title: GEX_1R

description: 10X Genomics

data_processing:
SnRNA-Seq data were aligned and quantified using the 10X Genomics Cell Ranger Software Suite (v3.1.0) against a custom "pre-mRNA" human reference (GRCh38-1.2.0.pre-mrna) generated according to the steps detailed by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
Assembly: GRCh38-1.2.0.pre-mrna
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
To isolate nuclei, the frozen tissue (50-60 mg) was thawed for 2 minutes in 2 mL of ice-cold Nuclei EZ Lysis Buffer (Sigma, Cat # NUC-101), supplemented with EDTA-free protease inhibitors (Sigma, Cat # 11836170001) and 0.4 U μL−1 recombinant RNase inhibitors (Takara Bio USA, Cat # 2313A) before homogenizing with a glass Dounce tissue grinder (10-15 strokes with pestle A, followed by 10 strokes with pestle B. Sigma, Cat # D8938). An additional 2 mL of lysis buffer supplemented with protease and RNase inhibitor was added to the homogenized tissue and incubated for 5 minutes. The nuclei suspension was then filtered through a 40-μm cell strainer (Corning, Cat # 352340), followed by centrifugation at 300 x g for 5 minutes. The nuclei pellet was resuspended with 900 μL debris removal solution (Miltenyi Biotech, Cat # 130-109-398) containing 0.4 U μL−1 RNase inhibitors and 3.1 mL of Dulbecco's phosphate-buffered saline (DPBS) without calcium and magnesium. Next, 4 mL of DPBS was overlaid carefully onto the top of the nuclei resuspension. The nuclei were then pelleted again by centrifugation for 5 minutes at 3,000 x g. After removing the supernatant, the nuclei were resuspended in 500 µL of 1% BSA in DPBS with 0.4 U μL−1 RNase inhibitors. All procedures for nuclei isolation were carried out on ice or at 4°C. The density of the nuclei suspension was determined using a C-chip-disposable hemocytometer (INCYTO, Cat # DHC-B02-5) with trypan blue staining (Bio-Rad, Cat # 1450013).
The 59 samples were processed in 10 batches. Each batch had 5 to 6 samples from individuals of the same sex randomly selected from each of the AD and APOE genotype groups, i.e., control APOE2 carriers, control APOE3 homozygotes, control APOE4 carriers, AD APOE2 carriers, AD APOE3 homozygotes, and AD APOE4 carriers (6 groups in total). The samples from males and females were processed in alternating batches. A total of 5000 nuclei per sample were loaded to the Chromium microfluidic chip for cDNA library preparation using the Chromium Single Cell 3' Library and Gel Bead kit v3 (10X Genomics, Cat # 1000075) following the manufacturer's instructions.

value: Brain (temporal cortex)

value: AD

value: male


title: nac in vitro 10x 1

status: Public on Mar 17 2025

type: SRA

city: Boston

first: James

last: Galagan

state: Massachusetts

address: 36 Cummington Mall

department: Biomedical Engineering

country: USA

institute: Boston University

description:
Library name: invitro_nac_500_rep1
in vitro ChIP-Seq of 500ng nac with C-terminal 6xHis 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)
Assembly: U00096.3
Supplementary files format and content: ChIP-Seq: GFF file containing peak calls that passed all filtering steps

molecule: genomic DNA

organism: Escherichia coli str. K-12 substr. MG1655

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.  DNA was sheared via sonication prior to TF-DNA binding.  Sheared DNA was immunoprecipitated (IP) using anti-6xHis mAb.  DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
ChIP-DNA was converted into NGS libraries compatible with the Illumina platform using the NEBNext Ultra DNA (NEB Cat. No. E7465).

treatment_protocol: Purified proteins were allowed to bind with 500ng sheared genomic DNA in IPP150 buffer at room temp for 1 hour prior to crosslinking and immunoprecipitation with anti-6xHis antibody.

tag: strain

tag: cell line

tag: transcription factor

value: nac

tag: chip antibody

value: anti-6xHis mAb

tag: antibody vendor/catalog#

value: Invitrogen/Cat. No. MA1-21315

tag: media

tag: time

value: 1 hour


title: Heart, TAB, wildtype, biol rep 4

city: Utrecht

first: Louk

last: Timmer

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: transcriptomic

data_processing:
Quality control of sequencing reads from FASTQ files was performed using FastQC (v0.11.8)
Reads were trimmed based on quality and adapter presence by TrimGalore (v0.6.5) and again checked for quality using FastQC.
rRNA reads were removed using SortMeRNA (v4.3.3)
reads were aligned to using the STAR (v2.7.3a) aligner
Mapped (bam) files were subjected to quality control using Sambamba (v0.7.0), RSeQC (v3.0.1) and PreSeq (v2.0.3). and annotated against reference genome to generate readcounts using the Subread FeatureCounts module (v2.0.0).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Heart (ventricular)

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher)
TruSeq Stranded mRNA libraries (Illumina, #20020594) were prepared using a total of 100ng RNA according to the manufacturers protocol.

tag: tissue

value: Heart (ventricular)

tag: genotype

value: sorbs2 knock-out

tag: treatment

value: sham


title: native allR libV2 postIP 2

description: Sequencing of Library-ChIP sequences in native-V5-tagged AllR strain after IP

library_source: other

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
Library strategy: Library-ChIP

molecule: other

organism: Escherichia coli K-12

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).

value: allR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: ADR+SI1

city: Zhengzhou

first: Mingyang

last: Hu

state: Henan

address: jinshui

country: China

institute: Department of Nephrology, First Affiliated Hospital of Zhengzhou University

data_processing:
The quality of the constructed library was verified with an Agilent 2100 Bioanalyzer and quantified via qPCR.
Sequencing was then performed using the Illumina NovaSeq 6000 sequencer.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNA samples were extracted and assessed for quality using agarose gel electrophoresis, followed by quantification with a nanodrop. RNA samples that met the quality criteria were enriched for mRNA using oligo(dT) magnetic beads.
For RNA sequencing library construction, the RNA was fragmented and reverse-transcribed into first-strand cDNA using random primers, followed by second-strand cDNA synthesis with dUTP incorporation. The double-stranded cDNA was subjected to end repair, A-tailing, adapter ligation, and polymerase chain reaction (PCR) amplification to generate the final library.

value: kidney

tag: cell type

value: podocytes


title: ADR3

value: ADR


title: native allR libV1 postIP


title: Heart, TAB, wildtype, biol rep 3


title: ADR2


title: Heart, TAB, wildtype, biol rep 2


title: native pdhR libV2 preIP 2

description: Sequencing of Library-ChIP sequences in native-SPA-tagged PdhR strain before IP

value: pdhR

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


title: nac in vitro 1x 1

description:
Library name: invitro_nac_50_rep1
in vitro ChIP-Seq of 50ng nac with C-terminal 6xHis tag

source_name: Escherichia coli str. K-12 substr. MG1655

value: nac


title: Heart, sham, sorbs2 knock-out, biol rep 3

value: wildtype

value: TAB


title: ADR1


title: Heart, TAB, wildtype, biol rep 1


title: ulaR in vitro 10x 1

description:
Library name: invitro_ulaR_500_rep1
in vitro ChIP-Seq of 500ng ulaR with C-terminal 6xHis tag

value: Escherichia coli str. K-12 substr. MG1655

value: ulaR

value: anti-6xHis mAb

value: Invitrogen/Cat. No. MA1-21315

value: 1 hour


title: glnG in vitro 10x 1

description:
Library name: invitro_glnG_500_rep1
in vitro ChIP-Seq of 500ng glnG with C-terminal 6xHis tag

value: glnG


title: Heart, sham, wildtype, biol rep 4

value: Heart (ventricular)

value: sham


title: Heart, sham, sorbs2 knock-out, biol rep 1


title: ADR+SI3


title: CON3

value: WT


title: Heart, sham, wildtype, biol rep 3


title: glnG in vitro 10x 2

description:
Library name: invitro_glnG_500_rep2
in vitro ChIP-Seq of 500ng glnG with C-terminal 6xHis tag


title: native allR libV2 postIP 1

value: allR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: inducible pdhR libV2 preIP 2

description: Sequencing of Library-ChIP sequences in inducible-FLAG-tagged PdhR strain before IP

value: pdhR

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


title: nac in vitro 1x 2

description:
Library name: invitro_nac_50_rep2
in vitro ChIP-Seq of 50ng nac with C-terminal 6xHis tag

value: nac


title: glnG in vitro 1x 1

description:
Library name: invitro_glnG_50_rep1
in vitro ChIP-Seq of 50ng glnG with C-terminal 6xHis tag

value: Escherichia coli str. K-12 substr. MG1655


title: native pdhR libV1 preIP


title: inducible pdhR libV2 preIP 1


title: Heart, sham, wildtype, biol rep 1

value: wildtype


title: SNr

city: New York

first: Alana

last: Mendelsohn

state: NY

address: 3227 Broadway

institute: Columbia University

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 and sequencing reads were processed and aligned to the mm10 transcriptome using Cell Ranger 5.0.1. 3999 cells were captured with 99874 mean reads per nucleus and 4304 median genes per nucleus.
Assembly: mm10
Supplementary files format and content: Tab-delineated file of barcodes
Supplementary files format and content: Tab-delineated file of features
Supplementary files format and content: Sparse matrix file of counts

molecule: nuclear RNA

source_name: Brain, substantia nigra pars reticulata

extract_protocol:
9 12-week old C57BL/6JN mice were used. Animals were euthanized in a CO2 chamber and decapitated, after which the brains were dissected out from the skull and submerged in ice-cold aCSF (92 mM NMDG, 2.5 mM KCl, 1.25 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 Na-ascorbate, 3 mM Na-pyruvate, 0.5 mM CaCl2·2H2O, and 10 mM MgSO4·7H2O). Coronal brain slices (400 µm thick) were cut using a vibrating-blade microtome (V1200S, Leica, USA) at 4°C. The SNr subregion was microdissected out in aCSF under a fluorescent dissection microscope (Leica M165FC) and transferred to microcentrifuge tubes. Excess aCSF was aspirated before flash-freezing the tubes on dry ice. Single nuclei preparations were performed pooling tissue from 3-4 mice, following the Allen Institute’s published V1 protocol. Briefly, each pooled sample was homogenized in a chilled 2 mL dounce (Sigma D8938) using 3.5 ml of freshly prepared homogenization buffer containing 3.375 ml of NIM (10 mM Tris-HCl, 250 mM sucrose, 25 mM KCl, 5mM MgCl2, 10mM Tris-HCl ), 3.5 µl of 100 mM DTT stock (Promega P1171), 70 µl of 50X Protease inhibitor cocktail (Promega G6521), 17.5 µl of 40 U/µl RNAsin Plus (Promega N2615), and 35 µl of 10% Triton X-100 (Sigma T8787). The homogenate was strained through a 30 µm cell strainer (Miltenyi Biotec 130-098-458) and centrifuged at 900 x g for 10 minutes at 4°C. After centrifugation, the pellet was resuspended in 500 µl of freshly prepared blocking buffer containing 410 µl nuclease-free water, 50 µl 10X PBS, 40 µl of 10% OmniPur BSA (Sigma 2905), and 2.5 µl of 40 U/µl RNAsin Plus. The nuclear resuspension as subsequently incubated on ice for 15 minutes. The suspension was labeled with Mouse anti-NeuN-488 to enrich for neuronal cells (1:500, Millipore Sigma), incubated on ice for 30 minutes, then centrifuged at 400 x g for 5 minutes. The supernatant was resuspended in 500 µl of blocking buffer, then labeled with 0.5 µl of DAPI. Prior to DAPI labeling, 5 µl of nuclear suspension was removed and labeled with 5 µl of Trypan Blue and loaded into a disposable hemocytometer slide (Invitrogen C10228) for quantification of yield and visual inspection of nuclear quality. Fluorescence-activated nuclei sorting (FANS) of single nuclei was performed using the Beckman Coulter MoFlo Astrios EQ. Cell analysis and sorting were performed on a Beckman Coulter MoFlo Astrios EQ.  These experiments required the use of the 405 nm (80 mW) laser for fluorescent excitation of the DAPI labeled nuclei and the 488 nm (200 mW) laser for forward, side scatter detection and GFP excitation. The sample and collection area were cooled to ~ 7° C. DAPI was detected with a 448 /59 band-pass filter. The PMT was set at 341V with an amplifier gain of 3. GFP was detected with a 513 /26 band-pass filter. The PMT was set at 360V with an amplifier gain of 3. The PMT was set at 310V with an amplifier gain of 4. DAPI+/GFP+ nuclei were collected into an Eppendorf tube containing blocking buffer.
Single-nucleus cDNA libraries were constructed according to the user guide of Chromium Single Cell 3’ Reagents Kit v3 (10× Genomics, Pleasanton, CA).

value: Brain, substantia nigra pars reticulata

value: Neuron


title: CON1

value: kidney

value: podocytes


title: native pdhR libV2 preIP 1

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


title: inducible glnG libV2 preIP 2

description: Sequencing of Library-ChIP sequences in inducible-FLAG-tagged GlnG strain before IP

value: glnG


title: Col5a1_UUO_D7_3

city: Los Angeles

first: Lianjiu

last: Su

address: 500 Landfair Ave.

institute: University of California, Los Angeles

description: Library name: Col5a1_UUO_D7_3

data_processing:
The quality of sequencing reads was evaluated by FastQC. The transcript quantification was performed by Salmon using mouse reference transcriptome (GRCm39). The transcript-level quantification of estimated counts, length, and abundance from Salmon were imported into DESeq2 using tximport package. DESeq2 uses a negative binomial model to model the variability of raw counts and Wald test to estimate differences between the conditions. DEseq function was performed with default setting. The transformed count data were used for PCA visualization. Using the results function, we selected genes with a adjusted p value < 0.05 and logFC > 1 or <-1 as differentially expressed genes (DEG). The p-values attained by the Wald test are corrected for multiple testing using Benjamini and Hochberg method by default. The cluster Profiler was used for GO pathway, GSEA analysis and visualization.
Assembly: GRCm39
Supplementary files format and content: quant.tar.gz file of each sample generated by Salmon stores the gene expression in quant.sf, and other information.

extract_protocol:
Total RNA was extracted with the RNeasy Mini kit (QIAGEN)
Strand-specific libraries were generated using 400 ng of total RNA using the TruSeq stranded RNA Sample Preparation Kit (Illumina).

value: Wild type

value: Unilateral ureteral obstruction model at Day 7


title: WT (JC450) replicate C (M2G)

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

description: Library name: JC450C

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Reads were aligned againstCaulobacter vibrioides NA1000 ASM2200v1 genome using STAR (v. 2.5.3a)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1) using Caulobacter vibrioides NA1000 ASM2200v1 gene annotation.
Assembly: Caulobacter vibrioides NA1000 ASM2200v1
Supplementary files format and content: tab-delimited text file includes read counts per gene locus for each sample

organism: Caulobacter vibrioides NA1000

growth_protocol: Cells were cultivated exponentially in M2G medium until they reach OD660 = 0.4

extract_protocol:
RNA samples were prepared from 10 ml bacterial cultures. Cells were harvested at 4°C by centrifugation at 8,000 rpm for 10 minutes and immediately frozen in liquid nitrogen. The samples were stored at -80°C until their processing. RNA were extracted using the RNeasy mini kit from Qiagen following the manufacturer’s recommendation. Any remaining DNA was removed by on-column DNA digestion with DNase I (RNase-free DNases set from Qiagen) followed by a TURBO DNA-freeTM DNase treatment (Invitrogen). RNA samples were then re-purified using a RNA clean-up procedure (RNeasy mini kit).
RNA-seq libraries were prepared from 1000 ng of total RNA with the Illumina Truseq stranded mRNA Prep reagents (Illumina) using a unique dual indexing strategy, and following the official protocol. The polyA selection step was replaced by an rRNA depletion step with the Ribo-off rRNA Depletion Kit (Bacteria)  (Vazyme).

value: WT


title: Col5a1_UUO_D7_2

description: Library name: Col5a1_UUO_D7_2


title: WT (JC450) replicate B (M2G)

description: Library name: JC450B


title: CD8TILs, Mannose, rep 2

city: Shanghai

first: Haiou

last: Liu

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

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited txt files include TPM values for each sample.

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mannose supplementation


title: inducible glnG libV2 preIP 1

value: M9 Minimal with 0.4% glycerol


title: CON2


title: glnG in vitro 1x 2

description:
Library name: invitro_glnG_50_rep2
in vitro ChIP-Seq of 50ng glnG with C-terminal 6xHis tag

value: anti-6xHis mAb

value: Invitrogen/Cat. No. MA1-21315

value: 1 hour


title: Col5a1_UUO_D7_1

description: Library name: Col5a1_UUO_D7_1


title: CD8TILs, Mannose, rep 1


title: Heart, sham, wildtype, biol rep 2

value: Heart (ventricular)

value: sham


title: WT (JC450) replicate A (M2G)

description: Library name: JC450A


title: CD8TILs, Control, rep 3

value: Control


title: inducible glnG libV1 preIP

value: Log-Phase

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


title: ∆scmA (JC2005) replicate C (M2G)

description: Library name: JC2005C

value: deltaCCNA_01085 (delta-scmA)


title: Col5a1_UUO_D14_3

description: Library name: Col5a1_UUO_D14_3

value: kidney

value: Unilateral ureteral obstruction model at Day 14


title: allR in vitro 1x 2

description:
Library name: invitro_allR_50_rep2
in vitro ChIP-Seq of 50ng allR with C-terminal 6xHis tag

value: Escherichia coli str. K-12 substr. MG1655

value: allR


title: ∆scmA (JC2005) replicate B (M2G)

description: Library name: JC2005B


title: inducible pdhR libV1 preIP

value: pdhR


title: native allR libV2 preIP 2

description: Sequencing of Library-ChIP sequences in native-V5-tagged AllR strain before IP


title: Col5a1_UUO_D14_2

description: Library name: Col5a1_UUO_D14_2

value: Wild type


title: CD8TILs, Mannose, rep 3

value: Mannose supplementation


title: Col5a1_UUO_D14_1

description: Library name: Col5a1_UUO_D14_1


title: ∆scmA (JC2005) replicate A (M2G)

description: Library name: JC2005A


title: CD8TILs, Control, rep 1


title: Co5a1-UUO_D3_3

description: Library name: Co5a1-UUO_D3_3

value: Unilateral ureteral obstruction model at Day 3


title: native allR libV1 preIP

value: M9 Minimal with 0.4% glycerol


title: Tumor tissues, Mannose, rep 5

source_name: tumor tissue

value: tumor tissue


title: Tumor tissues, Mannose, rep 4


title: Co5a1-UUO_D3_2

description: Library name: Co5a1-UUO_D3_2


title: yoeB inducible 2

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

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

value: yoeB

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: yjiR inducible 2

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

value: yjiR


title: Co5a1-UUO_D3_1

description: Library name: Co5a1-UUO_D3_1


title: Co5a1-UUO_CTR_3

description: Library name: Co5a1-UUO_CTR_3

value: sham


title: yhjC inducible 1

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

value: yhjC

value: Log-Phase

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


title: CD8TILs, Control, rep 2

value: Control


title: Tumor tissues, Mannose, rep 2


title: yhfR inducible 3

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

value: yhfR


title: Co5a1-UUO_CTR_2

description: Library name: Co5a1-UUO_CTR_2

value: kidney


title: native allR libV2 preIP 1

value: allR


title: Tumor tissues, Control, rep 4


title: Tumor tissues, Mannose, rep 1


title: Co5a1-UUO_CTR_1

description: Library name: Co5a1-UUO_CTR_1

value: Wild type


title: yfhH inducible 1

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

value: yfhH


title: Tumor tissues, Mannose, rep 3

value: Mannose supplementation


title: AD28-WT-2

description: Library name: AD28-WT-2

value: Wild type (cre-)

value: Adenine diet+PBS for 28 days


title: paaX inducible 1

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

value: paaX

value: M9 Minimal with 0.4% glycerol


title: yedW inducible 2

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

value: yedW

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: GEX_44R

city: Jacksonville

first: Zonghua

last: Li

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

institute: Mayo Clinic

description: 10X Genomics

library_source: transcriptomic single cell

organism: Homo sapiens

source_name: Brain (temporal cortex)

value: Brain (temporal cortex)

tag: pathological diagnosis

value: AD

tag: Sex

value: female


title: IAP knockout (IAP-KO) (Akp3-/-) mice liver_14days_600IIAEK (IIAEK)_rep3

type: RNA

city: Gifu

first: Satoshi

last: Nagaoka

address: 1-1 Yanagido

country: Japan

institute: Gifu university

hyb_protocol: Targets consisting of amplified and fluorescently labelled complementary RNA were hybridised to a microarray slide (SurePrint G3 Mouse GE Microarray 8 × 60 K Ver. 2.0; Agilent Technologies) using an Agilent Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: The slides were scanned using a microarray scanner (ArrayScan, Agilent Technologies) and Agilent Feature Extraction software (Agilent Technologies) for spot identification and quantification.

data_processing: Data analyses were performed according to the manufacturer’s instructions using GeneSpring GX 11.5 Expression Analysis Software (Agilent Technologies).

source_name: IAP knockout (IAP-KO) (Akp3-/-) mice liver, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt including the cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d)  once a day for 14week to the mice

label_protocol: Total RNA samples were labeled using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: After fasting for 8 h, the  liver was collected from mice and immediately immersed in RNAlater solution (Qiagen, Hilden, Germany).

treatment_protocol: The cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d) was  orally administered to mice once a day for 14d.

value: liver

tag: gender

value: male


title: IAP knockout (IAP-KO) (Akp3-/-) mice liver_14days_600IIAEK (IIAEK)_rep2


title: IAP knockout (IAP-KO) (Akp3-/-) mice liver_14days_600IIAEK (IIAEK)_rep1


title: Tumor tissues, Control, rep 5

value: tumor tissue

value: Control


title: Tumor tissues, Control, rep 2


title: AD28-WT-1

description: Library name: AD28-WT-1

value: kidney


title: envY inducible 2

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

value: envY

value: Log-Phase

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


title: AD28-CKO-Cilengitide-4

description: Library name: AD28-CKO-Cilengitide-4

value: Co5a1 CKO

value: Adenine diet + Cilengitide for 28 days


title: IAP knockout (IAP-KO) (Akp3-/-) mice liver_14days_0IIAEK (Control)_rep3

source_name: IAP knockout (IAP-KO) (Akp3-/-) mice liver, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt once a day for 14days to the mice


title: Wild-type mice liver_14days_600IIAEK (IIAEK)_rep2

source_name: Wild-type mice liver, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt including the cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d)  once a day for 14week to the mice


title: Tumor tissues, Control, rep 1


title: AD28-CKO-Cilengitide-3

description: Library name: AD28-CKO-Cilengitide-3


title: IAP knockout (IAP-KO) (Akp3-/-) mice liver_14days_0IIAEK (Control)_rep2


title: AD28-WT-3

description: Library name: AD28-WT-3

value: Wild type (cre-)

value: Adenine diet+PBS for 28 days


title: Enteric neurons P24 replicate 3

city: Stockholm

first: Ulrika

last: Marklund

state: - If in U.S, Select a State -

address: Tomtebodavägen 16

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
RNA libraries from P7 were sequenced by S1 reagent kit (100 cycles) and P24 was sequenced by S2 Reagent Kit (100 cycles). Both P7 and P24 libraries were sequenced using NovaSeq6000 platform.
Gene expression dataframe was constructed, using Seurat's Read10X(), from filtered_feature_bc_matrix outputs from CellRanger version 3.0.1 pipeline.
Assembly: mm10
Supplementary files format and content: The processed data present here were taken from filtered_feature_bc_matrix outputs from the Cell Ranger version 3.0.1 pipeline. Each sample consists of three processed files: Tab-separated value file barcodes.tsv.gz (cell IDs), Tab-separated value file features.tsv.gz (IDs of quantified genes), and matrix file matrix.mtx.gz (UMI counts).
Supplementary files format and content: ens_p7_lv2.rds: Seurat Object displaying processed datasets GSM8191470 and GSM8191471.
Supplementary files format and content: sm_p24_lv3.rds: Seurat Object displaying processed datasets GSM8191472, GSM8191473, and GSM8191474.
Supplementary files format and content: p7_metadata.csv: Metadata information for the seurat object: ens_p7_lv2.rds
Supplementary files format and content: sm_metadata.csv: Metadata information for the seurat object: sm_p24_lv3.rds

source_name: submucosal plexus

extract_protocol:
Small intestines from P7 Wnt1-CrexR26RtdTom mice were isolated and then treated with EDTA, followed by Dispase/Liberase TH, flow sorted and applied to 10xGenomics Chromium Single Cell Kit Version 2. Small intestines from P24 Baf53bCrexR26RtdTom mice were peeled and then treated with EDTA, followed by Dispase/Liberase TH, flow sorted and applied to 10xGenomics Chromium Single Cell Kit Version 3.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: submucosal plexus


title: zraR inducible 2

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

value: zraR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: AD28-CKO-Cilengitide-2

description: Library name: AD28-CKO-Cilengitide-2


title: yqjI native 2

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

value: yqjI


title: gadW inducible 1

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

value: gadW


title: ytfH inducible 2

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

value: ytfH


title: IAP knockout (IAP-KO) (Akp3-/-) mice liver_14days_0IIAEK (Control)_rep1

value: liver

value: male


title: Enteric neurons P24 replicate 2


title: Enteric neurons P24 replicate 1


title: AD28-CKO-Cilengitide-1

description: Library name: AD28-CKO-Cilengitide-1

value: kidney


title: Tumor tissues, Control, rep 3

value: tumor tissue

value: Control


title: AD28-CKO-3

description: Library name: AD28-CKO-3

value: Co5a1 CKO

value: Adenine diet for 28 days


title: yjjQ inducible 2

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

value: yjjQ

value: Log-Phase

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


title: ENS cells at P7 replicate 2

source_name: ENS

value: ENS


title: ypdC inducible 2

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

value: ypdC

value: anti-FLAG mAb


title: Wild-type mice liver_14days_0IIAEK (Control)_rep2

source_name: Wild-type mice liver, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt once a day for 14days to the mice


title: Wild-type mice liver_14days_0IIAEK (Control)_rep3


title: Wild-type mice liver_14days_0IIAEK (Control)_rep1


title: IAP knockout (IAP-KO) (Akp3-/-) mice jejunum_14days_600IIAEK (IIAEK)_rep2

source_name: IAP knockout (IAP-KO) (Akp3-/-) mice jejunum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt including the cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d)  once a day for 14week to the mice

extract_protocol: After fasting for 8 h, the jejunum was collected from mice and immediately immersed in RNAlater solution (Qiagen, Hilden, Germany).

value: Jejunum


title: AD28-CKO-2

description: Library name: AD28-CKO-2


title: ENS cells at P7 replicate 1


title: yidZ inducible 2

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

value: yidZ

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: Mouse 36, left hemisphere injected with NC

city: Zurich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190 Building 17

department: D-HEST

institute: ETH Zürich

data_processing:
Salmon pseudo-alignement
Salmon feature count
Filtered by expression using filterByExpr of edgeR
Surrogate variable analysis (SVA) to correct for batch effects
Normalization by estimateDisp (edgeR), Fit a negative binomial generalized log-linear model to the read counts for each gene (glmFit) followed by likelihood ratio tests for LNA-Treatment coefficients in the linear model (glmLRT)
Assembly: GRCm39 (Release 108)
Supplementary files format and content: Excel-matrix of raw counts (Excel-Sheet "RawCounts") and logcpm ( Excel-Sheet (logCPM), log counts per million, normalized and corrected by SVA) for every sample (Columns) and every gene (Rows)
Supplementary files format and content: edgeR-resultstable showing log-fold-change and significance for every gene between LNA218 vs NC conditions

molecule: polyA RNA

source_name: Brain, Cortex

extract_protocol:
RNA extraction according to manufacturer protocl (RNA-solv from Omega Bio-tek)
According to NEB Next Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Stereotactic Injection of miRNA-inhibitor LNA218 or NC

value: Brain, Cortex

tag: age

value: adult, 3months old

value: WT

value: NC


title: yihW inducible 2

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

value: yihW


title: AD28-CKO-1

description: Library name: AD28-CKO-1

value: kidney

value: Co5a1 CKO


title: Wild-type mice liver_14days_600IIAEK (IIAEK)_rep3

value: liver

value: male


title: Wild-type mice liver_14days_600IIAEK (IIAEK)_rep1


title: NC_2

description: Library name: NC_2

value: Wild type

value: chow diet


title: Mouse 36, right hemisphere injected with LNA218


title: NC_1

description: Library name: NC_1


title: Mouse 35, right hemisphere injected with NC


title: Mouse 35, left hemisphere injected with LNA218


title: yhaJ native 2

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

value: yhaJ

value: Log-Phase


title: Mouse 34, left hemisphere injected with NC


title: yhjC inducible 2

value: yhjC

value: anti-FLAG mAb

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


title: ygiT native 3

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

value: ygiT

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

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


title: ADE_7_3

description: Library name: ADE_7_3

value: Adenine diet for 7 days


title: IAP knockout (IAP-KO) (Akp3-/-) mice jejunum_14days_600IIAEK (IIAEK)_rep3

value: Jejunum


title: ADE_7_2

description: Library name: ADE_7_2

value: kidney


title: Mouse 34, right hemisphere injected with LNA218

value: Brain, Cortex

value: adult, 3months old

value: WT


title: IAP knockout (IAP-KO) (Akp3-/-) mice jejunum_14days_0IIAEK (Control)_rep3

source_name: IAP knockout (IAP-KO) (Akp3-/-) mice jejunum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt once a day for 14days to the mice

value: male


title: NC_3

description: Library name: NC_3

value: Wild type

value: chow diet


title: ygeH inducible 2

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

value: ygeH

value: Log-Phase


title: ADE_7_1

description: Library name: ADE_7_1


title: Mouse 33, left hemisphere injected with NC

value: NC


title: IAP knockout (IAP-KO) (Akp3-/-) mice jejunum_14days_0IIAEK (Control)_rep1


title: IAP knockout (IAP-KO) (Akp3-/-) mice jejunum_14days_0IIAEK (Control)_rep2


title: yhfZ inducible 2

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

value: yhfZ

value: anti-FLAG mAb

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


title: IAP knockout (IAP-KO) (Akp3-/-) mice jejunum_14days_600IIAEK (IIAEK)_rep1


title: Mouse 33, right hemisphere injected with LNA218


title: Wild-type mice jejunum_14days_600IIAEK (IIAEK)_rep2

source_name: Wild-type mice jejunum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt including the cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d)  once a day for 14week to the mice


title: yfhH inducible 2

value: yfhH

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: ADE_28_2

description: Library name: ADE_28_2

value: Adenine diet for 28 days


title: cKO

city: NEW BRUNSWICK

first: Xiaosheng

last: Tan

state: NJ

address: 89 French St

institute: RUTGERS

description: 10X Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v6.1.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 4.0.3 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
GRCm38Ensembl100
MTX file and TSV file contain counts for each barcodes and genes

source_name: thymus

growth_protocol: Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.

extract_protocol: RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

value: thymus

value: enriched by anti-CD25 beads


title: yfeT inducible 2

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

value: yfeT


title: ADE_28_1

description: Library name: ADE_28_1

value: kidney


title: yfiE inducible 1

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

value: yfiE


title: Wild-type mice jejunum_14days_600IIAEK (IIAEK)_rep3

value: Jejunum

value: male


title: ADE_28_3

description: Library name: ADE_28_3

value: Wild type


title: yfeC native 2

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

value: yfeC

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: Log-Phase


title: Wild-type mice jejunum_14days_0IIAEK (Control)_rep3

source_name: Wild-type mice jejunum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt once a day for 14days to the mice


title: WT_SP3

first: Jingsi

last: Jin

address: 280 South Chongqing Rd.

institute: Shanghai Jiaotong University

description: WT_TAM vs WT_SP.readcount

data_processing:
The raw reads were aligned to the mouse reference genome (mm10) using Tophat2 RNASeq alignment software Hisat2.
The raw reads alignment files were processed using Hisat SAMtools and HTSeq to generate read counts for every gene.
The read counts were then normalized using R package DESeq2. The normalized read counts were then centered and scaled for each gene, generating z-scores. The z-scores basically represent how many standard deviations one particular count is from the average count for that gene. P-values obtained from multiple tests were adjusted using Benjamini-Hochberg correction.
Assembly: mm10
Supplementary files format and content: excel file containing read count for each gene

source_name: Splenic macrophages

extract_protocol:
TAMs (CD45+ Ly6G- Ly6C- CD11b+ F4/80+) and splenic macrophages (CD45+ TCRβ- Ly6G- Ly6C- CD11blo F4/80+) from day14 LLC-bearing WT and cKO mice were FACS-sorted and total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6-8-week old paired Sin1fl/fl (WT) and LysMCre;Sin1fl/fl (cKO) mice were subcutaneously transplanted with 5×105 LLC cells. 14 days later, tumor tissue and spleen from LLC-bearing WT and cKO mice were obtained for further processing.

value: Spleen

value: 5×10^5 LLC cell inoculation subcutaneously


title: ADE_14_3

description: Library name: ADE_14_3

source_name: kidney

value: Adenine diet for 14 days


title: yeiI inducible 2

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

value: yeiI

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

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


title: Wild-type mice jejunum_14days_0IIAEK (Control)_rep1


title: ADE_14_2

description: Library name: ADE_14_2

value: kidney


title: Wild-type mice jejunum_14days_0IIAEK (Control)_rep2


title: Wild-type mice jejunum_14days_600IIAEK (IIAEK)_rep1


title: WT_SP2

description: WT_TAM vs WT_SP.readcount


title: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum_14days_600IIAEK (IIAEK)_rep3

source_name: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt including the cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d)  once a day for 16week to the mice

extract_protocol: After fasting for 8 h, the duodenum was collected from mice and immediately immersed in RNAlater solution (Qiagen, Hilden, Germany).

value: duodenum


title: WT_SP1

description: WT_TAM vs WT_SP.readcount


title: ADE_14_1

description: Library name: ADE_14_1


title: ydjF native 1

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

value: ydjF

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


title: yegW inducible 2

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

value: yegW


title: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum_14days_600IIAEK (IIAEK)_rep2

source_name: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt including the cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d)  once a day for 15week to the mice

value: male


title: D3

city: Wuhan

first: Jiawei

last: Jiang

state: Hubei

address: No.1095 Jiefang Avenue

department: Orthopedics

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT v2.1.0 with parameters --dta -t -p 4
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm8
Supplementary_files_format_and_content: FPKM

source_name: BMMs

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: BMM


title: KO_TAM4

description: WT_TAM vs KO_TAM.readcount

source_name: Tumor-associated macrophages

value: Day14 subcutaneous LLC tumor


title: D2


title: ydjF inducible 1

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

value: Log-Phase


title: KO_TAM3

description: WT_TAM vs KO_TAM.readcount


title: D1


title: ydfH inducible 2

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

value: ydfH


title: KO_TAM2

description: WT_TAM vs KO_TAM.readcount

value: 5×10^5 LLC cell inoculation subcutaneously


title: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum_14days_600IIAEK (IIAEK)_rep1

source_name: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt including the cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d)  once a day for 14week to the mice


title: ydcR native 3

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

value: ydcR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: C3

value: DMSO


title: KO_TAM1

description: WT_TAM vs KO_TAM.readcount


title: C2


title: WT_TAM4

description: WT_TAM vs KO_TAM.readcount


title: ydcN inducible 1

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

value: ydcN

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum_14days_0IIAEK (Control)_rep3

source_name: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt once a day for 14days to the mice

value: duodenum


title: ydaS inducible 2

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: C1


title: WT_TAM3

description: WT_TAM vs KO_TAM.readcount


title: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum_14days_0IIAEK (Control)_rep2

value: male


title: ycjZ inducible 2

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

value: ycjZ


title: Wild-type mice duodenum_14days_600IIAEK (IIAEK)_rep2

source_name: Wild-type mice duodenum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt including the cholesterol-lowering pentapeptide IIAEK (Ile-Ile-Ala-Glu-Lys) (600 mg/kg B.W./d)  once a day for 14week to the mice


title: xnp-1_L1_biological_replicate_3, smallRNA-seq

city: St Andrews

first: Helder

middle: C

last: Ferreira

address: North Haugh

country: United Kingdom

institute: University of St Andrews

description: Library name: WTCHG_954678_221

data_processing:
Quality control with fastQC before and after trimming with Trim_galore.
Trimmed reads were mapped to WS280 genome build (BioProject PRJNA13758) using STAR without limits on mapped length and with max. number of mismatches per pair = 2.
The reads were re-sorted by read name using Samtools. FeatureCounts was used to generate a count matrix.
Assembly: WS280
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Adult C. elegans were grown on standard NGM with OP50 at 20°C and lysed with hypochlorite to obtain embryos. L1 larvae were obtained by incubating embryos in M9 for ~11hrs at 20°C. L4 larvae were grown at 25°C from L1.

extract_protocol:
For each 100 μl of worm pellet, 1 ml of Trizol was added. 5 cycles of freeze‐cracking were carried out, freezing in liquid nitrogen, followed by thawing in a water bath at 37°C. Tubes were vortexed for 30 s on, 30 s off, for 5 min and incubated for 5 min at room temperature. 200 μl chloroform per ml of Trizol were added, tubes were shaked vigorously, incubated 2–3 min at room temperature and centrifuged at full speed for 10 min at 4°C. The top layer was transferred to a new tube, and RNA was precipitated overnight at −20°C with 1 μl glycogen and an equal volume of isopropanol.
RNA sequencing of embryos and L1 was carried out at the Oxford Genomics Centre and for the L4 samples was carried out at Novogene, Cambridge. All genotypes where sequences in biological triplicate. For small RNA library preparation, 1-2 µg (see Beltran et al., Nat Ecol Evo 2020 for details) of RNA were incubated for 1 h at 37 °C with RNA 5′ polyphosphatase (Epicentre) at a final concentration of 1 U µl−1 in a total volume of 20 µl to convert 5′-triphosphate 22G-RNAs into clonable 5′-phosphate 22G-RNAs. RNA was phenol–chloroform-extracted and precipitated overnight with 1 µl of glycogen, 1/10 volume 3M AcNA and 3 volumes of 100% ethanol. Small RNA libraries were generated using the Illumina TruSeq Small RNA Library Preparation Kit according to the manufacturer’s instructions and gel-purified to size-select 21–23-nucleotide (nt) inserts. The libraries were sequenced on an Illumina HiSeq2500 system.

treatment_protocol: L4 larvae were grown at 25°C from L1 to L4.

value: whole organism

tag: developmental stage

tag: biological replicate


title: N2_L1_biological_replicate_3, smallRNA-seq

description: Library name: WTCHG_954678_220


title: yciT inducible 2

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

tag: strain

value: yciT

value: Log-Phase


title: WT_TAM2

description: WT_TAM vs KO_TAM.readcount

value: Day14 subcutaneous LLC tumor

value: 5×10^5 LLC cell inoculation subcutaneously


title: xnp-1_embryo_biological_replicate_3, smallRNA-seq

description: Library name: WTCHG_954678_219

value: embryo


title: ybiH inducible 2

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

value: ybiH


title: SNr_MSC_plate_2

data_processing:
Sequences were de-multiplexed to generate a fastq file. Reads were aligned to annotated mRNAs in the mouse genome (UCSC, Mus musculus assembly mm10) and the read count for each gene was calculated using STAR aligner.
Assembly: mm10
Supplementary files format and content: tab-deliminated text file includes cell names
Supplementary files format and content: Sparse matrix file includes raw counts
Supplementary files format and content: tab-deliminated text file includes gene names

source_name: Brain, substantia nigra pars reticulata

extract_protocol:
Animals were euthanized in a CO2 chamber and decapitated, after which the brains were dissected out from the skull and submerged in ice-cold aCSF (92 mM NMDG, 2.5 mM KCl, 1.25 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 Na-ascorbate, 3 mM Na-pyruvate, 0.5 mM CaCl2·2H2O, and 10 mM MgSO4·7H2O). Coronal brain slices (400 µm thick) were cut using a vibrating-blade microtome (V1200S, Leica, USA) at 4°C. The SNr subregion was microdissected out in aCSF under a fluorescent dissection microscope (Leica M165FC) and transferred to microcentrifuge tubes. Excess aCSF was aspirated before flash-freezing the tubes on dry ice. Single nuclei preparations were performed pooling tissue from 3-4 mice, following the Allen Institute’s published V1 protocol. Briefly, each pooled sample was homogenized in a chilled 2 mL dounce (Sigma D8938) using 3.5 ml of freshly prepared homogenization buffer containing 3.375 ml of NIM (10 mM Tris-HCl, 250 mM sucrose, 25 mM KCl, 5mM MgCl2, 10mM Tris-HCl ), 3.5 µl of 100 mM DTT stock (Promega P1171), 70 µl of 50X Protease inhibitor cocktail (Promega G6521), 17.5 µl of 40 U/µl RNAsin Plus (Promega N2615), and 35 µl of 10% Triton X-100 (Sigma T8787). The homogenate was strained through a 30 µm cell strainer (Miltenyi Biotec 130-098-458) and centrifuged at 900 x g for 10 minutes at 4°C. After centrifugation, the pellet was resuspended in 500 µl of freshly prepared blocking buffer containing 410 µl nuclease-free water, 50 µl 10X PBS, 40 µl of 10% OmniPur BSA (Sigma 2905), and 2.5 µl of 40 U/µl RNAsin Plus. The nuclear resuspension as subsequently incubated on ice for 15 minutes, , then labeled with 0.5 µl of DAPI. Prior to DAPI labeling, 5 µl of nuclear suspension was removed and labeled with 5 µl of Trypan Blue and loaded into a disposable hemocytometer slide (Invitrogen C10228) for quantification of yield and visual inspection of nuclear quality. Fluorescence-activated nuclei sorting (FANS) of single nuclei was performed using the Beckman Coulter MoFlo Astrios EQ. Cell analysis and sorting were performed on a Beckman Coulter MoFlo Astrios EQ. A 405 nm (80 mW) laser was used for excitation of DAPI and a 561 nm (200 mW) laser was used for excitation of mCherry. DAPI was detected with a 448 /59 band-pass filter. mCherry was detected with a 614 /20 band-pass filter. DAPI+/mCherry+ nuclei were collected and sorted into 96-well plates preloaded with a lysis solution (6 µl per well) including 0.2% Triton X-100, 1 U/ul SuperaseIN (Invitrogen), 1 mM dNTPs and RT primer. Individual nuclei were sorted into the 96-well plates on “Single Cell” mode with a drop envelope of “1”. Sheath pressure was set at 28 PSI.  Sample pressure was kept below 28.5 PSI.  A 100 µm nozzle was used.  Cells were run at an event rate between 2000 – 5000 cells / second. For cell sorting experiments a droplet drive frequency of 49.6 KHz was used. After sorting, 96-well plates were briefly centrifuged, flash frozen on dry ice and stored at -80°C prior to library preparation.
Primer annealing was performed by incubating plates on a thermocycler at 72°C for 3 minutes, followed by hold at 4°C. A reverse transcription reaction mix (7.5 µl) was added to each well. Each 7.5 µl of reaction mix contained 40U Maxima H Minus Reverse Transcriptase (ThermoFisher), 4U SupernaseIN, 7.5% PEG and 1uM TSO and 1X Maxima Buffer. Reverse transcription was performed by incubating plates on a thermocycler at 42°C for 90 minutes, followed by 10 cycles of 50°C for 2 minutes and 42°C for 2 minutes. Reverse transcription was stopped by heating at 75°C for 10 minutes, followed by hold at 4°C. An ExoI digestion mix (0.22 U/ µl) was subsequently added to each well to remove excess primer or singled stranded products. ExoI digestion was performed by incubating plates on a thermocycler at 37°C for 30 minutes, 85°C for 15 minutes and 75°C for 30 seconds, followed by hold at 4°C. Pooling was performed on the Biomek 4000 (Beckman Coulter, Brea California). cDNA cleanup was performed using Silane beads (ThermoFisher) suspended in RLT Plus buffer (Qiagen) and ethanol. Bead incubation was performed at room temperature for 20 minutes followed by placement on a magnetic stand. The supernatant was removed and the beads were washed twice with 80% ethanol before being returned to the magnet and allowed to air dry for 10 minutes. The beads were resuspended in 50 µl of nuclease-free water, incubated for 2 minutes and returned to the magnet. The supernatant was then removed, transferred to a clean Eppendorf tube and then split into two tubes for cDNA amplification. cDNA amplification was performed using a master mix containing 25 µl of 2X Kapa HotStart Mix (Roche) per reaction and 2 µl of 5 µM SMART PCR primer (Takara Bio). Amplification was performed by incubating tubes on a thermocycler at 98°C for 3 minutes followed by 18 cycles of 98°C for 20 seconds, 67°C for 15 seconds and 72°C for 5 minutes. The reaction was then maintained at 72°C for 5 minutes, followed by hold at 4°C. The two reactions were pooled in one Eppendorf tube and 70 µl of AMPureXP beads (Beckman Coulter) were added to the sample and incubated for 5 minutes at room temperature. The sample was placed on a magnet and the supernatant was removed. The beads were then washed twice with 80% ethanol, returned to the magnet and dried for 5 minutes. The beads were then resuspended in 25 µl of nuclease-free water, incubated for 2 minutes and placed on the magnet for removal of the supernatant to a new tube. The quality and quantity of cDNA was examined using an Agilent Bioanalyzer and Qubit Fluorometer (ThermoFisher). Sequencing libraries were prepared using Nextera XT Library Prep Kit (Illumina). 0.6 ng of cDNA was used as input and tagmentation and neutralization was performed as directed. Indexing PCR was performed as directed using 10 cycles by adding 5 µl of 2 µM custom i5 primer, 5 µl N7 Nextera primer and 15 µl of NPM. PCR was followed by 2 AMPureXP cleanups as above, first with 0.6 beads:sample ratio and then with 1:1 beads:sample. The final volume was eluted in 20 µl of nuclease-free water. QC was repeated as before. Libraries were sequenced using an Illumina NextSeq 500/550.

value: Brain, substantia nigra pars reticulata

value: neuron


title: N2_embryo_biological_replicate_3, smallRNA-seq

description: Library name: WTCHG_954678_218


title: Wild-type mice duodenum_14days_600IIAEK (IIAEK)_rep3


title: ybhD inducible 2

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

value: ybhD

value: anti-FLAG mAb


title: Day7-3

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

country: Canada

institute: St. Michael's Hospital

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software
Transcript abundances for each sample were estimated with StringTie , and the FPKM  value for gene and transcript level were calculated with R package Ballgown
Assembly: GRCm38
Supplementary files format and content: FPKM

source_name: Primary kidney fibroblasts

growth_protocol: Adult kidney fibroblasts were isolated from C57BL/6 mouse control kidneys and UUO kidneys after tissue digestion and enriched in DMEM containing 10% FBS, L-glutamine and 1% penicillin/streptomycin

extract_protocol:
Total RNA from fibroblasts was isolated using Trizol and quantified using NanoDrop ND-1000
Total RNA was used to prepare sequencing libraries with a KAPA Stranded RNA-Seq Library Prep Kit (Illumina)
Sequencing was carried out using an Illumina NovaSeq 6000

tag: tissue source of cells

value: Kidneys

tag: surgical condition

value: 7 day UUO kidneys


title: Day7-4


title: Wild-type mice duodenum_14days_600IIAEK (IIAEK)_rep1

value: duodenum


title: SNr_MSC_plate_1


title: Day7-2


title: IAP knockout (IAP-KO) (Akp3-/-) mice duodenum_14days_0IIAEK (Control)_rep1


title: xnp-1_L1_biological_replicate_2, smallRNA-seq

description: Library name: WTCHG_954678_217


title: yagI inducible 2

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

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).

tag: transcription factor

value: yagI

tag: chip antibody

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

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


title: SNr_Med_plate_4


title: N2_L1_biological_replicate_2, smallRNA-seq

description: Library name: WTCHG_954678_216

value: whole organism


title: WT_TAM1

description: WT_TAM vs KO_TAM.readcount


title: Wild-type mice duodenum_14days_0IIAEK (Control)_rep1

source_name: Wild-type mice duodenum, oral administarion of a 5 g/L solution of carboxymethylcellulose sodium salt once a day for 14days to the mice

value: male


title: Wild-type mice duodenum_14days_0IIAEK (Control)_rep3


title: yafN inducible 2

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

value: yafN

tag: antibody vendor/catalog#

tag: media

value: Log-Phase


title: Wild-type mice duodenum_14days_0IIAEK (Control)_rep2

tag: tissue


title: Day3-4

value: 3 day UUO kidneys


title: uxuR inducible 2

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

value: uxuR

tag: time


title: SNr_Med_plate_2

value: Brain, substantia nigra pars reticulata


title: Day7-1


title: xnp-1_embryo_biological_replicate_2, smallRNA-seq

description: Library name: WTCHG_954678_215

value: embryo

tag: genotype


title: N2_embryo_biological_replicate_2, smallRNA-seq

description: Library name: WTCHG_954678_214


title: Day3-3


title: SNr_Med_plate_1

tag: cell type

value: neuron


title: uidR native 2

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

value: uidR

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: xnp-1_L1_biological_replicate_1, smallRNA-seq

description: Library name: WTCHG_954678_213


title: SNr_DR_plate_5


title: Day3-1

value: Kidneys


title: treR inducible 3

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

value: treR

value: anti-FLAG mAb

tag: treatment


title: treR inducible 2

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: SNr_DR_plate_4


title: xnp-1_embryo_biological_replicate_1, smallRNA-seq

description: Library name: WTCHG_954678_211

value: whole organism


title: SNr_Med_plate_3


title: Control-3

value: Control kidneys


title: sxy inducible 2

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

value: sxy

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


title: SNr_DR_plate_3


title: Control-2


title: N2_embryo_biological_replicate_1, smallRNA-seq

description: Library name: WTCHG_954678_210


title: xnp1_L1_biological_replicate_3, RNA-Seq

description:
Library name: WTCHG_945386_73475323
all_samples_counts_embryo_L1.txt


title: N2_L1_biological_replicate_3, RNA-Seq

description:
Library name: WTCHG_945386_73465322
all_samples_counts_embryo_L1.txt


title: ONPRC026_C

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

description: 10X Genomics

data_processing:
Raw GEX libraries were mapped to the Ensemble rhesus macaque reference genome (Macaca_mulatta.Mmul_10 release 109) using cellranger count (version 6.1.1) from 10x genomics. The aligned data was filtered using SoupX default parameters and quality assessment and filtering of UMIs and individual cells performed using the scater R package with experiment specific thresholds. Data set merging and normalization were performed using the Seurat R package (version 4.0) with default settings.
Assembly: Macaca_mulatta.Mmul_10 Release 109
Supplementary files format and content: Raw matrix files from CellRanger version 6.1.1 using Macaca_mulatta.Mmul_10 release 109.

organism: Macaca mulatta

source_name: Testis

extract_protocol:
Gonads were dissociated using a enzymatic mix (collagenase and dispase in FBS), washed and immdiately proceeded to GEM encapsulation.
Libraries for 10X genomics were produced according to manufacturer's instructions.

value: Testis

tag: embryonic day/stage


title: SNr_DR_plate_1


title: sgcR inducible 2

first: James

last: Galagan

address: 36 Cummington Mall

institute: Boston University

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

value: sgcR

value: Log-Phase


title: SNr_DR_plate_2

value: Brain, substantia nigra pars reticulata


title: Control-1


title: sfsB inducible 2

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

value: sfsB


title: xnp1_embryo_biological_replicate_3, RNA-Seq

description:
Library name: WTCHG_945386_73455321
all_samples_counts_embryo_L1.txt

value: embryo


title: ulaR inducible 2

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

value: ulaR


title: srlR inducible 2

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

value: srlR


title: N2_L1_biological_replicate_1, smallRNA-seq

description: Library name: WTCHG_954678_212


title: ONPRC026_B

description: 10X Genomics


title: sgrR inducible 2

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

value: sgrR


title: SNr_PNo_plate_4

value: neuron


title: SNr_PNo_plate_3


title: Day3-2

value: Kidneys

value: 3 day UUO kidneys


title: N2_embryo_biological_replicate_3, RNA-Seq

description:
Library name: WTCHG_945386_73445320
all_samples_counts_embryo_L1.txt


title: ONPRC026_A

description: 10X Genomics


title: SNr_PNo_plate_2


title: ONPRC023_C

description: 10X Genomics


title: xnp1_L1_biological_replicate_2, RNA-Seq

description:
Library name: WTCHG_945386_73435319
all_samples_counts_embryo_L1.txt


title: SNr_PNo_plate_1


title: ONPRC023_B

description: 10X Genomics


title: N2_L1_biological_replicate_2, RNA-Seq

description:
Library name: WTCHG_945386_73425318
all_samples_counts_embryo_L1.txt


title: pdhR native pyr

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

value: pdhR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

value: 40mM pyruvate


title: SNr_IC_plate_3


title: xnp1_embryo_biological_replicate_2, RNA-Seq

description:
Library name: WTCHG_945386_73415317
all_samples_counts_embryo_L1.txt

value: whole organism


title: ONPRC023_A

description: 10X Genomics

value: Testis


title: SNr_IC_plate_2


title: ONPRC015_B

description: 10X Genomics


title: N2_embryo_biological_replicate_2, RNA-Seq

description:
Library name: WTCHG_945386_73405316
all_samples_counts_embryo_L1.txt


title: SNr_IC_plate_1


title: pdhR native 3

value: Log-Phase


title: xnp1_L1_biological_replicate_1, RNA-Seq

description:
Library name: WTCHG_945386_73395315
all_samples_counts_embryo_L1.txt


title: pdhR inducible pyr

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


title: ONPRC015_A

description: 10X Genomics


title: SNr_LSC_plate_4

value: Brain, substantia nigra pars reticulata


title: ONPRC014_B

description: 10X Genomics


title: SNr_LSC_plate_3


title: nsrR native 2

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

value: nsrR

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


title: N2_L1_biological_replicate_1, RNA-Seq

description:
Library name: WTCHG_945386_73385314
all_samples_counts_embryo_L1.txt


title: rstA inducible 2

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

value: rstA

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


title: pdhR inducible 4


title: xnp1_embryo_biological_replicate_1, RNA-Seq

description:
Library name: WTCHG_945386_73375313
all_samples_counts_embryo_L1.txt

value: embryo


title: ONPRC014_A

description: 10X Genomics


title: relE inducible 2

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

value: relE


title: ONPRC013_B

description: 10X Genomics


title: SNr_LSC_plate_2

value: neuron


title: N2_embryo_biological_replicate_1, RNA-Seq

description:
Library name: WTCHG_945386_73365312
all_samples_counts_embryo_L1.txt


title: nhaR inducible 3

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

value: nhaR


title: SNr_LSC_plate_1


title: Q6_3, case batch 3

first: Joseph

middle: A.

last: Gogos

department: Zuckerman Institute

data_processing:
Raw reads were subjected to ACGT101-miR (LC Sciences, Houston, TX, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18∼26 nucleotide were mapped to specific species precursors in miRBase (v22.0) by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs
The unique sequences mapping to human mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known human  precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two mentioned mapped   5p and 3p sequences were defined as known miRNAs.
Assembly: Hg38, Ensembl version 98

source_name: hiPSC-derived cortical neurons

growth_protocol: Human iPSC-derived cortical neurons at DIV8 were generated using combined small molecule inhibitors as described in Thakur et al.

extract_protocol:
Total RNA extraction with miRNA enrichment was performed using the Vana™ miRNA Isolation Kit (Thermo Fisher Scientific, AM1561).
Approximately 1 ug of total RNA was used to prepare small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA) and single-end sequencing 50bp on an Illumina Hiseq 2500 (following the vendor’s recommended protocol) was conducted

value: hiPSC-derived cortical neurons

tag: cell line


title: ONPRC013_A

description: 10X Genomics


title: VSMC, IP, shMettl14, B

city: Sydney

first: Justin

middle: J-L

last: Wong

address: Charles Perkins Centre Lvl4 West, The University of Sydney, Camperdown, NSW, Australia

department: School of Medical Sciences, Faculty of Medicine and Health,

country: Australia

institute: University of Sydney

description: Library name: VSMC_IP_shMettl14_B

data_processing:
Reads were mapped using STAR. Non-uniquely mapping reads were filtered out using SAMtools.
MACS2 was used to call m6A peaks enriched in IP over corresponding input samples.
High-confidence peaks were determined by intersecting peaks from replicate runs.
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak
Supplementary files format and content: bedfile with overlapping peaks from each set of duplicates

source_name: Smooth muscle

extract_protocol:
Total RNA was extracted using TRIzol
3-5µg of total RNA underwnet zinc-mediated fragmentation into fragments of approximately  200nt. To enrich for RNA fragments containing m6A modifications, magnetic beads were first prepared in IP buffer and 5 μg anti-m6A antibody (Millipore) by mixing for 6 h at 4 ̊C. The antibody-bead mixtures were resuspended in IP reaction solutions containing fragmented total RNA. m6A-enriched fragmented RNA was eluted from the beads using the Rneasy Mini Kit (Qiagen). The eluates were resuspended in ethanol and transferred to an Rneasy MiniElute spin column (Qiagen) and centrifuged at high speed.

value: Smooth muscle

value: Vascular smooth muscle cells

value: Primary vascular smooth muscle cells


title: nagC native 3

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

value: nagC

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol


title: Q6_2, case batch 2


title: ONPRC011_B

description: 10X Genomics

value: Testis


title: VSMC, IP, shMettl14, A

description: Library name: VSMC_IP_shMettl14_A


title: mraZ inducible 2

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

value: mraZ

value: Log-Phase


title: modE native 2

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

value: modE


title: Q5_3, ctrl batch 3

value: Wild type


title: ONPRC011_A

description: 10X Genomics


title: VSMC, IP, shCTR, A

description: Library name: VSMC_IP_shCTR_A

value: shCTR


title: mlrA inducible 2

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

value: mlrA

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


title: VSMC, Input, shMettl14, B

description: Library name: VSMC_Input_shMettl14_B


title: metR inducible 1

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

value: metR


title: ONPRC010_B

description: 10X Genomics


title: ONPRC010_A

description: 10X Genomics


title: VSMC, Input, shMettl14, A

description: Library name: VSMC_Input_shMettl14_A


title: ∆scmA∆vsrA (JC2542) replicate C (M2G)

description: Library name: JC2542C

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 2.5).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Reads were aligned againstCaulobacter vibrioides NA1000 ASM2200v1 genome using STAR (v. 2.5.3a)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1) usingCaulobacter vibrioides NA1000 ASM2200v1 gene annotation.
Assembly: Caulobacter vibrioides NA1000 ASM2200v1
Supplementary files format and content: tab-delimited text file includes read counts per gene locus for each sample

extract_protocol:
RNA samples were prepared from 10 ml bacterial cultures. Cells were harvested at 4°C by centrifugation at 8,000 rpm for 10 minutes and immediately frozen in liquid nitrogen. The samples were stored at -80°C until their processing. RNA were extracted using the RNeasy mini kit from Qiagen following the manufacturer’s recommendation. Any remaining DNA was removed by on-column DNA digestion with DNase I (RNase-free DNases set from Qiagen) followed by a TURBO DNA-freeTM DNase treatment (Invitrogen). RNA samples were then re-purified using a RNA clean-up procedure (RNeasy mini kit).
RNA-seq libraries were prepared from 100 ng of total RNA with the Illumina Stranded mRNA Prep reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer). The polyA selection step was replaced by an rRNA depletion step with the RiboCop for Bacteria, mixed bacterial samples reagents (Lexogen).

value: deltaCCNA_01085 deltaCCNA_02930 (delta-scmA delta-vsrA)


title: melR inducible 2

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

value: melR


title: VSMC, Input, shCTR, B

description: Library name: VSMC_Input_shCTR_B

value: Smooth muscle

value: Vascular smooth muscle cells


title: Q5_1, ctrl batch 1

value: hiPSC-derived cortical neurons


title: ONPRC009_B

description: 10X Genomics


title: nanR inducible 2

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

value: nanR

value: anti-FLAG mAb


title: ONPRC009_A

description: 10X Genomics


title: mazE native 2

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

value: mazE

value: Sigma/Cat. No. F1804

value: M9 Minimal with 0.4% glycerol

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


title: ∆scmA∆vsrA (JC2542) replicate B (M2G)

description: Library name: JC2542B


title: Q6_1, case batch 1


title: ONPRC005_B

description: 10X Genomics

value: Testis


title: VSMC, Input, shCTR, A

description: Library name: VSMC_Input_shCTR_A

value: Primary vascular smooth muscle cells


title: VSMC, IP, shCTR, B

description: Library name: VSMC_IP_shCTR_B

value: shCTR


title: WT

description: 10X Genomics

source_name: thymus

value: thymus

value: WT

value: enriched by anti-CD25 beads


title: matA inducible 2

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

value: matA

value: Log-Phase

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


title: VSMC, B, shMettl14

description: Library name: VSMC_B_shMettl14

data_processing:
Reads were mapped to the genome using STAR, with gene quantification performed using FeatureCounts
Assembly: mm10
Supplementary files format and content: Table of counts for all genes

extract_protocol:
Total RNA was extracted using TRIzol
2µg of poky-A enriched mRNA library were treated with TURBO DNase, and prepared using the TruSeq Stranded Library Preparation Kit per manufacturers instructions. Sequencing was performed on an Illumina HiSeq 2500, aiming for 100 million paired-end reads per sample

value: Smooth muscle

value: Vascular smooth muscle cells


title: marA inducible 2

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

value: marA


title: ONPRC004_B

description: 10X Genomics


title: VSMC, B, shCTR

description: Library name: VSMC_B_shCTR


title: Q5_2, ctrl batch 2

value: hiPSC-derived cortical neurons

value: Wild type


title: lldR inducible 2

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

value: lldR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: VSMC, A, shMettl14

description: Library name: VSMC_A_shMettl14


title: ONPRC004_A

description: 10X Genomics

value: Testis


title: kdgR inducible 2

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

value: kdgR

value: M9 Minimal with 0.4% glycerol


title: ∆vsrA (JC2540) replicate A (M2G)

description: Library name: JC2540A

value: deltaCCNA_02930 (delta-vsrA)


title: ONPRC003_B

description: 10X Genomics


title: hipB inducible 2

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

value: hipB


title: VSMC, A, shCTR

description: Library name: VSMC_A_shCTR

value: Primary vascular smooth muscle cells

value: shCTR


title: ONPRC003_A

description: 10X Genomics


title: hipA inducible 3

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

value: hipA

value: Log-Phase


title: MB299

city: Heidelberg

first: Michele

last: Bortolomeazzi

address: TP3 B4.105.5, Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

description: Tissues were sectioned into 10 µm slices, and four samples were placed on a single Xenium slide. After sectioning, the slides were stored at -80°C for less than two weeks. On the day of the experiment, the tissue was fixed with PFA according to the manufacturer's protocol. Tissues were permeabilized with SDS, incubated in 70% ice-cold methanol, and washed with PBS. Hybridization of the human generic brain panel with 70 add-on genes (Supplementary Dataset 1) was performed at 50°C in a Bio-Rad C1000 touch cycler for 20 hours. The washing, ligation, and amplification steps were carried out according to the manufacturer’s instructions. ROIs were selected based on the tissue area, excluding non-tissue-covered tiles. Each transcript was imaged in a bright state five times across 60 cycle-channels (15 cycles x 4 channels). After the run on the Xenium analyzer, slides were removed, and buffer was exchanged with PBS-T for further storage at 4°C.

hyb_protocol: Hybridization of the human generic brain panel with 70 add-on genes was performed at 50°C in a Bio-Rad C1000 touch cycler for 20 hours

scan_protocol: Xenium In Situ Analyzer

data_processing: Xenium Onboard Analysis: 1.7.6.0

label: Xenium Human Probe Set

source_name: Brain with Medulloblastoma

label_protocol: Xenium Human Probe Set

tag: subtype

value: MBEN


title: ∆vsrA (JC2540) replicate C (M2G)

description: Library name: JC2540C


title: ∆scmA∆vsrA (JC2542) replicate A (M2G)

description: Library name: JC2542A

value: deltaCCNA_01085 deltaCCNA_02930 (delta-scmA delta-vsrA)


title: ONPRC005_A

description: 10X Genomics


title: MB295

extract_protocol: Tissues were sectioned into 10 µm slices, and four samples were placed on a single Xenium slide. After sectioning, the slides were stored at -80°C for less than two weeks. On the day of the experiment, the tissue was fixed with PFA according to the manufacturer's protocol. Tissues were permeabilized with SDS, incubated in 70% ice-cold methanol, and washed with PBS.


title: ONPRC027_B

description: 10X Genomics

source_name: Ovary

value: Ovary


title: hdfR inducible 2

city: Boston

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

value: hdfR

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


title: ONPRC002_A

description: 10X Genomics


title: ONPRC002_B

description: 10X Genomics


title: WT_CD8SP_3

first: Shaofeng

state: <None>

address: 8th floor, Dr. Tak Mak lab, Princess Margaret Cancer Centre

institute: UHN

description: SMARTer Mouse TCR a/b Profiling Kit

data_processing:
Data were analyzed using MiXCR and VDJtools. Statistical analyses were performed using Prism 5.0 (GraphPad), with the two-tailed paired t-test employed for comparison of repertoire properties.
Assembly: mm10
Supplementary files format and content: TSV files (MiXCR processed files)
Library strategy: TCR-Seq

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Micro Kit (50) (#74034).
TCR libraries were prepared using SMARTer Mouse TCR a/b Profiling Kit
Libraries were  sequenced using the MiSeq platform (Illumina)

treatment_protocol: Single cell suspensions were prepared from mouse thymus, thymocytes were stained with BV605-CD8 and BV711-CD4. CD4SP and CD8SP thymocytes were sorted by FACS (BD Aira Fusion)

value: thymus

value: thymocytes

value: wild type


title: MB266


title: P5 Human Colon Cancer

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

data_processing: During the Xenium Analyzer workflow, the Xenium In Situ Cell Segmentation Solution was used to identify cell boundaries (cell segmentation) in an automated fashion. The solution includes antibodies for labeling membranes, antibodies for labeling cell interiors, a universal interior label for ribosomal RNA, and a DAPI stain for nuclei. Probe hybridization, ligation, amplification, cell segmentation staining, and autofluorescence quenching followed the Xenium In Situ Gene Expression with Morphology-based Cell Segmentation Staining User Guide (CG000749).The Xenium Onboard Analysis pipeline v2.0 (10x Genomics) was run directly on the instrument for imaging processing, cell segmentation, image registration, decoding, deduplication, and secondary analysis.

source_name: Colon cancer

label_protocol: The 10x Genomics Xenium Human Colon Gene Expression Panel (322 genes) was supplemented with an additional 100 genes chosen to characterize the TME. Three genes, each with unique probesets, were designed for the two alpha and one beta chains of the TCR clonotype identified from the Single Cell Immune Profiling data in sample P5 CRC. The other 97 genes included markers that were enriched in different subsets of tumor cells from the single cell reference atlas and from the Visium HD data. They include marker genes for macrophages, neutrophils, cancer-associated fibroblasts, granulocytes, chemokines, and other TME markers. The panel was designed using Xenium Panel Designer following the guidance in the Xenium Add-on Panel Design Technical Note (CG000643, RevB).

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 Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578, Rev C).

value: colon cancer


title: hcaR inducible 2

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

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

value: hcaR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: Chrna9KO_CD8SP_3

description: SMARTer Mouse TCR a/b Profiling Kit

value: Chrna9 KO


title: P2 Human Colon Cancer


title: ONPRC025_B

description: 10X Genomics


title: ONPRC027_A

description: 10X Genomics


title: glnG inducible 5

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

value: glnG

value: Gutnick


title: Chrna9KO_CD8SP_2

description: SMARTer Mouse TCR a/b Profiling Kit


title: gadX inducible 2

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

value: gadX

value: M9 Minimal with 0.4% glycerol


title: P1 Human Colon Cancer


title: ∆vsrA (JC2540) replicate B (M2G)

first: Karolina

last: Bojkowska

address: Unil, Genopode

institute: University of Lausanne

description: Library name: JC2540B

value: deltaCCNA_02930 (delta-vsrA)


title: galR inducible 2

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

value: galR

value: Log-Phase


title: fucR inducible 2

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

value: fucR


title: WT_CD8SP_2

last: Liu

description: SMARTer Mouse TCR a/b Profiling Kit


title: Chrna9KO_CD4SP_3

description: SMARTer Mouse TCR a/b Profiling Kit


title: MB263

value: MBEN


title: WT_CD4SP_2

description: SMARTer Mouse TCR a/b Profiling Kit

value: thymus


title: AA FtHfl/fl and FtHΔ/Δ (FB)

city: Birmingham

first: Yanfeng

last: Zhang

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

description:
Library name: AA treated samples fb
10x genomics

data_processing:
Each sample of scRNA-seq was mapped to the mouse reference genome (GRCm38) provided by 10x Genomics and using the CellRanger software (v 7.0) with default parameters. The samples then were merged by loading the CellRanger output h5 file using Seurat (v 5.1) for data preprocessing, integration, and normalization. Cells with fewer than 200 genes, more than 6,000 unique molecular identifiers (UMIs), and > 10% mitochondrial UMIs were excluded
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz

source_name: CD45+ cells

extract_protocol:
Mice were harvested at Weeks 6 post-final injection, and CD45⁺ immune cells were sorted from kidneys using flow cytometry and subjected to scRNA-seq using the 10× Genomics platform.
Single-cell 3’ biased transcriptome and featuring barcoding libraries were prepared using a 3’ Library & Gel Bead Kit (PN-1000268) and 3’ Feature Barcode Kit ( PN-1000262) according to the 10x Genomics manual. Libraries were sequenced by illumina Novaseq X plus machine

treatment_protocol: Male FtHfl/fl and FtHΔ/Δ mice (8–10 weeks old) were randomly assigned to either the aristolochic acid (AA) injection group or the control (Saline) group. Mice in the AA group received intraperitoneal injections of AA (2 mg/kg body weight; Sigma-Aldrich, A9451) once daily for five consecutive days to induce kidney injury, while control mice received an equal volume of saline as a vehicle control. Mice were harvested at Weeks 6 post-final injection

value: CD45+ cells


title: ONPRC018_B

description: 10X Genomics

value: Ovary


title: Vehicle FtHfl/fl and FtHΔ/Δ (GEX)

description:
Library name: Vehicle treated samples gex
10x genomics


title: ONPRC017_B

description: 10X Genomics


title: dinJ inducible 2

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: fimZ inducible 2

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

value: fimZ

value: anti-FLAG mAb


title: ONPRC018_A

description: 10X Genomics


title: AA FtHfl/fl and FtHΔ/Δ (GEX)

description:
Library name: AA treated samples gex
10x genomics


title: WT_CD4SP_3

description: SMARTer Mouse TCR a/b Profiling Kit

value: thymocytes

value: wild type


title: Chrna9KO_CD4SP_1

description: SMARTer Mouse TCR a/b Profiling Kit

value: Chrna9 KO


title: dicA inducible 2

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

value: dicA

value: Sigma/Cat. No. F1804


title: ONPRC025_A

description: 10X Genomics


title: WT_CD8SP_1

description: SMARTer Mouse TCR a/b Profiling Kit


title: dicA native 4

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

value: M9 Minimal with 0.4% glycerol

value: Stationary Phase


title: dicA native 3

value: LB


title: 0.4mM THP-1 rep2

city: Tokyo

first: Gaku

last: Ichihara

address: 6-3-1 Niijuku, Katsushika-ku

institute: Tokyo University of Science

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Cutadpat-v2.10.
The filtered reads were mapped to reference RNA (GRCh38 release-101) using Bowtie2-2.4.2 (parameters: -p 2 -L 16 --very-sensitive-local -N 1 -nofw -seed 656565 -reorder) and read number of each gene were counted.
Between-sample normalization was performed against raw count data by using R 3.5.1. (https://cran.r-project.org/) and TCC package (EEE-E method).
Assembly: GRCh38 release 101
Supplementary files format and content: Text file (.txt) of raw count matrix for every gene and every sample

source_name: monocytes

growth_protocol:
MMNK-1 cells (JCRB, Osaka, Japan) were maintained in low-glucose DMEM (Wako, Osaka, Japan), supplemented with 5% heat inactivated FBS (Biowest, Riverside, MO) at 37°C under 5% CO2 atmosphere. The cells were detached with Accutase (Innovative Cell Technologies, San Diego, CA) and passaged every 2-3 days.
THP-1 cells (ATCC, Rockville, MD) were maintained in RPMI1640 (Wako, Japan) and supplemented with 10% heat inactivated FBS, penicillin, streptomycin, L-glutamine (Gibco, Thermo Fisher, Waltham, MA), and 2-mercapethanol (0.05 mM, Sigma Aldrich, St. Louis, MO), at 37°C in an atmosphere of 5% CO2. The cells were subcultured every 3-4 days.

extract_protocol:
PolyA RNAs were isolated from the cell lysates, using Dynabeads M-270 Streptavidin (Thermo Fisher Scientific, MA) conjugated with biotin-3’ WTA-EcoP-dT25 and amplified according to the previous report with some modifications (GSE110711). 100 ng of the whole-transcriptome library was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs Inc., Tokyo, Japan) with some modifications.
Standard illumina protocols were followed to generate RNA libraries.

treatment_protocol: 1,2-DCP was diluted in complete medium for co-cultures of MMNK-1 and differentiated THP-1 cells. The DMSO concentration was adjusted to 0.1%. The seeded cells were exposed to 1,2-DCP concentrations of 0, 0.1 and 0.4 mM, for 24 hours and then incubated at 37°C, sealed in a Tedlar polyvinyl fluoride (PVF) gas sampling bags

value: Blood

value: human macrophages differentiated by PMA

value: 0.4 mM 1,2-DCP for 24 hrs


title: ONPRC012_B

city: Los Angeles

description: 10X Genomics


title: ONPRC016_A

description: 10X Genomics


title: Vehicle FtHfl/fl and FtHΔ/Δ (FB)

description:
Library name: Vehicle treated samples fb
10x genomics

value: CD45+ cells


title: 0.4mM THP-1 rep1


title: dicA native 2

value: Log-Phase


title: SYOI, sgSSX, R2

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

description: Library name: SYOI_sgSSX_R2

data_processing:
FPKM were obtained using featurecounts and bigwig using Bowtie alignment to T2T and bamcoverage
FPKM and bigwig
Assembly: hg19 for FPKM, T2T for bigwigs
Supplementary files format and content: FKPM in xls, RNA profiles in bigwig

source_name: SYO-I

growth_protocol: DMEM, 10% fetal bovine serum and cultured at 37C at 5% CO2.

extract_protocol:
RNA was prepared using RNeasy mini kit (QIAGEN) according to the manufacturer’s protocoland including the DNaseI (QIAGEN) treatment.
RNA-Seq library preparation and sequencing were performed at the High Throughput Sequencing Unit of the Genomics & Proteomics core facility of DKFZ using TruSeq Stranded Total RNA Library Prep kit (Illumina) and HiSeq 2000 v4 single-read 50bp sequencing system.

treatment_protocol: Stable HSSY-II cells expressing Cas9 were first generated and subsequently infected with the corresponding sgRNA

value: SYO-I

value: Human synovial sarcoma cells

value: Stable Cas9 expression

value: Cas9, SS18-SSX knockout


title: ONPRC012_A

description: 10X Genomics

value: Ovary


title: Chrna9KO_CD8SP_1

description: SMARTer Mouse TCR a/b Profiling Kit

value: thymus

value: thymocytes


title: SYOI, sgSSX, R1

description: Library name: SYOI_sgSSX_R1


title: ONPRC016_B

description: 10X Genomics


title: cynR inducible 2

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

value: cynR

value: anti-FLAG mAb

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


title: ONPRC007_B

description: 10X Genomics


title: 0.1mM THP-1 rep3

value: 0.1 mM 1,2-DCP for 24 hrs