title: LecLALA_8w_2_Chip_Barcodes

description:
Library name: LecLALA_8w_2_Chip_Barcodes.fastq.gz
NovaST spatial transcriptome sequencing

data_processing:
A combined Human (hg38) and Mouse (mm10) STAR index was created from the 10x Genomics GRCh38-and-mm10-2020-A index using STAR (v2.7.11a). This index was used together with the NovaScope Pipeline v1.111, utilizing spatula (v1.0.0) and STAR (v2.7.11a) to pre-process, map and quantify the data via the following two workflows: sge-per-run, transcript-per-unit. Mapped and quantified data was loaded and binned into hexagonal bins (TDs) with a width, and center-to-center distance of 40μm using custom Python code, images were exported at a resolution of 1px:1μm and used for alignment with immunofluorescent images previously collected. Images were aligned to spatial data using the Landmark Correspondences plugin in Fiji. Multiple fiducial circles, visible in both the 488 IF channel and the spatial data, were selected as landmarks. An affine transformation was then applied to achieve precise alignment.
Further processing was done using SCANPY in python
Assembly: GRCh38/mm10
Supplementary files format and content: h5ad of all 40um TDs per sample: 40um.h5ad; h5ad of cortical 40um TDs: CRX_40um.h5ad; chip barcode layout file: layout.tsv; DAPI staining: c4.tif; D54D2 staining: c2.tif
Library strategy: Spatial Transcriptomics

extract_protocol:
Briefly, OCT-embedded hemispheres were cryosectioned sagittaly.
The tissue optimization for Nova-ST is performed using 10X Genomics Visium Spatial Tissue Optimization kit, according to the manufacturer’s protocol (Visium Spatial Tissue Optimization Reagents kit, User Guide CG000238.Ref F). The Nova-ST spatial transcriptomics analysis was performed using Nova-ST chips prepared from repurposed NovaSeq 6000 S4 flow cell as described in the publication. Spatial transcriptomics workflow was followed as per the publication.

treatment_protocol: The effect of Lecanemab's Fc effector function on the microglial transcriptome was assessed following chronic treatment of 4-month-old male and female AppNL-G-F Csf1rΔFIRE/ΔFIRE mice dosed weekly intraperitoneally for 8 weeks with 10 mg kg−1 Lecanemab or Lecanemab 101 LALA-PG.

value: Brain

value: APP-NLGF x FIRE KO

value: Lecanemab LALA-PG


title: tumor tissues, 5% glucose, rep3

status: Public on Jul 31 2025

type: SRA

city: Beijing

first: yanghong

last: liu

address: No.2 Nanwei Road, Xicheng District

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

library_source: transcriptomic

data_processing:
Bioinformatics analysis of RNA-seq data was performed with R software(V 4.1.0). Differentially expressed genes (DEGs) were got using the DESeq2 package (v1.26.0) (10.1186/s13059-014-0550-8), with the following creteria: p < 0.01 and absolute log2 fold change > 1. Pathway enrichment were performed using kobas (doi.org/10.1093/nar/gkab447). Gene pathway network were plotted using the cluster Profiler package (v 4.2.2). The heatmap was plotted using the pheatmap package (v1.0.12). Protein-protein interaction network analysis were performed by String DB.
Assembly: GRCm38

molecule: total RNA

organism: Mus musculus

source_name: tumor tissues

extract_protocol:
the total RNA of tumor tissues in 5% glucose and CM-ZIF8 at Ce6/Lon+L group were  extracted using Trizol reagent.
RNA-seq libraries were prepared according to the manufacturer's library construction protocol.RNA quality was evaluated by Agilent 2100 BioAnalyzer (Agilent RNA 6000 Nano Kit). mRNA was purified via an oligo (dT) and subjected to sequencing library constructions. The  library quality  was performed using an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System. RNA-seq was carried out using an Novaseq600 with 150 base pair reads.

tag: tissue

value: tumor tissues

tag: strain

value: BALB/c mice


title: ATCC19606 biol rep 1

city: Yangzhou

first: JIngchen

last: Hao

address: No. 136, Jiangyang Middle Road

institute: Yangzhou University

description: Library name: ATCC19606_1

data_processing:
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Genome assembly ASM903584v1
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841

source_name: Bacteria

extract_protocol:
Total bacterial RNA extraction was performed using RNAprep PureCell/Bacteria Kit (TIANGEN) following manufacturer's protocols.
Ribosomal RNA was removed from the total RNA and then precipitated with ethanol.   After fragmentation, the first strand cDNA was synthesized using random hexamer primers.   During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer.   The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

value: Bacteria

tag: cell line

tag: cell type

value: Gram-negative coccobacillus


title: H3K4_scr2

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description:
Library name: nxid21410
H3K4 scranble

library_source: genomic

data_processing:
Raw data were mapped using bowtie2 with --sensitive-local mode
Peaks were called using seacr with parameters stringent
Assembly: hg19
Supplementary files format and content: Bedfile as outputed by SEACR of the Cut&Tag peaks
Library strategy: Cut & Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK293T were grown in DMEM supplemented with FCS and PSG

extract_protocol:
According to protocol from Zhao et al ., 2020
BrdU-Seq (NEBNext UltraII DNA Library Prep for Illumina)
NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, cat. no. E7370)

treatment_protocol: No

value: Myeloid

tag: chip antibody

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9752


title: LecLALA_8w_1_Chip_Barcodes

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

description:
Library name: LecLALA_8w_1_Chip_Barcodes.fastq.gz
NovaST spatial transcriptome sequencing

source_name: Brain

growth_protocol: Mice were housed in groups of 2-5, under a 14/10 h light/dark cycle at 21°C, with food and water ad libitum.

tag: genotype

tag: treatment


title: ST-LPD1 (LPD treated  Raw264.7 cells with Salmonella infection)

city: Changchun

first: Jiazhang

last: Qiu

address: Xi'an Road 5333

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Mus musculus  Ensembl_v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Murine monocyte-macrophage leukemia cells


title: H3K9_93v4

description:
Library name: nxid21408
H3K9 ZNF93KD

value: Active Motif, RRID:AB_2532132, RRID:AB_2532132


title: ST3 (Salmonella infected  Raw264.7 cells)

value: Salmonella infected  Raw264.7 cells


title: Lec_8w_2_Chip_Barcodes

description:
Library name: Lec_8w_2_Chip_Barcodes.fastq.gz
NovaST spatial transcriptome sequencing

value: Lecanemab


title: ST2 (Salmonella infected  Raw264.7 cells)


title: Lec_8w_1_Chip_Barcodes

description:
Library name: Lec_8w_1_Chip_Barcodes.fastq.gz
NovaST spatial transcriptome sequencing


title: ST1 (Salmonella infected  Raw264.7 cells)


title: H3K9_93v3

description:
Library name: nxid21407
H3K9 ZNF93KD


title: H3K9_93v2

description:
Library name: nxid21406
H3K9 ZNF93KD


title: Healthy1_WTA

city: Stanford

first: Asiri

last: Ediriwickrema

address: 265 Campus Dr

department: Institute for Stem Cell Biology and Regenerative Medicine

country: USA

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
raw data was processed using sevenbridges per BD Rhapsody protocol recommendations
Assembly: hg38
Supplementary files format and content:  output files are count tables for both genes and adts in a csv file.

source_name: bone marrow

extract_protocol:
cryopreserved bone marrow cells were thawed and submitted for single cell capture and processing using the BD Rhapsody workflow
libraries were generated according to manufacter's instructions.

value: bone marrow

tag: age

tag: Sex

value: male

tag: ethnicity

value: White

tag: library type

value: GEX


title: LPD3 (LPD treated  Raw264.7 cells)

value: LPD treated  Raw264.7 cells


title: H3K4_scr3

description:
Library name: nxid21411
H3K4 scranble

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9753


title: H3K9_scr4

description:
Library name: nxid21404
H3K9 scamble


title: Lecanemab LALA-PG Rep 1, GEX

description:
Library name: LecLALA_8w_1
NovaST spatial transcriptome sequencing

value: Brain

value: APP-NLGF x FIRE KO

value: Lecanemab LALA-PG


title: Vessel_KO rat_male_Ang II_rep1

type: RNA

city: Imabari

first: Masashi

last: Mukohda

state: Ehime

address: 1-3 Ikoinooka, Imabari

country: Japan

institute: Okayama University of Science

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol /ug ) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1 (Agilent) using default parameters (Grid: 074036_D_F_2020909) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Vessel from KO rat with Ang II

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA, United States).  Dye incorporation and cRNA yield were checked with the NanoDrop ONEc Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, United States).

extract_protocol: Total RNA was prepared using Trizol, and RNA integrity was assessed using the 2200 TapeStation systems (Agilent Technologies, Santa Clara, CA, United States).

tag: tssue

value: Vessel

value: KO, Ang II

value: PKCbeta deletion


title: Lecanemab LALA-PG Rep 2, GEX

description:
Library name: LecLALA_8w_2
NovaST spatial transcriptome sequencing


title: Seed kernels, harvest date, September, biological replicates 3

city: Kunming

last: Li

state: Yunnan

address: Qingyun Street

institute: Southwest Forestry University

data_processing:
Pinus armandii
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, cDNA libraries were sequenced on Illumina high-throughput platform.
The raw reads were filtered using the fastp platform for quality control as follows.1.Remove reads containing adapter;2. Remove the reads with N ratio greater than 10%;3. Remove reads with all A bases;4.Remove low-quality reads (the number of bases with quality value Q less than or equal to 20 accounts for more than 50% of the whole read).
The reads were assembled using Trinity software, and assembly quality was assessed based on N50 values and GC content, and assembly integrity was assessed using BUSCO software.
The Unigene sequences were aligned to the protein databases nr, SwissProt, KEGG and COG/KOG by blastx (evalue<0.00001) to obtain the protein with the highest sequence similarity to a given Unigene, thus obtaining the protein functional annotation information for that Unigene. The assembled unigene was then quantified using RSEM software, and the expression was shown in raw reads count and FPKM.
Supplementary files format and content: raw counts, FPKM for each Sample

organism: Pinus armandii

source_name: Seed kernel

extract_protocol:
There are two time periods for harvesting the seed kernels of Pinus armandii : August and September
The mRNA of the seed kernel was collected in two time periods, August and September, respectively.

value: Seed kernel

tag: harvest time

value: September


title: H3K4_scr1

description:
Library name: nxid21409
H3K4 scranble

value: Myeloid

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9751


title: H3K9_scr3

description:
Library name: nxid21403
H3K9 scamble

value: Active Motif, RRID:AB_2532132, RRID:AB_2532132


title: Lecanemab Rep 2, GEX

description:
Library name: Lec_8w_2
NovaST spatial transcriptome sequencing

value: Lecanemab


title: Seed kernels, harvest date, September, biological replicates 2


title: H3K9_scr2

description:
Library name: nxid21402
H3K9 scamble


title: Vessel_WT rat_male_Ang II_rep1

source_name: Vessel from WT rat with Ang II

value: WT, Ang II

value: male

value: WT


title: Seed kernels, harvest date, September, biological replicates 1


title: LPD1 (LPD treated  Raw264.7 cells)

value: Murine monocyte-macrophage leukemia cells

value: LPD treated  Raw264.7 cells


title: Vessel_KO rat_male_control_rep1

source_name: Vessel from KO rat

value: KO


title: LPD2 (LPD treated  Raw264.7 cells)


title: Blank3 (untreated Raw264.7 cells)

value: untreated Raw264.7 cells


title: Vessel_WT rat_male_control_rep1

source_name: Vessel from WT rat


title: Lecanemab Rep 1, GEX

description:
Library name: Lec_8w_1
NovaST spatial transcriptome sequencing

value: Brain

value: APP-NLGF x FIRE KO


title: S. Typhimurium 14028s tolC, 10 µM MgSO4, rep 2

city: Seattle

first: William

middle: Ryan

last: Will

state: WA

address: 1959 NE Pacific Street

department: Laboratory Medicine and Pathology

institute: University of Washington

description: Library name: tolC_rep2

data_processing:
Galaxy Platform
Cutadapt was used to remove adapter sequences and reads below length and quality thresholds of 20.
Reads were mapped to the S. Typhimurium 14028s genome using Bowtie2.
Mapped read counts were generated using htseq-count.
Differential gene expression and normalized counts were determined using DEseq2.
Assembly: GCA_000022165.1; ASM2216v1
Supplementary files format and content: txt file containing normalized rlog counts for each library

organism: Salmonella enterica

source_name: bacterial culture

growth_protocol: Cultures were grown to 1.0 OD600 in LB, then washed three times in N-minimal medium containing 10 µM Mg SO4. Cultures were grown for an additional hour in N-minimal medium.

extract_protocol:
RNA was purified using TRIzol reagent (Life Technologies, Carlsbad, CA) and DirectZol columns (Zymo Research, Irvine, CA). rRNA was depleted using the method described in "Culviner PH, Guegler CK, Laub MT. A Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies. mBio. 2020 Apr 21;11(2):e00010-20. doi: 10.1128/mBio.00010-20. PMID: 32317317; PMCID: PMC7175087".
Libraries were prepared for RNA-Seq using NEBNext Ultra II RNA library prep kit (New England Biolabs, Ipswich, MA) according to the manufacturer's instructions.

value: bacterial culture

value: tolC

value: 10 µM MgSO4, N-minimal medium


title: g9NHC_shIFT88_5198-6_3

city: Austin

first: Estanislao

last: Peixoto

state: MN

address: 801 16th Ave NE

institute: Hormel Institute, University of Minnesota

data_processing:
The  University of Minnesota Research Informatics at MSI  analyzed the RNA Seq output. 2 x 75bp FastQ paired-end reads for 6 samples  were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC
Sequencing reads were mapped to the human reference genome (hg38, UCSC) using Hisat2.
Genes differentially expressed between NHC-NT and NHC-IFT88   were calculated using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Homo sapiens
Supplementary files format and content: Estanislao_RawReadCounts.txt

molecule: polyA RNA

growth_protocol: The NHC cell lines were cultured cultured in plastic flasks with media at 37°C and 5% CO2.

extract_protocol:
The analysis of differential gene expression between the NHC-NT and NHC-IFT88 cell lines was conducted using the RNA-seq technique. Total RNA was obtained using the Qiagen RNeasy kit, following the manufacturer's instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq stranded mRNA Protocols at the University of Minnesota Genomic Center (UMGC)

value: NHC


title: g9NHC_shIFT88_5198-6_2


title: g9NHC_shIFT88_5198-6_4


title: S. Typhimurium 14028s tolC, 10 µM MgSO4, rep 1

description: Library name: tolC_rep1


title: g9NHC_shIFT88_5198-6_1


title: Seed kernels, harvest date, August, biological replicates 2

value: Seed kernel

value: August


title: S. Typhimurium 14028s slyA, 10 µM MgSO4, rep 2

description: Library name: slyA_rep2

value: slyA


title: Blank1 (untreated Raw264.7 cells)


title: Ep KO_3

city: shanghai

first: li

last: zihao

address: dongchuan road 800

institute: shanghai jiao tong university

description: Library name: Sample6

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
Assembly: mm9
Supplementary files format and content: In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.
Supplementary files format and content: processed data.xlsx

source_name: Stomach

growth_protocol: no

extract_protocol:
Antral Epithelial cells were sorted by FACS, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Col1a2-creERT;Bmpr1a and ctrl mice (10 weeks-old) were gave 3 dose of TAM and then sorted Epithelial cells from antrum by FACS

value: Stomach

value: Epithelial cells

value: 3 dose of TAM treat for 14 day3


title: Seed kernels, harvest date, August, biological replicates 1


title: S. Typhimurium 14028s, 10 µM MgSO4, rep 2

description: Library name: WT_rep2

value: wildtype


title: S. Typhimurium 14028s slyA, 10 µM MgSO4, rep 1

description: Library name: slyA_rep1


title: Ep KO_2

description: Library name: Sample5


title: AP2P_KD_MicroC_schizont, 36 hpi, MicroC6

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Micro-C paired-end reads were mapped to the P. falciparum genome and processed into pairs and multi-resolution normalized contact matrix .mcool files using hicstuff
Assembly: P. falciparum genome (plasmoDB.org, version 3, release 55)
Supplementary files format and content: high resolution interaction matrices in .mcool format
Library strategy: Micro-C

organism: Plasmodium falciparum 3D7

growth_protocol: Blood stage 3D7 or NF54 P. falciparum parasites were cultured in human RBCs supplemented with 10% v/v Albumax I (Thermo Fisher 11020), hypoxanthine (0.1 mM final concentration, C.C.Pro Z‐41‐M) and 10 mg gentamicin (Sigma G1397) at 4% hematocrit and under 5% O2, 5% CO2 at 37 °C.

extract_protocol:
Parasites were cross-linked by adding methanol-free formaldehyde to 1% final concentration. The reaction was quenched by adding 1 M Tris-HCl pH 7.5. Parasites were washed with DPBS at 25°C, resuspended in the second cross-linking solution - 3 mM DSG in DPBS and incubated for 45 minutes. The reaction was quenched with 1 M Tris-HCl pH 7.5. The cell pellet was lysed and digested with the chosen concentration of MNase. Each pellet was resuspended in end-chewing mix [1X NEB Buffer 2.1, 2 mM ATP, 5 mM DTT, 0.5 U/μl T4 PNK] and incubated for 15 minutes. Klenow fragment was added, followed by 25 μl of end-labeling mix [0.2 mM Biotin-dATP, 0.2 mM Biotin-dCTP, 0.2 mM dTTP, 0.2 mM dGTP, 0.1 mg/ml BSA]. 500 mM EDTA was added and incubated for 30 minutes. Biotinylated DNA fragments were then covalently linked by proximity ligation by resuspending the pellet in ligation mix [1X T4 DNA ligase buffer, 0.1 mg/ml BSA, 33 U/μl T4 DNA ligase)]. The biotin-dNTPs were removed from unligated ends, the DNA was purified and decrosslinked. The DNA contained in the supernatant was recovered using the DNA Clean & Concentrator. The ligated DNA was loaded onto a 2% TAE agarose gel to separate dimers from monomers, and DNA was extracted. The biotinylated dimers were isolated with Dynabeads MyOne Streptavidin C1.
The library prep was performed with the samples on beads using the NEBNext® Ultra II Directional DNA Library Prep Kit (NEB E7645), with several modifications.


title: g8NHC_shIFT88_5198-4_3


title: Ep KO_1

description: Library name: Sample4


title: S. Typhimurium 14028s, 10 µM MgSO4, rep 1

description: Library name: WT_rep1


title: Ep con_3

description: Library name: Sample3


title: Blank2 (untreated Raw264.7 cells)

value: Murine monocyte-macrophage leukemia cells


title: g8NHC_shIFT88_5198-4_2


title: Ep con_2

description: Library name: Sample2


title: DesWithSec (Of B. subtilis treated with Plant secretion)-3

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description:
Descendents of Prined with secretions
Library 15

data_processing:
The number of uniquely mapped reads per gene was calculated with HTSeq (2).
Fastq reads were trimmed from their adapter with cutadapt and aligned to the B. subtilis genome (subsp. subtilis str. NCIB 3610, NZ_CM000488.1) with Bowtie 2 version 2.3.4.1
The number of uniquely mapped reads per gene was calculated with HTSeq (2). Normalization and testing for differential expression were performed with DESeq2 version 1.16.
Genes with normalized mean read ≥ 50, fold change ≥ 2, and adjusted P < 0.05 were considered as differentially expressed. DAVID (Database for Annotation, Visualization, and Integrated Discovery) (3-4) was used to perform gene annotation enrichment analysis. From 12 samples, one sample (of the descendants) was a clear outlier and was removed from further analysis following a consultation with Dr. Tsviya Olendenr
Assembly: NZ_CM000488.1
Supplementary files format and content: read count.txt,text

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: Bacillus subtilis 3610

growth_protocol: Roots: The bacteria were diluted to an OD of 0.02 in 1 ml liquid MSgg with 7-d-old A. thaliana seedlings and grown in a 12-well plate. Alternatively, cells were grown for a mid-logarithmic stage and transferred to MSgg for 4 hours (untreated), or to root secretions (with sec).  Cells primed by root secretions or with MSgg were transferred to LB for re-growth and analysis of the decedents

extract_protocol:
For RNA extraction, cells were treated with 250 μl 20g/L lysozyme for 20 minutes at 30oC. RNA extraction was done with TRIzolTM reagent (InvitrogenTM according to the manufacturer’s protocol, DNAse treatment was performed and rRNA was depleted
TURBO DNA-free (Ambion) kit was used to remove DNA contamination, as manufacturer’s protocol. rRNA was depeleted with Ribo-Zero rRNA Removal bacterial Kit (Illumina)
The preparation of the libraries and sequencing were performed by the G-INCPM unit at the Weizmann Institute of Science. Libraries were prepared with G-INCPM mRNA-Seq protocol without polyA capture. Sequencing was performed by HISeq Illumina Sequencer using high output mode.

treatment_protocol: Cells were harvested, pelleted and RNA was extracted

value: Bacillus subtilis 3610

value: bacteria cells

value: Growth with secretions, wash, re-growth in LB


title: AP2P_KD_MicroC_schizont, 36 hpi, MicroC7


title: DesWithSec (Of B. subtilis treated with Plant secretion)-2

description:
Descendents of Prined with secretions
Library 10


title: Control_MicroC_schizont, 36 hpi, MicroC1


title: g8NHC_shIFT88_5198-4_1


title: AP2P_KD_MicroC_schizont, 36 hpi, MicroC5


title: g8NHC_shIFT88_5198-4_4


title: Ep con_1

description: Library name: Sample1


title: g7NHC_shNT-2_4

source_name: NHC-NT

value: NHC-NT


title: DesWithSec (Of B. subtilis treated with Plant secretion)-1

description:
Descendents of Prined with secretions
Library 5


title: g7NHC_shNT-2_3


title: KO_3

description: Library name: Sample6

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
Assembly: mm9
Supplementary files format and content: In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.
Supplementary files format and content: processed data.txt

extract_protocol:
Antral stromal cells were sorted by FACS, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Col1a2-creERT;Bmpr1a and ctrl mice (10 weeks-old) were gave 3 dose of TAM and then sorted stromal cells from antrum by FACS

value: stromal cells

value: KO


title: Control_MicroC_schizont, 36 hpi, MicroC2


title: Descendents (of untreated bacteria)-3

description:
Descendents of untreated
Library 14

value: Growth with MSGG, wash, re-growth in LB


title: g7NHC_shNT-2_2


title: Control_MicroC_schizont, 36 hpi, MicroC3


title: KO_2

description: Library name: Sample5


title: Control_MicroC_schizont, 36 hpi, MicroC4


title: AP2P_KD_MicroC_schizont, 36 hpi, MicroC8


title: Descendents (of untreated bacteria)-2

description:
Descendents of untreated
Library 9


title: g7NHC_shNT-2_1


title: KO_1

description: Library name: Sample4


title: PC_30dpci_05

city: Oxford

first: Mathilda

last: Mommersteeg

address: | Institute of Developmental and Regenerative Medicine (IDRM) | IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive

department: Department off Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

data_processing:
Paired reads were demultiplexed using bcl2fastq (v2.20.0, Illumina) and only R1 used for expression (R2 mostly 3'UTR)
Adapter trimming and quality control was performed with Trim Galore! (v.0.6.4_dev)
Alignment and counting were performed using STAR (v.2.7.6a)
Assembly: Astyanax_mexicanus-2.0
Supplementary files format and content: extended_AstMex_surface_v103.gtf.gz (gzipped gene annotation files based on Ensembl v.103 release with extended 3'UTR)
Supplementary files format and content: ext103_raw_counts.tsv (tab-separated matrix of raw counts)
Supplementary files format and content: ext103_rLog2_counts.tsv (tab-separated matrix of regularized log2 counts)

organism: Astyanax mexicanus

source_name: cardiac ventricle

extract_protocol:
RNA was extracted from individual ventricles using the Quick-RNA MicroPrep kit (Zymo Research). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) from Lexogen.

treatment_protocol: Cryo-injury was induced on the tip of the ventricle using a copper probe pre-chilled in liquid nitrogen.

value: cardiac ventricle

tag: population

value: Pachon

value: cryo-injury

tag: time (hours)


title: Root-associated-3

description:
Associated with A. thaliana roots in MSgg
Library 13

value: Root


title: Descendents (of untreated bacteria)-1

description:
Descendents of untreated
Library 4


title: con_3

description: Library name: Sample3

value: con


title: MV411_RNA_vehicle_mouse2-4_240411_ATGTCA_S3

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38_v33/hg38) reference genome using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Assembly: Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Supplementary files format and content: GRCh38/hg38
Supplementary files format and content: HTSeq per-gene raw counts (Excel .xlsx format)

growth_protocol: 1 x 10^6 MV4;11 cells were intravenously injected per mouse and engraftment was confirmed in the peripheral blood by flow cytometry-based detection of human CD45+ cells using an LSR Fortessa, BD Biosciences (human CD45-PE, clone HI30, 1:200, mouse CD45-APC-Cy7, clone 30-F11, 1:100, BioLegend).

extract_protocol:
Mouse cell depletion was performed on whole bone marrow cells using the Mouse Cell Depletion Kit and LS columns (Miltenyi Biotec). For RNA isolation, 1x10^6 human cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions for cell ine experiments.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).

treatment_protocol: Upon confirmation of engraftment, mice were randomly assigned to treatment groups and received 3 doses of JS8-100(+) or (-) (50 mg/kg i.p. BID, i.e. every 12 hours) or vehicle. The compounds were dissolved in 5% DMAC and 95% PEG-300 (40%) + NaCl (0.9%) (60%). Mice were euthanized one hour after the last dosing.

value: vehicle

value: human acute myeloid leukemia cell line


title: PC_30dpci_04


title: MV411_RNA_vehicle_mouse2-0_240411_AGTCAA_S1


title: con_2

description: Library name: Sample2

value: Stomach

value: 3 dose of TAM treat for 14 day3


title: Root-associated-2

description:
Associated with A. thaliana roots in MSgg
Library 8


title: PC_30dpci_03


title: con_1

description: Library name: Sample1


title: MV411_RNA_vehicle_mouse1-2_240411_AGTTCC_S2


title: Root-associated-1

description:
Associated with A. thaliana roots in MSgg
Library 3


title: PC_30dpci_02


title: MV411_RNA_JS8-100p_mouse3-0_240411_GTCCGC_S6

value: 3 doses (S)-dHTC1, 50 mg/kg i.p. BID


title: MV411_RNA_JS8-100p_mouse2-3_240411_GTAGAG_S5


title: withSec (plant Secretion)-3

description:
MSgg with secretions
Library 12

value: Bacillus subtilis 3610

value: MSgg+A. thaliana secretions


title: PC_30dpci_01


title: psoriatic DRG4

city: wuhan

first: Jian

last: Jiang

address: jiefang avenue

institute: hospital

data_processing:
BGISEQ platform
Assembly: RNA-seq data is aligned to a reference genome assembly. The choice of genome build can affect the alignment accuracy and the subsequent analysis results.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: DRG

growth_protocol: C57BL/6J mice were used in the experiments, according to the guidelines of the Committee of Use of Laboratory Animals and Common Facilities. The male mice were used at 7–8 weeks of age.

extract_protocol:
The RNA of the tissue and cells were extracted using Trizol reagent according to the manufacturer’s manual.
Followed by total RNA extraction from each of the samples using an RNASimple Total RNA Kit (Tiangen, Beijing, China). The RNA from one representative symptomatic sample was used to construct an rRNA-depleted library using the Ribo-Zero rRNA Removal Kit (Plant Leaf) (Illumina, San Diego, CA). The library was subjected to RNA-Seq using a BGISEQ platform (Shenzhen Huada Gene Science and Technology Service Co., Shenzhen, China).

treatment_protocol: The mice were subjected to imiquimod-induced psoriasis-like inflammations, which were treated locally with a 62.5 mg daily dose of IMQ (5%) cream (Mingxin Pharmaceuticals, Sichuan, China) on the shaved dorsal skin for 5 consecutive days. Vaseline jelly was used as the control.

value: DRG

value: psoriatic

value: WT

value: IMQ


title: PC_14dpci_05


title: MV411_RNA_JS8-100p_mouse1-1_240411_CCGTCC_S4


title: withSec (plant Secretion)-1

description:
MSgg with secretions
Library 2

value: bacteria cells


title: withSec (plant Secretion)-2

description:
MSgg with secretions
Library 7


title: psoriatic DRG3


title: PC_14dpci_04

value: cardiac ventricle


title: MV411_RNA_JS8-100n_mouse3-1_240411_CGTACG_S9

value: 3 doses (R)-dHTC1, 50 mg/kg i.p. BID


title: psoriatic DRG2


title: noSec(liquidMsgg)-3

description:
MSgg no secretions
Library 11

value: MSgg


title: MV411_RNA_JS8-100n_mouse2-2_240411_GTTTCG_S8


title: psoriatic DRG1


title: psoriatic DRG5


title: PC_14dpci_03

value: Pachon

value: cryo-injury


title: noSec(liquidMsgg)-2

description:
MSgg no secretions
Library 6


title: PC_14dpci_02


title: noSec(liquidMsgg)-1

description:
MSgg no secretions
Library 1


title: naive DRG5

value: naive

value: control


title: naive DRG4


title: PC_7dpci_05


title: PC_14dpci_01


title: Sample8_DRG_B16F10_rep4

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

country: Canada

institute: Queen's University

description:
Library name: DRG_B16F10_rep4
10x Genomics

data_processing:
Reads were aligned to the mouse reference genome using Cell Ranger (10x Genomics)
Low-RNA-content and dead cells were excluded (nFeature_RNA > 100, percent.mt < 25%).
Assembly: GRCm38
Supplementary files format and content: Tab Separated Values (.tsv) files including counts data and matrix file

source_name: L3_L5 dorsal root ganglia

extract_protocol:
L3–L5 dorsal root ganglia (DRG) were harvested and digested. Most CD45+ cells were depleted using the MagniSort Mouse CD45 Depletion Kit (Invitrogen, #8804-6864). The remaining neurons were resuspended in FACS buffer (PBS with 2% fetal calf serum and EDTA) and stained with Viability Dye eFluor 780 (eBioscience, 65-0865-14) at 4 °C for 15 minutes. Subsequently, nuclei were stained with SYTO 40 (10 µM, Thermofisher, #S11351) for 5 minutes at room temperature to distinguish cells from axonal debris. Cells were then purified by FACS on a BD FACSAria IIu cell sorter
Single-cell barcoding was performed using the Chromium Next GEM Single Cell 3′ GEM, Library, and Gene Expression v3.1 system (10x Genomics).

value: L3_L5 dorsal root ganglia

value: Dorsal root ganglia neurons

value: B16F10 tumor cell injected in the left paw


title: PC_7dpci_04


title: Sample7_DRG_B16F10_rep3

description:
Library name: DRG_B16F10_rep3
10x Genomics


title: H1299 cells, 1.5uM AVJ16 2

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10 (ref 1). The processed reads were aligned to the human transcriptome and genome version GRCh38 with annotations from Ensembl release 99 using TopHat v2.1.1. Counts per gene quantification was done with htseq-count v2.01. Normalization and differential expression analysis were done with the DESeq2 package v 1.36.0.
Assembly: GRCh38 with annotations from Ensembl release 99
Supplementary files format and content: raw_and_norm_counts.xlsx.  Each row in the file contains a certain ensembl Gene ID, Symbol, name, raw counts and DESEq2 normalized counts per sample. Missing values are denoted by “?” are for genes with a too low expression that were filtered out prior to normalization (sum of counts in all samples lower than 10).

source_name: Lung

growth_protocol: H1299 cells were maintained in RPMI medium,  (Biological Industries - Israel). media contained 10% FCS (Biological Industries) and 10 μg/mL ciprofloxacin (Bayer).

extract_protocol:
RNA isolation was done with Qiagen RNeasy MinElute Spin Columns, according to the manufacturer’s protocol. RNA quality was assessed with tape station (Agilent TapeStation).
PolyA-selection, mRNA libraries were prepared using KAPA Stranded mRNA kit with mRNA Capture Beads (KAPA Biosystems, KK8421).
Single End 75bp length

treatment_protocol: H1299 cells were treated with 1.5µM of AVJ16 or an appropriate DMSO concentration, for 48 hours.

value: Lung

value: epithelial-like cell

value: 1.5uM AVJ16


title: naive DRG2

value: DRG


title: naive DRG3

value: WT


title: PC_7dpci_03


title: H1299 cells, DMSO control 3

value: DMSO


title: H1299 cells, 1.5uM AVJ16 3


title: Sample5_DRG_B16F10_rep1

description:
Library name: DRG_B16F10_rep1
10x Genomics


title: Sample6_DRG_B16F10_rep2

description:
Library name: DRG_B16F10_rep2
10x Genomics


title: MV411_RNA_JS8-100n_mouse1-3_240411_GTGGCC_S7

value: human acute myeloid leukemia cell line


title: PC_7dpci_02

value: cardiac ventricle


title: H1299 cells, 1.5uM AVJ16 1


title: H1299 cells, DMSO control 2


title: naive DRG1


title: H1, WT, R1, none, input

city: Philadelphia

first: Naiara

last: Akizu

state: PA

address: 3501 Civic Center Blvd

department: Pathology And Lab Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Bigiwg files were generated using rgt-THOR.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
1 x 106 million cells were double crosslinked with 2mM di (N-succinimidyl) glutarate DSG (45min) and 1% formaldehyde (15 min) at RT. The cells were lysed with a mild lysis buffer (0.1% SDS, 1% Triton, 0.15M NaCl, 1mM EDTA, 20mM Tris) and sonicated using a Qsonica Q700 prove sonicator (7 min ON, 1 min ON/OFF, 25% amp). Following sonication, the non-sonicated chromatin was removed by centrifugation. 300ul of chromatin extract was used per IP, and the  cell lysate was incubated with the 1-5 ug primary antibody overnight at 4°C. After overnight incubation, 10µl of protein A/G magnetic beads was added to the chromatin extracts for 4 hours at 4°C. After four hours, the IPs were washed four times (Wash buffer 1: 0.1% SDS, 0.1% NaDOC, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM HEPES. Wash buffer 2: 0.1% SDS, 0.1% NaDOC, 1% Triton X- 100, 0.5 M NaCl, 1 mM EDTA, 20 mM HEPES. Wash buffer 3: 0.25 M LiCl, 0.5% NaDOC, 0.5% NP-40, 1 mM EDTA, 20 mM HEPES. Wash buffer 4: 1 mM EDTA, 20 mM HEPES), and reverse crosslinked with elution buffer (1% SDS, 0.1 M NaHCO3) overnight at 65°C. The next day, DNA was purified using the Qiaquick PCR purification kit.
The DNA was quantified using a Qubit Flex and the libraries were prepared using the NEBNext DNA Library kit. The quality of the libraries was analyzed using the Agilent 4150 Tapestation. Samples were sequenced using a P2 flow cell and NextSeq 1000 instrument.

value: hESC

tag: replicate


title: Sample4_DRG_Con_rep4

description:
Library name: DRG_Con_rep4
10x Genomics

value: MPEK-BL6 non-tumorigenic keratinocyte injected in the left paw


title: H1299 cells, DMSO control 1


title: H1, YAPKO, R2, EZH2, ChIP

value: YAPKO


title: PC_3dpci_05

value: Pachon

value: cryo-injury


title: PC_7dpci_01


title: Sample3_DRG_Con_rep3

description:
Library name: DRG_Con_rep3
10x Genomics


title: H1, YAPKO, R1, EZH2, ChIP


title: SKNMC-sgGFP_ChIP_input_7d_REP1_230320_CGATGT_S2

description: SKNMC sgGFP H3K4me1/H3K4me2/H3K27ac ChIP Input

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human(Gencode GRCh38/hg38) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (tornado plots).
Assembly: GRCh38/hg38
Supplementary files format and content: Broad IGV (.tdf) files for visualization

source_name: SK-N-MC

growth_protocol: All Ewing Sarcoma cell lines were grown in RPMI in 10cm tissue culutre dishes. Cells were maintained by splitting 1/3 three times weekly.

extract_protocol:
In brief, cells were fixed in either 1% Formaldehyde (FA) for 10 minutes (histone modifications) or with 2uM DSG (30 mins) following by 1% FA (10 mins, for non histone proteins). Following fixation, cells were lysed and sonicated. Beads and antibody complexes were incubated with sonicated lysis overnight. ChIP material was washed 3x ChIP wash buffer and 1x TE+50mM NaCl. DNA-rpotein complexes were eluted from beads and de-crosslinked overnight. The following day, DNA clean up was performed using column purification.
1-10 ng of ChIP DNA was used for the library preparation using the SMARTer ThruPLEX DNA-Seq Kit (Takara)
ChIP-Sequencing was performed using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 37bp, paired-end reads.

treatment_protocol: Treatment/CRISPR time points are indicated per sample

tag: chip target

value: SK-N-MC

tag: guide rna

value: sgGFP

tag: time

value: 7 days


title: PC_3dpci_04

tag: tissue


title: Sample2_DRG_Con_rep2

description:
Library name: DRG_Con_rep2
10x Genomics

value: L3_L5 dorsal root ganglia

tag: cell type

value: Dorsal root ganglia neurons


title: Sample1_DRG_Con_rep1

description:
Library name: DRG_Con_rep1
10x Genomics


title: SKNMC-sgGFP_ChIP_H3K4me2_7d_REP1_230320_GGCTAC_S11

tag: cell line


title: SKNMC-sgGFP_ChIP_H3K4me1_7d_REP1_230320_TAGCTT_S10


title: PC_3dpci_03


title: H1, WT, R1, EZH2, ChIP

tag: chip antibody

tag: genotype


title: H1, WT, R2, EZH2, ChIP


title: PC_3dpci_02

tag: treatment


title: old (39wph) Female tRNA-seq replicate 2

first: Jae Ho

last: Lee

state: CA

address: 318 Campus Drive E200

department: Biology

library_source: other

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v3.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline (v1.3.8) using the parameters: -t notFur1_tRNAs.fa -m notFur1-mitotRNAs.fa -o notFur1-tRNAs-confidence-set.out --cluster-id 0.95 --threads 40 --control-condition young --max-mismatches 0.1 --remap --remap-mismatches 0.075 --max-multi 8 max-multi 6 --remap --remap-mismatches 0.075 --crosstalks.
Assembly: GRZ
Supplementary files format and content: Anticodon_counts_raw.txt Tab-delimited text files include: Column1: tRNA anticodon; Column2: Old Female Rep2 counts; Column3: Old Male Rep1 counts; Column4: Old Male Rep2 counts; Column5: Old Female Rep1 counts; Column 6: Young Female Rep1 counts; Column 7: Young Female Rep2 counts; Column8: Young Male Rep1 counts; Column9: Young Male Rep2 counts
Supplementary files format and content: CCAcounts.txt Tab-delimited text files include: Column1: tRNA gene; Column2: end type; Column3: sample; Column4: condition; Column5: count

molecule: other

organism: Nothobranchius furzeri

source_name: brain

extract_protocol:
Total RNA from killifish brains collected from young (5 weeks) or aged (39-40 weeks) animals was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta-elimination (Behrens and Nedialkova, 2022).
tRNA-seq libraries were prepared using the mim-tRNAseq workflow (Behrens and Nedialkova, 2022) and sequenced on an Illumina NovaSeq 6000 platform.

value: brain


title: Tumor_LN_Cre_WT

description:
Library name: Tumor_LN_Cre_WT
16 samples Multiplex library 10x Genomics

data_processing:
Reads were aligned to the mouse reference genome and demultiplexing based on the unique sample barcodes was performed using Cell Ranger multi (10x Genomics)
Low-quality cells (nFeature_RNA ≤ 100 or percent.mt ≥ 5%) were excluded from downstream analysis in Seurat.
Assembly: GRCm38
Supplementary files format and content: Tab Separated Values (.tsv) files including counts data and matrix file

source_name: B16F10-mCherry-OVA melanoma tissue

extract_protocol:
tumors were excised, minced with a razor blade, and digested for 30 minutes in DMEM containing 10 mM HEPES, 1.6 mg/mL collagenase IV (Sigma, #C5138), and 10 μg/mL DNase I (Sigma, #4942078001). The resulting cell suspensions were filtered through a 40 μm mesh, and samples from two mice were pooled for each experiment. After red blood cell lysis (Gibco, #A10492-01), cells were stained with Zombie Aqua viability dye (BioLegend, #423105) and a FITC anti-mouse CD45 antibody (BioLegend, #103107). Approximately 500,000 live immune cells, which included ~80% CD45+ cells, were sorted on a BD FACSAria III cell sorter into a collection buffer (PBS, 0.04% BSA, and 50% FBS; Sigma, #F4135), and then fixed.
Single-cell RNA sequencing (scRNA-seq) libraries were prepared using the Chromium 10x Fixed RNA kits (#PN-1000414 and #PN-1000497) following the manufacturer’s protocol. A total of eight Cre (knockout) and eight WT (wild-type) tumor-infiltrating immune cell and lymph nodes samples were uniquely barcoded during library preparation. For tumor-infiltrating immune cell, the library included Tumor_Cre_rep1, Tumor_Cre_rep2, Tumor_Cre_rep3, Tumor_Cre_rep4, Tumor_WT_rep1, Tumor_WT_rep2, Tumor_WT_rep3, and Tumor_WT_rep4. Following barcoding, all samples were pooled into a single tube and sequenced on an Illumina NovaSeq platform using paired-end sequencing. Sequencing was performed across seven lanes (L001 to L007), generating two FASTQ files per lane (one Read 1 [R1] and one Read 2 [R2]), resulting in a total of 14 FASTQ files.  Post-sequencing, raw FASTQ files were processed using the Cell Ranger pipeline for demultiplexing and alignment. Each of the eight Cre and eight WT samples has separate processed output files, including a matrix file (.mtx.gz), a barcode file (.tsv.gz), and a feature file (.tsv.gz). The processed data files for each sample are named accordingly, such as Tumor_Cre_rep1_barcodes.tsv.gz, Tumor_Cre_rep1_features.tsv.gz, and Tumor_Cre_rep1_matrix.mtx.gz for Tumor_Cre_rep1, with similar naming conventions for all other samples.

value: B16F10-mCherry-OVA melanoma tissue

value: B16F10-mCherry-OVA melanoma cell line

value: Melanoma cell

value: Intradermal innoculation of B16F10-mCherry-OVA cells


title: SKNMC-sgGFP_ChIP_H3K27ac_7d_REP1_230320_AGTCAA_S13


title: H1, YAPKO, R1, QSER1, ChIP


title: PC_24hpci_05


title: SKNMC-DKO_ChIP_input_7d_REP1_230320_TTAGGC_S3

description: SKNMC sgMLL3/4 H3K4me1/H3K4me2/H3K27ac ChIP Input


title: H1, YAPKO, R2, QSER1, ChIP


title: old (39wph) Female tRNA-seq replicate 1


title: SKNMC-DKO_ChIP_H3K4me2_7d_REP1_230320_ATGTCA_S15


title: H1, WT, R2, QSER1, ChIP

value: WT


title: old (39wph) Male tRNA-seq replicate 2


title: PC_3dpci_01

value: cardiac ventricle


title: PC_24hpci_04


title: old (39wph) Male tRNA-seq replicate 1


title: H1, WT, R1, QSER1, ChIP

value: hESC


title: SKNMC-DKO_ChIP_H3K4me1_7d_REP1_230320_AGTTCC_S14


title: Wild_type_MicroC_schizont, 36 hpi, MicroC9

organism: Plasmodium falciparum NF54

tag: strain


title: SKNMC-DKO_ChIP_H3K27ac_7d_REP1_230320_GTCCGC_S17


title: young (5wph) Female tRNA-seq replicate 2


title: PC_24hpci_03


title: young (5wph) Female tRNA-seq replicate 1


title: PC_24hpci_02


title: Seed kernels, harvest date, August, biological replicates 3

value: Seed kernel

value: August


title: SKNMC_ChIP_RNAPol2_dCBP1_100nM_6h_REP1_230320_GTGGCC_S19

value: RNA Polymerase II

value: 6 hours

value: 100nM dCBP1


title: PC_24hpci_01

value: Pachon

value: cryo-injury


title: PC_6hpci_05


title: Wild_type_MicroC_schizont, 36 hpi, MicroC11


title: SKNMC_ChIP_input_DMSO_6h_REP1_230809_CTTGTA_S1

description: DMSO H2BK120ac/H3K27ac ChIP Input

value: SK-N-MC

value: DMSO


title: young (5wph) Male tRNA-seq replicate 1

value: brain


title: PC_6hpci_04


title: Ribosome profiling of old brain replicate 2

description: Ribosome protected mRNA

data_processing:
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer
Ribosomal RNA reads were removed by alignment using Bowtie v1.3.1.
Remaining reads were aligned using Bowtie v1.3.1 (parameters ""-y -a -m 1 -v 2 --norc --best --strata"") to a library of coding sequences. This CDS library included only the longest transcript of each gene.
A nucleotide offset was empirically calculated from the 5' end of each fragment length that displayed three nucleotide periodicity, thereby assigning each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150927
Supplementary files format and content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.
Library strategy: Ribo-seq

extract_protocol:
10~15 frozen brain from fish were pooled and lysed using cryo-mill. Lysed samples were thawed and spun at 21,000g for 15 minutes to clear the lysate. RNA concentration of supernatant was measured and RNAse I was added to 0.4 units per ug of RNA. The sample was incubated for 45 minutes at room temperature and 0.02ul of SUPERaseIn RNAse Inhibitor was added per ug of RNA to stop digestion. Samples were immediately layered on 1M sucrose cushion and spun at 100,000rpm for 1 hour in TLA 100.3 rotor to isolate ribosomes. Resulting ribosome pellet was resuspended and RNA was extracted using TRIzol reagent following manufacturer’s instructions.
RNA fragments in the range of ~25-35 nucleotides were gel purified. After dephosphorylation, a DNA linker (CTGTAGGCACCATCAAT) was ligated to the 3' end of the RNA footprints. Samples were then depleted of rRNA using RiboCop (Lexogen) with the addition of custom-designed oligos to enhance depletion efficiency. Remaining RNA fragments were reverse transcribed into cDNA, followed by circularization. Libraries were barcoded during PCR amplification and sent for sequencing.

tag: age


title: Total RNA Brain Male 32wph Bortezomib 3

data_processing:
Sequence information was extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422, against the Nothobranchius furzeri reference genome (Nfu_20150522, annotation nfurzeri_genebuild_v1.150922). Alignment to the reference genome was performed using STAR with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique. The deduplication step was performed using the umi_tool v1.1.1, using the following parameters: extract --bcpattern= NNNNNNNNNNN`, `dedup --chimeric-pairs discard --unpaired-reads discard -- paired.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150922
Supplementary files format and content: Counts of each gene from different samples

source_name: Brain

extract_protocol:
Individual brains from the fish were collected and snap-frozen in liquid nitrogen. The protein amount was estimated based on fresh tissue weight (assuming 5% of protein w/w), and ice-cold 1x PBS with protease/ phosphatase inhibitors (Roche,11836170001, 4906837001) was added accordingly to a final concentration of 2 μg/μL. Samples were then vortexed (5 times) before sonication (Bioruptor Plus) for 10 cycles (60 sec ON/30 sec OFF) at the high setting, at 4 °C. The samples were then centrifuged at 3000 xg for 5 min at 4 °C, and the supernatant was transferred to 2 mL Eppendorf tubes. 1.5 mL of ice-cold Qiazol (Qiagen, 79306) reagent was added to 150 μL of homogenate, vortexed five times, and snap-frozen in liquid nitrogen. On the day of the experiment, samples were thawed on ice, vortexed five times, and incubated at room temperature for 5 min before adding 300 μL of chloroform. Samples were mixed vigorously, incubated for 3 min at room temperature, and centrifuged at 12000 xg for 20 min at 4 °C. The upper aqueous phase (600 μL) was carefully transferred into a fresh tube, and the remaining volume (phenol/chloroform phase) was kept on ice for DNA isolation. The aqueous phase was mixed with 1.1 volume of isopropyl alcohol, 0.16 volumes of sodium acetate (2 M; pH 4.0), and 1 μL of GlycoBlue (Invitrogen, AM9515) to precipitate RNA. After 10 min incubation at room temperature, samples were centrifuged at 12000 xg for 30 min at 4 °C. The supernatant was completely removed, and RNA pellets were washed by adding 80% (v/v) ethanol and centrifuging at 7500 xg for 5 min at 4 °C. The washing steps were performed twice. The resulting pellets were air-dried for no more than 5 min and dissolved in 10 μL nuclease-free water. To ensure full dissolution of RNA in water, samples were then incubated at 65 °C for 5 min, before storage at -80 °C.
quality check and quantification of total RNA was done using the Agilent Bioanalyzer 2100 in combination with the RNA 6000 pico kit (Agilent Technologies, 5067-1513). Total RNA library preparation was done by introducing 500 ng total RNA into Illumina’s NEBNext Ultra II directional mRNA (UMI) kit (NEB, E7760S), following the manufacturer’s instructions. The quality and quantity of all libraries were checked using Agilent’s Bioanalyzer 2100 and DNA 7500 kit (Agilent Technologies, 5067-1506).

value: Brain

tag: Sex

value: M

value: Bortezomib


title: PC_6hpci_03


title: SKNMC_ChIP_input_DMSO_6h_REP1_230320_TGACCA_S4

description: RNA Pol II ChIP Input (linked to dCBP1)


title: SKNMC_ChIP_input_DMSO_6h_REP1_230710_CAGATC_S7

description: DMSO H3K18ac ChIP Input (A485/dCBP1)


title: young (5wph) Male tRNA-seq replicate 2


title: Ribosome profiling of old brain replicate 1

description: Ribosome protected mRNA

data_processing:
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer
Ribosomal RNA reads were removed by alignment using Bowtie v1.3.1.
Remaining reads were aligned using Bowtie v1.3.1 (parameters ""-y -a -m 1 -v 2 --norc --best --strata"") to a library of coding sequences. This CDS library included only the longest transcript of each gene.
A nucleotide offset was empirically calculated from the 5' end of each fragment length that displayed three nucleotide periodicity, thereby assigning each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150926
Supplementary files format and content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.
Library strategy: Ribo-seq


title: Wild_type_MicroC_schizont, 36 hpi, MicroC10


title: PC_6hpci_02


title: SKNMC_ChIP_RNAPol2_DMSO_6h_REP1_230320_GTGAAA_S18


title: Total RNA Brain Female 32wph Bortezomib 3

value: F


title: PC_6hpci_01


title: Total RNA Brain Male 32wph Bortezomib 2


title: Ribosome profiling of adult brain replicate 2

description: Ribosome protected mRNA

data_processing:
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer
Ribosomal RNA reads were removed by alignment using Bowtie v1.3.1.
Remaining reads were aligned using Bowtie v1.3.1 (parameters ""-y -a -m 1 -v 2 --norc --best --strata"") to a library of coding sequences. This CDS library included only the longest transcript of each gene.
A nucleotide offset was empirically calculated from the 5' end of each fragment length that displayed three nucleotide periodicity, thereby assigning each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150925
Supplementary files format and content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.
Library strategy: Ribo-seq


title: SKNMC_ChIP_input_DMSO_24h_REP1_231017_GTGGCC_S7

description: DMSO H3K4me1 ChIp Input (linked to A485)

value: 24 hours


title: SKNMC_ChIP_input_dCBP1_100nM_6h_REP1_230710_GATCAG_S9

description: dCBP1 H3K18ac ChIP Input


title: Total RNA Brain Female 32wph Bortezomib 2


title: Wild_type_MicroC_schizont, 36 hpi, MicroC12


title: PC_3dps_05

value: cardiac ventricle

value: sham


title: PC_3dps_04


title: Ribosome profiling of young brain replicate 2

description: Ribosome protected mRNA

data_processing:
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer
Ribosomal RNA reads were removed by alignment using Bowtie v1.3.1.
Remaining reads were aligned using Bowtie v1.3.1 (parameters ""-y -a -m 1 -v 2 --norc --best --strata"") to a library of coding sequences. This CDS library included only the longest transcript of each gene.
A nucleotide offset was empirically calculated from the 5' end of each fragment length that displayed three nucleotide periodicity, thereby assigning each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150923
Supplementary files format and content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.
Library strategy: Ribo-seq


title: Total RNA Brain Female 32wph Bortezomib 1


title: Muscle FAP3

city: guangzhou

last: ruijie

state: State...

address: sun yat-sen university

institute: sun yat-sen university

data_processing:
Sequence reads were trimmed for adapter sequence and low-quality sequence by trim-galore.
Trimmed sequences were mapped to GRCm39 using STAR.
Unique mappings over genes were summarized by featureCounts .
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts of each sample.

source_name: Muscle

extract_protocol:
RNA was extracted using  RLT plus buffer (1053393, QIAGEN).
RNA library for RNA-seq was prepared using TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer's protocol

value: Muscle

value: MCAO

value: fibroadipogenic progenitors


title: SKNMC_ChIP_H3K4me1_A485_1uM_24h_REP1_231017_ACTGAT_S11


title: Total RNA Brain Female 32wph DMSO 3


title: Total RNA Brain Male 32wph Bortezomib 1


title: SKNMC_ChIP_H3K4me1_DMSO_24h_REP1_231017_GTTTCG_S8


title: PC_3dps_01


title: Muscle FAP2


title: SKNMC_ChIP_input_A485_1uM_6h_REP1_230710_ACTTGA_S8

description: A485 H3K18ac/H2BK120ac/H3K27ac ChIP Input

value: 6 hours


title: Muscle FAP1


title: SKNMC_ChIP_H3K27ac_DMSO_6h_REP1_230809_GATCAG_S5


title: PC_24hps_05


title: Circulating FAP3

source_name: Peripheral blood

value: Peripheral blood


title: PC_24hps_04

value: Pachon


title: PC_3dps_02


title: Total RNA Brain Female 32wph DMSO 2


title: Ribosome profiling of adult brain replicate 1

description: Ribosome protected mRNA

data_processing:
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer
Ribosomal RNA reads were removed by alignment using Bowtie v1.3.1.
Remaining reads were aligned using Bowtie v1.3.1 (parameters ""-y -a -m 1 -v 2 --norc --best --strata"") to a library of coding sequences. This CDS library included only the longest transcript of each gene.
A nucleotide offset was empirically calculated from the 5' end of each fragment length that displayed three nucleotide periodicity, thereby assigning each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150924
Supplementary files format and content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.
Library strategy: Ribo-seq


title: SF_3dps_03

value: Surface


title: Total RNA Brain Female 32wph DMSO 1


title: Ribosome profiling of young brain replicate 1

description: Ribosome protected mRNA

data_processing:
Illumina CASAVA 1.8 was used for base calling and demultiplexing.
Adaptor sequences (CTGTAGGCACCATCAAT) were trimmed using Cutadapt v1.4.2, followed by removal of the 5' nucleotide using FASTX-Trimmer
Ribosomal RNA reads were removed by alignment using Bowtie v1.3.1.
Remaining reads were aligned using Bowtie v1.3.1 (parameters ""-y -a -m 1 -v 2 --norc --best --strata"") to a library of coding sequences. This CDS library included only the longest transcript of each gene.
A nucleotide offset was empirically calculated from the 5' end of each fragment length that displayed three nucleotide periodicity, thereby assigning each read to a specific A-site nucleotide. Nucleotide reads were then summed for each codon.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150922
Supplementary files format and content: Tab-delimited text files include: Column1: ORF; Column2: codon position of each ORF, including 21 flanking nucleotides (7 triplets) before the start codon and after the stop codon; Column3: codon; Column4: counts of ribosome reads.
Library strategy: Ribo-seq


title: SKNMC_ChIP_input_A485_1uM_24h_REP1_231017_GAGTGG_S10

description: A485 H3K4me1 ChIP Input

value: SK-N-MC


title: Total RNA Brain Male 32wph DMSO 3

value: DMSO


title: Total RNA Brain Male 32wph DMSO 1


title: Circulating FAP1


title: Total RNA Brain Male 32wph DMSO 2


title: PC_24hps_02

data_processing:
Paired reads were demultiplexed using bcl2fastq (v2.20.0, Illumina) and only R1 used for expression (R2 mostly 3'UTR)
Adapter trimming and quality control was performed with Trim Galore! (v.0.6.4_dev)
Alignment and counting were performed using STAR (v.2.7.6a)
Assembly: Astyanax_mexicanus-2.0
Supplementary files format and content: extended_AstMex_surface_v103.gtf.gz (gzipped gene annotation files based on Ensembl v.103 release with extended 3'UTR)
Supplementary files format and content: ext103_raw_counts.tsv (tab-separated matrix of raw counts)
Supplementary files format and content: ext103_rLog2_counts.tsv (tab-separated matrix of regularized log2 counts)


title: SKNMC_ChIP_H3K18ac_dCBP1_100nM_6h_REP1_230710_TTAGGC_S3

value: 100nM dCBP1


title: SKNMC_ChIP_H3K27ac_A485_1uM_6h_REP1_230809_GTGAAA_S7


title: SKNMC_ChIP_H3K18ac_A485_1uM_6h_REP1_230710_CGATGT_S2


title: SKNMC_ChIP_H3K18ac_DMSO_6h_REP1_230710_ATCACG_S1


title: PC_24hps_03


title: DEL_OD3_rep2

city: Toronto

first: Alexander

last: Ensminger

state: Ontario

address: 661 University Avenue

institute: University of Toronto

data_processing:
Demultiplexing, quality control, and adapter trimming  were performed with bcl-convert
Raw sequencing reads were trimmed with trimmomatic and quality checked using FastQC
Filtered reads were aligned to a reference genome (Refseq ID: GCF_001941585.1) using STAR and mapped reads were quantified using featureCounts
Assembly: Refseq ID: GCF_001941585.1
Supplementary files format and content: Comma separated file with matrix of samples and genes, with raw counts dispayed for each gene in each count.

organism: Legionella pneumophila

growth_protocol: Grown in AYE media

extract_protocol:
PureLink RNA extraction kit (Invitrogen) and DNAse treatment (Invitrogen)
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices

value: bacteria


title: Circulating FAP2


title: SKNMC_ChIP_H2BK20ac_DMSO_6h_REP1_230809_TAGCTT_S6


title: Total RNA OpticTectum Male 39wph replicate 4

source_name: Optic tectum

value: Optic tectum

value: M


title: Total RNA OpticTectum Female 39wph replicate 4

value: F


title: SKNMC_ChIP_H2BK20ac_A485_1uM_6h_REP1_230809_GTGGCC_S8


title: PC_6hps_05


title: Total RNA OpticTectum Female 39wph replicate 2


title: Total RNA OpticTectum Female 39wph replicate 3


title: PC_24hps_01


title: DEL_OD1_rep2


title: PC_6hps_04


title: PC_6hps_02


title: SKNMC_ChIP_FLI1_A485_1uM_6h_REP1_230809_GTTTCG_S3


title: PC_6hps_03


title: SKNMC_ChIP_FLI1_DMSO_6h_REP1_230809_AGTTCC_S2


title: Total RNA OpticTectum Female 39wph replicate 1


title: EWS502_ChIP_input_dTAG_1uM_24h_REP1_231017_GCCAAT_S4

description: dTAG1 H3K4me1/H3K27ac ChIP Input

value: 24 hours

value: 1uM dTAG


title: EWS-502_ChIP_input_dTAG1_1uM_24h_REP1_230131_AGTCAA_S14

description: dTAG1 FLI1 ChIP Input


title: Total RNA OpticTectum Male 39wph replicate 2


title: WT_OD3_rep1

value: WT


title: SF_6hps_01

value: cardiac ventricle

value: sham


title: WT_OD1_rep2


title: PC_con_05

value: uninjured


title: WT_OD1_rep1


title: DEL_OD3_rep1


title: DEL_OD1_rep1


title: Total RNA OpticTectum Male 39wph replicate 1


title: PC_con_03


title: Total RNA OpticTectum Female 12wph replicate 4


title: PC_con_01


title: MT_T2_Rep2

data_processing:
Raw sequencing reads were trimmed with trimmomatic and quality checked using FastQC
Filtered reads were aligned to a reference genome (Refseq ID: GCF_001941585.1) using STAR and mapped reads were quantified using featureCounts
Assembly: Refseq ID: GCF_001941585.1
Supplementary files format and content: Excel spreadsheet with matrix of samples and genes, with raw counts dispayed for each gene in each count.

growth_protocol: Grown to exponential phase in AYE media

extract_protocol:
PureLink RNA extraction kit (Invitrogen)
Performed at sequencing facility

treatment_protocol: Non-control samples were treated with ciprofloxacin antibiotic for the indicarted times

value: 6 hr DNA stress


title: EWS502_ChIP_H3K4me1_dTAG_1uM_24h_REP1_231017_ACTTGA_S6


title: MT_T2_Rep1


title: WT_OD3_rep2


title: EWS502_ChIP_H3K4me1_dNEG_1uM_24h_REP1_231017_ACAGTG_S3

value: 1uM dNEG


title: Total RNA OpticTectum Male 12wph replicate 4


title: SF_30dpci_05

value: cryo-injury


title: SF_30dpci_04

value: Surface


title: Total RNA OpticTectum Male 39wph replicate 3


title: Total RNA OpticTectum Male 12wph replicate 3


title: Total RNA OpticTectum Female 12wph replicate 3


title: SF_30dpci_03


title: MT_T1_Rep1

value: 1 hr DNA stress


title: EWS502_ChIP_H3K27ac_dTAG_1uM_24h_REP1_231017_CAGATC_S5


title: EWS502_ChIP_input_dNEG_1uM_24h_REP1_231017_TTAGGC_S1

description: dNEG H3K4me1/H3K27ac ChIP Input


title: EWS502_ChIP_H3K27ac_dNEG_1uM_24h_REP1_231017_TGACCA_S2


title: MT_T0_Rep2


title: EWS-502_ChIP_EWS-FLI1_dTAG1_1uM_24h_REP1_230131_GAGTGG_S9


title: Total RNA OpticTectum Female 12wph replicate 2


title: EWS-502_ChIP_input_dNEG_1uM_24h_REP1_230131_GCCAAT_S12

description: dNEG FLI1 ChIP Input


title: SF_30dpci_02


title: SF_30dpci_01


title: MT_T0_Rep1


title: MT_T1_Rep2


title: EWS-502_ChIP_EWS-FLI1_dNEG_1uM_24h_REP1_230131_GTTTCG_S7


title: WT_T2_Rep2


title: Total RNA OpticTectum Male 12wph replicate 1


title: Total RNA OpticTectum Female 12wph replicate 1


title: SF_14dpci_05


title: WT_T2_Rep1


title: A673-sgLuc_ChIP_H3K4me1_steadystate_REP1_231017_AGTCAA_S15

value: sgLuciferase

value: 7 days


title: SF_14dpci_03


title: WT_T1_Rep2

value: bacteria


title: SF_14dpci_04


title: A673-sgLuc_ChIP_H3K27ac_steadystate_REP1_231017_CTTGTA_S14


title: A673-sgLuc_ChIP_input_steadystate_REP1_231017_GATCAG_S13

description: sgLuciferase control H3K4me1/H3K27ac ChIP Input


title: Total RNA OpticTectum Female 5wph replicate 4

value: Optic tectum


title: WT_T1_Rep1


title: Total RNA OpticTectum Female 5wph replicate 3


title: Total RNA OpticTectum Male 12wph replicate 2

value: M


title: SF_14dpci_01


title: WT_T0_Rep1


title: A673-sgGFP_ChIP_H3K4me2_7d_REP1_221108_CTTGTA_S2

description: sgGFP control ChIP linked to sgMLL3/4 H3K4me2 ChIP

value: sgGFP


title: A673-sgGFP_ChIP_input_7d_REP1_221013_ACTTGA_S9

description: sgGFP H3K4me2 Input


title: SF_14dpci_02


title: Total RNA OpticTectum Female 5wph replicate 2

value: F


title: Total RNA OpticTectum Male 5wph replicate 4


title: SF_7dpci_04


title: Total RNA OpticTectum Male 5wph replicate 3


title: A673-sgGFP_ChIP_FLI1_7d_REP1_221013_GCCAAT_S10

description: sgGFP control ChIP linked to sgMLL3/4 FLI1 ChIP


title: Total RNA OpticTectum Female 5wph replicate 1


title: SF_7dpci_03


title: A673-sgFLI1_ChIP_H3K4me1_steadystate_REP1_231017_CCGTCC_S18


title: WT_T0_Rep2


title: SF_7dpci_02


title: SF_7dpci_01


title: A673-sgFLI1_ChIP_H3K27ac_steadystate_REP1_231017_ATGTCA_S17


title: Total RNA OpticTectum Male 5wph replicate 1


title: A673-DKO_ChIP_input_steadystate_REP1_220705_CGATGT_S2

description: sgMLL3/4 H3K4me1/H3K27ac ChIP Input


title: Total RNA Muscle Female 39wph replicate 4

value: Muscle


title: SF_3dpci_05


title: Total RNA Muscle Female 39wph replicate 3


title: LNCaP cells, siVDR D3

city: Kaga, Itabashi-ku

first: Takao

last: Susa

state: Tokyo

institute: Teikyo University, School of Mediocine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: VDR siRNA transfected LNCaP cells, 10-7M of 1,25(OH)2D3 treatment.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Prostate cancer LNCaP cells were maintained in monolayer cultures in RPMI-1640 phenol red free medium supplemented with 5% (v/v) fetal bovine serum and antibiotics (Life Technologies) in humidified 5% CO2–95% air at 37°C.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: At 24 h before hormone or chemical treatment, the culture media was replaced with serum-free media, and the cells were exposed to the indicated hormones with serum-free media for 24 h.

value: Human prostate cancer cells

value: LNCaP

tag: transfection

value: siVDR


title: A673-DKO_ChIP_H3K4me2_7d_REP1_221108_CCGTCC_S4


title: A673-DKO_ChIP_H3K4me1_steadystate_REP1_220705_ACTTGA_S7


title: SF_3dpci_04

value: cardiac ventricle


title: LNCaP cells, siVDR v

source_name: VDR siRNA transfected LNCaP cells, vehicle treatment.

value: v


title: A673-sgFLI1_ChIP_input_steadystate_REP1_231017_AGTTCC_S16

description: sgFLI1 H3K4me1/H3K27ac ChIP Input


title: Total RNA Muscle Female 39wph replicate 2

city: Stanford

institute: Stanford University


title: SF_3dpci_03


title: Total RNA OpticTectum Male 5wph replicate 2


title: A673-DKO_ChIP_H3K27ac_steadystate_REP1_220705_TAGCTT_S9


title: LNCaP cells, siVDR DHT

source_name: VDR siRNA transfected LNCaP cells, 10-7M of DHT treatment.

value: DHT


title: LNCaP cells, siCT D3

source_name: Control siRNA transfected LNCaP cells, 10-7M of 1,25(OH)2D3 treatment.

value: siCT


title: AP2P_KD_MicroC_schizont, 36 hpi, MicroC5R

data_processing:
Micro-C paired-end reads were mapped to the P. falciparum genome and processed into pairs and multi-resolution normalized contact matrix .mcool files using hicstuff
Assembly: P. falciparum genome (plasmoDB.org, version 3, release 55)
Supplementary files format and content: high resolution interaction matrices in .mcool format
Library strategy: Micro-C

extract_protocol:
Parasites were cross-linked by adding methanol-free formaldehyde to 1% final concentration. The reaction was quenched by adding 1 M Tris-HCl pH 7.5. Parasites were washed with DPBS at 25°C, resuspended in the second cross-linking solution - 3 mM DSG in DPBS and incubated for 45 minutes. The reaction was quenched with 1 M Tris-HCl pH 7.5. The cell pellet was lysed and digested with the chosen concentration of MNase. Each pellet was resuspended in end-chewing mix [1X NEB Buffer 2.1, 2 mM ATP, 5 mM DTT, 0.5 U/μl T4 PNK] and incubated for 15 minutes. Klenow fragment was added, followed by 25 μl of end-labeling mix [0.2 mM Biotin-dATP, 0.2 mM Biotin-dCTP, 0.2 mM dTTP, 0.2 mM dGTP, 0.1 mg/ml BSA]. 500 mM EDTA was added and incubated for 30 minutes. Biotinylated DNA fragments were then covalently linked by proximity ligation by resuspending the pellet in ligation mix [1X T4 DNA ligase buffer, 0.1 mg/ml BSA, 33 U/μl T4 DNA ligase)]. The biotin-dNTPs were removed from unligated ends, the DNA was purified and decrosslinked. The DNA contained in the supernatant was recovered using the DNA Clean & Concentrator. The ligated DNA was loaded onto a 2% TAE agarose gel to separate dimers from monomers, and DNA was extracted. The biotinylated dimers were isolated with Dynabeads MyOne Streptavidin C1.
The library prep was performed with the samples on beads using the NEBNext® Ultra II Directional DNA Library Prep Kit (NEB E7645), with several modifications.


title: A673-DKO_ChIP_FLI1_7d_REP1_221013_GATCAG_S11


title: Total RNA Muscle Male 39wph replicate 4


title: SF_24hpci_05

value: Surface

value: cryo-injury


title: SF_3dpci_01


title: Total RNA Muscle Female 39wph replicate 1


title: SF_3dpci_02


title: LNCaP cells, siAR v

source_name: AR siRNA transfected LNCaP cells, vehicle treatment.

value: siAR


title: LNCaP cells, siCT DHT

source_name: Control siRNA transfected LNCaP cells, 10-7M of DHT treatment.


title: A673-DKO_ChIP_EP300_steadystate_REP1_221119_TAGCTT_S2

value: 7 days


title: Total RNA Muscle Male 39wph replicate 3


title: AP2P_KD_MicroC_schizont, 36 hpi, MicroC6R


title: AP2P_KD_MicroC_schizont, 36 hpi, MicroC8R


title: Total RNA Muscle Male 39wph replicate 2


title: SF_24hpci_04

source_name: cardiac ventricle


title: A673-dHALO_ChIP_WDR5_VH0032_24h_REP1_220802_CCGTCC_S4

value: 24 hours


title: A673-dHALO_ChIP_WDR5_DMSO_24h_REP1_220802_GCCAAT_S2

description: DMSO ChIP linked to 1µM VH0032 WDR5 ChIP

value: DMSO


title: Control_MicroC_schizont, 36 hpi, MicroC1R


title: SF_24hpci_02


title: A673-dHALO_ChIP_PAXIP1_steadystate_REP1_230320_ACTTGA_S8

description: No treatment, baseline cells


title: SF_24hpci_03


title: Control_MicroC_schizont, 36 hpi, MicroC2R


title: A673-dHALO_ChIP_RBBP5_steadystate_REP1_230320_GATCAG_S9

description: No treatment, baseline cells


title: Total RNA Muscle Male 12wph replicate 4

value: M


title: LNCaP cells, siAR D3

source_name: AR siRNA transfected LNCaP cells, 10-7M of 1,25(OH)2D3 treatment.


title: Total RNA Muscle Female 12wph replicate 3


title: Control_MicroC_schizont, 36 hpi, MicroC3R


title: SF_24hpci_01


title: LNCaP cells, siAR DHT

source_name: AR siRNA transfected LNCaP cells, 10-7M of DHT treatment.


title: Total RNA Muscle Male 39wph replicate 1


title: A673-dHALO_ChIP_MLL4_VH0032_1uM_24h_REP1_230131_AGTTCC_S4


title: Total RNA Muscle Female 12wph replicate 4


title: A673-dHALO_ChIP_MLL4_DMSO_24h_REP1_230131_TTAGGC_S1

description: DMSO ChIP linked to 1µM VH0032 MLL4 ChIP


title: Total RNA Muscle Male 12wph replicate 3


title: A673-dHALO_ChIP_KDM6A_VH0032_1uM_24h_REP1_230131_ATGTCA_S5


title: MORC, IP, 36hpi

data_processing:
Sequenced reads were mapped to the P. falciparum genome (plasmoDB.org, version 3, release 56) using bowtie. PCR duplicates were filtered using samtools’ fixmate and markdup commands and only alignments with a mapping quality ≥ 30 were retained (samtools view -q 30). The paired end deduplicated ChIP and input BAM files were used as treatment and control, respectively, for peak calling with the MACS2 subcommand.
Assembly: P. falciparum genome (plasmoDB.org, version 3, release 56)
Supplementary files format and content: IP/Input enrichment ratio in .bw format and macs2 output in narrowPeak format

growth_protocol: Clonal populations of AP2-P-3HA-glmS and MORC-3HA-glmS parasites were tightly synchronized and harvested at 36 hpi in human RBCs supplemented with 10% v/v Albumax I, hypoxanthine (0.1 mM final concentration) and 10 mg gentamicin under 5% O2, 5% CO2 at 37 °C.

extract_protocol:
For the AP2-P-3HA-glmS parasites, the parasites were cross-linked by adding methanol free formaldehyde (final concentration 1%)  for 10 minutes. The cross-linking reaction was quenched by adding glycine. For the MORC-3HA-glmS parasites, the supernatant was removed and MgCl2 was added. 80 μL of ChIP Cross-link Gold were added and sample was incubated for 30 min with gentle agitation. The parasites were resuspended in DPBS at 4°C and were further cross-linked by adding methanol‐free formaldehyde (final concentration 1%) and incubated for 15 minutes. The cross-linking reaction was quenched by adding glycine. The parasites were lysed, and the lysates were sonicated in a Diagenode Pico Bioruptor.
Libraries were prepared with the MicroPlex library preparation kit (Diagenode C05010014), with KAPA HiFi polymerase (KAPA biosystems) substituted for the PCR amplification.


title: SF_6hpci_04

extract_protocol:
RNA was extracted from individual ventricles using the Quick-RNA MicroPrep kit (Zymo Research). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) from Lexogen.


title: SF_6hpci_03


title: MORC, Input, 36hpi


title: SF_6hpci_02


title: A673-dHALO_ChIP_KDM6A_DMSO_24h_REP1_230131_ACAGTG_S2

description: DMSO ChIP linked to 1µM VH0032 UTX ChIP

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human(Gencode GRCh38/hg38) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (tornado plots).
Assembly: GRCh38/hg38
Supplementary files format and content: Broad IGV (.tdf) files for visualization


title: SF_6hpci_05


title: Total RNA Muscle Male 12wph replicate 2


title: LNCaP cells, siCT v

source_name: Control siRNA transfected LNCaP cells, vehicle treatment.


title: A673-dHALO_ChIP_input_VH0032_1uM_24h_REP1_230131_ATTCCT_S16

description: 1uM VH0032 A673 dHALO MLL4/UTX ChIP Input


title: SF_6hpci_01


title: Total RNA Muscle Female 12wph replicate 2


title: AP2-P Biological Replicate2, IP, 36 hpi


title: Total RNA Muscle Female 12wph replicate 1


title: AP2-P Biological Replicate2, Input, 36 hpi


title: A673-dHALO_ChIP_input_VH0032_1uM_24h_REP1_220525_ACTTGA_S5

description: 1uM VH0032 A673 dHALO H3K27ac/H3K4me1 ChIP Input


title: Control_MicroC_schizont, 36 hpi, MicroC4R


title: SF_3dps_05

value: sham


title: SF_3dps_04


title: A673-dHALO_ChIP_input_DMSO_24h_REP1_230131_ACTGAT_S15

description: DMSO control A673 dHALO MLL4/UTX ChIP Input


title: AP2-P Biological Replicate1, Input, 36 hpi


title: AP2-P Biological Replicate1, IP, 36 hpi


title: Total RNA Muscle Male 12wph replicate 1


title: A673-dHALO_ChIP_input_steadystate_REP1_230320_ATCACG_S1

description: ASH2L/CBP/PAXIP1/RbBP5 steadystate ChIP Input


title: SF_3dps_02


title: Total RNA Muscle Female 5wph replicate 3

value: F


title: A673-dHALO_ChIP_input_DMSO_24h_REP1_220802_CGATGT_S1

description: DMSO control A673 dHALO WDR5 ChIP Input


title: PC_3dps_03

value: Pachon


title: day1_wt3

city: zhejiang

first: Siyu

last: Chen

address: zhejiang

institute: zhejiang university

data_processing:
RNA-seq was performed using three biological replicates for all the samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm10) with STAR v2.7.11a and ERCC spike-in sequences using Hisat2 v2.2.1. Only uniquely mapped reads were assembled into transcripts using featureCounts v2.0.6. The expression level of each transcript was quantified to the normalized FPKM and normalized to the ERCC spike-in. Only transcripts with FPKM > 1 in at least one sample were considered in all analyses. Functional annotation was performed using clusterProfiler v4.10.1.
Assembly: mm10
Supplementary files format and content: FPKM

source_name: ovary

extract_protocol:
Briefly, after the hormone challenge, ovaries from animal were directly lysed in Lysis Buffer (DMEM, 13 WU/ml Liberase™ DH, Dnase I).
The ovary RNA-seq protocol was based on the well established protocol with Fast RNA-seq Lib Prep Kit V2 (ABclonal). Sequencing libraries were constructed from 500 pg of amplified cDNA using Fast RNA-seq Lib Prep Kit V2 for Illumina (Catalog number: RK20306, ABclonal) according to the manufacturer’s instructions.

value: ovary

tag: genetic modification

value: wild type


title: A673-dHALO_ChIP_input_DMSO_24h_REP1_220525_TGACCA_S1

description: DMSO control A673 dHALO H3K27ac/H3K4me1 ChIP Input


title: Total RNA Muscle Female 5wph replicate 1

value: Muscle


title: day1_wt1


title: day1_wt2


title: SF_3dps_01

value: cardiac ventricle

tag: population


title: day1_cko3

value: hnRNPL flox/flox;Stra8-cre


title: A673-dHALO_ChIP_H3K4me1_VH0032_1uM_24h_REP1_220525_CCGTCC_S10


title: SF_24hps_05

tag: time (hours)


title: day1_cko2


title: A673-dHALO_ChIP_H3K4me1_DMSO_24h_REP1_220525_CTTGTA_S6

description: DMSO ChIP linked to 1µM VH0032 H3K4me1 ChIP


title: Total RNA Muscle Male 5wph replicate 2


title: A673-dHALO_ChIP_H3K27ac_VH0032_1uM_24h_REP1_220525_ATTCCT_S15


title: SF_24hps_03


title: Total RNA Muscle Female 5wph replicate 4


title: Total RNA Muscle Male 5wph replicate 3


title: SF_24hps_02


title: SF_7dpci_05


title: A673-dHALO_ChIP_FLI1_VH0032_1uM_24h_REP1_220705_CCGTCC_S6


title: A673-dHALO_ChIP_H3K27ac_DMSO_24h_REP1_220525_GTTTCG_S11

description: DMSO ChIP linked to 1µM VH0032 H3K27ac ChIP


title: Total RNA Muscle Male 5wph replicate 1


title: day1_cko1


title: 03_input

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were trimmed using Trimmomatic (version 0.33) to remove poor quality reads.
The filtered sequences were aligned to the mouse reference genome (mm10) with Bowtie2 (version 2.4.1)
Non-unique aligned reads and PCR duplicates were filtered out to identify GR binding sites. GR binding sites were identified by the call peak function of MACS2 (version 2.2.7.1) (FDR<1e-4). Bigwig files of normalized coverage were created by deepTools (version 3.4.3).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: lymph nodes

growth_protocol: 1000000 Naïve CD4 T cells were isolated at ZT13.

extract_protocol:
Cells were fixed with 1% formaldehyde for 5 minutes at room temperature (RT) and sonicated by an ultrasonicator (Covaris). Soluble chromatin was immunoprecipitated with the mixture of anti-GR antibody (BuGR-2, Invitrogen MA1-150) and anti-GR polyclonal antibody (Invitrogen PA1-511A) or mouse IgG as isotype control (Jackson ImmunoResearch) overnight. Immunoprecipitated DNA was sized (150 to 600 bp) by AMPure XP (Beckman Coulter).
DNA was adapter-ligated and amplified by NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: lymph nodes

value: naive CD4 T cells

value: WT


title: Total RNA Muscle Female 5wph replicate 2


title: Ribosome profiling of old liver replicate 2

description: Ribosome protected mRNA

source_name: liver

extract_protocol:
5~10 frozen liver from fish were pooled and lysed using cryo-mill. Lysed samples were thawed and spun at 21,000g for 15 minutes to clear the lysate. RNA concentration of supernatant was measured and RNAse I was added to 0.4 units per ug of RNA. The sample was incubated for 45 minutes at room temperature and 0.02ul of SUPERaseIn RNAse Inhibitor was added per ug of RNA to stop digestion. Samples were immediately layered on 1M sucrose cushion and spun at 100,000rpm for 1 hour in TLA 100.3 rotor to isolate ribosomes. Resulting ribosome pellet was resuspended and RNA was extracted using TRIzol reagent following manufacturer’s instructions.
RNA fragments in the range of ~25-35 nucleotides were gel purified. After dephosphorylation, a DNA linker (CTGTAGGCACCATCAAT) was ligated to the 3' end of the RNA footprints. Samples were then depleted of rRNA using RiboCop (Lexogen) with the addition of custom-designed oligos to enhance depletion efficiency. Remaining RNA fragments were reverse transcribed into cDNA, followed by circularization. Libraries were barcoded during PCR amplification and sent for sequencing.

value: liver


title: SF_24hps_01

value: Surface


title: Ribosome profiling of old liver replicate 1

description: Ribosome protected mRNA


title: Total RNA Muscle Male 5wph replicate 4


title: 02_GR_ChIP_rep2


title: A673-dHALO_ChIP_EP300_VH0032_1uM_24h_REP1_230131_GTCCGC_S6


title: SF_24hps_04


title: SF_6hps_05


title: 01_GR_ChIP_rep1


title: SF_6hps_04


title: Ribosome profiling of adult liver replicate 1

description: Ribosome protected mRNA


title: SF_6hps_03


title: A673-dHALO_ChIP_EP300_DMSO_24h_REP1_230131_CCGTCC_S3

description: DMSO ChIP linked to 1µM VH0032 EP300 ChIP


title: GRcKO_mTh17_rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing reads were trimmed using Trimmomatic (version 0.33) to remove poor quality reads.
Read data was then aligned to the mouse genome (mm10) with Hisat2 (version 2.1.0)
The aligned reads were used for the transcript quantification by using featureCounts from the subread package (version 1.6.5)
Assembly: mm10
Supplementary files format and content: Csv file includes raw counts for each sample.

source_name: Small intestine

growth_protocol: mice were subjected to the stress of wet bedding and 2 hours of restraint for two days. Then, the mice were intraperitoneally injected with 5 ug of anti-CD3 antibody. At 3 days after treatment, 10000 small intestinal Th17 cells (TCRb+CD4+IL-17-GFP+)  were sorted by BD Aria II.

extract_protocol:
Sorted cells were lasated by Buffer RLT (QIAGEN).
Then total RNA was harvested using Agencourt AMPure XP (Beckman Coulter) size selection beads. Takara SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Cat#634890) was used with all extracted RNA for cDNA library.  Illumina Nextera XT DNA Library Preparation Kit (Cat#FC-131-1024) and Nextera XT Index Kit (Cat#FC-131-1001) were used with 1 ng of cDNA for the construction of sequencing libraries.

value: Small intestine

value: IL-17-GFP+CD4+TCRb+ primary cells

value: Th17 cells

value: CD4-Cre;GR flox/flox;IL-17-GFP/+

value: Stress and anti-CD3 antibody injection


title: A673-dHALO_ChIP_CBP_steadystate_REP1_230320_GCCAAT_S6

description: No treatment, baseline cells

value: CBP


title: SF_6hps_02

value: sham


title: GRcKO_mTh17_rep2


title: Ribosome profiling of young liver replicate 2

description: Ribosome protected mRNA


title: A673-dHALO_ChIP_ASH2L_steadystate_REP1_230320_ACAGTG_S5

description: No treatment, baseline cells


title: GRcKO_mTh17_rep1


title: A673_ChIP_input_steadystate_REP1_220705_ATCACG_S1

description: sgGFP H3K4me1/H3K27ac ChIP Input

value: sgGFP

value: 7 days


title: Ribosome profiling of young liver replicate 1

description: Ribosome protected mRNA


title: Control_mTh17_rep4

value: CD4-Cre;GR flox/+;IL-17-GFP/+


title: SF_con_03

value: cardiac ventricle

value: uninjured


title: Total RNA-seq of old brain replicate 4

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150939
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.

source_name: brain

extract_protocol:
Individual brains from the fish were collected and snap-frozen in liquid nitrogen. The protein amount was estimated based on fresh tissue weight (assuming 5% of protein w/w) and ice-cold 1x PBS with protease/ phosphatase inhibitors (Roche,11836170001, 4906837001) was added accordingly to a final concentration of 2 μg/μL. Samples were then vortexed (5 times) before sonication (Bioruptor Plus) for 10 cycles (60 sec ON/30 sec OFF) at the high setting, at 4 °C. The samples were then centrifuged at 3000 xg for 5 min at 4 °C, and the supernatant was transferred to 2 mL Eppendorf tubes. 1.5 mL of ice-cold Qiazol (Qiagen, 79306) reagent was added to 150 μL of homogenate, vortexed five times, and snap-frozen in liquid nitrogen. On the day of the experiment, samples were thawed on ice, vortexed five times, and incubated at room temperature for 5 min before the addition of 300 μL of chloroform. Samples were mixed vigorously, incubated for 3 min at room temperature, and centrifuged at 12000 xg for 20 min at 4 °C. The upper aqueous phase (600 μL) was carefully transferred into a fresh tube and the remaining volume (phenol/chloroform phase) was kept on ice for DNA isolation. The aqueous phase was mixed with 1.1 volume of isopropyl alcohol, 0.16 volumes of sodium acetate (2 M; pH 4.0), and 1 μL of GlycoBlue (Invitrogen, AM9515) to precipitate RNA. After 10 min incubation at room temperature, samples were centrifuged at 12000 xg for 30 min at 4 °C. The supernatant was completely removed, and RNA pellets were washed by adding 80% (v/v) ethanol and centrifuging at 7500 xg for 5 min at 4 °C. The washing steps were performed twice. The resulting pellets were air-dried for no more than 5 min and dissolved in 10 μL nuclease-free water. To ensure full dissolution of RNA in water, samples were then incubated at 65 °C for 5 min, before storage at -80 °C.
Total RNA library preparation was done by introducing 500 ng total RNA into Illumina’s NEBNext Ultra II directional mRNA (UMI) kit (NEB, E7760S), following the manufacturer’s instructions. The quality and quantity of all libraries were checked using Agilent’s Bioanalyzer 2100 and DNA 7500 kit (Agilent Technologies, 5067-1506).

value: brain


title: PC_6hps_01

value: Pachon


title: A673-dHALO_ChIP_FLI1_DMSO_24h_REP1_220705_AGTTCC_S4

description: DMSO ChIP linked to 1µM VH0032 FLI1 ChIP

extract_protocol:
In brief, cells were fixed in either 1% Formaldehyde (FA) for 10 minutes (histone modifications) or with 2uM DSG (30 mins) following by 1% FA (10 mins, for non histone proteins). Following fixation, cells were lysed and sonicated. Beads and antibody complexes were incubated with sonicated lysis overnight. ChIP material was washed 3x ChIP wash buffer and 1x TE+50mM NaCl. DNA-rpotein complexes were eluted from beads and de-crosslinked overnight. The following day, DNA clean up was performed using column purification.
1-10 ng of ChIP DNA was used for the library preparation using the SMARTer ThruPLEX DNA-Seq Kit (Takara)
ChIP-Sequencing was performed using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 37bp, paired-end reads.

value: 24 hours

value: DMSO


title: A673_ChIP_H3K4me1_steadystate_REP1_220705_TGACCA_S3

description: sgGFP control ChIP linked to sgMLL3/4 H3K4me1 ChIP


title: Control_mTh17_rep3


title: Ribosome profiling of adult liver replicate 2

description: Ribosome protected mRNA

value: liver


title: Total RNA-seq of old brain replicate 3

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150938
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: A673_ChIP_H3K27ac_steadystate_REP1_220705_GCCAAT_S5

description: sgGFP control ChIP linked to sgMLL3/4 H3K27ac ChIP


title: SF_con_02

value: Surface


title: Control_mTh17_rep1

value: Small intestine

value: IL-17-GFP+CD4+TCRb+ primary cells


title: A673_ChIP_EP300_steadystate_REP1_221119_CAGATC_S1

description: sgGFP control ChIP linked to sgMLL3/4 p300 ChIP


title: Control_mTh17_rep2

value: Th17 cells