title: TC32 cells with BCL6 KO guide 1 - Day 4 - replicate 3

description:
Library name: TC32_BCL6_G1_D4_R3
column name in day 4 knock out counts file

data_processing:
RNA-seq data analysis was performed according to the ENCODE standards (https://www.encodeproject.org/data-standards/rna-seq/long-rnas/ ). Quality check of unaligned reads was performed using FastQC v.0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC v.1.14 Using STAR v.2.7.11a9 the paired end reads were aligned to hg38/gencodev30
Gene level reads were counted and summarized across hg38 exons by using featureCounts v.2.0.3 from the Subread v2.0.0 package (https://subread.sourceforge.net/). Following alignment, quality control checks were performed using SARTools v.1.7.310. DESeq2 v.1.44.0 was used to normalize gene counts and quantify differential expression between experimental and control conditions11 using the apeglm v1.26.111 library. Gene level expression was estimated as log2(TPM +1) normalized reads
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts and log2(TPM+1) values for each sample

growth_protocol: Parental EWS502 cells and EWS502 cells expressing exogenous FKBP12(F36V)-EWS/FLI1 concurrent with Cas9 and a guide targeting an intron/exon junction of endogenous EWS/FLI1 were grown in RPMI media supplemented with 15% FBS and 1% penicllin-streptomycin. Parental TC32 cells were grown in RPMI media supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Approximately two million parental EWS502 or TC32 cells transduced with control or BCL6 sgRNAs from each well were washed with PBS and then detached from the plate using trypsin. Half of the cells were aliquoted into a 1.5 mL Eppendorf tube and were set aside for protein purification to confirm KO. The other half of cells were pelleted by centrifugation at 2500xg for 3 minutes (min) in a tabletop centrifuge (Eppendorf, 5425). Media was aspirated and total RNA was extracted using the RNAeasy Plus kit (Qiagen, 74134).  For RNA sequencing experiments of compound treated cells, 800,000 EWS502 FKBP-E/F cells were seeded into a 6 well plate. The next day, cells were treated in sextuplicate with DMSO, 2.5 µM BI3812, or 2.5 µM EB-TCIP, or 2.5 µM NEG-1. One set of triplicates was collect as described above 8 hrs post treatment and the second set of triplicates was collected as described above 24 hrs post treatment. At both time points cells collected for RNA harvesting were frozen in 350 µL of RLT plus buffer (Qiagen) at -80 oC. All samples were thawed at the same time and total RNA purified using the RNAeasy Plus kit.
Libraries were constructed by Novogene. Per there correspondence, RNA integrity was assessed using a Bioanalyzer 2100 System (Agilent Technologies). Libraries were then prepared by purifying messenger RNA (mRNA) from total RNA samples using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented and library prep completed using Fast RNA seq Lib Prep Kit V2 (AbClonal Technology, RK20306). Library quality and concentration were assessed using real-time PCR and Qubit fluorometric quantitation (Thermo Fisher Scientific).

value: Ewing sarcoma

value: day 4


title: TC32 cells with BCL6 KO guide 2 - Day 4 - replicate 2

status: Public on Mar 17 2025

type: SRA

city: Boston

first: Kimberly

last: Stegmaier

address: 450 Brookline Ave

country: USA

institute: Dana Farber Cancer Institue

description:
Library name: TC32_BCL6_G2_D4_R2
column name in day 4 knock out counts file

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment

tag: time


title: TC32 cells with BCL6 KO guide 2 - Day 4 - replicate 1

description:
Library name: TC32_BCL6_G2_D4_R1
column name in day 4 knock out counts file


title: yijO inducible 1

first: James

last: Galagan

state: Massachusetts

address: 36 Cummington Mall

department: Biomedical Engineering

institute: Boston University

description: ChIP-Seq of inducible yijO with C-terminal FLAG tag

library_source: genomic

data_processing:
For ChIP-Seq: Adapters were trimmed from reads using Cutadapt version 2.6
For ChIP-Seq: Reads were aligned to GenBank ID U00096.3 using Bowtie2 versioni 2.3.4.1
For ChIP-Seq: Peak calling was done using SPAT
For ChIP-Seq: Peaks with low shift (<45 bases) between forward and reverse coverage were filtered
For ChIP-Seq: Peaks with low enrichment compared to WT controls were filtered
For ChIP-Seq: Peaks from SPA-tagged TFs that matched NagC artifacts were filtered
For ChIP-Seq: Peaks with low overall enrichment (<4.75-fold over genomic average coverage) were filtered
For ChIP-Seq: Peaks mapped to strong tag-independent artifacts (described in manuscript) were filtered
For ChIP-Seq: Peaks mapped to weak tag-independent artifacts were filtered (described in manuscript)
For ChIP-Seq: Peaks adjacent to inducible watermarks were re-added (described in manuscript)
For Library-ChIP: Inserted sequences were counted from raw reads by identifying the anchor sequence (from the flank of the insertion site) "GGACGGATCCTCGAGCATGC", and taking the following 37 nucleotides after the anchor.
For Library-ChIP: Low abundance hits were dropped out (< 0.1% of preIP reads)
For Library-ChIP: Counts were normalized within-sample for sequencing depth by dividing counts by average counts for each insertion sequence
For Library-ChIP: Enrichment was determined as the ratio of normalized postIP:preIP counts
Assembly: U00096.3
Supplementary files format and content: ChIP-Seq: GFF file containing peak calls that passed all filtering steps
Supplementary files format and content: Library-ChIP: TSV file where first column is the inserted sequence identified in processing step 1, columns 2 and 3 are the number of times sequence was identified in R1 and R2 reads, column 4 is the identifier of the sequence from the designed insertion pool, and column 5 is the sum of R1 and R2 reads

molecule: genomic DNA

organism: Escherichia coli K-12

growth_protocol: Cells were grown in indicated media at 30°C with shaking in vented flasks

extract_protocol:
TF-DNA complexes were fixed with formaldehyde and glycine.  For in vivo ChIP-Seq, cells were sheared via sonication; for in vitro ChIP-Seq, DNA was sheared via sonication prior to TF-DNA binding.  Sheared DNA was immunoprecipitated (IP) using anti-FLAG, anti-V5, or anti-6xHis mAb (indicated in metadata).  DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  For Library-ChIP, preIP samples used sheared DNA purified via ProteinaseK digestion and Qiaquick PCR purification kit prior to addition of anti-tag antibody; postIP samples used sheared DNA that was immunoprecipitated, washed, purified, and extracted in the same way as ChIP-Seq.
ChIP-DNA was converted into NGS libraries compatible with the Illumina platform using the NEBNext Ultra DNA (NEB Cat. No. E7465).  For Library-ChIP, libraries were constructed similarly to Illumina's 16S metagenomic library prep (Illumina Ref #15044223 Rev. B).  Briefly, an initial PCR was performed on DNA with a universal primer pair targeting flanks of the insertion site on the pAMD plasmid where designed sequences were inserted.  These primers contained overhangs that could be targeted by Illumina Nextera XT Index Kit v2 (Illumina Cat. No. FC-131-2001) primers.  First PCR was cleaned up with Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  Second PCR used a unique pair of primers from the Illumina Nextera kit for each sample, and were cleaned up with AMPureXP beads (Fisher Scientific Cat. No. NC9933872).

treatment_protocol: Inducible strains were treated with arabinose prior to crosslinking, some native strains were treated with GlcNac for 5 minutes prior to crosslinking (treatments indicated in metadata).

tag: strain

tag: transcription factor

value: yijO

tag: chip antibody

value: anti-FLAG mAb

tag: antibody vendor/catalog#

value: Sigma/Cat. No. F1804

tag: media

value: M9 Minimal with 0.4% glycerol

value: Log-Phase

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: yjgJ native 1

description: ChIP-Seq of native yjgJ with C-terminal V5 tag

value: yjgJ

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: TC32 cells with LacZ KO control - Day 4 - replicate 3

description:
Library name: TC32_LacZ_D4_R3
column name in day 4 knock out counts file

value: LacZ


title: yijO native 1

description: ChIP-Seq of native yijO with C-terminal SPA tag


title: TC32 cells with BCL6 KO guide 1 - Day 4 - replicate 1

description:
Library name: TC32_BCL6_G1_D4_R1
column name in day 4 knock out counts file


title: yihW native 2

description: ChIP-Seq of native yihW with C-terminal V5 tag

value: yihW


title: TC32 cells with LacZ KO control - Day 4 - replicate 2

description:
Library name: TC32_LacZ_D4_R2
column name in day 4 knock out counts file


title: yihW inducible 1

description: ChIP-Seq of inducible yihW with C-terminal FLAG tag


title: yihW native 1


title: TC32 cells with LacZ KO control - Day 4 - replicate 1

description:
Library name: TC32_LacZ_D4_R1
column name in day 4 knock out counts file


title: yhfZ inducible 1

description: ChIP-Seq of inducible yhfZ with C-terminal FLAG tag

value: yhfZ


title: TC32 cells with BCL6 KO guide 2 - Day 4 - replicate 3

description:
Library name: TC32_BCL6_G2_D4_R3
column name in day 4 knock out counts file


title: TC32 cells with Chr2-2 KO control - Day 4 - replicate 1

description:
Library name: TC32_Chr2-2_D4_R1
column name in day 4 knock out counts file


title: TC32 cells with Chr2-2 KO control - Day 4 - replicate 2

description:
Library name: TC32_Chr2-2_D4_R2
column name in day 4 knock out counts file


title: TC32 cells with Chr2-2 KO control - Day 4 - replicate 3

description:
Library name: TC32_Chr2-2_D4_R3
column name in day 4 knock out counts file


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BAK-04-212 treatment - 24 hours - replicate 2

description:
Library name: EFLI502_BAK212_24hr_R2
column name in EB-TCIP experiment counts file

source_name: EWS502 FKBP(F36V)-EWS/FLI1

value: EWS502 FKBP(F36V)-EWS/FLI1

value: 24 hours


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BAK-04-212 treatment - 24 hours - replicate 3

description:
Library name: EFLI502_BAK212_24hr_R3
column name in EB-TCIP experiment counts file


title: yhfR inducible 1

description: ChIP-Seq of inducible yhfR with C-terminal FLAG tag

value: yhfR

value: LB


title: yhfR inducible 2


title: yhfR native 1

description: ChIP-Seq of native yhfR with C-terminal V5 tag


title: yjiR inducible 1

description: ChIP-Seq of inducible yjiR with C-terminal FLAG tag

value: yjiR


title: TC32 cells with BCL6 KO guide 1 - Day 4 - replicate 2

description:
Library name: TC32_BCL6_G1_D4_R2
column name in day 4 knock out counts file

value: Ewing sarcoma

value: day 4


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BAK-04-212 treatment - 24 hours - replicate 1

description:
Library name: EFLI502_BAK212_24hr_R1
column name in EB-TCIP experiment counts file


title: yjgJ native 2

description: ChIP-Seq of native yjgJ with C-terminal V5 tag


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BI3812 treatment - 24 hours - replicate 3

description:
Library name: EFLI502_BI_24hr_R3
column name in EB-TCIP experiment counts file

value: BI


title: yidZ inducible 1

description: ChIP-Seq of inducible yidZ with C-terminal FLAG tag

value: yidZ

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: yhaJ native 1

description: ChIP-Seq of native yhaJ with C-terminal SPA tag

value: yhaJ

value: Log-Phase


title: yheO inducible 1

description: ChIP-Seq of inducible yheO with C-terminal FLAG tag

value: yheO

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: ygiT native 2

description: ChIP-Seq of native ygiT with C-terminal SPA tag

value: ygiT


title: Stool sample6 pre-treament

city: Shanghai

first: Haiou

last: Liu

address: No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.

country: China

institute: Fudan University

description: Library name: sample6 pre-treament

data_processing:
Raw FASTQ files were de-multiplexed using an in-house perl script, and then quality-filtered by fastp version 0.19.6 and merged by FLASH version 1.2.11 with the following criteria: (i) the PE300 reads were truncated at any site receiving an average quality score of <20 over a 50 bp sliding window, and the truncated reads shorter than 50 bp were discarded, reads containing ambiguous characters were also discarded; (ii) only overlapping sequences longer than 10 bp were assembled according to their overlapped sequence. The maximum mismatch ratio of overlap region is 0.2. Reads that could not be assembled were discarded; (iii) Samples were distinguished according to the barcode and primers, and the sequence direction was adjusted, exact barcode matching, 2 nucleotide mismatch in primer matching. Then the optimized sequences were clustered into operational taxonomic units (OTUs) using Usearch 11 with 97% sequence similarity level. The most abundant sequence for each OTU was selected as a representative sequence. The OTU table was manually filtered, i.e., chloroplast sequences in all samples were removed. To minimize the effects of sequencing depth on alpha and beta diversity measure, the number of 16S rRNA gene sequences from each sample were rarefied to 20,000, which still yielded an average Good's coverage of 99.09% , respectively. The taxonomy of each OTU representative sequence was analyzed by RDP Classifier version 2.13 against the 16S rRNA gene database (eg. Silva v138) using confidence threshold of 0.7. The metagenomic function was predicted by PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) based on OTU representative sequences. PICRUSt2 is a software containing a series of tools as follows: HMMER was used to aligns OTU representative sequences with reference sequences. EPA-NG and Gappa were used to put OTU representative sequences into a reference tree. The castor was used to normalize the 16S gene copies. MinPath was used to predict gene family profiles, and locate into the gene pathways. Entire analysis process was accord to protocols of PICRUSt2.
Assembly: hg38
Supplementary files format and content: otu_summary.txt
Library strategy: 16S rRNA-seq

organism: human feces metagenome

source_name: Stool sample

extract_protocol:
Total microbial genomic DNA was extracted from 12 samples using the FastPure Stool DNA Isolation Kit (MJYH, shanghai, China) according to manufacturer’s instructions.
The quality and concentration of DNA were determined by 1.0% agarose gelelectrophoresis and a NanoDrop® ND-2000 spectrophotometer (Thermo Scientific Inc., USA) and kept at -80 ℃ prior to further use. The hypervariable region V3-V4 of the bacterial 16S rRNA gene were amplified with primer pairs 338F (5'-ACTCCTACGGGAGGCAGCAG-3') and806R(5'-GGACTACHVGGGTWTCTAAT-3') by an T100 Thermal Cycler (BIO-RAD, USA). The PCR reaction mixture including 4 μL 5 × Fast Pfu buffer, 2 μL 2.5 mM dNTPs, 0.8 μL each primer (5 μM), 0.4 μL Fast Pfu polymerase, 10 ng of template DNA, and ddH2O to a final volume of 20 µL. PCR amplification cycling conditions were as follows: initial denaturation at 95 ℃ for 3 min, followed by 27 cycles of denaturing at 95 ℃ for 30 s, annealing at 55 ℃ for 30 s and extension at 72 ℃for 45 s, and single extension at 72 ℃ for 10 min, and end at 4 ℃. All samples were amplified in triplicate. The PCR product was extracted from 2% agarose gel and purified. Then quantified using Synergy HTX (Biotek, USA)

tag: tissue

value: Stool sample


title: Stool sample6 post-treament

description: Library name: sample6 post-treament


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BI3812 treatment - 24 hours - replicate 2

description:
Library name: EFLI502_BI_24hr_R2
column name in EB-TCIP experiment counts file

value: EWS502 FKBP(F36V)-EWS/FLI1

value: 24 hours


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BI3812 treatment - 24 hours - replicate 1

description:
Library name: EFLI502_BI_24hr_R1
column name in EB-TCIP experiment counts file


title: ygiT native 1


title: Stool sample5 post-treament

description: Library name: sample5 post-treament


title: Stool sample5 pre-treament

description: Library name: sample5 pre-treament


title: Stool sample4 post-treament

description: Library name: sample4 post-treament


title: ygbI native 2

description: ChIP-Seq of native ygbI with C-terminal V5 tag

value: ygbI

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with RPG-02-089 treatment - 24 hours - replicate 3

description:
Library name: EFLI502_O89_24hr_R3
column name in EB-TCIP experiment counts file

value: Ewing sarcoma


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with RPG-02-089 treatment - 24 hours - replicate 2

description:
Library name: EFLI502_O89_24hr_R2
column name in EB-TCIP experiment counts file


title: Stool sample4 pre-treament

description: Library name: sample4 pre-treament


title: Stool sample3 post-treament

description: Library name: sample3 post-treament


title: ygbI native 1


title: ygbI inducible 1

description: ChIP-Seq of inducible ygbI with C-terminal FLAG tag


title: yfeT inducible 1

description: ChIP-Seq of inducible yfeT with C-terminal FLAG tag

value: yfeT


title: yfiE native 1

description: ChIP-Seq of native yfiE with C-terminal V5 tag

value: yfiE


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with RPG-02-089 treatment - 24 hours - replicate 1

description:
Library name: EFLI502_O89_24hr_R1
column name in EB-TCIP experiment counts file


title: yheO native 1

description: ChIP-Seq of native yheO with C-terminal V5 tag


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with ortho-AP1867 control - 24 hours - replicate 3

description:
Library name: EFLI502_OAP_24hr_R3
column name in EB-TCIP experiment counts file

value: OAP


title: yfhH native 1

description: ChIP-Seq of native yfhH with C-terminal SPA tag

value: yfhH

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: yheO native 2

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: yfeT native 2

description: ChIP-Seq of native yfeT with C-terminal V5 tag


title: yfeT native 1


title: ygeH inducible 1

description: ChIP-Seq of inducible ygeH with C-terminal FLAG tag

value: ygeH

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: yfeC native 1

description: ChIP-Seq of native yfeC with C-terminal V5 tag

value: yfeC


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with ortho-AP1867 control - 24 hours - replicate 2

description:
Library name: EFLI502_OAP_24hr_R2
column name in EB-TCIP experiment counts file

value: EWS502 FKBP(F36V)-EWS/FLI1


title: Stool sample2 post-treament

description: Library name: sample2 post-treament

value: Stool sample


title: yeiI inducible 1

description: ChIP-Seq of inducible yeiI with C-terminal FLAG tag

value: yeiI


title: yeiE inducible 2

description: ChIP-Seq of inducible yeiE with C-terminal FLAG tag

value: yeiE


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with ortho-AP1867 control - 24 hours - replicate 1

description:
Library name: EFLI502_OAP_24hr_R1
column name in EB-TCIP experiment counts file

value: 24 hours


title: yeiE inducible 1


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with DMSO control - 24 hours - replicate 3

description:
Library name: EFLI502_DMSO_24hr_R3
column name in EB-TCIP experiment counts file

value: Ewing sarcoma

value: DMSO


title: Stool sample2 pre-treament

description: Library name: sample2 pre-treament


title: Stool sample1 post-treament

description: Library name: sample1 post-treament


title: yegW inducible 1

description: ChIP-Seq of inducible yegW with C-terminal FLAG tag

value: yegW


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with DMSO control - 24 hours - replicate 2

description:
Library name: EFLI502_DMSO_24hr_R2
column name in EB-TCIP experiment counts file


title: yegW native 1

description: ChIP-Seq of native yegW with C-terminal FLAG tag

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: yeiE native 1

description: ChIP-Seq of native yeiE with C-terminal V5 tag

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: Stool sample1 pre-treament

description: Library name: sample1 pre-treament


title: yedW inducible 1

description: ChIP-Seq of inducible yedW with C-terminal FLAG tag

value: yedW

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: Stool sample3 pre-treament

description: Library name: sample3 pre-treament


title: yeaT native 1

description: ChIP-Seq of native yeaT with C-terminal V5 tag

value: yeaT

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: yeaM inducible 1

description: ChIP-Seq of inducible yeaM with C-terminal FLAG tag

value: yeaM

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with DMSO control - 24 hours - replicate 1

description:
Library name: EFLI502_DMSO_24hr_R1
column name in EB-TCIP experiment counts file

value: EWS502 FKBP(F36V)-EWS/FLI1


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BAK-04-212 treatment - 8 hours - replicate 3

description:
Library name: EFLI502_BAK212_8hr_R3
column name in EB-TCIP experiment counts file

value: 8 hours


title: Fig4_VDJ_JP0076N

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description:
Library name: JP0076_N_VDJ
VDJ library

library_source: transcriptomic single cell

data_processing:
Gene expression unique molecular identifier (UMI) sample HTO counts were generated with CellRanger v6.0.1, v7.0.1, or v8.0.1 with mm39 reference.
BCR libraries were processed with CellRanger “vdj” with default parameters.
Transciptomic analysis was carried out using Seurat v. 5.1.0.
Assembly: Mus Musculus mm39
Supplementary files format and content: Tab separated value files and matrix files

organism: Mus musculus

source_name: Lymph node

extract_protocol:
Single cell suspension from lymph nodes was prepared in PBS supplemented with 0.5% BSA and 2 mM EDTA (PBE). Live GC cells were sorted using BD FACSymphony S6 or BD S8 FACSDiscover sorter
Library was  generated using a Chromium Next GEM Single Cell 5' Reagent Kit v2 or v3(Dual Index) with Feature Barcode technology for Cell Surface Protein, according to the manufacturer’s protocol.

value: Lymph node

value: GC B cell

tag: library type

value: mRNA


title: yeaM native 2

description: ChIP-Seq of native yeaM with C-terminal V5 tag


title: yeaM native 1


title: ydjF native 2

description: ChIP-Seq of native ydjF with C-terminal SPA tag

value: ydjF


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BAK-04-212 treatment - 8 hours - replicate 2

description:
Library name: EFLI502_BAK212_8hr_R2
column name in EB-TCIP experiment counts file

value: Ewing sarcoma


title: Fig4_GEX_JP0076N

description:
Library name: JP0076_N_GEX
GEX (5') library


title: ydfH inducible 1

description: ChIP-Seq of inducible ydfH with C-terminal FLAG tag

value: ydfH


title: yeiE native 2

value: yeiE

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BAK-04-212 treatment - 8 hours - replicate 1

description:
Library name: EFLI502_BAK212_8hr_R1
column name in EB-TCIP experiment counts file


title: ydfH native 1

description: ChIP-Seq of native ydfH with C-terminal V5 tag


title: yddM native 2

description: ChIP-Seq of native yddM with C-terminal V5 tag

value: yddM


title: Fig4_VDJ_JP0076C

description:
Library name: JP0076_C_VDJ
VDJ library


title: yddM native 1


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BI3812 treatment - 8 hours - replicate 3

description:
Library name: EFLI502_BI_8hr_R3
column name in EB-TCIP experiment counts file

value: BI


title: Fig4_HTO_JP0076C

description:
Library name: JP0076_C_HTO
HTO library

value: HTO


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BI3812 treatment - 8 hours - replicate 2

description:
Library name: EFLI502_BI_8hr_R2
column name in EB-TCIP experiment counts file


title: Fig4_GEX_JP0076C

description:
Library name: JP0076_C_GEX
GEX (5') library


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with BI3812 treatment - 8 hours - replicate 1

description:
Library name: EFLI502_BI_8hr_R1
column name in EB-TCIP experiment counts file


title: ydcN native 1

description: ChIP-Seq of native ydcN with C-terminal SPA tag

value: ydcN

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: ydaS inducible 1

description: ChIP-Seq of inducible ydaS with C-terminal FLAG tag

value: ydaS

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: Fig2g_VDJ_JP0071

description:
Library name: JP0071_VDJ
VDJ library

value: Lymph node

value: GC B cell

value: mRNA


title: ycjZ inducible 1

description: ChIP-Seq of inducible ycjZ with C-terminal FLAG tag

value: ycjZ


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with RPG-2-089 treatment - 8 hours - replicate 3

description:
Library name: EFLI502_O89_8hr_R3
column name in EB-TCIP experiment counts file

value: EWS502 FKBP(F36V)-EWS/FLI1

value: Ewing sarcoma

value: 8 hours


title: Fig4_HTO_JP0076N

description:
Library name: JP0076_N_HTO
HTO library


title: ycjZ native 2

description: ChIP-Seq of native ycjZ with C-terminal V5 tag

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: Fig2g_HTO_JP0071

description:
Library name: JP0071_HTO
HTO library

value: HTO


title: Fig2g_GEX_JP0071

description:
Library name: JP0071_GEX
GEX (5') library


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with RPG-2-089 treatment - 8 hours - replicate 2

description:
Library name: EFLI502_O89_8hr_R2
column name in EB-TCIP experiment counts file


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with RPG-2-089 treatment - 8 hours - replicate 1

description:
Library name: EFLI502_O89_8hr_R1
column name in EB-TCIP experiment counts file


title: ycjW inducible 1

description: ChIP-Seq of inducible ycjW with C-terminal FLAG tag

value: ycjW


title: ycjW native 3

description: ChIP-Seq of native ycjW with C-terminal V5 tag


title: ycjW inducible 2

value: anti-FLAG mAb


title: ycjZ native 1


title: Fig2g_VDJ_JP0063

description:
Library name: JP0063_VDJ
VDJ library


title: ydcR native 2

description: ChIP-Seq of native ydcR with C-terminal V5 tag

value: ydcR


title: ycjW native 1

value: M9 Minimal with 0.4% glycerol


title: Fig2g_HTO_JP0063

description:
Library name: JP0063_HTO
HTO library


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with ortho-AP1867 control - 8 hours - replicate 3

description:
Library name: EFLI502_OAP_8hr_R3
column name in EB-TCIP experiment counts file

value: OAP


title: yciT inducible 1

description: ChIP-Seq of inducible yciT with C-terminal FLAG tag

value: yciT

value: Sigma/Cat. No. F1804

value: Log-Phase


title: yciT native 2

description: ChIP-Seq of native yciT with C-terminal V5 tag


title: ydcR native 1


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with ortho-AP1867 control - 8 hours - replicate 1

description:
Library name: EFLI502_OAP_8hr_R1
column name in EB-TCIP experiment counts file


title: yciT native 1


title: Fig2g_GEX_JP0063

description:
Library name: JP0063_GEX
GEX (5') library

value: Lymph node

value: GC B cell


title: ycgE native 1

description: ChIP-Seq of native ycgE with C-terminal SPA tag

value: ycgE


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with ortho-AP1867 control - 8 hours - replicate 2

description:
Library name: EFLI502_OAP_8hr_R2
column name in EB-TCIP experiment counts file

value: EWS502 FKBP(F36V)-EWS/FLI1


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with DMSO control - 8 hours - replicate 3

description:
Library name: EFLI502_DMSO_8hr_R3
column name in EB-TCIP experiment counts file

value: Ewing sarcoma

value: DMSO


title: ybiH inducible 1

description: ChIP-Seq of inducible ybiH with C-terminal FLAG tag

value: ybiH

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: ybcM native 2

description: ChIP-Seq of native ybcM with C-terminal V5 tag

value: ybcM

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with DMSO control - 8 hours - replicate 2

description:
Library name: EFLI502_DMSO_8hr_R2
column name in EB-TCIP experiment counts file

value: 8 hours


title: ybcM native 1

value: M9 Minimal with 0.4% glycerol


title: TOP52, Replicate 3, pH 6.8

city: St. Louis

first: Petra

middle: Anne

last: Levin

state: MISSOURI

address: 1 Brookings Drive, Rebstock Hall, Room 323

department: Biology

institute: Washington University in St. Louis

description:
Library name: Sample 6
Column name in raw and processed files = PAL4422-Isol3-pH6-8

data_processing:
QC and adapter trimming was performed with bcl2fastq.
Read mapping was done using HISAT2.
Read counts were loaded into R, normalized with edgeR's Trimmed Mean of M values, and then values were converted to counts per million (cpm).
Differential gene expression was calculated with edgeR's quasi-linear F-test (qlfTest) functionality against treatment groups.
Assembly: ASM395745v1; ASM584v2
Supplementary files format and content: Tab-delimited file contains raw, quantified read counts
Supplementary files format and content: tab-delimited file containing the subset of all quantified genes that meet |logFC|>1 and p <0.05.

organism: Klebsiella pneumoniae

source_name: bacterial cells

growth_protocol: Cells were cultured in LB buffered to indicated pH with MMT buffer until early exponential phase (OD600 ~= 0.2).

extract_protocol:
RNA was extracted using Invitrogen Ribopure RNA extraction kit following manufacturer's instructions.
RNA was submitted to Microbial Genome Sequencing Center for library prep and sequencing.  Libraries were generated using Illumina's Stranded Total RNA Prep with Ribo-Zero plus following manufacturer's instructions.

value: bacterial cells

tag: genotype

value: WT

value: neutral pH


title: Fig2a_HTO_JP0069

description:
Library name: JP0069_HTO
HTO library

value: HTO


title: ybaQ native 2

description: ChIP-Seq of native ybaQ with C-terminal V5 tag

value: ybaQ

value: Log-Phase


title: EWS502 FKBP(F36V)-EWS/FLI1 cells treated with DMSO control - 8 hours - replicate 1

description:
Library name: EFLI502_DMSO_8hr_R1
column name in EB-TCIP experiment counts file


title: yafN native 1

description: ChIP-Seq of native yafN with C-terminal SPA tag

value: yafN

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: EWS502 cells with BCL6 KO guide 2 - Day 4 - replicate 3

description:
Library name: EWS_BCL6_G2_D4_R3
column name in day 4 knock out counts file

value: Ewing sarcoma

value: day 4


title: ybaQ native 1


title: TOP52, Replicate 2, pH 6.8

description:
Library name: Sample 5
Column name in raw and processed files = PAL4422-Isol2-pH6-8


title: yagI inducible 1

description: ChIP-Seq of inducible yagI with C-terminal FLAG tag

value: yagI

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: ycgE inducible 1

description: ChIP-Seq of inducible ycgE with C-terminal FLAG tag

value: ycgE


title: yafN inducible 1

description: ChIP-Seq of inducible yafN with C-terminal FLAG tag


title: TOP52, Replicate 1, pH 6.8

description:
Library name: Sample 4
Column name in raw and processed files = PAL4422-Isol1-pH6-8


title: TOP52, Replicate 3, pH 4.8

description:
Library name: Sample 3
Column name in raw and processed files = PAL4422-Isol3-pH4-8

value: acidic pH


title: yafC inducible 2

description: ChIP-Seq of inducible yafC with C-terminal FLAG tag

value: yafC


title: EWS502 cells with BCL6 KO guide 2 - Day 4 - replicate 1

description:
Library name: EWS_BCL6_G2_D4_R1
column name in day 4 knock out counts file


title: yafC inducible 1

value: M9 Minimal with 0.4% glycerol


title: uxuR inducible 1

description: ChIP-Seq of inducible uxuR with C-terminal FLAG tag

value: uxuR


title: TOP52, Replicate 2, pH 4.8

description:
Library name: Sample 2
Column name in raw and processed files = PAL4422-Isol2-pH4-8

value: bacterial cells

value: WT


title: EWS502 cells with BCL6 KO guide 2 - Day 4 - replicate 2

description:
Library name: EWS_BCL6_G2_D4_R2
column name in day 4 knock out counts file


title: Fig2a_VDJ_JP0069

description:
Library name: JP0069_VDJ
VDJ library

value: Lymph node

value: GC B cell

value: mRNA


title: uvrY native 4

description: ChIP-Seq of native uvrY with C-terminal SPA tag

value: uvrY

value: Log-Phase

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: EWS502 cells with BCL6 KO guide 1 - Day 4 - replicate 3

description:
Library name: EWS_BCL6_G1_D4_R3
column name in day 4 knock out counts file

value: Ewing sarcoma


title: TOP52, Replicate 1, pH 4.8

description:
Library name: Sample 1
Column name in raw and processed files = PAL4422-Isol1-pH4-8


title: uvrY native 3

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: EWS502 cells with BCL6 KO guide 1 - Day 4 - replicate 2

description:
Library name: EWS_BCL6_G1_D4_R2
column name in day 4 knock out counts file

value: day 4


title: uvrY native 2


title: uvrY native 1


title: ulaR inducible 1

description: ChIP-Seq of inducible ulaR with C-terminal FLAG tag

value: ulaR

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: CD11b, CD103 Doulbe-positive, Non-granuloma, R3

city: Glasgow

first: Andrew

middle: George

last: Farthing

state: Scotland

address: Institute of Infection, Immunity and Inflammation, 120 University Place, Sir Graeme Davies Building

country: United Kingdom

institute: University of Glasgow

description:
Library name: DP_NG3
Column name in raw_counts.csv: DP_NG3

data_processing:
RNA-Seq fastQ files were quality control checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, v0.11.7) and aligned to the Mus musculus reference genome (GRCm39, vM30) using STAR (v 2.7.9a).
Genes with a mean expression <1 read per sample were removed from merged counts files. Expression and differential expression values were generated using DESeq2 (v 1.42.1) using a pairwise model with no additional covariates. Genes with a median expression < 20 across samples were excluded from downstream analysis.
The processed data was then visualised using RStudio and Searchlicht2 according to the multiple differential expression (MDE) workflow using an absolute log2-fold cut-off of 0.58 and an adjusted p-value of 0.05 across all comparisons.
Assembly: GRCm39, vM30
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Small intestine lamina propria

growth_protocol: Mice were infected with 200 Hpb L3 larvae (a gift from Professor Rick Maizels) by oral gavage and tissues were harvested 7 days post infection.Small intestine (SI) were removed, cut open longitudinally and rinsed in cold PBS, with Peyer’s patches being removed from the small intestines. Intestinal tissue was enzymatically digested as described previously (Webster and Andrusaite et al., 2019). In brief, the epithelium and mucus were first removed by washingtissues 3 times in warm calcium/magnesium free HBSS containing 2mM EDTA (Gibco) for 15 minutes at 37°C with shaking at 250rpm. Small intestines were then digested by incubationwith 0.5mg/mL collagenase VIII (Sigma), while colons were digested with 0.5mg/mL collagenase V (Sigma), 0.65mg/mL collagenase D (Roche), 1mg/mL Dispase (Gibco) and 30ug/mL DNase (Roche) each for 15-20 minutes at 37°C with shaking. Digestion was stopped by adding cold complete RPMI medium (RPMI 1640 contained 10% heat inactivated foetal calf serum (FCS), 2mM L-glutamine, 100μm/mL penicillin/streptomycin and 50μm b-mercaptoethanol (all Gibco). Cells were then passed through a 100μm and then a 40μm mesh EASYstrainer (Greiner), before being washed twice with cold complete RPMI medium for 10 minutes in 4°C at 400g at stored at 4°C before use. For separation of individual granuloma-associated tissue, SI was processed the same way, but visible granuloma tissue were removed using dissection scissors. For each granuloma, a comparable size non-granuloma tissue in the proximity to the paired granuloma was removed for control. Comparable size naïve tissue was removed at the same location down the length of the SI from naïve animals to be used as control. Tissue was processed, washed and enzymatically digested in the same manner as the whole gut tissue. Each individual collection tube was weighed before and after tissuecollection to determine the tissue weight that was used for normalisation. Cells isolate from granuloma, non- granuloma and naïve SI LP tissue were FACS-isolated on an BD FACSAriaTM III using anti-CD3(1:100), anti-CD19-BV605 (1:100), anti-NK1.1 (1:100), anti-B220 (1:200), anti-CD64 (1:200), and anti-MHCII (1:200), anti-CD11c (1:100), anti-CD11b (1:200) and anti-CD103 (1:200). Each sample was pooled from 4 individual animals. Immediately after cell sort, cells were washed and resuspended in RLT supplemented with 0.1% b-ME. Cells were lysed by vigorous vortex for 1 min and flash-frozen using dry ice.

extract_protocol:
RNA was extracted immediately after using RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions
RNA library preparation and sequencing was performed commercially by Novogene and sequenced using NovaSeq X Plus (PE150) platform

value: Small intestine lamina propria

value: Intesitnal DC2

value: Non-granuloma

value: C57/Bl6 background

value: 200 L3 Hpb larvae by oral gavage

tag: batch


title: ulaR native 1

description: ChIP-Seq of native ulaR with C-terminal SPA tag

value: M9 Minimal with 0.4% glycerol


title: CD11b, CD103 Doulbe-positive, Non-granuloma, R2

description:
Library name: DP_NG2
Column name in raw_counts.csv: DP_NG2


title: uidR native 1

description: ChIP-Seq of native uidR with C-terminal V5 tag

value: uidR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: CD11b, CD103 Doulbe-positive, Non-granuloma, R1

description:
Library name: DP_NG1
Column name in raw_counts.csv: DP_NG1


title: tyrR native 1

description: ChIP-Seq of native tyrR with C-terminal SPA tag

value: tyrR

value: Log-Phase


title: EWS502 cells with LacZ KO control - Day 4 - replicate 2

description:
Library name: EWS_LacZ_D4_R2
column name in day 4 knock out counts file

value: Ewing sarcoma

value: LacZ


title: CD11b, CD103 Double-positive, Naive, R3

description:
Library name: DP_N3
Column name in raw_counts.csv: DP_N3

value: Naive

value: 200 PBS by oral gavage


title: ttk native 2

description: ChIP-Seq of native ttk with C-terminal V5 tag

value: ttk


title: trpR native 2

description: ChIP-Seq of native trpR with C-terminal SPA tag

value: trpR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: CD11b, CD103 Double-positive, Naive, R2

description:
Library name: DP_N2
Column name in raw_counts.csv: DP_N2

value: Small intestine lamina propria

value: Intesitnal DC2


title: EWS502 cells with Chr2-2 KO control - Day 4 - replicate 3

description:
Library name: EWS_Chr2-2_D4_R3
column name in day 4 knock out counts file

value: day 4


title: ttk native 3

value: M9 Minimal with 0.4% glycerol


title: treR inducible 1

description: ChIP-Seq of inducible treR with C-terminal FLAG tag

value: treR

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: EWS502 cells with LacZ KO control - Day 4 - replicate 3

description:
Library name: EWS_LacZ_D4_R3
column name in day 4 knock out counts file


title: CD11b, CD103 Double-positive, Granuloma, R3

description:
Library name: DP_G3
Column name in raw_counts.csv: DP_G3

value: Granuloma

value: C57/Bl6 background

value: 200 L3 Hpb larvae by oral gavage


title: EWS502 cells with Chr2-2 KO control - Day 4 - replicate 2

description:
Library name: EWS_Chr2-2_D4_R2
column name in day 4 knock out counts file

value: Ewing sarcoma


title: EWS502 cells with LacZ KO control - Day 4 - replicate 1

description:
Library name: EWS_LacZ_D4_R1
column name in day 4 knock out counts file

value: LacZ


title: EWS502 cells with Chr2-2 KO control - Day 4 - replicate 1

description:
Library name: EWS_Chr2-2_D4_R1
column name in day 4 knock out counts file


title: torR native 1

description: ChIP-Seq of native torR with C-terminal V5 tag

value: torR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: Log-Phase


title: CD11b, CD103 Double-positive, Granuloma, R2

description:
Library name: DP_G2
Column name in raw_counts.csv: DP_G2


title: stpA native 2

description: ChIP-Seq of native stpA with C-terminal V5 tag

value: stpA


title: siKAT8 H4s, replicate 6, sequencing batch 3

city: London

first: Amy

last: Hicks

address: 30 Guilford Street

institute: UCL

description: Library name: N7_KAT8_S6

data_processing:
FASTQ files were processed using a Nextflow pipeline available here: github.com/Jbrenton191/RNAseq_splicing_pipeline.git. The final pipeline outputs for each sample are Salmon .quant files containing transcript-level abundance, which are imported and summarised into transcripts per million (TPM) matrices using the tximport package.
Assembly: Processed reads were mapped to the GRCh38 human reference genome, using gene annotations from Gencode v.41.
Supplementary files format and content: Processed data is provided in the format of TPM files, one for each cell type.

molecule: polyA RNA

growth_protocol: Cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, 11995-065) containing foetal bovine serum (FBS) (10%, Gibco, 10500-064) in a humidified incubator at 37◦C, 5%/95% CO2/air mixture

extract_protocol:
Total RNA was extracted from dry cell pellets following the manufacturer’s protocol for the Monarch Total RNA Miniprep Kit (New England Bioscience). All centrifugation steps were performed at 16,000 g and at room temperature, and the DNase 1 treatment step was completed. RNA was eluted in 30 μL water and concentration was measured using a NanoDrop 1 (Thermofisher). RNA extracted for sequencing was diluted to 50 ng/μL in water.
Bulk RNA-sequencing libraries were constructed and sequenced by the UCL Genomics Facility. Total RNA (500 ng) was used as input for the construction of complementary DNA (cDNA) libraries with the KAPA messenger RNA (mRNA) HyperPrep kit (Roche), as per manufacturer’s instructions. First, magnetic oligodT beads were used to capture mRNA, which was then fragmented using heat and magnesium. Random priming was used for first strand cDNA synthesis, followed by combined second strand synthesis and A-tailing. Adapter ligation was then performed, followed by strand-specific library amplification (further details of which can be found here: https://elabdoc-prod.roche.com). xGen Dual Index UMI Adapters (Integrated DNA Technologies, Inc.) were used to minimise read misassignment in later de-multiplexing of samples. Libraries were multiplexed on the NovaSeq SP v1.5 for paired-end 100 bp sequencing on the NovaSeq 6000 Sequencing System (Illumina), aiming for a mean read depth of 66 million paired-end reads per sample. Sequenced reads were de-multiplexed and BCL Convert software (Illumina) was used to generate FASTQ files.

treatment_protocol: Three types of short interfering RNA (siRNA) were purchased as pre-designed siGENOME SMARTpools and transfected as per the manufacturer’s instructions: non-targeting/SCR (D-001206-13), KAT8 (M-014800-00) and KANSL1 (M-031748-00). 40,000 SH-SY5Ys or 26,000 H4s were reverse transfected with 100nM siRNA and 0.5% v/v Dharmafect1. Following 72 hours incubation, culture media was removed, cells were washed in ice-cold phosphate-buffered saline (PBS) (Gibco, 14190-094) and either centrifuged for 5 minutes at 300 g, 4◦C and stored at -80◦ as dry pellets, or snap frozen within the plate at -80◦.

value: Astroglioma

value: KAT8 knockdown

value: KAT8 siRNA

tag: biological replicate

tag: sequencing batch


title: tyrR native 2

value: tyrR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: CD11b, CD103 Double-positive, Naive, R1

description:
Library name: DP_N1
Column name in raw_counts.csv: DP_N1

value: Small intestine lamina propria

value: Intesitnal DC2

value: Naive

value: 200 PBS by oral gavage


title: stpA native 1

value: M9 Minimal with 0.4% glycerol


title: srlR inducible 1

description: ChIP-Seq of inducible srlR with C-terminal FLAG tag

value: srlR

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: siKANSL1 H4s, replicate 6, sequencing batch 3

description: Library name: N7_KANSL1_S5

value: KANSL1 knockdown

value: KANSL1 siRNA


title: ttk native 1

description: ChIP-Seq of native ttk with C-terminal FLAG tag

value: ttk

value: Log-Phase


title: EWS502 cells with BCL6 KO guide 1 - Day 4 - replicate 1

description:
Library name: EWS_BCL6_G1_D4_R1
column name in day 4 knock out counts file

value: Ewing sarcoma

value: day 4


title: sxy inducible 1

description: ChIP-Seq of inducible sxy with C-terminal FLAG tag

value: sxy


title: CD11b, CD103 Double-positive, Granuloma, R1

description:
Library name: DP_G1
Column name in raw_counts.csv: DP_G1

value: Granuloma

value: C57/Bl6 background

value: 200 L3 Hpb larvae by oral gavage


title: CD11b+, Non-granuloma, R3

description:
Library name: CD11b_NG3
Column name in raw_counts.csv: CD11b_NG3

value: Small intestine lamina propria

value: Non-granuloma


title: sgrR inducible 1

description: ChIP-Seq of inducible sgrR with C-terminal FLAG tag

value: sgrR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: sgcR inducible 1

description: ChIP-Seq of inducible sgcR with C-terminal FLAG tag

value: sgcR

value: M9 Minimal with 0.4% glycerol


title: CD11b+, Non-granuloma, R2

description:
Library name: CD11b_NG2
Column name in raw_counts.csv: CD11b_NG2

value: Intesitnal DC2


title: trpR native 1

description: ChIP-Seq of native trpR with C-terminal SPA tag

value: trpR


title: sfsB inducible 1

description: ChIP-Seq of inducible sfsB with C-terminal FLAG tag

value: sfsB

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: siSCR H4s, replicate 6, sequencing batch 3

description: Library name: N7_SCR_S4

value: Astroglioma

value: Control

value: SCR siRNA


title: torR native 2

value: torR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: Log-Phase


title: siKAT8 H4s, replicate 5, sequencing batch 3

description: Library name: N6_KAT8_S3

value: KAT8 knockdown

value: KAT8 siRNA


title: rutR inducible 1

description: ChIP-Seq of inducible rutR with C-terminal FLAG tag

value: rutR

value: anti-FLAG mAb


title: CD11b+, Non-granuloma, R1

description:
Library name: CD11b_NG1
Column name in raw_counts.csv: CD11b_NG1

value: Small intestine lamina propria

value: Non-granuloma

value: C57/Bl6 background

value: 200 L3 Hpb larvae by oral gavage


title: rutR inducible 2

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: siKANSL1 H4s, replicate 5, sequencing batch 3

description: Library name: N6_KANSL1_S2

value: Astroglioma

value: KANSL1 knockdown

value: KANSL1 siRNA


title: siSCR H4s, replicate 5, sequencing batch 3

description: Library name: N6_SCR_S1

value: Control

value: SCR siRNA


title: racR inducible 3

description: ChIP-Seq of inducible racR with C-terminal FLAG tag

value: racR

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: CD11b+, Naive, R2

description:
Library name: CD11b_N2
Column name in raw_counts.csv: CD11b_N2

value: Intesitnal DC2

value: Naive

value: 200 PBS by oral gavage


title: racR inducible 1

value: anti-FLAG mAb

value: Log-Phase


title: racR inducible 2


title: purR native 3

description: ChIP-Seq of native purR with C-terminal V5 tag

value: purR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: siKAT8 H4s, replicate 4, sequencing batch 3

description: Library name: N15_KAT8_S18

value: KAT8 knockdown

value: KAT8 siRNA


title: CD11b+, Naive, R1

description:
Library name: CD11b_N1
Column name in raw_counts.csv: CD11b_N1

value: Small intestine lamina propria

value: C57/Bl6 background


title: purR native 2

value: M9 Minimal with 0.4% glycerol


title: siKANSL1 H4s, replicate 4, sequencing batch 3

description: Library name: N15_KANSL1_S17

value: Astroglioma

value: KANSL1 knockdown

value: KANSL1 siRNA


title: relE inducible 1

description: ChIP-Seq of inducible relE with C-terminal FLAG tag

value: relE

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: CD11b+, Granuloma, R3

description:
Library name: CD11b_G3
Column name in raw_counts.csv: CD11b_G3

value: Intesitnal DC2

value: Granuloma

value: 200 L3 Hpb larvae by oral gavage


title: pspF inducible 1

description: ChIP-Seq of inducible pspF with C-terminal FLAG tag

value: pspF

value: anti-FLAG mAb

value: Log-Phase


title: purR native 1

value: purR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: siSCR H4s, replicate 4, sequencing batch 3

description: Library name: N15_SCR_S16

value: Control

value: SCR siRNA


title: pspF native 1

description: ChIP-Seq of native pspF with C-terminal SPA tag

value: M9 Minimal with 0.4% glycerol


title: CD11b+, Granuloma, R2

description:
Library name: CD11b_G2
Column name in raw_counts.csv: CD11b_G2

value: Small intestine lamina propria

value: C57/Bl6 background


title: pepA inducible 1

description: ChIP-Seq of inducible pepA with C-terminal FLAG tag

value: pepA


title: CD11b+, Granuloma, R1

description:
Library name: CD11b_G1
Column name in raw_counts.csv: CD11b_G1


title: rstA inducible 1

description: ChIP-Seq of inducible rstA with C-terminal FLAG tag

value: rstA

value: Sigma/Cat. No. F1804


title: pdhR inducible 3

description: ChIP-Seq of inducible pdhR with C-terminal FLAG tag

value: pdhR

value: LB

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: pepA native 1

description: ChIP-Seq of native pepA with C-terminal V5 tag


title: siKAT8 H4s, replicate 3, sequencing batch 3

description: Library name: N13_KAT8_S15

value: Astroglioma

value: KAT8 knockdown

value: KAT8 siRNA


title: siKANSL1 H4s, replicate 3, sequencing batch 3

description: Library name: N13_KANSL1_S14

value: KANSL1 knockdown

value: KANSL1 siRNA


title: CD11b+, Naive, R3

description:
Library name: CD11b_N3
Column name in raw_counts.csv: CD11b_N3

value: Intesitnal DC2

value: Naive

value: 200 PBS by oral gavage


title: siSCR H4s, replicate 3, sequencing batch 3

description: Library name: N13_SCR_S13

value: Control

value: SCR siRNA


title: pdhR inducible 2

value: anti-FLAG mAb

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: pdhR inducible 1

value: Sigma/Cat. No. F1804


title: H3K9ME3 KO HT rep2

city: NEW BRUNSWICK

first: Xiaosheng

last: Tan

state: NJ

address: 89 French St

institute: RUTGERS

description:
Library name: H3K9ME3 KO HT rep2
H3K9ME3 KO HT rep2

data_processing:
Adapter sequences and low-quality reads in the raw Cut&Tag data were filtered using BBDuk
The filtered reads were then aligned to the mouse mm10 reference genome using Bowtie2
Duplicate reads were removed with the MarkDuplicates function in GATK
Coverage (bigWig) files were generated from the resulting BAM files using the bamCoverage tool in deepTools
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

source_name: Spleen

extract_protocol:
Briefly, after harvesting, CD25+ enriched T cells were counted and divided into groups of 200,000 cells each. The cells were centrifuged at 600 g for 5 minutes at room temperature. Each sample was resuspended in 100 μl of pre-cooled NE Buffer, mixed gently, and incubated on ice. Following incubation, the cells were centrifuged again at 600 g for 5 minutes at room temperature, and the pellets were resuspended in 100 μl of wash buffer.
Next, 10 μl of Concanavalin A-coated magnetic beads, pre-activated at room temperature, were added to each sample and incubated for 10 minutes. The unbound supernatant was removed, followed by an overnight reaction between the H3K9me3 group sample and anti-H3K9me3 antibodies (1:50, Proteintech), as well as between the SETDB1 group sample and anti-SETDB1 antibodies (2 μg, Proteintech) in Antibody Buffer at 4°C. After washing, the bound antibodies were reacted with secondary antibodies and then incubated with pA/G-Tnp Pro (0.04 μM). Next, the samples were fragmented with TTBL, followed by the addition of 10% SDS and DNA spike-in to each sample. To extract the genomic DNA, DNA Extract Beads Pro were activated and added to each sample. The extracted DNA fragments were amplified by PCR with indexing primers (Vazyme, TD202), and the library was purified using VAHTS DNA Clean Beads (Vazyme, N411).

value: Spleen

value: T cell

value: KO

value: HEART TRANSPLANT


title: pdhR native 2

description: ChIP-Seq of native pdhR with C-terminal SPA tag

value: pdhR

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: H3K9ME3 KO HT rep1

description:
Library name: H3K9ME3 KO HT rep1
H3K9ME3 KO HT rep1


title: ybhD inducible 1

description: ChIP-Seq of inducible ybhD with C-terminal FLAG tag

value: ybhD

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: pdhR native 1


title: siKAT8 H4s, replicate 2, sequencing batch 3

description: Library name: N12_KAT8_S12

value: Astroglioma

value: KAT8 knockdown

value: KAT8 siRNA


title: siKANSL1 H4s, replicate 2, sequencing batch 3

description: Library name: N12_KANSL1_S11

value: KANSL1 knockdown

value: KANSL1 siRNA


title: ompR inducible 1

description: ChIP-Seq of inducible ompR with C-terminal FLAG tag

value: ompR

value: anti-FLAG mAb


title: H3K9ME3 KO control rep2

description:
Library name: H3K9ME3 KO control rep2
H3K9ME3 KO control rep2

value: NO TREATMENT


title: ompR native 1

description: ChIP-Seq of native ompR with C-terminal FLAG tag

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: H3K9ME3 KO control rep1

description:
Library name: H3K9ME3 KO control rep1
H3K9ME3 KO control rep1

value: Spleen

value: T cell

value: KO


title: nsrR native 1

description: ChIP-Seq of native nsrR with C-terminal SPA tag

value: nsrR


title: siSCR H4s, replicate 2, sequencing batch 3

description: Library name: N12_SCR_S10

value: Control

value: SCR siRNA


title: H3K9ME3 WT HT rep2

description:
Library name: H3K9ME3 WT HT rep2
H3K9ME3 WT HT rep2

value: WT

value: HEART TRANSPLANT


title: siKAT8 H4s, replicate 1, sequencing batch 3

description: Library name: N11_KAT8_S9

value: Astroglioma

value: KAT8 knockdown

value: KAT8 siRNA


title: nrdR native 1

description: ChIP-Seq of native nrdR with C-terminal V5 tag

value: nrdR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: nrdR native 2


title: nhaR inducible 2

description: ChIP-Seq of inducible nhaR with C-terminal FLAG tag

value: nhaR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: siKANSL1 H4s, replicate 1, sequencing batch 3

description: Library name: N11_KANSL1_S8

value: KANSL1 knockdown

value: KANSL1 siRNA


title: H3K9ME3 WT HT rep1

description:
Library name: H3K9ME3 WT HT rep1
H3K9ME3 WT HT rep1

value: Spleen

value: T cell


title: nhaR inducible 1

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: nanR inducible 1

description: ChIP-Seq of inducible nanR with C-terminal FLAG tag

value: nanR


title: siSCR H4s, replicate 1, sequencing batch 3

description: Library name: N11_SCR_S7

value: Astroglioma

value: Control

value: SCR siRNA


title: H3K9ME3 WT control rep1

description:
Library name: H3K9ME3 WT control rep1
H3K9ME3 WT control rep1

value: WT

value: NO TREATMENT


title: nac inducible 6

description: ChIP-Seq of inducible nac with C-terminal FLAG tag

value: nac

value: LB


title: H3K9ME3 WT control rep2

description:
Library name: H3K9ME3 WT control rep2
H3K9ME3 WT control rep2


title: nagC native 1

description: ChIP-Seq of native nagC with C-terminal SPA tag

value: nagC

value: anti-FLAG mAb


title: siKAT8 SH-SY5Ys, replicate 8, sequencing batch 2

description: Library name: 8KAT8_S12

value: Neuroblastoma

value: KAT8 knockdown

value: KAT8 siRNA


title: nac inducible 7

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: paaX native 1

description: ChIP-Seq of native paaX with C-terminal V5 tag

value: paaX

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol


title: nagC native 2

value: Log-Phase


title: siKANSL1 SH-SY5Ys, replicate 8, sequencing batch 2

description: Library name: 8KANSL1_S11

value: KANSL1 knockdown

value: KANSL1 siRNA


title: nac inducible 5


title: SETDB1 KO HT rep1

description:
Library name: SETDB1 KO HT rep1
SETDB1 KO HT rep1

value: Spleen

value: T cell

value: KO

value: HEART TRANSPLANT


title: SETDB1 KO HT rep2

description:
Library name: SETDB1 KO HT rep2
SETDB1 KO HT rep2


title: nac inducible 4

value: nac

value: anti-FLAG mAb

value: LB


title: siSCR SH-SY5Ys, replicate 8, sequencing batch 2

description: Library name: 8SCR_S10

value: Neuroblastoma

value: Control

value: SCR siRNA


title: nac inducible 3

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: nac inducible 2


title: nac inducible 1


title: siKAT8 SH-SY5Ys, replicate 7, sequencing batch 2

description: Library name: 7KAT8_S9

value: KAT8 knockdown

value: KAT8 siRNA


title: SETDB1 KO control rep2

description:
Library name: SETDB1 KO control rep2
SETDB1 KO control rep2

value: NO TREATMENT


title: mraZ native 2

description: ChIP-Seq of native mraZ with C-terminal V5 tag

value: mraZ

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: siKANSL1 SH-SY5Ys, replicate 7, sequencing batch 2

description: Library name: 7KANSL1_S8

value: KANSL1 knockdown

value: KANSL1 siRNA


title: SETDB1 WT HT rep2

description:
Library name: SETDB1 WT HT rep2
SETDB1 WT HT rep2

value: Spleen

value: T cell

value: WT

value: HEART TRANSPLANT


title: mraZ native 1


title: modE inducible 1

description: ChIP-Seq of inducible modE with C-terminal FLAG tag

value: modE

value: anti-FLAG mAb


title: modE native 1

description: ChIP-Seq of native modE with C-terminal SPA tag

value: Sigma/Cat. No. F1804


title: SETDB1 WT HT rep1

description:
Library name: SETDB1 WT HT rep1
SETDB1 WT HT rep1


title: SETDB1 KO control rep1

description:
Library name: SETDB1 KO control rep1
SETDB1 KO control rep1

value: KO


title: mngR inducible 1

description: ChIP-Seq of inducible mngR with C-terminal FLAG tag

value: mngR

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: mngR native 2

description: ChIP-Seq of native mngR with C-terminal V5 tag


title: mlrA inducible 1

description: ChIP-Seq of inducible mlrA with C-terminal FLAG tag

value: mlrA


title: siKAT8 SH-SY5Ys, replicate 6, sequencing batch 2

description: Library name: 6KAT8_S6

value: Neuroblastoma

value: KAT8 knockdown

value: KAT8 siRNA


title: siKANSL1 SH-SY5Ys, replicate 6, sequencing batch 2

description: Library name: 6KANSL1_S5


title: SETDB1 WT control rep1

description:
Library name: SETDB1 WT control rep1
SETDB1 WT control rep1

value: NO TREATMENT


title: mngR native 1

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: mlrA native 1

description: ChIP-Seq of native mlrA with C-terminal V5 tag


title: siSCR SH-SY5Ys, replicate 6, sequencing batch 2

description: Library name: 6SCR_S4

value: Control

value: SCR siRNA


title: SETDB1 WT control rep2

description:
Library name: SETDB1 WT control rep2
SETDB1 WT control rep2

value: Spleen

value: T cell

value: WT


title: Combine 6

description:
Library name: Combine 6
P_combine_7

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: mm39
Supplementary files format and content: text

source_name: Peritoneum

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer's instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/23≥ 2.0, RIN≥ 6.5, 28S:18S ≥ 1.0, > 1 μ g) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for15 PCR cycles.

value: Peritoneum

value: propionate and butyrate


title: siKAT8 SH-SY5Ys, replicate 5, sequencing batch 2

description: Library name: 5KAT8_S3


title: mraZ inducible 1

description: ChIP-Seq of inducible mraZ with C-terminal FLAG tag

value: mraZ

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: mhpR native 2

description: ChIP-Seq of native mhpR with C-terminal V5 tag

value: mhpR


title: mhpR native 1


title: siKANSL1 SH-SY5Ys, replicate 5, sequencing batch 2

description: Library name: 5KANSL1_S2

value: Neuroblastoma

value: KANSL1 knockdown

value: KANSL1 siRNA


title: metR native 3

description: ChIP-Seq of native metR with C-terminal SPA tag

value: metR

value: M9 Minimal with 0.4% glycerol


title: metR native 2

value: Log-Phase

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: siSCR SH-SY5Ys, replicate 5, sequencing batch 2

description: Library name: 5SCR_S1

value: Control

value: SCR siRNA


title: siSCR SH-SY5Ys, replicate 7, sequencing batch 2

description: Library name: 7SCR_S7


title: Combine 4

description:
Library name: Combine 4
P_combine_5


title: melR inducible 1

description: ChIP-Seq of inducible melR with C-terminal FLAG tag

value: melR


title: Combine 3

description:
Library name: Combine 3
P_combine_3

value: Peritoneum


title: mazE native 1

description: ChIP-Seq of native mazE with C-terminal SPA tag

value: mazE


title: Combine 2

description:
Library name: Combine 2
P_combine_2

value: propionate and butyrate


title: marA inducible 1

description: ChIP-Seq of inducible marA with C-terminal FLAG tag

value: marA

value: anti-FLAG mAb


title: mhpR inducible 1

description: ChIP-Seq of inducible mhpR with C-terminal FLAG tag

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: siKAT8 SH-SY5Ys, replicate 4, sequencing batch 1

description: Library name: 4KAT8_S12

value: Neuroblastoma

value: KAT8 knockdown

value: KAT8 siRNA


title: siSCR SH-SY5Ys, replicate 4, sequencing batch 1

description: Library name: 4SCR_S10


title: lexA inducible 3

description: ChIP-Seq of inducible lexA with C-terminal FLAG tag

value: lexA

value: Arabinose added to 0.2% final volume for TF induction 30 minutes prior to crosslink


title: lldR inducible 1

description: ChIP-Seq of inducible lldR with C-terminal FLAG tag

value: lldR

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: marA native 1

description: ChIP-Seq of native marA with C-terminal FLAG tag

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: But 6

description:
Library name: But 6
P_but_8

value: butyrate


title: siKAT8 SH-SY5Ys, replicate 3, sequencing batch 1

description: Library name: 3KAT8_S9


title: Combine 5

description:
Library name: Combine 5
P_combine_6

value: Peritoneum


title: lexA inducible 2


title: But 5

description:
Library name: But 5
P_but_7


title: lexA inducible 1

value: Arabinose added to 0.2% final volume for TF induction 15 minutes prior to crosslink


title: lexA native 1

description: ChIP-Seq of native lexA with C-terminal FLAG tag


title: lacI inducible 1

description: ChIP-Seq of inducible lacI with C-terminal FLAG tag

value: lacI


title: siSCR SH-SY5Ys, replicate 3, sequencing batch 1

description: Library name: 3SCR_S7

value: Control

value: SCR siRNA


title: metR native 1

value: metR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: siKAT8 SH-SY5Ys, replicate 2, sequencing batch 1

description: Library name: 2KAT8_S6

value: Neuroblastoma

value: KAT8 knockdown


title: But 4

description:
Library name: But 4
P_but_6


title: lacI native 1

description: ChIP-Seq of native lacI with C-terminal V5 tag

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: But 3

description:
Library name: But 3
P_but_5


title: siKANSL1 SH-SY5Ys, replicate 2, sequencing batch 1

description: Library name: 2KANSL1_S5

value: KANSL1 knockdown

value: KANSL1 siRNA


title: matA inducible 1

description: ChIP-Seq of inducible matA with C-terminal FLAG tag

value: matA

value: M9 Minimal with 0.4% glycerol

value: Log-Phase

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: Combine 1

description:
Library name: Combine 1
P_combine_1

value: Peritoneum

value: propionate and butyrate


title: kdgR native 1

description: ChIP-Seq of native kdgR with C-terminal V5 tag

value: kdgR


title: kdgR native 2


title: siKANSL1 SH-SY5Ys, replicate 4, sequencing batch 1

description: Library name: 4KANSL1_S11


title: But 2

description:
Library name: But 2
P_but_3

value: butyrate


title: iscR native 2

description: ChIP-Seq of native iscR with C-terminal V5 tag

value: iscR


title: siKAT8 SH-SY5Ys, replicate 1, sequencing batch 1

description: Library name: 1KAT8_S3

value: KAT8 siRNA


title: iscR native 1


title: Pro 6

description:
Library name: Pro 6
P_pro_8

value: propionate


title: iclR native 2

description: ChIP-Seq of native iclR with C-terminal V5 tag

value: iclR


title: iclR native 1


title: hipB inducible 1

description: ChIP-Seq of inducible hipB with C-terminal FLAG tag

value: hipB

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: hipA inducible 2

description: ChIP-Seq of inducible hipA with C-terminal FLAG tag

value: hipA


title: hipA inducible 1


title: lacI native 2

value: lacI

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: Pro 4

description:
Library name: Pro 4
P_pro_6


title: Pro 3

description:
Library name: Pro 3
P_pro_5


title: kdgR inducible 1

description: ChIP-Seq of inducible kdgR with C-terminal FLAG tag

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: hipA native 1

description: ChIP-Seq of native hipA with C-terminal V5 tag


title: hcaR inducible 1

description: ChIP-Seq of inducible hcaR with C-terminal FLAG tag

value: hcaR

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: glpR native 2

description: ChIP-Seq of native glpR with C-terminal V5 tag

value: glpR


title: hdfR inducible 1

description: ChIP-Seq of inducible hdfR with C-terminal FLAG tag

value: hdfR


title: Pro 1

description:
Library name: Pro 1
P_pro_1

value: Peritoneum


title: siSCR SH-SY5Ys, replicate 2, sequencing batch 1

description: Library name: 2SCR_S4

value: Neuroblastoma

value: Control

value: SCR siRNA


title: glnG inducible 4

description: ChIP-Seq of inducible glnG with C-terminal FLAG tag

value: glnG


title: But 1

description:
Library name: But 1
P_but_2

value: butyrate


title: glpR native 1


title: glnG inducible 3

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: glnG inducible 2

value: LB


title: siSCR SH-SY5Ys, replicate 1, sequencing batch 1

description: Library name: 1SCR_S1


title: glnG inducible 1


title: Pro 5

description:
Library name: Pro 5
P_pro_7

value: propionate


title: gcvR inducible 1

description: ChIP-Seq of inducible gcvR with C-terminal FLAG tag

value: gcvR


title: P5 Colon Normal Adjacent Tissue

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

data_processing:
Space Ranger v3.0 (10x Genomics) was used to map FASTQ files to the human reference, detect the tissue section, align the sequencing data to the microscope image and the CytAssist image, and output gene-barcode matrices for further analysis.
Assembly: GRCh38
Supplementary files format and content: image.tif: CytAssist Image
Supplementary files format and content: alignment_file.json: Manual alignment file
Supplementary files format and content: tissue_lowres_image.png: Downsampled version of the original, full-resolution image
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: scalefactors_json.json: Relative scales of the user-supplied image, the images in the spatial outs and the Visium array
Supplementary files format and content: filtered_feature_bc_matrix.h5: UMI count matrix h5 format
Supplementary files format and content: probe_set.csv: Used probeset
Library strategy: Spatial Transcriptomics

source_name: Colon Normal Adjacent

extract_protocol:
5 µm sections were taken from the FFPE tissue blocks with a microtome (Epredia HM355S). Sections were adjacent or near-adjacent (within 5-10 µm of each other). Sectioning followed the Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide (CG000518, Rev C).
5 µm FFPE serial sections were placed on standard glass slides and H&E-stained following the Demonstrated Protocol Visium CytAssist Spatial Gene Expression for FFPE – Deparaffinization, H&E Staining, Imaging & Decrosslinking (CG000520). Imaging was performed on the slide scanner Olympus V200 at 20x magnification. The CytAssist instrument was used to facilitate the transfer of transcriptomic probes from the standard glass slide to the Visium CytAssist Spatial Gene Expression Slide, v2, 11 mm capture area. Probe hybridization, probe ligation, release, extension, pre-amplification, and library preparation followed the Visium CytAssist Spatial Gene Expression Reagent Kits User Guide (CG000495). Sequencing was performed on the NovaSeq 6000 (28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2).

value: Colon Normal Adjacent


title: Control 5

description:
Library name: Control 5
P_control_6


title: gcvR native 1

description: ChIP-Seq of native gcvR with C-terminal V5 tag

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: P3 Colon Normal Adjacent Tissue


title: Control 4

description:
Library name: Control 4
P_control_5


title: gcvA native 2

description: ChIP-Seq of native gcvA with C-terminal V5 tag

value: gcvA


title: gcvA native 3


title: Control 3

description:
Library name: Control 3
P_control_4

value: Peritoneum


title: Pro 2

description:
Library name: Pro 2
P_pro_4


title: gcvA native 1


title: P2 Human Colon Cancer

source_name: Colon Cancer

value: Colon Cancer


title: galS inducible 1

description: ChIP-Seq of inducible galS with C-terminal FLAG tag

value: galS

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: Human Colon Cancer DTCs (Rep9), VDJ

data_processing:
We used Cell Ranger v8.0.0 (10x Genomics) to process FASTQ data for both gene expression and TCR libraries. The cellranger count pipeline was used to align 5' reads to the reference genome (GRCh38) and output gene-barcode matrices that could be used to cluster cells and run differential gene expression. We used the cellranger vdj pipeline to assemble TCR sequences and group cells into clonotypes based on their CDR3 sequences.
Assembly: GRCh38
Supplementary files format and content: count_filtered_feature_bc_matrix.h5: UMI count matrix in h5 format
Supplementary files format and content: clonotypes.csv: High-level descriptions of each clonotype
Supplementary files format and content: consensus.fasta: The consensus sequence of each assembled contig
Supplementary files format and content: filtered_contig_annotations.csv: Annotations of each high-confidence cell barcode
Supplementary files format and content: consensus_annotations.csv: High-level and detailed annotations of each clonotype consensus sequence

extract_protocol:
We used DTCs that were obtained from the same tumor samples as our FFPE blocks to obtain TCR profiling data on three samples. Cryovials were thawed in a water bath for 2–3 minutes at 37°C with gentle shaking. Thawed cells were transferred into a 15 mL centrifuge tube containing 9 mL of pre-warmed complete growth medium (RPMI + 10% FBS) and the centrifuged at 150 rcf for 10 minutes at room temperature using a swinging bucket rotor. All but ~200 μL of the supernatant was removed and then the pellet was resuspended in this remaining 200 μL, followed by the addition of 200 μL of complete media. Cells were strained using a 40 μm Flowmi cell strained and transferred to a 1.5 mL Eppendorf tube before being counted on a Cellaca MX using AOPI. 5 μL of CD3 BV510 stain and 2.5uL of CD45 APC was added to the cell suspension and it was incubated on ice for 30 minutes in the dark. Cells were then centrifuged at 300 rcf for 10 minutes at 4°C. The supernatant was removed without disturbing the cell pellet and 1 mL of chilled PBS + 10% FBS added to the tube with gentle mixing. Cells were centrifuged at 300 rcf for 10 minutes at 4°C and the pellet resuspended in 250 μL of chilled PBS + 10% FBS. Cells were then sorted on a SONY MA900 cell sorter. Live single DTCs were gated using forward scatter (relative size) and back scatter (relative granularity) and 7AAD for live/dead cell discrimination. CD45 and CD3 were used to identify T cells. Sorts were performed on a 100 µm nozzle at 20 psi sheath pressure. The sample pressure was set to low-medium with a consistent event rate maintained throughout the sort. Cells were sorted into 30 μL 10% FBS in PBS, in a pre-coated 1.5 mL Eppendorf tube.
Sorted cells were directly loaded onto the 10x chip for generation of 5′ gene expression and TCR libraries following the Chromium Next GEM Single Cell 5′ Reagent Kits v2 (Dual Index) User Guide (CG000331) on the Chromium X instrument.

value: Dissociated Tumor Cells

value: VDJ


title: galS native 1

description: ChIP-Seq of native galS with C-terminal V5 tag


title: galR inducible 1

description: ChIP-Seq of inducible galR with C-terminal FLAG tag

value: galR

value: anti-FLAG mAb


title: Human Colon Cancer DTCs (Rep9), GEX

value: Gene Expression


title: Control 1

description:
Library name: Control 1
P_control_1


title: gadX inducible 1

description: ChIP-Seq of inducible gadX with C-terminal FLAG tag

value: gadX

value: Sigma/Cat. No. F1804


title: Control 6

description:
Library name: Control 6
P_control_7


title: CD8_Combine3

description:
Library name: CD8_Combine3
CD8_combine_3

source_name: CD8+ Tcells

value: CD8+ Tcells

value: propionate and butyrate


title: gadW native 2

description: ChIP-Seq of native gadW with C-terminal V5 tag

value: gadW

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: Human Colon Cancer DTCs (Rep8), VDJ


title: gadW native 1

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: Human Colon Cancer DTCs (Rep8), GEX

value: Colon Cancer


title: CD8_Combine2

description:
Library name: CD8_Combine2
CD8_combine_2


title: fimZ inducible 1

description: ChIP-Seq of inducible fimZ with C-terminal FLAG tag

value: fimZ


title: fucR inducible 1

description: ChIP-Seq of inducible fucR with C-terminal FLAG tag

value: fucR

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: fabR native 2

description: ChIP-Seq of native fabR with C-terminal V5 tag

value: fabR


title: CD8_Combine1

description:
Library name: CD8_Combine1
CD8_combine_1


title: fabR native 1


title: exuR native 2

description: ChIP-Seq of native exuR with C-terminal V5 tag

value: exuR


title: Human Colon Cancer DTCs (Rep6), GEX

value: Dissociated Tumor Cells


title: CD8_Ctrl4

description:
Library name: CD8_Ctrl4
CD8_control_4


title: Human Colon Cancer DTCs (Rep5), VDJ

value: VDJ


title: envY inducible 1

description: ChIP-Seq of inducible envY with C-terminal FLAG tag

value: envY

value: anti-FLAG mAb


title: galR native 1

description: ChIP-Seq of native galR with C-terminal FLAG tag

value: galR

value: Sigma/Cat. No. F1804


title: Human Colon Cancer DTCs (Rep6), VDJ


title: CD8_Ctrl3

description:
Library name: CD8_Ctrl3
CD8_control_3

value: CD8+ Tcells


title: Human Colon Cancer DTCs (Rep5), GEX

value: Gene Expression


title: ebgR native 2

description: ChIP-Seq of native ebgR with C-terminal V5 tag

value: ebgR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: Control 2

description:
Library name: Control 2
P_control_3

value: Peritoneum


title: Human Colon Cancer DTCs (Rep4), VDJ

value: Colon Cancer


title: exuR native 1

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: CD8_Ctrl2

description:
Library name: CD8_Ctrl2
CD8_control_2


title: CD8_Ctrl1

description:
Library name: CD8_Ctrl1
CD8_control_1


title: dinJ inducible 1

description: ChIP-Seq of inducible dinJ with C-terminal FLAG tag

value: dinJ

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: dinJ native 2

description: ChIP-Seq of native dinJ with C-terminal V5 tag


title: Human Colon Cancer DTCs (Rep4), GEX

value: Dissociated Tumor Cells


title: dinJ native 1


title: dicC inducible 4

description: ChIP-Seq of inducible dicC with C-terminal FLAG tag

value: dicC


title: Human Colon Cancer DTCs (Rep3), VDJ

value: VDJ


title: dicC inducible 3

value: anti-FLAG mAb

value: LB


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 7 hours, biol rep 2

city: Gif-sur-Yvette

first: Mathieu

last: Rougemaille

address: 1 avenue de la Terrasse

country: France

institute: Institute for Integrative Biology of the Cell

data_processing:
Demultiplexing was performed with bcl2fastq v2.20 and adapters were trimmed with fastp v0.23.1.
Reads were aligned using STAR v2.6.1d (--outSAMtype BAM SortedByCoordinate \ --quantMode GeneCounts \ --outSAMunmapped Within \ --outSAMattributes Standard \)
Read count was performed using featureCounts from subread v2.0.6
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa.gz and Schizosaccharomyces_pombe_all_chromosomes.gff3.gz from Pombase
Supplementary files format and content: tab-delimited text files include raw counts for each Sample.

organism: Schizosaccharomyces pombe

source_name: haploid, h- cells

growth_protocol: Schizosaccharomyces pombe cells carrying the pat1-L95G allele were grown in EMM at 30°C prior to over-night (15 to 16h) incubation in EMM lacking nitrogen (EMM-N) to synchronize cells in G1. The following day, cultures were supplemented with 50 mg/L L-leucine, 500 µg/mL NH4Cl and 25 µM 3-MB-PP1 to induce meiosis and aliquots were harvested every hour for up to 8h.

extract_protocol:
Total RNAs were extracted using the hot acid phenol method.
PolyA RNAs were enriched from total RNAs using oligodT-attached magnetic beads and mRNA librairies were constructed using the Novogene NGS RNA Library Prep Set (PT042).

treatment_protocol: Meiosis was induced by adding 25 µM 3-MB-PP1 to cell cultures for up to 8 hours.

value: haploid, h- cells

value: meiosis induction, 25 uM 3-MB-PP1

value: 7 hours


title: Human Colon Cancer DTCs (Rep3), GEX

value: Gene Expression


title: dicC inducible 1

value: Sigma/Cat. No. F1804


title: dicC inducible 2


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 6 hours, biol rep 2

value: 6 hours


title: ebgR inducible 1

description: ChIP-Seq of inducible ebgR with C-terminal FLAG tag

value: ebgR


title: Human Colon Cancer DTCs (Rep2), VDJ

value: Colon Cancer


title: dicA inducible 1

description: ChIP-Seq of inducible dicA with C-terminal FLAG tag

value: dicA

value: M9 Minimal with 0.4% glycerol


title: ebgR native 1

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: Log-Phase


title: dgsA native 2

description: ChIP-Seq of native dgsA with C-terminal V5 tag

value: dgsA


title: dgsA native 1


title: dicA native 1

description: ChIP-Seq of native dicA with C-terminal FLAG tag

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: Human Colon Cancer DTCs (Rep1), VDJ

value: Dissociated Tumor Cells

value: VDJ


title: Human Colon Cancer DTCs (Rep2), GEX


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 4 hours, biol rep 2

value: haploid, h- cells

value: 4 hours


title: dgoR inducible 1

description: ChIP-Seq of inducible dgoR with C-terminal FLAG tag

value: dgoR

value: anti-FLAG mAb

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 8 hours, biol rep 2

value: meiosis induction, 25 uM 3-MB-PP1

value: 8 hours


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 5 hours, biol rep 2

value: 5 hours


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 2 hours, biol rep 2

value: 2 hours


title: dgoR native 2

description: ChIP-Seq of native dgoR with C-terminal V5 tag

value: M9 Minimal with 0.4% glycerol


title: deoR inducible 2

description: ChIP-Seq of inducible deoR with C-terminal FLAG tag

value: deoR

value: Sigma/Cat. No. F1804


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 3 hours, biol rep 2

value: 3 hours


title: Human Colon Cancer DTCs (Rep1), GEX

value: Colon Cancer

value: Gene Expression


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 3 Library 4)

data_processing:
Cell Ranger v8.0 (10x Genomics) was used to align reads in FASTQ format to the human probe set and reference genome (GRCh38), producing feature-barcode matrices for analysis. Each GEM well was processed using a separate instance of the cellranger multi pipeline. Matrices across all eight tissue blocks were aggregated with the cellranger aggr pipeline.
Assembly: GRCh38
Supplementary files format and content: UMI count matrix in H5 file format

extract_protocol:
Cells were dissociated from 50 µm FFPE curls from CRC tissue samples (n=5 patients) and a subset of paired normal adjacent tissues (n = 3 patients) using the Demonstrated Protocol for Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling (CG000632)
Flex library preparation followed the Chromium Fixed RNA Profiling for Multiplexed Samples User Guide (CG000527, RevD). Each sample was hybridized with a unique probe barcode in an individual reaction. After hybridization, samples were multiplexed in equal cell proportions, washed, and processed collectively, across multiple GEM lanes as technical replicates, using the Chromium X instrument.

value: Colon Normal Adjacent

tag: samples (multiplexed)

value: P5NAT BC003 Pool3 Library4

value: P3NAT BC004 Pool3 Library4


title: deoR inducible 3

value: Log-Phase


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 1 hour, biol rep 2

value: haploid, h- cells

value: 1 hour


title: deoR inducible 1

value: anti-FLAG mAb

value: LB

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: cysB native 3

description: ChIP-Seq of native cysB with C-terminal FLAG tag

value: cysB

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 3 Library 3)

value: P5NAT BC003 Pool3 Library3

value: P3NAT BC004 Pool3 Library3


title: cysB native 1

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: snR107kloopmut nitrogen-starved cells, EMM-N, biol rep 2

value: over-night nitrogen starvation


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 3 Library 2)

value: P5NAT BC003 Pool3 Library2

value: P3NAT BC004 Pool3 Library2


title: cynR inducible 1

description: ChIP-Seq of inducible cynR with C-terminal FLAG tag

value: cynR


title: cysB native 2


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 3 Library 1)

value: Colon Normal Adjacent

value: P5NAT BC003 Pool3 Library1

value: P3NAT BC004 Pool3 Library1


title: vegetative snR107kloopmut cells, EMM, biol rep 2

value: haploid, h- cells

value: none, vegetative growth


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 8 hours, biol rep 1

value: meiosis induction, 25 uM 3-MB-PP1

value: 8 hours


title: csiR inducible 1

description: ChIP-Seq of inducible csiR with C-terminal FLAG tag

value: csiR

value: anti-FLAG mAb

value: Log-Phase

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: dgoR native 1

value: dgoR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: csgD inducible 4

description: ChIP-Seq of inducible csgD with C-terminal FLAG tag

value: csgD

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 2 Library 4)

value: Colon Cancer

value: P1CRC BC001 Pool2 Library4

value: P3CRC BC002 Pool2 Library4

value: P5CRC BC003 Pool2 Library4

value: P2NAT BC004 Pool2 Library4


title: csgD inducible 3


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 7 hours, biol rep 1

value: haploid, h- cells

value: meiosis induction, 25 uM 3-MB-PP1

value: 7 hours


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 2 Library 3)

source_name: Colon Cancer and Colon Normal Adjacent

value: Colon Cancer and Colon Normal Adjacent

value: P1CRC BC001 Pool2 Library3

value: P3CRC BC002 Pool2 Library3

value: P5CRC BC003 Pool2 Library3

value: P2NAT BC004 Pool2 Library3


title: csgD inducible 1

value: anti-FLAG mAb

value: Log-Phase

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: csgD inducible 2

value: csgD

value: Sigma/Cat. No. F1804

value: LB


title: cpxR native 2

description: ChIP-Seq of native cpxR with C-terminal SPA tag

value: cpxR

value: M9 Minimal with 0.4% glycerol


title: cbl inducible 1

description: ChIP-Seq of inducible cbl with C-terminal FLAG tag

value: cbl


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 2 Library 2)

value: P1CRC BC001 Pool2 Library2

value: P3CRC BC002 Pool2 Library2

value: P5CRC BC003 Pool2 Library2

value: P2NAT BC004 Pool2 Library2


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 4 hours, biol rep 1

value: haploid, h- cells

value: meiosis induction, 25 uM 3-MB-PP1

value: 4 hours


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 6 hours, biol rep 1

value: 6 hours


title: cadC inducible 2

description: ChIP-Seq of inducible cadC with C-terminal FLAG tag

value: cadC

value: anti-FLAG mAb


title: cadC inducible 1

value: Log-Phase

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: cbl native 1

description: ChIP-Seq of native cbl with C-terminal SPA tag

value: Sigma/Cat. No. F1804


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 5 hours, biol rep 1

value: 5 hours


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 1 Library 4)

value: Colon Cancer

value: P2CRC BC001 Pool1 Library4

value: P4CRC BC002 Pool1 Library4


title: betI inducible 1

description: ChIP-Seq of inducible betI with C-terminal FLAG tag

value: betI

value: M9 Minimal with 0.4% glycerol


title: cusR inducible 1

description: ChIP-Seq of inducible cusR with C-terminal FLAG tag

value: cusR


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 2 Library 1)

value: Colon Cancer and Colon Normal Adjacent

value: P1CRC BC001 Pool2 Library1

value: P3CRC BC002 Pool2 Library1

value: P5CRC BC003 Pool2 Library1

value: P2NAT BC004 Pool2 Library1


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 3 hours, biol rep 1

value: haploid, h- cells

value: meiosis induction, 25 uM 3-MB-PP1

value: 3 hours


title: betI native 1

description: ChIP-Seq of native betI with C-terminal V5 tag

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: Log-Phase


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 1 Library 3)

value: Colon Cancer

value: P2CRC BC001 Pool1 Library3

value: P4CRC BC002 Pool1 Library3


title: basR inducible 1

description: ChIP-Seq of inducible basR with C-terminal FLAG tag

value: basR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 2 hours, biol rep 1

value: 2 hours


title: betI native 2

value: betI

value: M9 Minimal with 0.4% glycerol


title: asnC native 1

description: ChIP-Seq of native asnC with C-terminal SPA tag

value: asnC


title: meiosis-induced snR107kloopmut cells, 25µM 3-MB-PP1 for 1 hour, biol rep 1

value: haploid, h- cells

value: 1 hour


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 1 Library 2)

value: P2CRC BC001 Pool1 Library2

value: P4CRC BC002 Pool1 Library2


title: ascG native 2

description: ChIP-Seq of native ascG with C-terminal V5 tag

value: ascG

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: ascG native 1

value: Log-Phase


title: Human Colon Cancer and Normal Adjacent Tissue (Pool 1 Library 1)

value: Colon Cancer

value: P2CRC BC001 Pool1 Library1

value: P4CRC BC002 Pool1 Library1


title: snR107kloopmut nitrogen-starved cells, EMM-N, biol rep 1

value: over-night nitrogen starvation


title: arsR native 1

description: ChIP-Seq of native arsR with C-terminal V5 tag

value: arsR


title: argR native 2

description: ChIP-Seq of native argR with C-terminal FLAG tag

value: argR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: HNO, D120, HOM, Bio Rep 2

city: Columbus

first: Hongjun

last: Fu

state: OH

address: 616 Biomedical Research Tower, 460 W. 12th Ave

department: Department of Neuroscience

institute: The Ohio State University Wexner Medical Center

description: 10x Genomics Chromium

data_processing:
Raw sequencing data was demultiplexed and converted to FASTQ format using bcl2fastq v2.20. Cell Ranger v6.1.2 (10X Genomics) was used for barcode identification, read alignment, and UMI quantification with default parameters and aligning to the human reference genome GRCh38.
Assembly: Human reference genome GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human iPSC derived neural organoids (HNOs)

extract_protocol:
On Day 70 and Day 120, ten healthy HNOs of similar size were selected from each line. Five HNOs were combined to form a technical replicate. Each replicate was gently dissociated following the Single Cell Preparation Guide established by 10x Genomics.
Approximately 10,000 live cells were used to generate scRNA-seq libraries with the 10x Chromium single-cell 3′ V2 library kit (10x Genomics) according to the manufacturer's instructions and paired-end sequencing was performed with a NovaSeq600 S2 flow cell using an Illumina NovaSeq 600 sequencer.

value: iPSC GIH-143 (HOM:MAPT R406W/R406W homozygous)

tag: technical replication

value: 5 HNOs pooled per library


title: argP inducible 3

description: ChIP-Seq of inducible argP with C-terminal FLAG tag

value: argP

value: M9 Minimal with 0.4% glycerol

value: Arabinose added to 20% final volume for TF induction 1 hour prior to crosslink


title: HNO, D120, HOM, Bio Rep 1

description: 10x Genomics Chromium

value: Human iPSC derived neural organoids (HNOs)

tag: cell line


title: argR native 1


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 8 hours, biol rep 2

tag: cell type

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR

value: meiosis induction, 25 uM 3-MB-PP1

value: 8 hours


title: argP inducible 2

value: Log-Phase

tag: treatment

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: argP inducible 1

tag: time


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 7 hours, biol rep 2

value: 7 hours


title: HNO, D120, HET, Bio Rep 2

description: 10x Genomics Chromium

value: iPSC F11362.11F10 (HET:MAPT R406W/R406R heterozygous)


title: Sheep pancreas WT Term scRNAseq donor 4 scRNA-seq

city: Cleveland

first: Ann

last: Harris

address: 2109 Adelbert Road

department: Genetics

institute: Case Western Reserve University

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger v3.1.0
Assembly: Oar_v4.0/oviAri4 (Texel)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ovis aries

source_name: Pancreas

extract_protocol:
For single cell isolation from fresh pancreas, ~ 300 mg of tissue was cut into 2-3 mm pieces and subjected to two rounds of digestion: First in 5ml of collagenase solution (200 U/ml collagenase, 40 IU/mL, DNAse I 250 μg/mL, soybean trypsin inhibitor (SBTI) (all from Worthington), 3 mM CaCl2, at 37°C, with continuous stirring for 30-40 min. Tissue clumps were then disassociated by pipetting 10 times in a 5 ml serological pipette and left to settle for 3-4 minutes at which point the supernatant was collected and stored on ice as cell suspension 1. Second, 5 ml of fresh collagenase digestion solution as above was added to the settled tissue clumps remaining after the first digestion and again stirred at 37°C for 30-40 min, at which point very little tissue debris remained. The supernatant (cell suspension 2) was pooled with cell suspension 1 and together passed through a cell strainer (200 µm, pluriSelect) to remove any tissue debris. The strained cell suspension was then centrifuged at 300 ×g for 5 min, washed once in HBSS (Sigma Aldrich) + 2% FBS and centrifuged again. 4 ml of 1× Red Blood Cell Lysis Solution (Miltenyi Biotec 130-094-183) was added to the cell pellet which was vortexed for 5 seconds and then incubated for 5 minutes at room temperature. After 10 mL of HBSS with 2% FBS was added, the mixture was centrifuged at 300 ×g for 5 min, and the supernatant was removed. The cell pellet was then digested with 3 mL of Accutase (Stem Cell Technologies) for 15-25 min with frequent gentle pipetting with a wide-bore pipette, after which time the cells were visualized under a microscope. If any cell clumps persisted, they were collected by centrifugation and further digested with replace with 3 mL of Accutase, and digested for 10-15 min. Accutase was removed by washing the cells with 5 mL HBSS + 2% FBS, followed by centrifugation to collect the cells. The supernatant was discarded, and the cell pellet was resuspended in 0.5-1.0 ml HBSS, passed through a 20-µm mini cell strainer (pluriSelect) and cells counted. ~ 2000 - 6,000 cells were used for scRNA-seq using the 10x Genomics Chromium system.
Libraries generated from single cells according to the manufacturer's protocol for 10X Genomics Chromium Single Cell 3' Reagent Kits v3 or 3.1.

value: Pancreas

tag: Sex

value: Male

tag: disease state


title: HNO, D120, WT, Bio Rep 2

description: 10x Genomics Chromium

value: WT:CRISPR-Cas9 edited isogenic control


title: Sheep pancreas WT Term scRNAseq donor 3 scRNA-seq

description: 10x Genomics

value: Female


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 6 hours, biol rep 2

value: 6 hours


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 5 hours, biol rep 2

value: 5 hours


title: allR native 11

description: ChIP-Seq of native allR with C-terminal V5 tag

tag: strain

tag: transcription factor

value: allR

tag: chip antibody

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 4 hours, biol rep 2

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR

value: 4 hours


title: Sheep pancreas CF Term scRNAseq donor 3B scRNA-seq

description: 10x Genomics

tag: tissue

value: CF


title: HNO, D120, WT, Bio Rep 1

description: 10x Genomics Chromium

value: Human iPSC derived neural organoids (HNOs)

value: 5 HNOs pooled per library


title: allR native 9

tag: antibody vendor/catalog#

tag: media

value: Log-Phase


title: HNO, D72, HOM, Bio Rep 2

description: 10x Genomics Chromium

tag: genotype

value: iPSC GIH-143 (HOM:MAPT R406W/R406W homozygous)


title: vegetative snR107kloopmut cells, EMM, biol rep 1

value: none, vegetative growth


title: Sheep pancreas CF Term scRNAseq donor 3A scRNA-seq

description: 10x Genomics

value: Pancreas

value: Male


title: allR native 8

description: ChIP-Seq of native allR with C-terminal SPA tag

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: N-acetyl-D-glucosamine added to 0.2% final volume 5 min prior to crosslink


title: HNO, D72, HOM, Bio Rep 1

description: 10x Genomics Chromium


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 3 hours, biol rep 2

value: meiosis induction, 25 uM 3-MB-PP1

value: 3 hours


title: Sheep pancreas CF 120 day scRNAseq donor 6 scRNA-seq

description: 10x Genomics

value: Female


title: allR native 7

value: allR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol


title: meiosis-induced wt cells, 25µM 3-MB-PP1 for 2 hours, biol rep 2

value: haploid, h- cells

value: leu1-32, pat1-L95G::kanR

value: 2 hours