coulter). Quality control and quantification of the amplified cDNA was performed on a Tapestation 4200 (Agilent) using D5000 High Sensitivity ScreenTapes (Agilent, 5067-5592). 5’ single nuclei RNA-seq libraries were generated using 50ng of the amplified cDNA. After fragmentation, end-repair, A-tailing and size selection purification, the cDNA was ligated with Illumina adaptors and subsequently purified with SPRISelect reagent. Libraries were amplified and barcoded by PCR with dual index oligonucleotides from the Chromium Dual Index TT Set A kit (10X Genomics), for a total of 15 PCR cycles. The final PCR products were subjected to double-sided size selection with SPRISelect beads (0.6x and 0.8x). The library fragment size distribution was analyzed on the Agilent 4200 Tapestation, and library yields and concentrations were determined by qPCR using the KAPA Illumina Library Quantification PCR kit (Roche Diagnostics). Sequencing of the libraries (min. depth: 20,000 paired reads/nucleus) was performed on an Illumina NovaSeq instrument operated by a commercial provider, with the following paired-end sequencing settings: Read1, 151 cycles; i7 index, 10 cycles; i5 index, 10 cycles; Read2, 151 cycles.

value: Lung

value: Lung cells


title: ROI 94, Patient 17, Primary tumor bed, NMPR

description: Library name: ROI 94


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 3 biological replicate 2

description:
Library name: E32
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 3, biological replicate 2; column name in processed expression matrix: E32


title: ROI 93, Patient 17, Primary tumor bed, NMPR

description: Library name: ROI 93


title: Granuloma at 90 days_2

description:
Library name: G90_2
10X Genomics


title: ROI 92, Patient 17, Primary tumor bed, NMPR

description: Library name: ROI 92


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 3 biological replicate 1

description:
Library name: E31
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 3, biological replicate 1; column name in processed expression matrix: E31


title: ROI 91, Patient 16, Lymph node, NMPR

description: Library name: ROI 91


title: Ly6Clow monocyte, Naïve, Biol rep 2

description:
Library name: Sample 6
P10-Naive-2


title: ROI 106, Patient 19, Primary tumor bed, NMPR

description: Library name: ROI 106


title: Treatment naïve EAC tissue 13

description: Library name: Sample 13

value: Esophageal


title: ROI 90, Patient 16, Lymph node, NMPR

description: Library name: ROI 90


title: Granuloma at 90 days_1

description:
Library name: G90_1
10X Genomics


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 2 biological replicate 4

description:
Library name: E24
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 2, biological replicate 4; column name in processed expression matrix: E24


title: ROI 89, Patient 16, Lymph node, NMPR

description: Library name: ROI 89


title: ROI 88, Patient 16, Primary tumor bed, NMPR

description: Library name: ROI 88


title: Granuloma at 60 days_3

description:
Library name: G60_3
10X Genomics


title: ChIPseq_Cbx3_sh33_1_input_Rep1

description: Input DNA in sh-Cbx3 (KD sh #2) replicate 1

source_name: Keratinocytes

value: Keratinocytes

value: Input


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 2 biological replicate 3

description:
Library name: E23
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 2, biological replicate 3; column name in processed expression matrix: E23


title: ROI 87, Patient 16, Primary tumor bed, NMPR

description: Library name: ROI 87


title: Anopheles gambiae infected with late-selected Vavraia culicis lineage 3 biological replicate 4

description:
Library name: L34
Pool of 10 adult female Anopheles gambiae infected with late-selected Vavraia culicis lineage 3, biological replicate 4; column name in processed expression matrix: L34


title: ChIPseq_Cbx3_sh33_1_Ac_Rep1

description: H3K27ac IP in sh-Cbx3 (KD sh #2) replicate 1


title: Treatment naïve EAC tissue 3

description: Library name: Sample 3


title: ROI 86, Patient 16, Primary tumor bed, NMPR

description: Library name: ROI 86


title: Granuloma at 60 days_2

description:
Library name: G60_2
10X Genomics


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 2 biological replicate 2

description:
Library name: E22
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 2, biological replicate 2; column name in processed expression matrix: E22


title: Granuloma at 60 days_1

description:
Library name: G60_1
10X Genomics


title: ROI 85, Patient 15, Primary tumor bed, NMPR

description: Library name: ROI 85


title: Treatment naïve EAC tissue 1

description: Library name: Sample 1


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 2 biological replicate 1

description:
Library name: E21
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 2, biological replicate 1; column name in processed expression matrix: E21


title: ROI 83, Patient 15, Primary tumor bed, NMPR

description: Library name: ROI 83


title: ROI 84, Patient 15, Primary tumor bed, NMPR

description: Library name: ROI 84


title: ChIPseq_Cbx3_sh12_1_input_Rep1

description: Input DNA in sh-Cbx3 (KD sh #1) replicate 1


title: Granuloma at 30 days_3

description:
Library name: G30_3
10X Genomics


title: ROI 82, Patient 14, Lymph node, NMPR

description: Library name: ROI 82

value: Non-small cell lung cancer, Lymph node


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 1 biological replicate 4

description:
Library name: E14
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 1, biological replicate 4; column name in processed expression matrix: E14


title: ROI 81, Patient 14, Lymph node, NMPR

description: Library name: ROI 81


title: Granuloma at 30 days_2

description:
Library name: G30_2
10X Genomics


title: ROI 79, Patient 14, Lymph node, NMPR

description: Library name: ROI 79


title: Granuloma at 30 days_1

description:
Library name: G30_1
10X Genomics


title: ROI 80, Patient 14, Lymph node, NMPR

description: Library name: ROI 80


title: ROI 78, Patient 14, Primary tumor bed, NMPR

description: Library name: ROI 78


title: Root,2,5-D,24hours,rep2

description:
Library name: Sample8
Root_Proceed_Data.txt

value: Root

value: WT


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 1 biological replicate 3

description:
Library name: E13
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 1, biological replicate 3; column name in processed expression matrix: E13


title: ROI 77, Patient 14, Primary tumor bed, NMPR

description: Library name: ROI 77

value: Non-small cell lung cancer, Primary tumor bed


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 1 biological replicate 2

description:
Library name: E12
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 1, biological replicate 2; column name in processed expression matrix: E12

value: whole adult female mosquito


title: ROI 76, Patient 14, Primary tumor bed, NMPR

description: Library name: ROI 76


title: WT-infected mice_2

description:
Library name: WT_2
10X Genomics


title: Anopheles gambiae infected with early-selected Vavraia culicis lineage 1 biological replicate 1

description:
Library name: E11
Pool of 10 adult female Anopheles gambiae infected with early-selected Vavraia culicis lineage 1, biological replicate 1; column name in processed expression matrix: E11


title: ROI 74, Patient 13, Primary tumor bed, NMPR

description: Library name: ROI 74


title: Anopheles gambiae infected with reference Vavraia culicis biological replicate 4

description:
Library name: R14
Pool of 10 adult female Anopheles gambiae infected with the unselected reference Vavraia culicis lineage, biological replicate 4; column name in processed expression matrix: R14

value: infected with reference Vavraia culicis


title: ROI 72, Patient 12, Primary tumor bed, NMPR

description: Library name: ROI 72


title: Anopheles gambiae infected with reference Vavraia culicis biological replicate 3

description:
Library name: R13
Pool of 10 adult female Anopheles gambiae infected with the unselected reference Vavraia culicis lineage, biological replicate 3; column name in processed expression matrix: R13


title: ROI 71, Patient 12, Primary tumor bed, NMPR

description: Library name: ROI 71


title: Uninfected mice_2

description:
Library name: UN_2
10X Genomics


title: ROI 70, Patient 12, Primary tumor bed, NMPR

description: Library name: ROI 70


title: Anopheles gambiae infected with reference Vavraia culicis biological replicate 2

description:
Library name: R12
Pool of 10 adult female Anopheles gambiae infected with the unselected reference Vavraia culicis lineage, biological replicate 2; column name in processed expression matrix: R12


title: ROI 73, Patient 13, Primary tumor bed, NMPR

description: Library name: ROI 73


title: Uninfected mice_3

description:
Library name: UN_3
10X Genomics


title: ROI 69, Patient 11, Lymph node, MPR

description: Library name: ROI 69


title: Uninfected mice_1

description:
Library name: UN_1
10X Genomics


title: ROI 68, Patient 11, Lymph node, MPR

description: Library name: ROI 68


title: Anopheles gambiae infected with reference Vavraia culicis biological replicate 1

description:
Library name: R11
Pool of 10 adult female Anopheles gambiae infected with the unselected reference Vavraia culicis lineage, biological replicate 1; column name in processed expression matrix: R11


title: ROI 67, Patient 11, Lymph node, MPR

description: Library name: ROI 67


title: d17_10%_874

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description:
Library name: d17-10-874
PCR amplicon

library_source: other

data_processing:
Reads were trimmed using Trim Galore and aligned to the sgRNA sequences using Bowtie aligner v2.3.3. Synthetic rescue/positive selection and synthetic lethality/negative selection beta scores, as well as statistical significance, were determined using MAGeCK-MLE method.
Supplementary files format and content: Tab-delimited file where each column contains the readcount associated to each sgRNA.  Column 2 is the gene associated with the sgRNA from column 1.
Library strategy: CRISPR Screen

molecule: other

growth_protocol: Cells were maintained at 300,000c/ml with counting every 2 - 3 days (Mon, Wed, Fri). Induction of Cas9 with 1/5,000 Doxycyclin for 7 days in media with 10% FBS, before addition of compounds for additional up to 17 days, taking samples every 2-3 days.  AML1 cells grown in DMEM +GM-CSF +Blast +Puro + @ FBS 10%          up to 17 days with compounds at 1/10,000 dilution vs. DMSO at same dilution (compounds added at each split according to volume of fresh media added)          gDNA isoaltion by proteinase K, followed by protein ppt by Ammonium sulfate, Isopropanol ppt of gDNA          PCR1 amplification of the integrated sg casette done on 277ug gDNA (42M genomes) for 23-26 cycles (pre-saturation).  Nested PCR2 adding Illumina adapters and indexes was done on 1/20 dilution of PCR1 for 13 cycles.          samples assembled at 10ng/ul with 7ul/sample. 2X PCR2 added for d0 samples, 1.5X added for DMSO end point samples

extract_protocol:
gDNA isoaltion by proteinase K, followed by protein ppt by Ammonium sulfate, Isopropanol ppt of gDNA - Modified from Neville Sanjana’s protocol.  Ref: Sidi Chen, Neville E. Sanjana, et al. Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis, Cell, Volume 160, Issue 6, 2015, Pages 1246-1260, https://doi.org/10.1016/j.cell.2015.02.038.
Followed protocol from Bertomeu, T., Coulombe-Huntington, J., Chatr-aryamontri, A., Bourdages, K. G., Coyaud, E., Raught, B., … Tyers, M. (2018). A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome. Molecular and Cellular Biology, 38(1). https://doi.org/10.1128/MCB.00302-17

value: Blood

value: Acute myeloid leukemia cells

value: time:day 17


title: ROI 66, Patient 11, Primary tumor bed, MPR

description: Library name: ROI 66


title: Anopheles gambiae uninfected control biological replicate 4

description:
Library name: U14
Pool of 10 adult female Anopheles gambiae, uninfected control, biological replicate 4; column name in processed expression matrix: U14

value: Kisumu

value: uninfected control


title: ROI 64, Patient 11, Primary tumor bed, MPR

description: Library name: ROI 64


title: Anopheles gambiae uninfected control biological replicate 3

description:
Library name: U13
Pool of 10 adult female Anopheles gambiae, uninfected control, biological replicate 3; column name in processed expression matrix: U13


title: d17_10%_DMSO

description:
Library name: d17-10-DMSO
PCR amplicon


title: ROI 62, Patient 10, Lymph node, MPR

description: Library name: ROI 62


title: ROI 63, Patient 10, Lymph node, MPR

description: Library name: ROI 63


title: Anopheles gambiae uninfected control biological replicate 2

description:
Library name: U12
Pool of 10 adult female Anopheles gambiae, uninfected control, biological replicate 2; column name in processed expression matrix: U12


title: d0_10%FBS

description:
Library name: d0-10
PCR amplicon

value: time:day 0 post-dox


title: ROI 61, Patient 10, Lymph node, MPR

description: Library name: ROI 61


title: combo_gskj4_24

city: Cambridge

first: Simon

last: Koplev

address: Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Puddicombe Way

department: Cambridge Stem Cell Institute

institute: University of Cambridge

description: Library name: S24

data_processing:
Resulting .fastq raw files were quality checked using FASTQC v. 0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MULTIQC v. 1.14. (https://github.com/MultiQC/MultiQC), before quantification using KALLISTO (https://github.com/pachterlab/kallisto) v. 0.48.0 with default settings. Processing of raw files was run in a Python virtual (v. 3.10.8) environment using CGATcore v. 12.2.0 pipeline framework (https://doi.org/10.12688/f1000research.18674.2).
Assembly: hg38
Supplementary files format and content: matrix of kallisto unnormalised counts for all samples (.csv)

source_name: intestine

growth_protocol: The Ccd-18Co colon fibroblast cell line was obtained from ATCC (#CRL-1459) up to passage 20. Ccd-18Co were maintained and expanded and maintained in full growth medium (MEM-alpha Sigma #12571063), Penicillin-Streptomycin (Thermo # 15140148) and 20% FBS (Thermo #A5209501). For experiments, fibroblast cultures were seeded at 25,000 cells in 200ul full growth medium in 48-well format tissue culture plates, unless stated otherwise.

extract_protocol:
RNA was isolated using the Qiagen RNeasey Mini kit (Qiagen #74104) or Zymo Quick-RNA 96 kits (ZymoResearch #R-1052) with the optional on-column DNA digestion step. Isolates from cell cultures were prepared by direct lysis in RNA lysis buffer, followed by RNA isolation with the Zymo RNA extraction kits including on-column DNase treatment. Isolated RNA was stored at –80C until further processing or shipped to service providers.
Libraries were prepared according to manufacturer's instructions, using NEBNext Ultra II RNA Library Prep Kit for Illumnia. Resulting libraries were sequenced on an Illumina NextSeq500.

treatment_protocol: Ccd-18Co were seeded at 25,000 cells in 200ul of full growth medium in 48-well format tissue culture plates. After attachment, cells were subjected to three pulses (1 pulse: 72h of cytokines in serum-free medium followed by 96h of recovery in full growth medium) of cytokine cocktail (TNF, OSM and IL-17A at 10ng/ml each; IL-1B at 0.1 ng/ml) stimulations. After a resting period of 1 week, Ccd-18Co were subjected to either DMSO, 250nM Belinostat or 10uM GSKJ4, each diluted 1:5000 in serum-free medium for a total of 5 days. After the 5 days, cells were returned to full growth medium. Cell extracts for RNAseq were prepared 2 weeks after the final epigenetic modulator treatment.

value: intestine

value: fibroblast


title: Anopheles gambiae uninfected control biological replicate 1

description:
Library name: U11
Pool of 10 adult female Anopheles gambiae, uninfected control, biological replicate 1; column name in processed expression matrix: U11


title: ROI 59, Patient 10, Primary tumor bed, MPR

description: Library name: ROI 59