title: Cardiac fibroblasts Yap+Wwtr1 siRNA treatment 2

description:
Allgene_normalized_counts.csv, diffgene_control_yap-wwtr.csv
Yap+Wwtr1 2

data_processing:
Sequencing was performed using a DNBSEQ-G400 platform at 20M, 100bp pair-end reads per sample.
Adapter sequences were removed from the output sequence and reads with low base quality (<13) were further trimmed using Trim_Galore v0.6.5 (Babraham Bioinformatics).
Trimmed reads were then aligned to the rat genome (rn6) using Hisat2 v 2 2.1.
Transcripts were assembled from RNA-seq alignments using Stringtie2 v2.1.5.
Expression was quantified by fragments per kilobase of transcript per million reads mapped (FPKM).
Genome_build: rn6
Supplementary_files_format_and_content: excel file with FPKM values for each sample
Supplementary_files_format_and_content: excel files comapring log2 fold change between experimental groups and negative control

organism: Rattus norvegicus

source_name: neonatal heart ventricles

growth_protocol: Cardiac fibroblasts were incubated in DMEM supplemented with 15% FBS and penicillin-streptomycin.

extract_protocol:
Cell were homogenized in TRIzol. RNA was subsequently collected and purified by phenol/chloroform extraction. RNA quality was determined using an Agilent BioAnalyzer.  RNA libraries were prepared by BGI Americas
Prepared by BGI Americas

treatment_protocol: After 16 hours, the cells were transfected using mission siRNA transfection reagent (Sigma) with two different siRNAs each at a concentration of 25 nM designed against the target gene of interest. Forty-eight hours post transfection cells were collected in Trizol for RNA extraction.

value: Cardiac Fibroblasts

tag: sirna treatment

value: Wwtr1 siRNA - SASI_Rn01_00120445 and SASI_Rn01_00120446 (Sigma)

value: Sprague Dawley


title: a1-7d

status: Public on Oct 29 2022

type: SRA

city: Jinan

first: Boya

last: Liang

address: No.336, West Nanxinzhuang Road, Qixian Street

country: China

institute: University of Jinan

library_source: transcriptomic

data_processing:
In order to ensure the quality of information analysis, the software FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_tool kit/) is used to filter the original data and get clean reads.
Use fastx_clipper to remove connector sequences from reads
Use fastq_quality_filter to remove N from the read 3'to 5 'direction (N indicates that the base information cannot be determined) to the first base that is not N.
Use fastq_quality_filter to remove continuously occurring low-quality bases from the read 3'to 5 'direction, and delete the read itself and its paired sequences when the low-quality clean reads length is lower than 36bp.
Use local scripts to pair pair end reads (used for PE sequencing).
samtools was used to calculate read counts and RPKM
Assembly: draft genomes of strains Brevundimonas diminuta R79 and Pseudomonas balearica R90 not yet published.  FASTA files of transcript sequences are available on the series record.
Supplementary files format and content: RPKM

molecule: total RNA

organism:
Brevundimonas diminuta
Stutzerimonas balearica

growth_protocol: Strains R79 and R90 were inoculated separately and mixed at 1:1 in the domestication medium, and the samples were collected at 30 ℃ for 0h, 4d and 7d, respectively, and the total RNA was extracted for transcriptome analysis.

extract_protocol:
RNA was extracted from the samples by column fecal RNAout Kit (TIANDZ). After the feces (0.5g) were ground to powder in liquid nitrogen, buffer A preheated by 1ml at 65 °C was added and mixed with 300ul buffer B and 200ul chloroform for 20 seconds. After swirling for 30 seconds, the supernatant was centrifuged, and then the buffer C of the same volume was mixed upside down and transferred to the adsorption column. After centrifugation, the penetrating solution was discarded and the 700ul universal column solution was washed once and then washed with 300ul universal column solution, and RNA was eluted with 100ulRNA elution solution. RNA is quantified using Qubit (Invitrogen, USA).
RNA digested by DNase was removed rRNA by Ribo-Zero digestion Magnetic Kit (Gram-Negative Bacteria or Gram-positive Bacteria) (Epicentre, USA): adding Ribo-Zero Reaction Buffer and Ribo-Zero rRNA Removal Solution (Gram-Negative Bacteria or Gram-positive Bacteria), adding Ribo-Zero Reaction Buffer and Ribo-Zero rRNA Removal Solution (Gram-Negative Bacteria or Gram-positive Bacteria) to 40 μ l, reacting 10min at 68 ℃, then placing 5min at room temperature, adding the treated RNA to the pre-washed magnetic beads, mixing thoroughly immediately, placing 5min at room temperature, then reacting 5min at 50 ℃, immediately placing above 1min on the magnetic rack. Absorb the supernatant, add water to 180 μ l, add 3 M Sodium Acetate and Glycogen (10 mg/ml), add 600ul anhydrous ethyl alcohol, place at-20 ℃ for more than 1 h, centrifuge to get precipitation, add water to dissolve rRNA-depleted RNA.
Take 10ng rRNA-depleted RNA from RNA library, construct library with KAPA Stranded mRNA-Seq Kit (KAPA Biosystems, USA): add KAPA Fragment,Prime and Elute Buffer (2X) to interrupt mRNA, react 6min at 94 °C, quickly put on ice; add 1stStrand synthesis Buffer and KAPA Script to synthesize the first chain of cDNA, reaction procedure: 25 °C 10 minutes, 42 °C 15 minutes, 70 °C 15 minutes; and then add 2ndStrand Marking Buffer (2x) and 2ndStrand Synthesis EnzymeMix for cDNA second chain synthesis, 16 °C reaction for 1 h. After purification with AMPure XP Beads (Agencourt, USA), add KAPA A-Tailing Buffer (10x) and A-Tailing Enzyme for terminal repair and add A, reaction procedure: 30 °C 30min, 65 °C 30 min; add Adaptor, KAPA Ligation Buffer (5x) and KAPA T4 DNA Ligase joint, 20 °C DNA Ligase reaction for 15 min; 200~300bp range of ligated cDNA was obtained by two-step AMPure XP Beads purification. PCR amplification was carried out by adding KAPA HiFi HotStart Ready Mix (2x) and KAPA Library Amplification Primer Mix (10x). The PCR reaction conditions were as follows: pre-denaturation at 98 °C for 45 Sec, denaturation at 98 °C for 15 Sec, annealing at 60 °C for 30 Sec, extension at 72 °C for 30 Sec;, and then purified with 1-fold volume of AMPure XP Beads to obtain a library for sequencing.

tag: strain

tag: medium

value: CH3COONa 5 g/L;(NH4)2SO4 0.16 g/L;K2HPO4•3H2O 0.121 g/L;KH2PO4 0.045 g/L;NaCl 16 g/L;trace element solution 1 mL/L

tag: culture time


title: Cardiac fibroblasts Yap+Wwtr1 siRNA treatment 3

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

country: USA

institute: Medical College of Wisconsin

description:
Allgene_normalized_counts.csv, diffgene_control_yap-wwtr.csv
Yap+Wwtr1 3

tag: cell type

tag: age


title: CHLA90, shERK5-4, 3

type: RNA

city: Barcelona

first: Carlos

last: Jimenez

state: Barcelona

address: Pg. Vall dHebron 119-129, Edificio Collserola, lab 207

department: Pediatric Oncology

country: Spain

institute: Vall d'Hebron Institut de Recerca

hyb_protocol: Three hundred nanograms of total RNA were hybridized to Human Clariom S assay (Affymetrix, Santa Clara, CA, USA) arrays with the GeneChip WT Terminal Labeling Hybridization Kit (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Transcription analysis console (Applied Biosystem, version 4.0.0.25)

label: biotin

organism: Homo sapiens

growth_protocol: SK-N-BE(2) and CHLA-90 cells were grown in Iscove’s modified Dulbecco’s medium (Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 20% heat-inactivated fetal bovine serum (South America Premium, Biowest, Nuaillé, France) and 1% of insulin–transferrin–selenium Supplement (Life Technologies).

extract_protocol: RNA was then isolated using the miRNeasy mini kit (Qiagen, #509217004). RNA quality was evaluated using Agilent Bioanalyzer 2100 Eukaryote Total RNA Pico assay (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SK-N-BE(2) and CHLA-90 cells (250000 cells per well) were seeded in 6-well plates with 1.5 ml of lentiviral supernatant produced in HEK-293T containing pLKO-shNSC, shERK5-4 or shERK5-5 lentiviral particles.

tag: cell line

value: neuroblastoma cell

tag: treatment


title: CHLA90, shERK5-5, 3

label_protocol: GeneChip WT Terminal Labeling Hybridization Kit


title: CHLA90, shERK5-4, 2


title: CGRT_3D_C_i

city: Oxford

first: Allison

middle: M

last: Barry

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were mapped to the GRCm38 (mm10) Mouse Genome using STAR alignment (Dobin et al 2013). Samtools was used to sort, index, and merge BAM files (Li et al 2009). Quality control (QC) was performed with both FastQC and Samtools prior to gene counting with HTSeq (Andrews 2010, Li et al 2009, Anders et al 2015).
Counts were corrected for effective library size in R using DESeq2 (Love et al 2014). Normalized gene counts were fitted to a negative binomial distribution. A batch effect was introduced during sample collection, and a model that included this batch effect was fitted to every gene. The significance of the model's coefficients was assessed using the Wald test.
Assembly: GRCm38 (mm10)
Supplementary files format and content: csv files contained count data (toc) from samples that pass quality control along with column data (colData), for use with DESeq2

molecule: polyA RNA

organism: Mus musculus

source_name: DRG

extract_protocol:
Cold saline perfusion, lumbar DRG dissection and dissociation, FACS into lysis buffer (NEBnext)
NEB/SMARTER

treatment_protocol: spared nerve injury (SNI) at 3 days (3D) or 4 weeks (4W). Ipsilateral lumbar DRG (L3-L5) were compared to their contralateral counterparts in paired samples.

tag: tissue

value: DRG

value: primary

value: PEP

tag: time

value: 3 day

tag: Sex

value: F

value: Ipsilateral

tag: batch


title: CHLA90, shNSC, 3

value: shNSC


title: CHLA90, shNSC, 2


title: Cardiac fibroblasts Yap+Wwtr1 siRNA treatment 1

description:
Allgene_normalized_counts.csv, diffgene_control_yap-wwtr.csv
Yap+Wwtr1 1


title: CGRT_3D_E_i

value: M


title: CHLA90, shNSC, 1


title: SKNBE2, shERK5-5, 3


title: a1-4d


title: Cardiac fibroblasts Wwtr1 siRNA treatment 3

description:
Allgene_normalized_counts.csv, diff_gene_control_wwtr.csv
Wwtr1 3


title: CGRT_3D_C_c

value: Contralateral


title: CHLA90, shERK5-4, 1


title: CHLA90, shERK5-5, 2


title: CHLA90, shERK5-5, 1


title: CGRT_3D_B_i


title: a2-4d


title: Cardiac fibroblasts Wwtr1 siRNA treatment 2

description:
Allgene_normalized_counts.csv, diff_gene_control_wwtr.csv
Wwtr1 2


title: CGRT_3D_B_c


title: a2-7d


title: R90-3-7d

organism: Stutzerimonas balearica


title: Cardiac fibroblasts Wwtr1 siRNA treatment 1

description:
Allgene_normalized_counts.csv, diff_gene_control_wwtr.csv
Wwtr1 1


title: R90-3-4d


title: CGRT_3D_A_i


title: CGRT_3D_A_c


title: SKNBE2, shERK5-5, 1


title: R90-3-0d


title: SKNBE2, shERK5-4, 3


title: Cardiac fibroblasts Yap siRNA treatment 3

description:
Allgene_normalized_counts.csv, diff_gene_control_yap.csv
Yap 3

value: Yap siRNA - SASI_Rn01_00114054 and SASI_Rn02_00203876 (Sigma)


title: Cardiac fibroblasts Yap siRNA treatment 2

description:
Allgene_normalized_counts.csv, diff_gene_control_yap.csv
Yap 2


title: Cardiac fibroblasts Yap siRNA treatment 1

description:
Allgene_normalized_counts.csv, diff_gene_control_yap.csv
Yap 1


title: SKNBE2, shERK5-4, 1


title: R90-2-4d


title: SKNBE2, shERK5-4, 2


title: Fos-creERT2,eWAT, hM3D-2

city: Binzhou

first: Bin

last: Liu

state: Shandong

address: No. 661 Huanghe 2nd Road, Binzhou City, Shandong

institute: Binzhou Medical University Hospital

description: hM3D All_gene_fpkm.list

data_processing:
CLC Genomics Workbench v 11.0.1
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud(www.biocloud.net) online platform.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing.
These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: GRCm38(Mus musculus)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: visceral epididymal WAT (eWAT)

extract_protocol:
Total RNA was extracted from iWAT or eWAT using TRIzol reagent for Illumina sequencing and 1 μg RNA per sample was used as input material for the RNA  sample preparations.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: visceral epididymal WAT (eWAT)

tag: stress

value: repeated activaiton of PVN neurons

value: every 3 days for  42 days


title: R90-2-7d


title: Cardiac fibroblasts negative siRNA treatment 2

description:
Allgene_normalized_counts.csv, diff_gene_control_yap.csv, diff_gene_control_wwtr.csv, diffgene_control_yap-wwtr.csv
Negative 2

value: Cardiac Fibroblasts

value: MISSION siRNA Universal Negative Control #1 + #2 (Sigma)


title: Cardiac fibroblasts negative siRNA treatment 3

description:
Allgene_normalized_counts.csv, diff_gene_control_yap.csv, diff_gene_control_wwtr.csv, diffgene_control_yap-wwtr.csv
Negative 3

value: Sprague Dawley


title: SKNBE2, shNSC, 3

value: neuroblastoma cell


title: Ad libitum male liver biol rep 4

city: Stanford

first: Jingxun

last: Chen

state: CA

address: 290 Jane Stanford Way, Room E365

institute: Stanford University - Stanford, CA

data_processing:
Raw sequencing data (FASTQ files) were processed and checked for quality using Trim-galore v0.4.5.
The processed reads were aligned to the African turquoise killifish reference genome downloaded from NCBI (Nfu_20140520, GCF_001465895.1). The read alignment was performed using STAR v2.7.1a with the default parameters.
Next, we used samtools v1.5 to remove the reads that map to multiple genomic regions, using the parameters of MAPQ<255 (“samtools view -q255 -b”).
These uniquely mapped reads were then used to generate the read counts for each gene, for which we used the “featureCounts” program from subread v2.0.1 using the default parameters.
We used DESeq2 v1.32.0 to analyze the differential gene expression.
Assembly: NCBI African turquoise killifish reference genome (Nfu_20140520, GCF_001465895.1).
Supplementary files format and content: Comma-separated text file includes raw counts for all samples in a matrix ("Counts_ALDR_220325.csv").
Supplementary files format and content: Comma-separated text file includes normalized counts for all liver samples in a matrix ("CountsNormDEseq2_Liver_ALDR_220331.csv").

organism: Nothobranchius furzeri

source_name: Liver

growth_protocol: All fish were raised from embryos collected from 15 male-female pairs, when these breeders were 9-10 weeks of age (within their reproductive peak). Collected embryos were treated with mild iodine (0.2%, diluted from Povidone-iodine solution (10% w/v, 1% w/v available iodine, RICCA #3955-16)) on Day 1 to reduce contamination, incubated in embryo solution with 0.01% methylene blue (Kordo, #37344), and then placed on moist coco fiber on the 14th day after collection. After two weeks on coco fiber, fish were hatched in ~1 cm-deep cold 1 g/L humic acid solution, at room temperature. For the next four days, the fish were housed on the countertop of the animal facility at 25C. System water was added to the hatching containers, and fish were fed live brine shrimp daily. For the following 2 weeks, fish were housed at a density of 4 fish per 0.8 L tank and fed with brine shrimps daily. In the following 2 weeks, housing density was reduced to 2 fish per 0.8 L tank and fish were fed as before. After 4 weeks post hatching, the fish was individually placed in 2.8 L tanks (singly housed) and fed dry food pellets according to specific dietary treatments.

extract_protocol:
We isolated RNA from liver and brain using Qiagen RNeasy Mini kit (Qiagen, #74106) according the manufacturer’s instructions. The processing order of each organ was randomized. The tissues were transferred to the 1.2 mL Collection Microtubes (Qiagen, #19560) on dry ice in a 4°C cold room to reduce tissue thawing. Next, an autoclaved metal bead (Qiagen, #69997) and 700 µL of QIAzol (Qiagen, #79306) were added to each tube. Two rounds of tissue homogenization were performed on the TissueLyserII machine (Qiagen, #85300) at 25 Hz, 5 min each, at room temperature. The lysate was transferred to new 1.5 mL tubes, 140 µL chloroform (Fisher Scientific, #C298-500) was added, and the tubes were vortexed for 15 sec. After incubation at room temperature for 2-3 min, lysates were centrifuged at 12,000 x g at 4°C for 15 min. The aqueous phase was mixed with 350 µL ethanol (200 Proof, Gold Shield Distributors, #412804) by inverting the tubes 10 times. The mixture was transferred to the RNeasy column, washed with 350 µL RW1 buffer (provided by the RNeasy Mini kit), and treated with DNase I (following the kit’s protocol) at room temperature, for 15 min. The column was washed 2 times with 500 µL RPE buffers, and the RNA was eluted with 50 µL nuclease-free water (Invitrogen, #10977023). RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer and the Agilent Nano Eukaryotic RNA Kit (Agilent, #5067-1511).
10 ng of RNA of each sample was used for cDNA synthesis. cDNA synthesis was performed using the Takara SMART-seq v4 PLUS kit (Takara, #634889) according to the manufacturer’s instructions. The cDNA libraries were prepared using the Illumina NexteraXT DNA library prep kit (Illumina, #FC-131-1096) based on the manufacturer’s protocol. The Illumina Nextera XT Index Kit v2 (Illumina, #131-2001) was used for library indexing.

treatment_protocol: For ad libitum treatment, fish were fed 7 feedings of 5 mg per feeding spread throughout from 7 am to 7 pm (i.e., feed 5 mg every 2 hours). For dietary restriction treatment, fish were fed 3 feedings of 5 mg per feeding in the morning (from 7 am to 9 am). Dietary treatment began when the fish was placed into 2.8 L tanks at 4 weeks of age and lasted for 5 weeks. Brains and livers were harvested from these killifish in two batches on two days (4 males and 4 females on each day). Fish were randomly assigned to a harvest batch, with each batch having 2 fish from each condition (AL-Male, DR-Male, AL-Female, DR-Female). On harvest day, the automatic feeders were first removed from the tank. Next, 1.5 h after the light turned on, for AL treatment, fish were manually fed 17.5 mg of dry food; and for DR treatment, fish were fed 7.5 mg of dry food. This quantity of food corresponded to half of the total daily food amount and maintained the differential ratio of food intake for the two diet regimens. From 12 PM to 3 PM, 8 fish were euthanized on ice, and organs were extracted and snap-frozen in liquid nitrogen. All organs were stored at -80˚C until RNA isolation.

value: Liver

value: GRZ

tag: genotype

value: WT

value: AL - ad libitum


title: Fos-creERT2,iWAT, hM3D-3

description: hM3D All_gene_fpkm.list

source_name: subcutaneous inguinal WAT (iWAT)

value: subcutaneous inguinal WAT (iWAT)


title: R90-1-7d

value: CH3COONa 5 g/L;(NH4)2SO4 0.16 g/L;K2HPO4•3H2O 0.121 g/L;KH2PO4 0.045 g/L;NaCl 16 g/L;trace element solution 1 mL/L


title: R90-2-0d


title: Cardiac fibroblasts negative siRNA treatment 1

description:
Allgene_normalized_counts.csv, diff_gene_control_yap.csv, diff_gene_control_wwtr.csv, diffgene_control_yap-wwtr.csv
Negative 1


title: Dietary restriction female liver biol rep 4

value: DR - dietary restriction


title: R90-1-4d


title: Fos-creERT2,eWAT, hM3D-1

description: hM3D All_gene_fpkm.list


title: Fos-creERT2,eWAT, hM3D-3

description: hM3D All_gene_fpkm.list


title: SKNBE2, shNSC, 2

value: shNSC


title: R79-3-7d

organism: Brevundimonas diminuta


title: R79-3-4d


title: Cl19 g1Hira_3

city: Cologne

first: Lorea

last: Valcarcel

address: FREZZA Lab, CECAD Research Center Faculty of Medicine University Hospital Cologne Joseph-Stelzmann-Str. 26

country: Germany

institute: CECAD

data_processing:
RNA-Seq was done on a single end run using the Truseq Stranded mRNA from Illumina, and the library preparation was performed following the manufacturer’s instructions
The sequencing was done on a 75-cycle high output NextSeq 500 kit
The quality control of the reads was done using FastQC [1] v0.11.4
Assembly: GRCm39
Supplementary files format and content: Raw count

source_name: Kidney mouse epithelial Cells

extract_protocol:
RNA extraction from the cells was performed using a RNeasy kit (Qiagen) following the manufacturer’s protocol. RNA was further purified using the RNA Clean and Concentrator kit (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Knock out of Hira was carried out using the CRISPR/Cas9 technology.

value: Fh1-/- g1Hira

value: Kidney mouse epithelial Cells


title: Dietary restriction male liver biol rep 4


title: R90-1-0d


title: Fos-creERT2,iWAT, hM3D-2

description: hM3D All_gene_fpkm.list


title: Fos-creERT2,eWAT, mcherry-3

description: hM3D All_gene_fpkm.list

value: visceral epididymal WAT (eWAT)

value: untreated mcherry

value: 42 days


title: Fos-creERT2,eWAT, mcherry-2

description: hM3D All_gene_fpkm.list


title: Cl19 g1Hira_2


title: R79-3-0d


title: Dietary restriction male brain biol rep 4

source_name: Brain

value: Brain


title: Ad libitum female brain biol rep 4


title: Dietary restriction female brain biol rep 4


title: Cl19 g1Hira_1


title: Fos-creERT2,eWAT, mcherry-1

description: hM3D All_gene_fpkm.list


title: Fos-creERT2,iWAT, mcherry-3

description: hM3D All_gene_fpkm.list


title: Ad libitum male brain biol rep 4


title: R79-2-7d


title: Fl g1Hira_2

value: Fh1 fl/fl g1Hira


title: Fos-creERT2,iWAT, mcherry-2

description: hM3D All_gene_fpkm.list


title: SKNBE2, shNSC, 1


title: Dietary restriction female liver biol rep 3


title: Fl g1Hira_1


title: Cl19_3

value: Fh1 deficient (Fh1-/-)


title: Ad libitum female liver biol rep 4


title: C57BL/6,eWAT, chronic restraint-3

description: restraint All_gene_fpkm.list

value: Chronic restraint stress


title: R79-2-4d


title: Fos-creERT2,iWAT, mcherry-1

description: hM3D All_gene_fpkm.list


title: Cl19_2


title: Dietary restriction female brain biol rep 3


title: R79-1-4d


title: C57BL/6,eWAT, chronic restraint-2

description: restraint All_gene_fpkm.list


title: R79-1-0d


title: Dietary restriction male liver biol rep 3

value: Liver


title: Fl g1Hira_3


title: C57BL/6,eWAT, chronic restraint-1

description: restraint All_gene_fpkm.list


title: Ad libitum male liver biol rep 3

value: GRZ


title: Ad libitum female brain biol rep 3

value: WT


title: Dietary restriction male brain biol rep 3


title: Fl_3

value: Fh1 fl/fl


title: Fl_2


title: C57BL/6,iWAT, chronic restraint-2

description: restraint All_gene_fpkm.list

value: subcutaneous inguinal WAT (iWAT)


title: CD7 PDX chordoma, palbociclib treatment, biol rep 1

city: PARIS

first: Sophie

last: VACHER

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
RNA sequencing data were analyzed using the BlueBee Genomics Plateform (Lexogen, Vienna, Austria).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts for each sample

source_name: chordoma PDX

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA)
Library preparation was performed using QuantSeq 3’ mRNA-Seq reverse (REV) Library Prep Kit (Lexogen, Vienna, Austria) using 150 ng of total RNA, and according to manufacturer’s instruction.

treatment_protocol: Palbociclib was administered orally at a dose of 75 mg/kg/day, 5 days per week from day 1 to mouse sacrifice. Xenografted mice were sacrificed when tumor volume reached a mean volume 500 mm3.

value: chordoma PDX

value: palbociclib


title: CD7 PDX chordoma, palbociclib treatment, biol rep 3


title: CD7 PDX chordoma, palbociclib treatment, biol rep 2


title: Ad libitum male brain biol rep 3

value: AL - ad libitum


title: Cl19_1


title: C57BL/6,iWAT, chronic restraint-1

description: restraint All_gene_fpkm.list


title: Fl_1


title: Ad libitum female liver biol rep 3


title: CD3 PDX chordoma, palbociclib treatment, biol rep 3


title: C57BL/6,iWAT, chronic restraint-3

description: restraint All_gene_fpkm.list


title: Dietary restriction female liver biol rep 2

value: DR - dietary restriction


title: C57BL/6,eWAT, control-3

description: restraint All_gene_fpkm.list

value: untreated control


title: Dietary restriction female brain biol rep 2


title: CD3 PDX chordoma, palbociclib treatment, biol rep 1


title: CD7 PDX chordoma, without treatment, biol rep 3


title: C57BL/6,eWAT, control-1

description: restraint All_gene_fpkm.list

value: visceral epididymal WAT (eWAT)


title: Ad libitum male brain biol rep 2


title: CD7 PDX chordoma, without treatment, biol rep 2


title: C57BL/6,iWAT, control-3

description: restraint All_gene_fpkm.list


title: GC038108: Hypertrophya

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

description: RNA isolated from extracellal vescicles

data_processing:
Mapping Tophat
HtSeq-count
DESeq
Assembly: mm10

source_name: Serum

extract_protocol: Illumina Truseq Stranded mRNA

value: Serum

value: extracellal vescicles

value: MAGIC F1

value: Hypertrophya


title: GC038109: Hypertrophya

description: RNA isolated from extracellal vescicles


title: GC038107: Hypertrophya

description: RNA isolated from extracellal vescicles


title: C57BL/6,iWAT, control-2

description: restraint All_gene_fpkm.list

value: 42 days


title: CD3 PDX chordoma, palbociclib treatment, biol rep 2


title: CD3 PDX chordoma, without treatment, biol rep 3


title: C57BL/6,iWAT, control-1

description: restraint All_gene_fpkm.list


title: Dietary restriction male brain biol rep 2

value: Brain


title: Dietary restriction male liver biol rep 2

value: Liver


title: CD3 PDX chordoma, without treatment, biol rep 2


title: C57BL/6,eWAT, control-2

description: restraint All_gene_fpkm.list


title: Ad libitum male liver biol rep 2

value: GRZ


title: CD19+ICOSL-B CELL

city: Suzhou

first: Cuiping

state: Jiangsu

address: Ganjiang Road 178#

institute: Jiang Su institue of immunology

description: gene expression after cell sorting

hyb_protocol: Klenow enzyme labeling strategy was applied after reverse transcription using CbcScript Ⅱ reverse transcriptase. Labeled cDNA was then purified and resuspended in elution buffer. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in an Agilent Hybridization Oven overnight.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CD19+ICOSL-B CELL

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification and enzymatic reaction. After completion of double-stranded cDNA (dsDNA) synthesis, the amplified cRNA was purified.

extract_protocol: Briefly, total RNA was extracted by using the Trizol reagent and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA).

treatment_protocol: After the second immunization, spleens of CIA mice were collected and single-cell suspensions were generated by density gradient centrifugation. CD19+ICOSL+ B cell and CD19+ICOSL- B cell subsets were sorted by FACSAriaTM Ⅱ Cell Sorter (BD Biosciences). Microarray analysis of sorted CD19+ICOSL+ B and CD19+ICOSL- B cells were carried out by Capitalbio Technology Corporation

tag: icosl

value: negative


title: GC034320: Hypertrophya

description: RNA isolated from extracellal vescicles


title: CD19+ICOSL+B CELL

description: gene expression after cell sorting

source_name: CD19+ICOSL+B CELL

value: positive


title: Dietary restriction male brain biol rep 1

value: WT


title: GC034321: Hypertrophya

description: RNA isolated from extracellal vescicles


title: GC034319: Hypertrophya

description: RNA isolated from extracellal vescicles


title: CD3 PDX chordoma, without treatment, biol rep 1

value: chordoma PDX


title: SKNBE2, shERK5-5, 2

value: neuroblastoma cell


title: mESC, WT, Adr

city: Guangzhou city

first: Mangmang

last: Li

state: Guangdong province

address: 1838 N Guangzhou Ave

department: Department of Cell Biology School of Basic Medical Sciences

institute: Southern Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore( Version 0.3.4)(parameters:trim_galore -q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired ./01.fastqc_data/RS_1.fq.gz ./01.fastqc_data/RS_2.fq.gz --gzip -o ./)
Trimmed sequence reads were mapped to mm9 using hisat2(version 2.0.4)
Read count was performed by featurecount(Version 1.6.0)(parameters:featureCounts -p -t exon -g gene_id -a /annotation.mm10 -o RS_count.txt RS.bam)
Different expression genes analysis was analyzed by DESeq2 (1.16.1) with P-value < 0.05 and the absolute value of Log2 > 1 were called differentially expressed .
Assembly: mm9
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads

source_name: mESC R1E

growth_protocol: Cells were maintained in mESC growth medium composed of DMEM (Corning, 10-013CVRC), 15% fetal bovine serum (TrinityTek, 1010102), 0.1 mM β-mercaptoethanol (Sigma, 516732), 100 mM MEM non-essential amino acids (Corning, 25-025-CIR), 1 × penicillin/streptomycin (Corning, 30-002-CIa), and 1000 U/mL leukemia inhibitory factor (LIF) (Genscript, Z03077-1).

extract_protocol:
1ug total RNAs were extracted with the TRIzol® Reagent (Thermo fisher, 15596018).
RNA libraries for RNA-seq were prepared using NEB Next® Ultra RNA Library Prep Kit for Illumina®（#7530） following manufacturer's protocols.

treatment_protocol: R1E cells were treated with 0.5 μM Adriamycin for 8 hours in growth medium.

value: mESC R1E

value: mouse embryonic stem cells

value: Adriamycin treatment

value: 8 h


title: GC038106: Dystrophya

description: RNA isolated from extracellal vescicles

value: Serum

value: Sgcb null

value: Dystrophya


title: CD39 patient germline

library_source: genomic

data_processing:
Variants were called using Varscan2 (v2.4.3-0)
All variants passed the following thresholds were validated : allelic ratio above 5% and population frequency lower than 0.1% in 1000 g, ESP or gnomAD.
Assembly: hg19
Supplementary files format and content: D182_table_report.xlsx file : include all variants called for all samples
Supplementary files format and content: D182.cnv_report.table.xlsx file : include copy number variations for all samples
Library strategy: target-seq

molecule: genomic DNA

source_name: blood

extract_protocol:
DNA was extracted from frozen tumor samples using a standard phenol/chloroform procedure.
The library preparation was performed using the Agilent Sureselect XT HS kit, and sequencing was completed on an Illumina NovaSeq 6000 sequencer.

value: blood


title: mESC, WT, Ctr

value: 0 h


title: Ad libitum male brain biol rep 1

value: Brain

value: AL - ad libitum


title: CD7 PDX chordoma, without treatment, biol rep 1


title: R1E_Adr8h_Input

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore( Version 0.3.4)(parameters:trim_galore -q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired ./01.fqc_data/RS_1.fq.gz ./01.fqc_data/RS_2.fq.gz --gzip -o ./)
Trimmed sequence reads were mapped to mm9 using bowtie2(Version 2.3.5 ).Only uniquely mapping reads  were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Bedtools(Version 2.29.2) was used for peaks overlap analysis and two peaks were defined as the overlapped peaks if they have 1bp intersection.
Finally, R package ChIPseeker(Version 1.30.3 ) was used to annotate with the position of the peaks in the genome, in which −1 to 1 kb of gene TSS were defined as gene promoter. we assigned the peak to the gene which is less than 25 kb away from the binding sites.
Motif analysis was performed using homer（v4.10）with the parameter ‘-size 200 -len 8,10,12’.
bigWig files were generated using bamCoverage(v3.5.0)
Assembly: mm9
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Briefly, 40 million cells were fixed with 1% formaldehyde for 10 min at room temperature. Chromatin fraction was prepared step by step using Lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), Lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and Lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholdate, 0.5% N-lauroylsarcosine). All the buffers were freshly supplemented with protease inhibitor cocktails (Roche, 4693116001) and 1 mM fresh PMSF. Chromatin fraction was sonicated with a Bioruptor® Plus (Diagenode) to shear DNA to a size of 300-500 bp. 5 μg of antibody and 50 ul Protein G beads (Genscript，L00664-25) were used to immunoprecipitate DNA-protein complex. After washing 5 times with Wash buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-Deoxycholdate), the DNA-protein complex was eluted in TES (10 mM Tris-HCl+1% SDS). After reverse-cross linking and DNA purification, the DNA was quantified using QubitTM 3.0 (Thermo Fisher Scientific, Q33216). 30 ng ChIPed DNA was sent to Novogen for library construction and sequencing.
(1) The DNA fragments are repaired, dA-tailed.(2) The DNA fragments with A tail are ligated to sequencing adaptors(3) The final DNA library is obtained by size selection and PCR amplification. After the construction of the library, the initial quantification was done with Qubit 2.0, and the library is diluted to 1ng/l. Then the insertion size of the library is detected with NGS3K. If meeting the expectation, the accurate concentration of the library is quantified by Q-PCR (library effective concentration > 2nM) to ensure the accurate molar amount that will pooled for sequencing.

treatment_protocol: Cells were either untreated or treated with 0.5 micromolar Adriamycin for 8 hours in growth medium.

value: Mouse embryonic stem cell

tag: chip antibody


title: Ad libitum female brain biol rep 2

value: GRZ


title: CD39 PDX chordoma


title: R1E_Ctr_Input


title: GC038104: Dystrophya

description: RNA isolated from extracellal vescicles

value: extracellal vescicles


title: Ad libitum female liver biol rep 2

value: Liver

value: WT


title: CD7 PDX chordoma

value: chordoma PDX


title: GC034318: Dystrophya

description: RNA isolated from extracellal vescicles


title: Dietary restriction female brain biol rep  1

value: DR - dietary restriction


title: CD3 patient germline


title: Dietary restriction male liver biol rep 1


title: GC034317: Dystrophya

description: RNA isolated from extracellal vescicles


title: CD3 PDX chordoma


title: GC034316: Dystrophya

description: RNA isolated from extracellal vescicles


title: R1E_H3K27ac_Ctr_ABCAM


title: hCM

city: Cheonansi

first: Ji-Young

last: Yoon

state: Chungnam

address: Dandaero 119

department: Nanbiomedical science

country: South Korea

institute: Dankook University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: human dental pulp

growth_protocol: DPSC were cultured in growth medium αMEM supplemented with 15% fetal bovine serum, 2 mM L-gluatamine, and 0.1 mM L-ascorbic acid phosphate.

extract_protocol:
Total RNA was isolated using RibospinTM (cat. no. 304-150; GeneAll Biotechnology) according to manufactural protocol.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: DPSC were cultured in osteogenic differentiation media diluted HGF-CM, heated HGF-CM and SFM at a 1:1 ratio each for 7 days.

value: primary human dental pulp stem cells

tag: culture condition

value: Culture condition :cultured at osteogenic medium diluted with heated HGF-CM at a 1:1 ratio for 7 days


title: GC034315: Wild Type

description: RNA isolated from extracellal vescicles

value: no


title: Ad libitum male liver biol rep 1


title: GC038105: Dystrophya

description: RNA isolated from extracellal vescicles

value: Serum


title: R1E_P53_Adr8h_RD


title: F

value: Culture condition :cultured at osteogenic medium diluted with serum free medium at a 1:1 ratio for 7 days


title: GC034314: Wild Type

description: RNA isolated from extracellal vescicles


title: Ad libitum female brain biol rep 1


title: Dietary restriction female liver biol rep 1


title: CD7 patient germline


title: R1E_P53_Ctr_RD


title: R1E_H3K4me3_Adr8h_ABCAM


title: Ad libitum female liver biol rep 1


title: CM

value: Culture condition :cultured at osteogenic medium diluted with HGF-CM (human gingival fibroblast derived-conditioned medium) at a 1:1 ratio for 7 days


title: R1E_H3K4me3_Ctr_ABCAM


title: R1E_H3K27ac_Adr8h_ABCAM


title: R79-2-0d

value: CH3COONa 5 g/L;(NH4)2SO4 0.16 g/L;K2HPO4•3H2O 0.121 g/L;KH2PO4 0.045 g/L;NaCl 16 g/L;trace element solution 1 mL/L


title: GC034313: Wild Type

description: RNA isolated from extracellal vescicles


title: a1-0d


title: NP-1

status: Public on Oct 28 2022

city: Potsdam

first: Petra

last: Kraus

state: NY

address: 8 Clarkson Avenue

department: Biology

country: Uruguay

institute: Clarkson University

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software.
Bioinformatic workflow followed the Genewiz protocol using GeneSCF v.1.1-p
Assembly: Bos taurus Btau_5.0.

organism: Bos taurus

source_name: IVD/adipose 2D culture

growth_protocol: D10SL 2D

extract_protocol:
RNA extraction was carried out at passage 2 (p2) from ~10exp6 cells per sample with the RNEasy Micro Kit (Qiagen) following the manufacturer’s guidelines.
NEBNext Ultra RNA Library Prep Kit (NEB)

value: nucleus pulposus

value: stromal cell

value: 2D culture


title: AF-3

value: annulus fibrosus


title: NP-3


title: FAT-2

value: adipose


title: AF-1


title: H9_ESC, scATAC-seq, Microwell ATAC-seq

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description: Microwell ATAC-seq

data_processing:
The original FASTQ files were converted to BAM format firstly. Then the cell barcodes were extracted and tagged with CB in the offered BAM files. Three 6bp barcodes and one 10bp Tn5 barcode ware combined to identify a single cell (a single cell barcode consists of four barcode fragments). Reads with the quality of cell barcodes less than 10 were tagged with XQ and removed afterwards. The processing above was based on Drop-seq_tools-2.5.1. Next, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each barcode fragments. Before alignment, the cell barcodes were added to the query names, the BAM files were converted to the FASTQ files and the 28bp barcodes at the 5’ end were trimmed simultaneously.
BWA (version 0.7.15), which is encapsulated in Snaptools, was used for reads alignment in paired-end mode. The teratoma data were aligned to a merged hg19-mm10 reference genome, and the ESCs data were aligned to hg19. For the teratoma data, the aligned BAM files would be divided into human.bam and mouse.bam subsequently. To correct the 9bp gap caused by the transposition reaction, we shifted all plus-strand insertions by +4bp and all minus-strand insertions by −5bp using alignmentSieve function in deepTools. Snaptools was again used to convert the aligned and shifted BAM files to SNAP files, which was then converted to Fragment files (BED format). The sorted and compressed Fragment files in BED format were required as inputs for subsequent analysis.
Assembly: Teratoma: a merged hg19-mm10 reference genome; ESCs: hg19
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq
Supplementary files format and content: Tab-delimited text files containing metadata (sample and cell_type)

source_name: H9 ESC

extract_protocol:
Tissues were quickly transferred into cold DPBS, then washed and subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into pre-labelled and pre-chilled 1.5 ml nuclease-free tubes. Aliquots of powdered tissues can be stored at -80°C. After that, the powder in each tube was suspended in 1 ml Nuclear Permeabilization Buffer [1 × DPBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1 × Protease inhibitor], and followed by incubation for 3 minutes to isolate the nuclei. The suspension was transferred to a 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, filtered through 40 μm strainers and centrifuged at 600 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.  For H9 ESCs, after digestion with Accutase solution (Sigma) for 5minutes, cells were centrifuged at 300 × g for 5 minutes at 4°C, then suspended in 1 ml Nuclear Permeabilization Buffer and followed by incubation for 6 minutes to isolate the nuclei. The suspension was transferred to 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, centrifuged at 500 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.
Library preparations were performed with the Microwell ATAC-seq protocol

value: H9 ESC


title: Teratoma_H9, scATAC-seq, Microwell ATAC-seq

description: Three teratoma samples cannot be distinguished simply by eight technical replicates. They are separated by Tn5 barcodes. The sample information can be found directly in the processed data file scATAC_metadata.txt.gz. Only human cells of the teratoma are contained in the offerred BAM files.

value: NOD/SCID

value: 15-17 weeks

value: female


title: H9_ESC, scRNAseq, Microwell-seq

library_source: transcriptomic single cell

data_processing:
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim ployA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The teratoma data were aligned to a merged hg19-mm10 reference genome, the ESCs data were aligned to GRCh38, and the mouse data were mapped to mm10. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. The TagReadWithGeneExon function was employed to recognize the reads that were mapped to the exonic regions of genes. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat. For teratoma data that mix human cells with mouse cells, the aligned BAM files should be divided into human.bam and mouse.bam before generating the digital expression matrices.
Assembly: Teratoma: A merged hg19-mm10 reference genome; ESCs: GRCh38; Mouse: mm10
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.

extract_protocol:
Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol


title: Lungs for High-Fat Diet Mice

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

institute: VIB/KU Leuven

description: 10x Genomics Single-Cell Gene Expression 3' v2

data_processing:
Single-cell libraries were sequenced on an Illumina NovaSeq 6000 System. Sequenced reads were then mapped to the mouse genome (mm10 build GRCm38.p6) using the 10x Genomics Cell Ranger software, and the resulting single-cell gene expression data was analyzed within the R/Bioconductor framework. Specifically, raw UMI count matrices for all samples were first imported and merged using Seurat v4.1.0, and then converted for further processing with Monocle3-alpha v2.99.3.
Low-quality cells were then filtered based on standard quality-control metrics, with thresholds chosen based on evaluating quality-control histograms. In particular, cells were filtered based on their mitochondrial RNA content (allowing for a maximum of 20%), library size (removing cells with total UMI counts below 1000) and number of detected genes (removing cells expressing less than 250 genes). Genes expressed in less than 5 cells were additionally ignored in all subsequent analyses.
Size-factor and variance-stabilizing normalization (based on fitting to a negative binomial distribution) were then applied to the filtered data set, and highly variable genes (HVGs) were identified based on their departure from the average normalized dispersion versus expression trend observed among all genes. After excluding mitochondrial, ribosomal-protein, and cell cycle-associated genes, the top 1000 HVGs with size-factor normalized expression levels above 0.01 were selected. Principal component analysis (PCA) was then performed on the size factor-normalized and variance-stabilized count matrix restricted to these genes only, followed by 2D UMAP dimensional reduction based on the resulting top 50 principal components (with correlation distance metric, number of neighbors = 15, and minimum distance = 0.1, and without further PCA scaling). After that, cells were clustered in the UMAP plane by applying the Louvain graph-based algorithm at high resolution (resolution = 0.001, with kNN = 15), in order to attain a fine-grained cluster structure (51 clusters).
Fine-grained clusters were then manually annotated to specific cell types, based on evaluating the cluster-averaged normalized expression profiles of several cell type-specific markers.
Assembly: mm10 build GRCm38.p6
Supplementary files format and content: The raw-count output of the 10x Genomics CellRanger pipeline is provided in the form of MatrixMarket sparse matrices with gene|barcode|counts triplets (matrix.mtx.gz), together with the corresponding gene (features.tsv.gz) and barcode (barcodes.tsv.gz) index files, within a separate tar archive for each sample (Counts_SID.tar, where SID = CD/FD for the Control/High-Fat Diet samples, respectively). In addition, analogous supplementary files are provided containing a merged gene|barcode|counts sparse matrix for the combination of both the CD and HFD samples (Counts_FINAL.tar), after filtering out cells based on quality-control metrics (mitochondrial RNA content, library size, and number of detected genes), and removing genes expressed in less than 5 cells. The latter are accompanied by text-based tables (GeneMetaData_FINAL.txt, CellMetaData_FINAL.txt) with all relevant gene/cell meta data needed to reproduce the results of the final analysis, including quality-control metrics, cell-type annotations, fine-grained cluster assignments, and UMAP coordinates. A description of the full contents of these meta data tables is provided in a separate text file (MetaDataDescription_FINAL.txt).

source_name: Lung

extract_protocol:
After 16 weeks under either CD or HFD feeding, mice were anesthetized with Ketamine (100mg/kg) + Xylazne (10mg/kg), and lungs were perfused through the right ventricle. Lungs were then extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL; Roche) and DNAse1 (1 μg/mL) for 45 min at 37°C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70μm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer (Merck). After red blood cell lysis, cells were washed once more and transferred through a 40 μm cell strainer. The resulting single-cell suspensions were then counted, adjusted to a density of 10^6 cells/mL, and immediately processed for single-cell library preparation.
Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 3’ v2 Library, Gel Bead, Chip, and Multiplex Kit, following the manufacturer’s guidelines, and aiming for a total of 10000 cells per library.

treatment_protocol: 4-week-old female BALB/c mice were randomized into two groups, and maintained under either control diet (CD, E15742-33 ssniff Spezialdiäten GmbH) or long-chain high-fat diet (HFD, S8655-E220 sniff Spezialdiäten GmbH) for 16 weeks. The energy balance between fat (from lard)/protein/carbohydrates was 13/27/60% and 60/20/20% for CD and HFD, respectively.

value: BALB/c

value: Female

value: 20 weeks-old

value: Lung

value: High-Fat Diet


title: Alox15- Alveolar macrophages replicate 2

city: Montreal

first: Jun

last: Ding

state: QC

address: 1001 Decarie Blvd.

department: Department of Medicine

country: Canada

institute: McGill University

data_processing:
All the raw reads were mapped to mouse genome mm10 using HISAT (version 2.1.0)
after quality control and reads trimming (fastp version 0.20.1) with the default settings.
We then employed HTSeq-count (version 0.12.4) to quantify the raw counts for all genes.
DESeq2 (version 1.26.0) was used to normalize the raw gene expression count matrix and identify differentially expressed genes
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
Supplementary files format and content: tab-delimited text file contains all processed gene expression for all samples

source_name: Bronchoalveolar lavage

growth_protocol: Alveolar macrophages were cultured for 1 hour at 37°C in 5% CO2 in RPMI 1640 supplemented with 10% FBS, penicillin (100 units/ml), streptomycin (100µg/ml) and amphotericin B (0.25µg/ml).

extract_protocol:
GENEzol TriRNA Pure kit – following manufacturer's instructions
Illumina TruSeq protocol

treatment_protocol: After 1 hour adhesion, cells were washed three times with PBS before RNA extraction.

value: Bronchoalveolar lavage

value: Primary cells

value: Alveolar macrophages

value: none – steady state


title: Alox15- Alveolar macrophages replicate 1


title: Alox15- Alveolar macrophages replicate 3


title: wild type Alveolar macrophages  replicate 2

value: Wild-type


title: wild type Alveolar macrophages  replicate 3


title: wild type Alveolar macrophages  replicate 1


title: AF-2

value: stromal cell

value: WT

value: 2D culture


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, control, biol rep 5

city: Hannover

first: Maximilian

last: Lenz

address: Carl-Neuberg-Straße 1

department: Institute of Neuroanatomy and Cell Biology

institute: Hannover Medical School

data_processing:
Data analysis was performed at the Galaxy platform (usegalaxy.eu). All files contained more than 10 M high-quality reads (after mapping to the reference genome; mm10) having at least a phred quality of 30 (>90% of total reads).
RNA sequencing data were uploaded to the Galaxy web platform (public server: usegalaxy.eu; (Afgan et al., 2018; Galaxy, 2022; Goecks et al., 2010)) and transcriptome analysis was performed using the Galaxy platform in accordance with the reference-based RNA-seq data analysis tutorial (Batut et al., 2021).
Adapter sequences, low quality, and short reads were removed via the CUTADAPT tool (Galaxy version 3.5+galaxy0).
Reads were mapped using RNA STAR (Galaxy version 2.7.8a+galaxy0) with the mm10 full reference genome (Mus musculus).
The evidence-based annotation of the mouse genome (GRCm38), version M25 (Ensembl 100), served as gene model (GENCODE). For an initial assessment of gene expression, unstranded FEATURECOUNT (Galaxy version 2.0.1+galaxy2) analysis was performed from RNA STAR output.
Assembly: mm10
Supplementary files format and content: FEATURE COUNT output (tabular files)

source_name: Brain, organotypic entorhino-hippocampal culture

growth_protocol: Entorhino-hippocampal tissue cultures were prepared at postnatal day 3-5 from C57BL/6J (wildtype, Synpo+/+) and B6.129-Synpotm1Mndl/Dllr [Synpo-/-, (Deller et al., 2003; Lenz et al., 2021a; Lenz et al., 2021b)] mice of either sex as previously described (Del Turco and Deller, 2007). Cultivation medium contained 50% (v/v) MEM, 25% (v/v) basal medium eagle, 25% (v/v) heat-inactivated normal horse serum, 25 mM HEPES buffer solution, 0.15% (w/v) bicarbonate, 0.65% (w/v) glucose, 0.1 mg/ml streptomycin, 100 U/ml penicillin, and 2 mM glutamax. The pH was adjusted to 7.3. All tissue cultures were allowed to mature for at least 18 days in a humidified atmosphere with 5% CO2 at 35°C. Cultivation medium was replaced 3 times per week. For entorhinal cortex lesion, the entorhinal cortex of mature slice cultures (≥18 days in vitro) was transected with a sterile scalpel from the rhinal to the hippocampal fissure to achieve a complete lesion of the perforant path. Except for the lesion-induced partial denervation of the hippocampus, cytoarchitecture of both the hippocampus and the entorhinal cortex remained unchanged.

extract_protocol:
regional transcriptome:
RNA Library preparations for transcriptome analysis were performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs, #E6420) according to the manufacturer's instructions. Briefly, isolation of the dentate gyrus and CA3 area from individual tissue cultures was performed using a scalpel. One isolated dentate gyrus or CA3 area respectively was transferred to 7.5 µl lysis buffer (supplemented with murine RNase inhibitor) and homogenized using a pestill. Samples were centrifuged for 30 seconds at 10,000g and 5 µl of supernatant were collected from individual samples and further processed. After cDNA synthesis, cDNA amplification was performed according to the manufacturer's protocol with 12 PCR cycles. cDNA yield was consecutively analyzed by a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). cDNA amount was adjusted to 10 ng for further downstream applications.
synaptopodin-coIP transcriptome:
Six tissue cultures per biological replicate were washed in coIP-solution and dounce homogenized on ice in a solution containing (150 µl per sample, coIP-solution, in mM): 10 HEPES, 120 NaCl, 0.05% (v/v) NP-40, cOmplete protease inhibitor (Roche, according to manufacturers’ instructions), murine RNase inhibitor (1:1000, New England Biolabs, #M0314) and cycloheximide (0.5 mg/ml, Sigma Aldrich, #C-4859). Input was precleared twice with protein A beads (10 µl per 100 µl sample/supernatant) to reduce unspecific binding. Protein A beads (10 µl, New England Biolabs, #S1425) were washed twice in coIP-solution and consecutively incubated for 1 hour at 4°C with an anti-Synaptopodin antibody (rabbit anti-Synaptopodin, Synaptic Systems, #163002). Beads were carefully washed twice to remove unbound antibodies and incubated for 1 hour with the precleared supernatant (‘input’) at 4°C with head-over-tail rotation. 10 µl of the precleared supernatant were kept as input control. After incubation, beads were washed twice with coIP-solution and finally dissolved in RNA protection buffer (New England Biolabs). RNA was released from the beads through Protein K lysis (Monarch® Total RNA Miniprep Kit; #T2010S New England Biolabs). After lysis, beads were removed from the solution in a magnetic rack and the RNA containing supernatant was transferred to fresh tubes. RNA isolation on coIP- and input-samples was then performed according to the manufacturer’s instructions. RNA content was determined using the Agilent RNA 6000 Pico Kit (#5067-1513 Agilent) with a 2100 Bioanalyzer (#G2939BA Agilent).  RNA Library preparations for Synpo-related transcriptome analysis were performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs, #E6420) according to the manufacturer's instructions.
After fragmentation and adaptor ligation, dual index primers (New England Biolabs, #E7600S) were ligated in a library amplification step. Libraries were finally cleaned up with 0.8X SPRI Beads following a standard bead purification protocol. Library purity and size distribution was assessed with a High Sensitivity DNA assay on a Bioanalyzer instrument (Agilent). We quantified the libraries using the NEBNext Library Quant Kit for Illumina (New England Biolabs, #E7630) based on the mean insert size provided by the Bioanalyzer. A 10 nM sequencing pool (120 µl in Tris-HCl, pH 8.5) was generated for sequencing on the NovaSeq6000 Sequencing platform (Illumina; service provided by CeGaT GmbH, Tübingen, Germany). We performed a paired-end sequencing with 101 bp read length (regional transcriptome) or 151 bp read length (SP-coIP transcriptome and their respective input controls). Data analysis was performed at the Galaxy platform (usegalaxy.eu). All files contained more than 10 M high-quality reads (after mapping to the reference genome; mm10) having at least a phred quality of 30 (>90% of total reads).

value: wildtype [C57BL/6]; Synpo+/+


title: FAT-1

value: adipose


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, control, biol rep 4

value: Brain, organotypic entorhino-hippocampal culture


title: wild type Alveolar macrophages  replicate 4


title: Alox15- Alveolar macrophages replicate 4


title: NP-2

value: nucleus pulposus


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, control, biol rep 3


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, control, biol rep 2


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, control, biol rep 1


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, control, biol rep 5


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, control, biol rep 4


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, ECL, biol rep 5


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, control, biol rep 1


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, control, biol rep 2


title: Lungs from Control Diet Mice

value: BALB/c

value: Control Diet


title: H1_ESC, scRNAseq, Microwell-seq

value: H1 ESC

value: female


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, ECL, biol rep 4


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, ECL, biol rep 3


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, ECL, biol rep 2


title: Fos-creERT2,iWAT, hM3D-1

description: hM3D All_gene_fpkm.list

value: subcutaneous inguinal WAT (iWAT)

value: repeated activaiton of PVN neurons

value: every 3 days for  42 days


title: Tissue culture, wildtype [C57BL/6], SP-coIP-RNA, ECL, biol rep 1


title: R79-1-7d

first: Boya

address: No.336, West Nanxinzhuang Road, Qixian Street

institute: University of Jinan

data_processing:
In order to ensure the quality of information analysis, the software FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_tool kit/) is used to filter the original data and get clean reads.
Use fastx_clipper to remove connector sequences from reads
Use fastq_quality_filter to remove N from the read 3'to 5 'direction (N indicates that the base information cannot be determined) to the first base that is not N.
Use fastq_quality_filter to remove continuously occurring low-quality bases from the read 3'to 5 'direction, and delete the read itself and its paired sequences when the low-quality clean reads length is lower than 36bp.
Use local scripts to pair pair end reads (used for PE sequencing).
samtools was used to calculate read counts and RPKM
Assembly: draft genomes of strains Brevundimonas diminuta R79 and Pseudomonas balearica R90 not yet published.  FASTA files of transcript sequences are available on the series record.
Supplementary files format and content: RPKM

extract_protocol:
RNA was extracted from the samples by column fecal RNAout Kit (TIANDZ). After the feces (0.5g) were ground to powder in liquid nitrogen, buffer A preheated by 1ml at 65 °C was added and mixed with 300ul buffer B and 200ul chloroform for 20 seconds. After swirling for 30 seconds, the supernatant was centrifuged, and then the buffer C of the same volume was mixed upside down and transferred to the adsorption column. After centrifugation, the penetrating solution was discarded and the 700ul universal column solution was washed once and then washed with 300ul universal column solution, and RNA was eluted with 100ulRNA elution solution. RNA is quantified using Qubit (Invitrogen, USA).
RNA digested by DNase was removed rRNA by Ribo-Zero digestion Magnetic Kit (Gram-Negative Bacteria or Gram-positive Bacteria) (Epicentre, USA): adding Ribo-Zero Reaction Buffer and Ribo-Zero rRNA Removal Solution (Gram-Negative Bacteria or Gram-positive Bacteria), adding Ribo-Zero Reaction Buffer and Ribo-Zero rRNA Removal Solution (Gram-Negative Bacteria or Gram-positive Bacteria) to 40 μ l, reacting 10min at 68 ℃, then placing 5min at room temperature, adding the treated RNA to the pre-washed magnetic beads, mixing thoroughly immediately, placing 5min at room temperature, then reacting 5min at 50 ℃, immediately placing above 1min on the magnetic rack. Absorb the supernatant, add water to 180 μ l, add 3 M Sodium Acetate and Glycogen (10 mg/ml), add 600ul anhydrous ethyl alcohol, place at-20 ℃ for more than 1 h, centrifuge to get precipitation, add water to dissolve rRNA-depleted RNA.
Take 10ng rRNA-depleted RNA from RNA library, construct library with KAPA Stranded mRNA-Seq Kit (KAPA Biosystems, USA): add KAPA Fragment,Prime and Elute Buffer (2X) to interrupt mRNA, react 6min at 94 °C, quickly put on ice; add 1stStrand synthesis Buffer and KAPA Script to synthesize the first chain of cDNA, reaction procedure: 25 °C 10 minutes, 42 °C 15 minutes, 70 °C 15 minutes; and then add 2ndStrand Marking Buffer (2x) and 2ndStrand Synthesis EnzymeMix for cDNA second chain synthesis, 16 °C reaction for 1 h. After purification with AMPure XP Beads (Agencourt, USA), add KAPA A-Tailing Buffer (10x) and A-Tailing Enzyme for terminal repair and add A, reaction procedure: 30 °C 30min, 65 °C 30 min; add Adaptor, KAPA Ligation Buffer (5x) and KAPA T4 DNA Ligase joint, 20 °C DNA Ligase reaction for 15 min; 200~300bp range of ligated cDNA was obtained by two-step AMPure XP Beads purification. PCR amplification was carried out by adding KAPA HiFi HotStart Ready Mix (2x) and KAPA Library Amplification Primer Mix (10x). The PCR reaction conditions were as follows: pre-denaturation at 98 °C for 45 Sec, denaturation at 98 °C for 15 Sec, annealing at 60 °C for 30 Sec, extension at 72 °C for 30 Sec;, and then purified with 1-fold volume of AMPure XP Beads to obtain a library for sequencing.

value: CH3COONa 5 g/L;(NH4)2SO4 0.16 g/L;K2HPO4•3H2O 0.121 g/L;KH2PO4 0.045 g/L;NaCl 16 g/L;trace element solution 1 mL/L


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, ECL, biol rep 4


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, ECL, biol rep 5


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, ECL, biol rep 3


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, ECL, biol rep 2


title: DG-tissue, wildtype [C57BL/6], ECL, biol rep 4

source_name: Brain, organotypic entorhino-hippocampal culture, dentate gyrus isolate


title: DG-tissue, wildtype [C57BL/6], ECL, biol rep 5

value: Brain, organotypic entorhino-hippocampal culture, dentate gyrus isolate


title: DG-tissue, wildtype [C57BL/6], ECL, biol rep 7


title: DG-tissue, wildtype [C57BL/6], ECL, biol rep 6


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, control, biol rep 3


title: DG-tissue, wildtype [C57BL/6], ECL, biol rep 2


title: DG-tissue, wildtype [C57BL/6], ECL, biol rep 3


title: DG-tissue, wildtype [C57BL/6], control, biol rep 4


title: DG-tissue, wildtype [C57BL/6], ECL, biol rep 1


title: DG-tissue, wildtype [C57BL/6], control, biol rep 3


title: CA3-tissue, wildtype [C57BL/6],ECL, biol rep 3

source_name: Brain, organotypic entorhino-hippocampal culture, CA3 isolate


title: DG-tissue, wildtype [C57BL/6], control, biol rep 1


title: CA3-tissue, wildtype [C57BL/6],ECL, biol rep 2

value: Brain, organotypic entorhino-hippocampal culture, CA3 isolate


title: DG-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 4

value: synaptopodin deficient [SP-KO]; Synpo-/-


title: CA3-tissue, wildtype [C57BL/6], control, biol rep 1


title: CA3-tissue, wildtype [C57BL/6], control, biol rep 2


title: DG-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 3


title: Tissue culture, wildtype [C57BL/6], INPUT-RNA, ECL, biol rep 1


title: DG-tissue, synaptopodin deficient [SP-KO], control, biol rep 6


title: DG-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 1


title: DG-tissue, synaptopodin deficient [SP-KO], control, biol rep 5


title: DG-tissue, wildtype [C57BL/6], control, biol rep 2


title: DG-tissue, synaptopodin deficient [SP-KO], control, biol rep 2


title: DG-tissue, synaptopodin deficient [SP-KO], control, biol rep 1


title: DG-tissue, synaptopodin deficient [SP-KO], control, biol rep 3


title: CA3-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 6


title: DG-tissue, synaptopodin deficient [SP-KO], control, biol rep 4


title: CA3-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 5


title: CA3-tissue, synaptopodin deficient [SP-KO], control, biol rep 5


title: CA3-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 1


title: CA3-tissue, synaptopodin deficient [SP-KO], control, biol rep 6


title: CA3-tissue, synaptopodin deficient [SP-KO], control, biol rep 4


title: CA3-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 2


title: CA3-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 3


title: CA3-tissue, wildtype [C57BL/6],ECL, biol rep 1


title: CA3-tissue, synaptopodin deficient [SP-KO], control, biol rep 1


title: CA3-tissue, synaptopodin deficient [SP-KO], control, biol rep 2


title: DG-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 2


title: DG-tissue, synaptopodin deficient [SP-KO], control, biol rep 7


title: Mouse liver tissue, MTX2 KO, biol rep1 [MTX2-LKO-4]

city: Beijing

first: Baiyu

last: He

address: No. 7, Science Park Road, Zhongguancun Life Science Park

institute: National Institute of Biological Sciences

data_processing:
All sequencing raw reads were trimmed using Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default settings.
Trimmed reads were aligned to the Mus musculus reference genome (Mm10) using STAR v2.7.7a (Dobin et al., 2013) in paired-end mode with default parameters.
Gene level counts were generated using FeatureCounts from Subread v1.6.
Generated matrix file from read quantification was then used for differential expression (DE) analysis. DE analysis was performed using Bioconductor package DESeq2 with contrast of control and treat groups (as indicated).
Genes having corrected Padj <0.05 (FDR) and absolute log-fold change greater than 1 were considered to be significantly differentially expressed (DE).
Assembly: Mm10
Supplementary files format and content: ProcessedDataMatrix.txt, this file include RPKM values for each sample

source_name: Mouse liver tissue

extract_protocol:
Cells were lysed in 500 μL TRIzol reagent and incubated at room temperature for 5 minutes. 100 μL chloroform was added and fully mixed. Samples were centrifuged at 14,400 rpm for 15 minutes at 4°C and 250 μL aqueous phase containing RNA was transferred to a new tube. 250 μL isopropanol was added to the aqueous phase and mixed well to precipitate RNA. After incubation 10 min at room temperature, RNA pellet was collected through centrifuging at 14,400 rpm for 15 minutes at 4°C and washed with 500 μL 75% ethanol. The RNA pellet was air-dried for 10 min and resuspended in nuclease-free H2O. Mouse tissue samples were first weighted and homogenized as described above with 1ml TRIzol reagent per 100 mg. After homogenization, chloroform was added and the following steps are same with cell samples. A total amount of 2 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit for Illumina following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using fragmentation buffer. First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated. Then the PCR was performed. At last, Qubit HS quantification, Agilent 2100 Bioanalyzer/Fragment Analyzer 5300 quality control, the final library size of about 350bp. The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.

value: Mouse liver tissue

value: MTX2 knockout, Cas9 knockin

value: No


title: Mouse liver tissue, MTX2 KO, biol rep2 [MTX2-LKO-6]


title: Mouse liver tissue, MTX2 KO, biol rep4 [MTX2-LKO-15]


title: Mouse liver tissue, MTX2 KO, biol rep5 [MTX2-LKO-29]


title: Mouse liver tissue, MTX2 KO, biol rep3 [MTX2-LKO-12]


title: Mouse liver tissue, non targeting control, biol rep5 [NTC-19]

value: Cas9 knockin


title: Mouse liver tissue, non targeting control, biol rep3 [NTC-13]


title: Mouse liver tissue, non targeting control, biol rep4 [NTC-18]


title: Mouse liver tissue, non targeting control, biol rep2 [NTC-8]


title: CA3-tissue, synaptopodin deficient [SP-KO], ECL, biol rep 4


title: MEF cells, MIC60 shRNA3, DOX-induced KD, biol rep3 [MIC60-DOX-3]

source_name: Mouse embryonic fibroblasts

value: Mouse embryonic fibroblasts

value: MIC60 knockdown

value: 1 mg/ml doxycycline (DOX)

tag: time point

value: Day 9


title: CA3-tissue, synaptopodin deficient [SP-KO], control, biol rep 3


title: MEF cells, MIC60 shRNA1, DOX-induced KD, biol rep1 [MIC60-DOX-1]


title: Mouse liver tissue, non targeting control, biol rep1 [NTC-7]


title: MEF cells, MIC60 shRNA3, uninduced control, biol rep3 [MIC60-3]

value: WT

value: ethanol (same volume with DOX)


title: MEF cells, MIC60 shRNA2, uninduced control, biol rep2 [MIC60-2]


title: MEF cells, MIC60 shRNA2, DOX-induced KD, biol rep2 [MIC60-DOX-2]


title: MEF cells, MIC60 shRNA1, uninduced control, biol rep1 [MIC60-1]


title: MEF cells, OPA1 shRNA1, DOX-induced KD, biol rep1 [OPA1-DOX-1]

value: OPA1 knockdown


title: MEF cells, OPA1 shRNA1, uninduced control, biol rep1 [OPA1-1]


title: MEF cells, OPA1 shRNA2, uninduced control, biol rep2 [OPA1-2]


title: MEF cells, OPA1 shRNA3, uninduced control, biol rep3 [OPA1-3]


title: MEF cells, OPA1 shRNA2, DOX-induced KD, biol rep2 [OPA1-DOX-2]


title: MEF cells, OPA1 shRNA3, DOX-induced KD, biol rep3 [OPA1-DOX-3]


title: MEF cells, non targeting shRNAcontrol, DOX-induced KD, biol rep1 [NC-DOX-1]


title: MEF cells, non targeting shRNAcontrol, uninduced control, biol rep1 [NC-1]


title: MEF cells, non targeting shRNAcontrol, uninduced control, biol rep2 [NC-2]


title: MEF cells, non targeting shRNAcontrol, DOX-induced KD, biol rep3 [NC-DOX-3]


title: MEF cells, non targeting shRNAcontrol, DOX-induced KD, biol rep2 [NC-DOX-2]


title: MEF cells, MTX2 KO, biol rep2 [MTX2-KO-2]

value: MTX2 knockout


title: MEF cells, MTX2 KO, biol rep3 [MTX2-KO-3]


title: MEF cells, DNAJC11 KO, biol rep1 [DNAJC11-KO-1]

value: DNAJC11 knockout


title: MEF cells, non targeting shRNAcontrol, uninduced control, biol rep3 [NC-3]


title: MEF cells, DNAJC11 KO, biol rep3 [DNAJC11-KO-3]


title: MEF cells, MIC19 KO, biol rep3 [MIC19-KO-3]

value: MIC19 knockout


title: MEF cells, MIC19 KO, biol rep1 [MIC19-KO-1]


title: MEF cells, Control, biol rep3 [WT-3]


title: MEF cells, MIC19 KO, biol rep2 [MIC19-KO-2]


title: MEF cells, Control, biol rep1 [WT-1]


title: Eosinophils, papain, cKO 4

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

description: Eos ko4

data_processing:
Raw reads were mapped to the mouse (GENCODE M12.GRCm38.p5, scaffolds removed) genome with STAR (2.7.3a).
The reads were assigned to genes with featureCounts (SUBREAD v2.0.0) setting -t exon -g gene_id (Gene annotation: gencode.vM12/GRCm38) .
Assembly: GENCODE M12.GRCm38.p5
Supplementary files format and content: tsv file contains tab separated counts per gene

growth_protocol: mice were kept under SPF conditions, were treated for 7 days with papain, on day 7 mice were sacrifised and lungs were taken for cell isolation

extract_protocol:
Eosinophils were sort-purified as Sytox blue- CD45+ Lineage (CD3, CD5, CD19, Ly6G)-CD11b+ Siglec F+ from the lung of Nmur1Cre-T2A-GFP Id2flox/flox and control mice on day 7 after papain administration. Cells were sorted into RLT Plus Lysis Buffer supplemented with 40 mM DTT and RNA was isolated using the RNeasy Plus Micro kit (Qiagen) according to the protocol provided by the manufacturer.
RNA libraries for RNA-Seq were prepared using theSMARTer Stranded Total RNA-Seq Kit – Pico (Takara)

treatment_protocol: papain treatment on day 1, 2 and 3

value: Lung

value: Eosinophils

value: Nmur1Cre-T2A-GFP Id2flox/flox

value: papain


title: colon epithelium from ILC2-deficient animals, N.b. infected

data_processing:
The processing and gene counting were made with the Cell Ranger software v5.0.0
Assembly: mm10
Supplementary files format and content: filtered gene matrix with counts and barcodes (Cell Ranger output)

source_name: colon

growth_protocol: not applicable

extract_protocol:
The intestine was incubated in PBS supplemented with 30 mM EDTA (Roboklon) and 1.5 mM DTT (Sigma-Aldrich) for 20 min on ice. Next, the tissue was transferred to prewarmed PBS/30 mM EDTA and incubated on a shaker at 37°C for 10 minutes and vortexed afterwards to remove the epithelium. The epithelium was washed in PBS/10% FCS and afterwards incubated in HBSS (Sigma-Aldrich) supplemented with dispase (0.5 U/ml; Corning) on a shaker at 37°C for 10 minutes and another 5 minutes after addition of FCS (1% final concentration) and DNaseI (100 μg/ml; Sigma-Aldrich) and filtered through a 70 µm and a 40 µm cell strainer.
The purified cDNA was amplified using 11 cycles of PCR and then used for 3’ gene expression (GEX) library preparation. Through fragmentation, adapter ligation and index PCR the final libraries were obtained. The quality of single cell 3’ GEX was assessed by Qubit quantification and Tapestation analysis (HS D1000, Agilent).
The sequencing was performed on a NovaSeq6000 (Illumina) with a S1 xp flow cell, paired-end sequencing with 400mln reds per library and otherwise the recommended sequencing conditions for 3’ GEX (read1: 28nt, read2: 90nt, index i7: 10nt, index i5: 10nt).

treatment_protocol: Mice received 500 L3 stage larvae of Nippostrongylus brasiliensis by subcutaneous injection. Analysis was performed 7 days after infection.

value: colon

value: epithelium

value: Id2fl/+ or Nmur1Cre-T2A-GFP Id2fl/+

value: day 7 after Nippostrongylus brasiliensis infection


title: MEF cells, DNAJC11 KO, biol rep2 [DNAJC11-KO-2]

value: Mouse embryonic fibroblasts

value: No


title: colon epithelium from ILC2-proficient animals, N.b. infected

value: Nmur1Cre-T2A-GFP Id2fl/fl


title: Liver CDAA Rat4

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

institute: The University of British Columbia

data_processing:
Reads were quality trimmed and Illumina TruSeq adapter sequences were removed. FastQC and FastX were run to ensure quality of data before and after trimming. Reads were aligned to the rat rn6 reference genome using Tophat2
Bioconductor packages Cufflinks, DESeq2, and EdgeR were used for differential expression analysis
Assembly: rn6
Supplementary files format and content: Excel file with differential log2 fold change between CDAA and CSAA in three packages, Cufflinks, DESeq2, and EdgeR

source_name: Liver

extract_protocol:
Livers were removed, 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

tag: strain

value: Fischer 344 (F344)

value: Liver

value: 1 year old

value: wild type

tag: diet

value: CDAA


title: Eosinophils, papain, cKO 1

description: Eos ko1


title: MEF cells, Control, biol rep2 [WT-2]

value: WT


title: Liver CDAA Rat3


title: Liver CDAA Rat2


title: Eosinophils, papain, Ctrl 3

description: Eos wt4

value: Lung


title: Eosinophils, papain, Ctrl 4

description: Eos wt5

value: Eosinophils


title: Liver CDAA Rat1


title: Eosinophils, papain, Ctrl 2

description: Eos wt2


title: Liver CSAA Rat4

value: CSAA


title: Liver CSAA Rat3


title: PROTAC RNA-seq Rep 2

city: Boston

first: Chad

middle: Brandon

last: Stein

state: MA

address: 240 Longwood Ave

institute: Harvard Medical School

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 50 nt.
DMSO and PROTAC samples were first mapped to an ERCC spike genome, and reads not mappping to spike were subsequently mapped to mm10 using STAR (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
bigWigs output from STAR were used for downstream analysis and visualization.
Assembly: mm10
Supplementary files format and content: bigWigs represent DEseq-normalized coverage

growth_protocol: INTS11Halo cells were maintained in SFES+2i/LIF.

extract_protocol:
RNA was extracted in Trizol and purified.
Libraries were generated with the llumina TruSeq Stranded Total RNA kit using standard protocols.

treatment_protocol: Cells were treated with DMSO or 500 nM PROTAC for 16 hours.

value: Embryonic stem cell

value: PROTAC


title: Liver CSAA Rat2


title: PROTAC RNA-seq Rep 3


title: Liver CSAA Rat1


title: PROTAC RNA-seq Rep 1


title: DMSO RNA-seq Rep 3

value: DMSO


title: DMSO RNA-seq Rep 2


title: preGTS1_DOX_2

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
preGTS1_DOX_3
CPM.Treatment.mm.txt

data_processing:
All RNA sequence reads were mapped against the mouse genome assembly mm9 using STAR v2.4.0 in a two step aproach previously described by Veeneman, B.A., et al. in Bioinformatics, 2016. Unmapped reads were realigned using Bowtie2 v2.2 and default parameters. Duplicate reads were removed with Piccard v1.127 and default parameters. Read counts were measured with Subread 1.5.2. The transcriptome profile was quantified with Limma or edgR with default parameters.
For single cell RNA seq, the Cell Ranger v3.3.0 pipeline was used to process data generated using the 10x Chromium platform. This aligns sequencing reads to the mouse reference genome mm10 v3.0.0. Following alignment, gene expression matrices were generated. Using Seurat v3.0 package in R, We first removed cells with a low number (<200) of unique detected genes and genes (<3) with low number of cells, then we removed the cells unique detected genes less than 500 or great than 7000, finally, we removed cells in which the proportion of the UMI count attributable to mitochondrial genes was greater than 20%.
ATAC-sequence reads were mapped against the mouse genome assembly mm9 using Bowtie2 and duplicate reads were removed by Piccard. Peak calling was performed with MACS2, than quantified and normalized to cpm values with edgeR.
Genome_build: mm10 for single cell analysis, otherwice mm9
Supplementary_files_format_and_content: Conventional RNA-seq: Tab delimeted files with CPM values. scRNA-seq: Count matrix. ATAC-seq: CPM values.

source_name: preGTS1 medulloblastoma tumor

extract_protocol:
RNA-Seq were prepared for sequencing using standard Ion-Torrent protocols.
Cells were lysed in Trizol (Life Technologies) and RNA was prepared using Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer´s recommendations.

value: DOX

value: tumor


title: preGTS1_DOX_1

description:
preGTS1_DOX_2
CPM.Treatment.mm.txt


title: Eosinophils, papain, cKO 2

description: Eos ko2

value: Nmur1Cre-T2A-GFP Id2flox/flox

value: papain


title: DMSO RNA-seq Rep 1


title: PROTAC Ser5P ChIP-seq Rep 2

data_processing:
Sequencing reads were filtered (requiring a mean quality score over 20) and trimmed to 50 bp.
Data from INTS11Halo cells were first mapped to the Drosophila dm3 genome (spike) and reads not mapping here were subsequently mapped mm10 using Bowtie 1.2.2 (-v2 -k1 --best)
Mapped reads were converted to bedGraphs representing deduplicated fragment midpoints using extract_fragments.pl (DOI 10.5281/zenodo.5519914), which were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: bigWigs represent deduplicated, normalized fragment centers.

growth_protocol: Cells were maintained in SFES+2i/LIF.

extract_protocol:
Cells were crosslinked with formaldehyde for 5 minutes and quenched with glycine. After washing, cell pellets were resuspended in sonication buffer and sonicated using the Qsonica Q800R3 system. INTS11Halo chromatin was spiked with Drosophila chromatin prior to IP. Chromatin was pre-cleared with Protein A agarose and incubated with the indicated antibody overnight. Protein A agarose beads were added and allowed to bind antibody-epitope complexes. IPs were washed extensively and eluted twice. DNA was purified using phenol/chloroform.
All libraries were constructed with the NEB NEBNext Ultra II DNA Library kit .

treatment_protocol: Cells were treated with DMSO or 500 nM PROTAC for 4 hours.

value: RNAPII Ser5P (Abcam, ab5131)


title: preGTS1_DMSO_3

description:
preGTS1_DOX_1
CPM.Treatment.mm.txt


title: preGTS1_DMSO_2

description:
preGTS1_DMSO_3
CPM.Treatment.mm.txt


title: PROTAC Ser5P ChIP-seq Rep 1


title: preGTS1_DMSO_1

description:
preGTS1_DMSO_2
CPM.Treatment.mm.txt


title: DMSO Ser5P ChIP-seq Rep 2


title: GTML3_DOX_3

description:
preGTS1_DMSO_1
CPM.Treatment.mm.txt

source_name: GTML medulloblastoma tumor


title: GTML3_DOX_1

description:
GTML3_DOX_2
CPM.Treatment.mm.txt


title: Eosinophils, papain, Ctrl 1

description: Eos wt1


title: GTML3_DOX_2

description:
GTML3_DOX_3
CPM.Treatment.mm.txt


title: GTML3_DMSO_3

description:
GTML3_DOX_1
CPM.Treatment.mm.txt


title: GTML3_DMSO_2

description:
GTML3_DMSO_3
CPM.Treatment.mm.txt


title: DMSO Ser5P ChIP-seq Rep 1


title: MEF cells, MTX2 KO, biol rep1 [MTX2-KO-1]

value: Mouse embryonic fibroblasts

value: MTX2 knockout

value: No


title: preGTS1_DOX_3

description: CPM.Treatment.mm.txt


title: GTML3_DMSO_1

description:
GTML3_DMSO_2
CPM.Treatment.mm.txt


title: GTML 6864

description:
GTML3_DMSO_1
GTML_vs_GTS_CPM.mm.txt


title: GTS 6313

source_name: GTS medulloblastoma tumor


title: GTS 5854


title: GTML 5569


title: GTS 5906


title: C57BL/6J mouse heart, P1d, biol rep 3

city: Nanjing

first: Danyang

last: Chong

address: 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing Medical University

data_processing:
Raw data were filtered and processed by Q30 and aligned to the mouse reference genome GRCm38/mm10 with STAR software.
Assembly and quantification of the transcripts were accomplished with RESM software guided by the Ensembl gtf gene annotation file (http://www.ensembl.rog/).
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were used for the measurements of the relative abundances of the transcripts.
Assembly: mm10
Supplementary files format and content: Comma separated-values (CSV) include FPKM values for each sample.

source_name: Heart

extract_protocol:
Total RNA was extracted with TrizolTM X-100 (Thermo Fisher Scientific, USA) treatment and a total amount of 2 µg RNA per sample was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit (Illumina, USA).

value: Heart

tag: developmental stage

value: Postnatal 1st day

value: Male

value: No treatment


title: GTS 4944


title: C57BL/6J mouse heart, P7d, biol rep 2

value: WT

value: Postnatal 7th day6J


title: C57BL/6J mouse heart, P1d, biol rep 1


title: C57BL/6J mouse heart, P7d, biol rep 1

value: Postnatal 7th day


title: C57BL/6J mouse heart, P1d, biol rep 2


title: C57BL/6J mouse heart, P7d, biol rep 3


title: C57BL/6J mouse heart, E18.5d, biol rep 3

value: Embryonic day 18.5


title: GTS1905


title: C57BL/6J mouse heart, E18.5d, biol rep 1


title: C57BL/6J mouse heart, E18.5d, biol rep 2


title: GTS1

description:
GTML_vs_GTS_CPM.mm.txt
GTS_120_1


title: GTML21527


title: ExperimentCCxcl12neg

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
Sequencing data was trimmed using Trimmomatic (version 0.36) and aligned to the mm10 genome using STAR (version 2.7.3a)
Reads were assigned to genes using HTSeq (intersection non-empty, version 0.12.4)
Assembly: mm10
Supplementary files format and content: Gene counts

source_name: cortical thymic epithelial cells

extract_protocol:
RNA was extracted using the QIagen RNAeasy kit.
RNA was processed using the SMARTer Ultra Low Input RNA Kit for Sequencing method.

value: Untreated

tag: sort

value: DsRed negative


title: ExperimentCCxcl12pos

value: DsRed positive


title: GTML1317

value: tumor


title: GTML15369


title: GTML1306


title: GTML1129


title: ExperimentBCxcl12pos


title: ExperimentBCxcl12neg


title: TKO_3_M

city: Lexington

first: Allison

last: Owen

state: KY

address: 441/CTW, 900 S. Limestone St.

institute: University of Kentucky

data_processing:
RNASeq raw data in FASTQ format were analyzed by Novogene (Durham, NC). Low quality reads as well as reads containing adapter and poly-N (N>10%) sequences were cleaned, and quality was further assessed by calculating Q20, Q30, and GC content.
Assembly: mm10
Supplementary files format and content: processed_readcount

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells were flushed and differntiated in RPMI 1640 supplemented with glutamine, 25 mM HEPES, 10% fetal bovine serum, 1% antibiotic-antimycotic, and 10 ng/mL mouse recombinant M-CSF

extract_protocol:
Total RNA was isolated from BMDMs under RNase-free conditions. Cells were lysed using QIAshredder homogenizers and RNA was isolated using the RNeasy Mini Kit (Qiagen)
NEBNext Poly(A) selection. Sequencing was performed at paired-end 150 bp with at least 50 million reads per sample.

treatment_protocol: Differentiated BMDMs were treated with MPLA (1ug/mL) for 24h, washed off, and rested for 3 days prior to RNA harvest

tag: cell type

value: Bone marrow-derived macrophages

value: TRIF knockout (i.e. Ticam1-/-)

value: 3 days post-treatment with 1ug/mL monophosphoryl lipid A (MPLA)


title: CART_9_pre_CD3

city: Heidelberg

first: Michael

last: Kilian

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CAR-T dataset, sort CD3, T & NK cell subset bmref

extract_protocol:
Serial blood samples and BM aspirates were collected from patients treated with anti-BCMA TCE at variable time points, prior and post initiation of therapy and at relapse. Bone marrow mononuclear fractions were isolated through Ficoll density gradients coupled with magnetic sorting of CD3+ or CD45+ T cells.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
5' scRNA/TCR-seq

value: human bone marrow mononuclear cells

value: T and NK cells

value: relapsed-refractory multiple myeloma


title: CART_8_pre_CD3


title: CART_7_pre_CD3


title: CART_6_pre_CD3


title: TKO_1_M


title: MKO_1_M

value: MyD88 knockout


title: MKO_2_M


title: MKO_3_M


title: GTML24618


title: CART_3_pre_CD3


title: CART_4_pre_CD3


title: CART_5_pre_CD3


title: WT_2_M

value: Wild type (C57BL/6)


title: CART_2_pre_CD3


title: CART_1_pre_CD3


title: WT_1_M


title: ExperimentACxcl12neg


title: HDIV5_CD3

source_name: In vitro dataset5, sort CD3, T & NK cell subset bmref


title: ExperimentACxcl12pos


title: TKO_3_US

value: Unstimulated control


title: TKO_2_US


title: HDIV4_CD3

source_name: In vitro dataset4, sort CD3, T & NK cell subset bmref


title: TKO_1_US


title: HDIV1_CD3

source_name: In vitro dataset1, sort CD3, T & NK cell subset bmref


title: PT10_pre_CD45

source_name: PT10_pre, sort CD45

value: CD45+ immune cells


title: MKO_3_US


title: HDIV3_CD3

source_name: In vitro dataset3, sort CD3, T & NK cell subset bmref


title: MKO_2_US


title: PT11_late_CD45

source_name: PT11_late, sort CD45


title: PT11_pre_CD45

source_name: PT11_pre, sort CD45


title: WT_3_M


title: MKO_1_US


title: WT_2_US


title: PT13_pre_CD45

source_name: PT13_pre, sort CD45


title: PT14_late_CD45

source_name: PT14_late, sort CD45


title: PT14_pre_CD45

source_name: PT14_pre, sort CD45


title: PT8_late_CD45

source_name: PT8_late, sort CD45


title: WT_3_US


title: PT8_pre_CD45

source_name: PT8_pre, sort CD45


title: Day14_1

first: Tao

last: Zou

address: 27, Taipingroad

institute: Beijing Institute of Basic Medical Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: NOT PROVIDED
Supplementary files format and content: Tab-delimited text files include FPKM and count values for each sample

source_name: cranial dura

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: age

value: wild type

value: cranial dura


title: PT13_late_CD45

source_name: PT13_late, sort CD45

tag: treatment


title: Day14_2

tag: tissue


title: Day7_1


title: Day1_2


title: WT_1_US


title: PT9_late_CD45

source_name: PT9_late, sort CD45


title: PT9_late_CD3

source_name: PT9_late, sort CD3, T & NK cell subset bmref


title: PT9_pre_CD3

source_name: PT9_pre, sort CD3, T & NK cell subset bmref


title: Day1_1


title: PROTAC TT-seq Rep 3

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

description: Other: 4sU RNA

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 100 nt.
Samples were mapped to the Drosophila dm3 (spike) genome, and nonmapping reads subsequently mapped to mm10 using STAR 2.7.3a (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Assembly: mm10
Supplementary files format and content: bigWigs representing DEseq-normalized read coverage
Library strategy: TT-seq

source_name: Embryonic stem cell

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse. RNA was then fragmented. 4sU-containing RNA was biotinylated, pulled down, and washed. RNA was then eluted and purified.
4sU-labeled RNA was used as input to the Illumina TruSeq stranded totl RNA kit using the manufacturer's protocol.

treatment_protocol: Cells were treated with DMSO or 500 nM PROTAC for 4 hours and labled with 4sU for the final 20 minutes.

value: Embryonic stem cell

tag: cell line

value: 500 nM PROTAC


title: PT9_pre_CD45

source_name: PT9_pre, sort CD45


title: PROTAC TT-seq Rep 2

description: Other: 4sU RNA


title: PT8_pre_CD3

source_name: PT8_pre, sort CD3, T & NK cell subset bmref


title: PROTAC TT-seq Rep 1

description: Other: 4sU RNA


title: TKO_2_M

source_name: Bone marrow-derived macrophages


title: PT7_pre_CD3

source_name: PT7_pre, sort CD3, T & NK cell subset bmref


title: DMSO TT-seq Rep 2

description: Other: 4sU RNA

value: DMSO


title: DMSO TT-seq Rep 1

description: Other: 4sU RNA