title: Walnut_19W_pellicle rep2


title: RNA-Seq_RUVBL2_Auxin_6h_rep2

status: Public on Aug 30 2022

type: SRA

city: Beijing

first: Xiong

last: Ji

address: Yiheyuan Road

department: School of life science

country: China

institute: Peking University

description: RUVBL2 degron

library_source: transcriptomic

data_processing:
The paired-end sequencing fastq files were removed adaptors and low-quality reads with Cutadapt V1.18 (Martin, 2011), then the filtered reads were aligned to mm10 genome with STAR V 2.7.3a (Dobin et al., 2013).
And the bam files after removing duplicates were used to count the genes with annotation files from GENCODE (version M23) (Frankish et al., 2019) with RSEM V1.3.1  (Li and Dewey, 2011).
Differential analysis was performed with DESeq2 V1.24.0 (Love et al., 2014), and the significant genes were selected with foldchange >1.5 and FDR <0.05. For the clustering analysis of Ruvbl2 RNA-seq, a method like Gkountela et al., 2013 (Gkountela et al., 2013) was used.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq rawcount, TPM count and DESeq2 results

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: For RNA- seq, Ruvbl2-mAID tagged cell lines were cultured in 0.2 % gelatin coated 6 well plates with irradiated mouse embryonic fibroblasts (MEF) in DMEM-KO (Gibco, 10829018) containing 15% FBS, 1000 U/ml mouse leukemia inhibiting factor (mLIF), 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1× nonessential amino acids, and 1× penicillin/ streptomycin at 37 °C with 5% CO2, as described previously (Jiang et al., 2020).

extract_protocol:
Cells were lysed in Trizol reagent and extracted RNA according to the manufacture’s protocol
examination the concentration and integrity of the total RNA, the untreated (Mock), doxycycline treatment (Dox), and time series auxin treated samples were delivered for poly A RNA library generation by Novogene Com

treatment_protocol: after two passages, 2 μg/ml Doxycycline (Dox) were added into the medium for 24 h to induce the OsTir1 expression, and then 500 μM auxin (3-indole acetic acid) were appended for 0.5h, 1h, 6h, 12h, 24h and 48h to induce the RUVBL2 degradation. Then cells were lysed by Trizol reagent for RNA extraction.

tag: agent

value: RUVBL2 degron auxin

tag: cell type

value: embryonic stem cells

tag: time point


title: RNA-Seq_RUVBL2_Dox_rep1

description: RUVBL2 degron

value: RUVBL2 degron Dox


title: Control-13

city: shenzhen

first: Yueying

last: Xiang

state: Guangdong

address: 1098 Xueyuan Avenue, Nanshan District,Shenzhen 518000,China

department: Shenzhen University General Hospital health management center

institute: shenzhen university

library_source: genomic

data_processing:
The sequence signatures with adapter ligation, low quality, and containing the unknown base > 5 were removed to obtain clean sequences.
The clean sequences were aligned to the human reference genome (UCSC hg19) by Burrows-Wheeler Aligner, and the alignment results were saved in BAM format files.
Further advanced analysis for the final BAM files, single nucleotide polymorphisms (SNPs) are detected by GATK and Insertion and Deletions (InDels) are detected by SAMtools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files.

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood, control

extract_protocol:
Genomic DNA was extracted from all donors using Magbead Blood DNA Kit (CWBIOTech, CW2361S) according to the manufacturer’s methods.
Products were purified using Agencourt AMPure XP beads (Beckman, p/n A63880) after sequencing library were constructed, the mitochondrial genome were captured with AI-Mito-Cap Kit (iGeneTech, Beijing, China) and sequenced on Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA) with 150 base paired‐end reads.

tag: diagnosis

value: Control

tag: tissue

value: blood

tag: Sex

value: female

tag: age


title: Walnut_17W_pellicle rep3

city: Alar

first: Qiang

last: Jin

email: jqzky@163.com, qiangjin@taru.edu.cn

address: Alar 843300, China

institute: College of Horticulture and Forestry，Tarim University

data_processing:
After removing the adapter and primer sequences, low quality reads with more than 20% low quality bases (quality < 20) were filtered out using FastQC packages (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Clean reads were mapped to M. viride genome using Hisat2 v2.1.051. Gene expression levels (FPKM) were calculated using Cufflinks with default parameters. Differentially expressed genes (DEGs) were identified by DEseq2 package, and only transcripts with fold change ≥ 2 and FDR ≤ 0.01 were considered as DEGs.
Assembly: JrSerr_v1.0
Supplementary files format and content: tab-delimited text files include FPKM values and counts for each sample.

organism: Juglans regia

source_name: pellicle tissues

growth_protocol: Walnut plant materials were planted and collected in a field in Aksu city, Xingjiang Province.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies). Samples were then subjected to poly(A) purification using oligo-dT beads (Life Technologies) followed by rRNA removal using Ribo-Zero Kit (Epicenter) according to the manufacturer’s instructions. RNA integrity was measured using 2100 RNA Nano 6000 Assay Kit (Agilent Technologies).
Library construction were done using TruSeq® Stranded mRNA Library Prep Kit following the manufacturer’s instructions (Illumina). 16 paired-end libraries were constructed and sequenced according to the Illumina HiSeqTM platform sequencing protocols.

value: pellicle

value: 17-week-old pellicle tissues after pollination

tag: cultivar


title: Walnut_19W_pellicle rep1

value: 19-week-old pellicle tissues after pollination


title: Control-8


title: RNA-Seq_RUVBL2_Auxin_6h_rep1

description: RUVBL2 degron


title: Control-6

value: male


title: RNA-Seq_RUVBL2_Auxin_48h_rep2

description: RUVBL2 degron


title: Walnut_17W_pellicle rep2


title: Control-5


title: H3K27ac_ESC_500_rep1

city: Boston

first: Yi

last: Zhang

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

country: USA

institute: Boston Children's Hospital / Harvard Medical School

data_processing:
For CUT&RUN sequencing data, the raw paired-end reads were trimmed with Trimmomatic (v0.39) (Bolger et al, 2014) to remove adaptors and the trimmed reads with length at least 35bp were retained. The cleaned reads were mapped to GRCm38 reference genome using bowtie2 (v2.4.2) (Langmead & Salzberg, 2012) with parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 --soft-clipped-unmapped-tlen. PCR duplicates were removed with Picard MarkDuplicates (v2.23.4). The mapped reads were further filtered to retain proper paired reads with fragment length at least 140 and mapping quality at least 30. The signal tracks were generated by bamCoverage in deeptools (v3.5.1) (Ramirez et al, 2016) with 100bp bin size and normalized with FPKM.    Since the H3K27ac showed different broad or narrow patterns in different stages of early embryos, the FPKM values were not directly comparable among stages. To make the FPKM values comparable, we followed the scaling method used in the previous study of H3K4me3 (Dahl et al., 2016), which also showed broad and narrow patterns in different stages. We used the signals in ESCs as reference so the ESCs had a scale factor of 1. We ranked the gene promoters by their H3K27ac signals. Then for each stage, we chose the median signal of the top 3,000 promoters, dividing from the median signals of the top 3,000 promoters in ESCs to obtain the sale factor for that stage. The FPKM signals in each stage were multiplied by the scale factor to derive the scaled FPKM, which was used in all the downstream analysis.    For allelic analysis, we used SNPsplit (v0.5.0) (Krueger & Andrews, 2016) to assign the mapped reads to maternal or paternal allele based on the SNPs information between B6D2F1and PWK/PhJ. The SNPs were downloaded from the Mouse Genomes Project (https://www.sanger.ac.uk/data/mouse-genomes-project/). The SNPs that were identical between C57BL/6J and DBA/2J while different with PWK/PhJ were used.
For the raw sequencing reads of total RNA-seq, the three leading nucleotides of read2 generated from TSO were removed. Then the adaptors were removed with Trimmomatic (v0.39) if present. The cleaned reads were mapped to GRCm38 reference genome using STAR (v2.7.8a) (Dobin et al, 2013). RSEM (v1.3.1) (Li & Dewey, 2011) was employed to quantify the genes expression levels with the transcriptome alignments generated by STAR as input. For differentially expression analysis, R package DESeq2 (v1.32.0) (Love et al, 2014) was utilized with raw counts from RSEM as input. The significantly changed genes were identified with adjusted p-value cutoff 0.05, fold change cutoff 2 and mean FPKM cutoff 1.
For analyzing ATAC-seq sequencing data, we used the ENCODE ATAC-seq pipeline (v2.1.2, https://github.com/ENCODE-DCC/atac-seq-pipeline). ATAC-seq peaks within 1kb upstream or downstream of any known TSS were treated as promoter peaks, while ATAC-seq peaks with distance greater than 2.5kb to TSS were treated as distal peaks.
Assembly: mm10
Supplementary files format and content: bigWig files contain scaled H3K27ac CUT&RUN FPKMs and ATAC-seq fold changes; txt files contain gene-level reads counts of RNA-seq; bed files contain ATAC-seq peaks
Library strategy: CUT&RUN

source_name: ESC

growth_protocol: All animal experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee at Harvard Medical School. Collection of oocytes and in vitro fertilized embryos were described previously (Chen et al., 2021; Chen & Zhang, 2019). For allelic H3K27ac CUT&RUN profiling experiments, oocytes were collected from 6- to 8-week-old B6D2F1/J female mice (Jax 100006) and sperm were collected from 8- to 10-week-old PWK/PhJ male mice (Jax 003715). For CBP/p300 and HDACs inhibition experiments, both oocytes and sperm were retrieved from 6- to 8-week-old B6D2F1/J mice. The time when capacitated sperm were added to cumulus oocyte complexes in Human Tubal Fluid (HTF, Millipore) was considered as 0 hour post in vitro fertilization (0hpi). Embryos were cultured in potassium simplex optimized medium (KSOM, Milliplore) at 37°C under 5% CO2 with air.

extract_protocol: CUT&RUN libraries were generated based on the original protocol (Meers et al, 2019) with some modifications to optimize for low-input cell numbers. For each library, 10μl BioMag Plus Concanavalin A beads (Polysciences) were washed twice in 1ml Binding Buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) and resuspended in 5μl Binding Buffer. Then embryos were added in 45μl Wash Buffer (20mM HEPES-NaOH pH7.5, 150mM NaCl, 0.5mM Spermidine, 1X Roche Protease Inhibitor Cocktail), mixed with the 5μl Binding Buffer containing beads and rotated for 10min at room temperature. After removing the liquid by putting the tube on the magnet stand, the beads were resuspended in 80μl antibody Incubation Buffer (1X Wash Buffer with 0.02% Digitonin and 2mM EDTA) with 1:100 diluted H3K27ac antibody (Millipore, 07-360) and rotated at 4oC overnight. Then the beads were washed twice with 100μl Wash Buffer with 0.02% Digitonin and pulled off the liquid. The beads were resuspended in 100μl Wash Buffer with 0.02% Digitonin and 500ng/ml pA-MNase, then rotated for 3h at 4oC. After washing the beads twice with 200μl Wash Buffer with 0.02% Digitonin, the beads were resuspended in 200μl ice-cold Wash Buffer with 0.02% Digitonin and 4μl 100mM CaCl2 and incubated at 0oC for 30min. The reaction was stopped by adding 23μl 10X Stop Buffer (1,700mM NaCl, 100mM EDTA, 20mM EGTA, 0.02% Digitonin, 250µg/ml RNase A, 250µg/ml Glycogen). Then the tube was incubated at 37oC for 10min to release the cut fragments into supernatant. The tube was put on a magnet stand and the supernatant was transferred to a new 1.5ml LoBind tube (Eppendorf) while the beads were discarded. 2.5μl 10% SDS and 2.5μl Proteinase K (20mg/ml) were added to the supernatant and incubated at 55oC for 1h. Then 25ng carrier RNA (Qiagen, 1068337) was added to the supernatant. The supernatant was mixed with 200μl Phenol:Chloroform:Isoamyl Alcohol (Invitrogen, 15593031) by vortexing then transferred to a phase-lock tube (QuantaBio, 2302830) and centrifuged at 16,000g for 5min at room temperature. The supernatant was transferred to a new 1.5ml LoBind tube, added 26μl 3M Sodium Acetate, 1μl Glycogen (20mg/ml) and 750μl cold 100% Ethanol, mixed by vortexing and stored at -20oC overnight. Then the tube was centrifuged at 16,000g for 20min at 4oC and the supernatant was discarded. The precipitate DNA pellet was washed with 1ml cold 80% Ethanol then centrifuged at 16,000g for 5min at 4oC and the supernatant was discarded. Finally the precipitate DNA pellet was dissolved in 25μl ultrapure H2O. The library was constructed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) following the manufacturer protocol.

treatment_protocol: To transiently inhibit CBP/p300, embryos were cultured in KSOM containing 10μM A-485 (Tocris) between 4 and 20hpi. For transient inhibition of HDACs, embryos were cultured in KSOM containing 50nM TSA (Sigma) between 0-20 or 8-28hpi. Embryos were washed at least six times when they were transferred between different culture conditions.

value: ESC

tag: strain

tag: genotype

value: WT

tag: treatment

value: untreated


title: RNA-Seq_RUVBL2_Auxin_48h_rep1

description: RUVBL2 degron


title: Walnut_15W_pellicle rep3

value: 15-week-old pellicle tissues after pollination


title: Walnut_17W_pellicle rep1


title: Walnut_15W_pellicle rep2


title: Control-3


title: RNA-Seq_RUVBL2_Auxin_24h_rep2

description: RUVBL2 degron


title: Control-7


title: Walnut_13W_pellicle rep3

value: 13-week-old pellicle tissues after pollination


title: Control-1


title: Control-4


title: T2D-10

source_name: Blood, T2D

value: Type 2 diabetes


title: RNA-Seq_RUVBL2_Auxin_24h_rep1

description: RUVBL2 degron


title: Control-2


title: Walnut_11W_pellicle rep3

value: 11-week-old pellicle tissues after pollination


title: RNA-Seq_RUVBL2_Auxin_12h_rep2

description: RUVBL2 degron

value: RUVBL2 degron auxin


title: RNA-Seq_RUVBL2_Auxin_1h_rep2

description: RUVBL2 degron

value: embryonic stem cells


title: T2D-9


title: Walnut_15W_pellicle rep1


title: RNA-Seq_RUVBL2_Auxin_1h_rep1

description: RUVBL2 degron


title: Walnut_13W_pellicle rep1


title: Walnut_11W_pellicle rep2


title: RNA-Seq_RUVBL2_Auxin_0.5h_rep2

description: RUVBL2 degron


title: RNA-Seq_RUVBL2_Auxin_12h_rep1

description: RUVBL2 degron


title: Walnut_13W_pellicle rep2


title: T2D-7


title: T2D-6


title: T2D-5


title: Walnut_11W_pellicle rep1


title: RNA-Seq_RUVBL2_Auxin_0.5h_rep1

description: RUVBL2 degron


title: Walnut_9W_pellicle rep3

value: 9-week-old pellicle tissues after pollination


title: T2D-4


title: PRO-Seq_RUVBL2_Dox_rep1

description: TELP libraries

data_processing:
Library strategy: PRO-Seq
Cutadapt V1.18 (Martin, 2011) was used to remove the adaptors (TELP libraries adaptor) and low-quality reads from the paired-end sequencing reads, then the filtered reads were mapped to the mm10 genome with bowtie2 (--very-sensitive-local) (Langmead and Salzberg, 2012).
In order to obtain the more reliable nascent RNA signals, the duplicate, discordant and multi-mapping reads were removed, rRNA reads were also removed with split_bam.py from RseQC V 2.6.6 (Wang et al., 2012).
Because Ruvbl1/2 have important effects on Pol II, to get the more accurately transcription changes, the spike-in of drosophila cells was used to normalized the PRO-Seq signals.
In order to display the information of the plus and minus chains at the same time, bamCoverage (Ramirez et al., 2014) was used to make the tracks for plus and minus chains separately with parameters –filterRNAstrand forward/reverse and –scaleFactor, and the scaling factord were determined by drosophila reads per million in the final unique bam files.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

growth_protocol: For PRO- seq, Ruvbl2-mAID tagged cell lines were cultured in 0.2 % gelatin coated 15 cm plates with irradiated mouse embryonic fibroblasts (MEF) in DMEM-KO (Gibco, 10829018) containing 15% FBS, 1000 U/ml mouse leukemia inhibiting factor (mLIF), 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1× nonessential amino acids, and 1× penicillin/ streptomycin at 37 °C with 5% CO2, as described previously (Jiang et al., 2020).

extract_protocol:
Total RNA were extracted using Trizol reagent, and nascent RNA were enriched with biotin according to the protocol described by Mahat et al., 2016.
The enriched RNAs were reverse transcribed on beads, simply, SuperScript IV RT buffer included N9 random primers were added into the RNA bound beads to synthesis first strand cDNA on beads according to user’s manual, the excess RT primers were removed by addition of 3 μl Exonuclease I (Exo I) (NEB, M0293S), digested for 1h at 37 °C. The RNA was eliminated by adding 2 µl of 1M NaOH and incubating for 20 min at 98 °C. The reaction was then neutralized with 2 µl 1M HCl, the released cDNAs were extracted using Tris saturated equilibrium phenol (pH 8.0). Finally, the purified cDNA was subjected to library preparation according to the TELP protocol (Peng et al., 2015), the 150~400 bps length amplified DNA were selected for library analysis and finally subject to HiSeq X-ten PE150 sequencing (Novogene, Beijing). Each condition performed two technical duplicates.

treatment_protocol: after two passages, 2 μg/ml Doxycycline (Dox) were added into the medium for 24 h to induce the OsTir1 expression, and then 500 μM auxin (3-indole acetic acid) were appended for 0.5h and 1h to induce the RUVBL2 degradation. Then cells were harvested by cell scraper for PRO-Seq.

value: RUVBL2 untreated


title: Walnut_9W_pellicle rep1


title: PRO-Seq_RUVBL2_Auxin_1h_rep1

description: TELP libraries

value: RUVBL2 degron


title: PRO-Seq_RUVBL2_Dox_rep2

description: TELP libraries


title: PRO-Seq_RUVBL2_Auxin_1h_rep2

description: TELP libraries


title: Walnut_8W_pellicle rep2

value: 8-week-old pellicle tissues after pollination


title: Walnut_8W_pellicle rep1

value: pellicle


title: T2D-2

value: blood

value: female


title: T2D-1

value: male


title: PRO-Seq_RUVBL2_Auxin_0.5h_rep2

description: TELP libraries


title: T2D-8


title: Walnut_8W_pellicle rep3


title: PRO-Seq_RUVBL2_Auxin_0.5h_rep1

description: TELP libraries


title: O14_3

status: Public on Aug 29 2022

city: Shenyang

first: Jianhua

last: Fu

address: 36 Sanhao Street

institute: China medical university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: lung

growth_protocol: The neonatal rats were delivered on the 21st to 23rd day of gestation, and were randomly divided into a model group and a control group after birth, with 12 rats in each group. According to our previous experimental method, the model group was exposed to hyperoxia (FiO2=0.85) within 24 hours after birth, and the control group was exposed to normoxic air (FiO2=0.21). Soda lime is used to absorb CO2, so that the concentration of CO2 is less than 0.5%, and silica gel removes the water vapor in the oxygen tank. The model group and the control group were exchanged every 24 hours to avoid differences in nursing ability. Cages were opened regularly for 30 minutes a day, bedding was changed, and clean drinking water and food were provided.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: About 40 mg of lung tissue was taken, the trachea section was removed, washed with pre-cooled PBS, and stored in liquid nitrogen for subsequent operations.

value: lung

value: 21percent O2

tag: time


title: Walnut_9W_pellicle rep2


title: O10_3


title: O10_2


title: A14_3

value: 85percent O2


title: A10_3


title: O10_1


title: A14_1


title: O14_2


title: O14_1


title: A14_2


title: T2D-3


title: A10_1


title: A7_3

value: Day 7


title: O7_1


title: A7_2


title: O7_2


title: A45

city: Lausanne

first: Tomas

last: Kay

state: Vaud

address: Biophore building

country: Switzerland

institute: University of Lausanne

description: 8-day-old individual of genotype B in social environment B

data_processing:
Reads were mapped using STAR 2.7.8a (to the reference genome and annotation), using default parameter settings
Reads were counted using FeatureCounts, using default parameter settings
Assembly: Genome: GCF_003672135.1_Obir_v5.4; Annotation: GCF_003672135.1_Obir_v5.4_genomic.gtf
Supplementary files format and content: csv file: unnormalised counts matrix

organism: Ooceraea biroi

source_name: Whole individual brain

extract_protocol:
RNA was extracted using Tri reagent, following manufacturers protocol
RNA libraraies were prepared using the KAPA Stranded mRNASeq Library Preparation Kit, following manufacturers protocol

value: Whole individual brain

value: B

value: Social environment B

value: 8 days


title: A33


title: A28


title: A26


title: A37


title: O3_3

value: Day 3


title: O7_3


title: A32


title: A25


title: O3_2


title: A3_3


title: A3_1


title: A10_2


title: A24


title: A14


title: O3_1


title: A1_3

value: Day 1


title: A1_1


title: O1_3


title: A3_2


title: A18

description: 8-day-old individual of genotype B in social environment M

value: Social environment M


title: A16


title: A30


title: A15


title: A23


title: O1_1


title: A7_1


title: A27


title: A12


title: A19


title: A17


title: A1_2


title: A21


title: A48

description: 8-day-old individual of genotype M in social environment B

value: M


title: Rpd3_Jhd2S2A

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

data_processing:
Fastq files for chip-seq samples were generated with bcl2fastq 1.8.3 from Illumina.
ChIP-seq data was aligned to sacCer3 genome from UCSC with bowtie2 (2.2.0) using -k 1
bigWig files were created by using deeptool bamCoverage command, normalizing to reads per kilomillion by multiplying by 1 kilomillion and dividing by the total number of alignments for each sample.
Genome_build: sacCer3
Supplementary_files_format_and_content: rpkm normalized bigWig files

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD until mid-log phase

extract_protocol:
Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with antibody against  H3 (ab1791, Abcam),H3K4me3 (Abclonal; A2357),FLAG (F1804-1MG; Sigma-Aldrich),Rpd3 (sc-514160; Santa Cruz Biotechnology)
Libraries were prepared using the HTP KAPA kit

value: Jhd2 S2A mutant

tag: mediam

value: YPD

tag: chip antibody


title: WT-rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: sacCer3
Supplementary_files_format_and_content: raw counts

treatment_protocol: No treatment

value: wild type


title: Rpd3_WT

value: Rpd3 (sc-514160; Santa Cruz Biotechnology)


title: JhS2Arep2


title: JhS2Arep3


title: A46


title: JhS2Arep1


title: IP_WT

value: FLAG (F1804-1MG; Sigma-Aldrich)


title: O1_2

value: lung


title: WT-rep2


title: A9


title: H3K4me3_WT

value: H3K4me3 (Abclonal; A2357)


title: A40


title: WT-rep1


title: A44


title: A50


title: IP_Jhd2S2A


title: A47


title: A51

description: 8-day-old individual of genotype M in social environment M


title: A49


title: A42


title: codY_mutant_2

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-seq were mapped onto each reference genome using bowtie with the maximum insert size of 2000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM files generated from bowtie, then, were then used for DESeq(https://bioconductor.org/packages/release/bioc/html/DESeq.html)
DESeq2 was run with default options with the library type of dUTP RNA-seq and the default normalization method
Genome_build: The reference genome used in this study is: NC_007793.1 for WT and cody mutant strains
Supplementary_files_format_and_content: tab-delimited text file containing TPM values for each sample

organism: Staphylococcus aureus

source_name: bacteria cells

growth_protocol: glycerol stocks of S. aureus JE2 and cody mutant strains were inoculated into RPMI-1640 with 10% Lysogeny broth (LB) . The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (gram-positive bacterial kit) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the media was RPMI-1640 with 10% Lysogeny broth (LB) ; no other treatments

tag: medium

value: RPMI-1640 with 10% Lysogeny broth (LB)

tag: phase

value: mid-log phase

value: codY mutant


title: A39

value: Whole individual brain


title: A41

value: Social environment B


title: A43

value: 8 days


title: Input_WT

value: none (INPUT)


title: Input_Jhd2S2A


title: A34


title: codY_mutant_1


title: H3_Jhd2S2A

value: H3 (Abcam; ab1791)


title: H3K4me3_Jhd2S2A


title: A4


title: A8


title: A36

value: Social environment M


title: H3_WT


title: WT_1


title: A13

value: M


title: A7


title: A29


title: A38


title: WT_2


title: A5


title: A6


title: A35


title: A31


title: MM_20

description: 1-day-old individual of genotype M in social environment M

value: 1 day


title: MM_19


title: A10


title: A3


title: MM_16


title: MM_15


title: MM_17


title: MM_14


title: MM_13


title: MM_12


title: MM_11


title: MM_18


title: MM_10


title: MM_9


title: MM_8


title: MM_7


title: MM_6


title: MM_5


title: MM_4


title: Lean_M2

type: genomic

city: Rancagua

first: Bernardo

middle: J.

last: Krause

state: VI Region

address: Alameda 611

country: Chile

institute: Universidad de O'Higgins

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Differentially methylated CpG probes (DMC) at a genomic level were determined by applying the pipeline and considerations suggested by Wright and colleagues for 450K and 850K arrays]. The primary analysis of the data was performed by a bioinformatician that was not informed of the origin of the samples. Raw values from the Infinium MethylationEPIC BeadChip were assessed to verify the quality of the data. The original data was received in the form of methylation beta values.
After the quality control, data normalization was performed using Beta Mixture Quantile Dilation (BMIQ) method, considering the β-value as the level of methylation for a defined probe, suitable for EPIC array data with a beta distribution. BMIQ is an internal array normalization strategy that adjusts the beta values assigning probes to different methylation states or quantiles, preserving the continuity of the data. All steps were performed with the statistical analysis program R version 3.5.1 (https://cran.r-project.org/), using the Bioconductor package ChAMP version 2.10.2.

label: Cy5 and Cy3

source_name: Umbilical cord blood

label_protocol: Standard Illumina protocol

growth_protocol: Cord blood samples were obtained at delivery using a cord blood sterile collection bag (TERUMO, Tokyo, Japan). Based on the timing necessary to develop a proper isolation protocol, all samples were collected from deliveries that took place in the morning and processed in the following 6 hours after collection. Cord blood mononuclear cells were separated shortly after birth by Ficoll density gradient using Histopaque-1077 (Sigma-Aldrich, Missouri, US) centrifugation, incubated in RPMI 1640 medium (Sigma-Aldrich, Missouri, US) and seeded at a density of 8 to 10 × 106 cells/mL in 100 mm culture dishes at 5% CO2 for 2 h at 37°C. Non-adherent cells were removed by Phosphate-buffered saline (PBS) wash, then adherent cells were extracted and stored at -80°C until further analysis.

extract_protocol: Whole monocyte DNA was extracted, at the same time for all the samples analyzed, from frozen cells with the DNeasy Blood & Tissue kit (#69504, Qiagen, Germany) and submitted to bisulfite conversion using the Epitect Bisulfite kit (#59104, Qiagen, Germany)

value: Male

tag: maternal bmi group

value: Lean

value: Umbilical cord blood

value: Monocytes


title: MM_3


title: Obese_F2

value: Female

value: Obese


title: Obese_F13


title: Obese_M3


title: Obese_M6


title: Obese_F1


title: Lean_M14


title: MM_2


title: Obese_F3


title: pCHiC_patients_CD14

city: Manchester

first: chenfu

last: shi

address: AV Hill Building, Upper Brook Street, room 1.023

country: United Kingdom

institute: the university of manchester

description:
Promoter Capture Hi-C library, data for patient CD14 samples
chicdiff_CD14_PatvsContr.csv.gz

data_processing:
pCHiC sequencing data was filtered and the adapters were removed using fastp v0.19.4
pCHiC mapping was performed using HICUP 0.7.4 on hg38 genome. CHICAGO 1.13.1 was used to identify significant interactions
RNA-seq sequencing data was filtered and the adapters were removed using fastp v0.19.4
RNA-seq reads were mapped using STAR v2.7.3a on hg38 gencode v32 annotation
RNA-seq counts were generated using Htseq
Assembly: hg38
Supplementary files format and content: .RDs files contain chicago classes containing data for the specified samples
Supplementary files format and content: washU_track.txt.gz files contain the longrage interaction files for washu browser
Supplementary files format and content: csv.gz files contain the data from the differential interaction analysis from chicdiff
Supplementary files format and content: .count file contain the counts from the RNA-seq
Library strategy: Capture Hi-C (pCHiC)

source_name: Primary CD14 Monocytes

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from blood using Ficoll density gradient centrifugation. EasySep Human CD14+ Positive selection kit (StemCell Technologies, ref:17858) was used to isolate CD14+ cells from PBMCs and, subsequently, Easysep CD4+ T cell isolation kit (StemCell Technologies, ref:17952) was used to isolate CD4+ T cells from the remaining PBMCs, according to the manufacturer’s instructions.
pCHiC: 5-10 million isolated CD4+ T cells and CD14+ monocytes were crosslinked for 10 min in 1% formaldehyde and agitated at room temperature, the reaction was then quenched with ice cold 0.125 M glycine for 5 min. Crosslinked cells were washed in ice-cold PBS, and the supernatant was discarded, the pellets were then stored at -80ºC.  Each Hi-C library was prepared from fixed cells following the Arima HiC kit (Arima Genomics) and the KAPA HyperPrep kit (KAPA Biosystems) following the manufacturer’s protocol. Briefly, crosslinked cells were lysed, and DNA was digested by two different restriction enzymes, and ligated.  The ligated DNA was reverse-crosslinked and fragmented by sonication (Covaris S220), followed by DNA size selection, biotin enrichment, adaptor ligation, and final library amplification. A quality control step to determine the number of PCR cycles needed for library amplification was performed for each library using the NEBNext Library Quant kit (NEBNext, ref: E7630). Final quality and quantity were assessed by Bioanalyzer 2100 (Agilent) and Qubit (Thermo Fisher).  Hi-C samples were then hybridized with the SureSelect custom capture library by following Agilent SureSelectXT HS reagents (ref: G9702A, G9496A) and protocols (ref: G9702-9000). Briefly, target regions are hybridized with designed probes, followed by capture enrichment of these regions through streptavidin pulldown using Dynabeads MyOne Streptavidin T1 (ThermoFisher, ref: 65601). Post-capture amplification was carried out using nine PCR cycles. Final quality and quantity were assessed by Bioanalyzer 2100 (Agilent) and Qubit (Thermo Fisher).   RNA: A total of 0.5 million purified cells was resuspended in 700 uL Qiazol lysis reagent (QIAGEN, ref: 79306) to isolate RNA, then 140 uL of chloroform was added. After centrifugation at 12000 x g for 15 min, approximately 350 uL of the upper layer containing the RNA was transferred and mixed with 525 uL of 100% ethanol. RNA isolation was continued from this point using the RNeasy microkit (QIAGEN, ref: 74004) reagents and protocol. Final quantity was assessed by Qubit (Thermo Fisher). Libraries for RNA-seq were prepared using Illumina Truseq Stranded Total RNA reagents and protocol, except for Control 1 CD4+ and CD14+ samples, for which library preparation failed. Library quality and quantity was assessed by Bioanalyzer. The 28 libraries generated were sequenced using three lanes on Illumina HiSeq4000, generating 75 bp paired-end reads, and leading to an average of 30 million reads per sample (Genomics Facility, University of Manchester).

tag: disease

value: Systemic sclerosis

value: Primary CD14 Monocytes


title: pCHiC_controls_CD14

description:
Promoter Capture Hi-C library, data for control CD14 samples
chicdiff_CD14_PatvsContr.csv.gz

value: healthy

tag: cell type


title: Lean_M12


title: MM_1

value: Whole individual brain


title: Obese_M5


title: Lean_M7


title: Lean_M1


title: pCHiC_controls_CD4

description:
Promoter Capture Hi-C library, data for control CD4 samples
chicdiff_CD4_PatvsContr.csv.gz

source_name: Primary CD4 T cells

value: Primary CD4 T cells


title: Obese_F7


title: Lean_F10


title: Obese_F4


title: Lean_F12


title: pCHiC_CD14

description:
Promoter Capture Hi-C library, data for all CD14 samples
chicdiff_CD4vsCD14.csv.gz


title: MB_12

description: 1-day-old individual of genotype M in social environment B

value: Social environment B


title: Obese_M11


title: Obese_F6


title: Obese_F14


title: MB_11


title: Obese_M4


title: Obese_M8


title: MB_9


title: Obese_F15


title: Obese_F9


title: MB_10


title: MDA-MB-231 cells, shControl bio rep2

city: NanJing

first: Zheng

last: Fang

state: Jiang Su

address: Guangzhou Road

department: Department of General Surgery, the First Affiliated Hospital

institute: Nanjing Medical University

data_processing:
a reference genome sequence of human species and gene model annotation files were downloaded and indexed, and a transcript profiling analysis was performed using Hisat2 software for alignment to reference genomes.
GFF annotation files are converted to fasta format for expression analysis.
HTSeq (v0.6.1) calculated the gene and isoform expression levels based on the pair-end clean data and the reference gene file.
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were maintained in RPM1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen, CA, USA). 1ug of total RNA was used for the construction of sequencing libraries  according to the manufacturer's instructions. VAHTS mRNA‐seq V2 Library Prep Kit for Illumina (NR601, Vazyme)
For the preparation of the following libraries, 1 ug of total RNA was used and isolation of poly(A) mRNA was performed using Oligo(dT) beads. Using divalent cations and high temperatures, mRNA fragmentation was achieved and the priming process was carried out using random primers. Two strands of cDNA were synthesized, one from the first strand and one from the second strand. As soon as the double-stranded cDNA was purified, adaptors were added to both ends after dA tailing and T-A ligation. DNA Clean Beads were then used to select the size of adaptor-ligated DNA. Amplification of each sample was then conducted using P5 and P7 primers, and the obtained products were validated by PCR.

tag: cell line

value: MDA-MB-231 cells

value: breast cancer cells

value: shRNA control


title: MB_13

value: M


title: MDA-MB-231 cells , shPUS1 bio rep1

value: PUS1 knockdown


title: MDA-MB-231 cells, shControl bio rep3


title: Lean_M13

value: Male


title: MDA-MB-231 cells , shPUS1 bio rep2


title: MB_8

value: 1 day


title: MB_5


title: MB_3


title: pCHiC_patients_CD4

description:
Promoter Capture Hi-C library, data for patient CD4 samples
chicdiff_CD4_PatvsContr.csv.gz


title: Lean_F5

value: Lean

value: Umbilical cord blood


title: MDA-MB-231 cells, shControl bio rep1


title: Lean_M10

value: Monocytes


title: MB_2


title: Obese_F11

value: Female

value: Obese


title: Visium sample partial_response_P6

city: Perth

first: Alistair

middle: R. R.

last: Forrest

state: WA

address: 6 Verdun Street, Nedlands

country: Australia

institute: Harry Perkins Institute of Medical Research, The University of Western Australia

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed using Space Ranger 1.0.0 with GRCh38-3.0.0 reference in the manual alignment mode. Filtered gene-barcode matrices from Space Ranger output were used for downstream analyses; barcodes with less than 400 genes were excluded.
Output of Space Ranger including "filtered_feature_bc_matrix" and "spatial" folders.
Assembly: GRCh38

source_name: Ovarian tumour

extract_protocol: Single-cell libraries were constructed using the 10x Chromium 3′ v2 workflow according to the manufacturer’s protocol. Visium libraries were prepared according to the Visium Gene Expression User Guide (CG000239, Rev A, 10X Genomics).

value: Ovarian tumour


title: Visium sample poor_response_P7

description: 10x Genomics


title: Visium sample good_response_P5

description: 10x Genomics


title: MB_7


title: BB_7

description: 1-day-old individual of genotype B in social environment B

value: B


title: MB_6

value: Whole individual brain


title: Visium sample poor_response_P1

description: 10x Genomics


title: Visium sample good_response_P3

description: 10x Genomics


title: MB_4


title: Obese_M9


title: Visium sample good_response_P2

description: 10x Genomics


title: BB_3


title: Visium sample poor_response_P8

description: 10x Genomics


title: BB_9


title: BB_2


title: BM_9

description: 1-day-old individual of genotype B in social environment M

value: Social environment M


title: MB_1

value: Social environment B


title: BB_4


title: BB_6


title: scRNA-seq sample Y5

description: 10x Genomics

data_processing:
FASTQ files were processed using Cell Ranger 3.0.2 with refdata-cellranger-GRCh38-3.0.0 reference. Raw gene-barcode matrices from Cell Ranger output were used for downstream processing. Cells were distinguished from background noise using EmptyDrops. Genes detected in a minimum of 3 cells were retained; cells with at least 500 genes, at least 1000 UMIs and under 15% of mitochondrial reads were retained.
Tab-separated files with matrices of gene by cell counts, post-filtering.
Assembly: GRCh38


title: scRNA-seq sample MJ11

description: 10x Genomics


title: BM_8


title: Lean_F8


title: Visium sample partial_response_P4

description: 10x Genomics


title: BM_6


title: BM_7


title: scRNA-seq sample MJ10

description: 10x Genomics


title: scRNA-seq sample Y2

description: 10x Genomics


title: BM_5


title: scRNA-seq sample Y3

description: 10x Genomics


title: BB_1


title: Epidermis_multiome_S1_RNA

city: Heidelberg

first: Llorenç

last: Solé Boldo

address: Im Neuenheimer Feld, 580

country: Germany

institute: DKFZ

description: single cell RNA

data_processing:
Alignment of the raw fastq-data with CellRanger v.2.1.0 to reference genome.
QC and data filtereing with CellRanger v.2.1.0.
Sample combination with CellRanger v.2.1.0.
QC and sample integration with Seurat v.4.0.5. & Signac v1.5.0.
Clustering and visualization with Seurat v.3.1.1. & Signac v.1.5.0.
Assembly: hg38
Supplementary files format and content: Fragment files for scATAC-seq and per barcode metrics, filtered barcode-feature matrix for scRNA-seq

source_name: Healthy epidermis

extract_protocol:
Healthy whole skin biopsies were obtained from two male donors of fair-skin type (55 and 72 y/o) and preserved in MACS Tissue Storage Solution (Miltenyi Biotec). Samples were subsequently cut into small pieces that were further processed using the human Epidermis Dissociation Kit (Miltenyi Biotec) and the Gentle MACS Dissociator (Miltenyi Biotec), following the manufacturer’s instructions. Nuclei were isolated from the resulting single-cell suspension using the lysis buffer recipe described in (Wysocka et al., 2001) In brief, epidermal cells were resuspended in Buffer A (10 mM HEPES pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 1 mM DTT, and 1X protease inhibitor cocktail) containing freshly added Triton X-100 at a final concentration of 0.1% . Cells were resuspended in a 1x106 cells/25 µL of Buffer A ratio and were incubated for 10 minutes on ice. Nuclei were recovered by centrifugation at 1,300 g for 5 minutes at 4ºC and resuspended in 1X Nuclei Buffer (10X Genomics).
Approximately 10,000 nuclei per sample were loaded into the Chromium Controller system, and libraries were subsequently prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit (10X Genomics), following the manufacturer’s instructions. Libraries were sequenced on a NovaSeq 6000 device (Illumina) using paired-end (28+90bp) settings for 100 cycles for the scRNA-seq, and paired-end (50+50bp) for 100 cycles for the scATAC-seq.

value: Healthy epidermis


title: BM_10


title: Epidermis_multiome_S2_ATAC

description: single cell DNA


title: Epidermis_multiome_S2_RNA

description: single cell RNA


title: MB_14


title: NCAL1overexpresion

city: Changchun

first: Chao

last: Niu

state: Jilin

address: Xinmin Street #1

department: Cancer Center

institute: The First Hospital of Jilin University

data_processing:
CLC Genomics Workbench v 11.0.1
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the hg38.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

growth_protocol: NK92MI cells were cultured in α-minimum essential medium containing 2 mM L-glutamine, 1.5 g/L sodium bicarbonate, 0.2 mM inositol, 0.1 mM β-mercaptoethanol, 0.02 mM folic acid, 12.5% horse serum, and 12.5% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol. To ensure the quality of the library, the effective concentration of the library is higher than 2nM.
RNA libraries for RNA-seq were prepared using NEB method.

treatment_protocol: NK92MI cells were seeded in a six-well plate at 500,000 cells/well with 2 mL medium containing 8 mg/mL polybrene. Cells were infected with NCAL1 overexpression lentiviruses or control lentiviruses at a multiplicity of infection of 10 and centrifuged at 2000 rpm for 2 h at 37 °C and then cultured in the incubator at 37 °C. After 12–14 h of incubation, the medium was replaced with fresh medium every 2 days.

value: cell line

value: Natural killer cells

value: NCAL1 overexpresion

value: Lentivirus transfection


title: Control

value: Control


title: BM_3

value: 1 day


title: Epidermis_multiome_S1_ATAC

description: single cell DNA


title: CR28 24h CB2

city: Liège

first: Christelle

last: Sanchez

address: Quai G. Kurth 45

country: Belgium

institute: ULiege

data_processing:
Raw data were demultiplexed into individual libraries. After filtering out reads mapping to rRNA, tRNA, mitochondrial RNA, and other contaminants (e.g., adapters, etc.) using bowtie2
Assembly: GRCh38
Supplementary files format and content: reads were aligned onto the human reference genome (GRCh38 and Ensembl 105 annotation) and quantified with Star to give the Counts file.

source_name: Chondrocytes

growth_protocol: Primary OA chondrocytes were isolated from cartilage after enzymatic digestion and growth in alginate beads in high glucose DMEM containing 1% FBS, 2mM glutamine, 50 µg/ml ascorbic acid and 20 µg/ml proline during 3 days

extract_protocol:
18 beads were pooled, degelified in 0,1M cold citrate and cells were homogenized in 600 µl RTL lysis buffer (Qiagen) then extract using Rneasy mini kit from Qiagen according to the manufacturer's instructions. Dnase step were performed during extraction. Samples were eluted in 30 µl RNase free H2O
0,1 µg of RNA from each culture condition was used for this analysis. Libraries were prepared with the Illumina Truseq stranded mRNA sample prep kit according to the manufacturer's instructions

treatment_protocol: Chondrocytes are cultured in 1% FBS, glutamine, ascorbic acid and proline with or without CL and BS for 6h or 24h

value: Chondrocytes

tag: patient

tag: cl treatment

tag: bs treatment


title: BM_4

tag: tissue

tag: age


title: MDA-MB-231 cells,  shPUS1 bio rep3

value: MDA-MB-231 cells

value: breast cancer cells

value: PUS1 knockdown


title: BM_1


title: CR28 24h BS1


title: domestic_pig_cerebrum 3 [RC3; re-analysis]

city: Chengdu

first: hengkuan

last: li

state: Sichuan

address: Hui ming

institute: Sichuan Agricultural University

description: re-analysis of GSM4943026

data_processing:
Sequence reads are aligned to pig reference genome by alignment tool STAR (version 2.6.0c) or BWA (version 0.7.17).
CIRCExplorer2 and CIRI2 were used to retrieve RNA-seq reads that are mapped to back-splicing junction sites for circRNA prediction, respectively.
Assembly: Sscrofa 11.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Sus scrofa

source_name: Cerebrum

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Technologies).
Ribosomal RNAs (rRNAs) were removed from total RNA using an rRNA depletion protocol (Ribo-Zero kit, Epicentre) and further fragmented. Subsequently, the Illumina TruSeq stranded RNA-seq library protocol was used to construct the RNA-seq libraries.

tag: breed

value: Rongchang pig

tag: Sex

value: Female


title: domestic_pig_cerebrum 2 [RC2; re-analysis]

description: re-analysis of GSM4943025


title: domestic_pig_cerebrum 1 [RC1; re-analysis]

description: re-analysis of GSM4943024


title: CR28 24h CL2


title: CR28 24h CB1


title: Wild_boar3_brain [WB3]

source_name: Brain

value: Wild boar


title: Wild_boar2_brain [WB2]


title: Wild_boar1_brain [WB1]


title: CR28 6h CB2


title: CR28 24h CL1


title: CR28 24h CTRL


title: CR28 6h CL2


title: CR28 6h CTRL


title: CR28 6h CB1


title: CR28 6h BS1


title: CR28 6h CL1


title: CR28 6h BS2


title: CR28 24h BS2


title: CR27 24h CB2


title: CR27 24h CB1


title: MDA-MB-436

city: Bethesda

first: Yoshimi

middle: E

last: Greer

state: MD

address: Bldg.10, Room 4B50, 9000 Rockville Pike, Line 2 (Optional)

institute: National Cancer Institute

data_processing:
Illumina HiSeq 2000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat
The Bam files were quantified using the Tuxedo suite (cufflinks, cuffdiff).
Assembly: hg19
Supplementary files format and content: format: xlsx content: log2 (rpkm+0.001)

source_name: breast cancer cells

growth_protocol: Breast cancer cell lines were grown in RPMI media supplemented with 10% heat-inactivated FBS, 1% streptomycin/penicillin.

extract_protocol:
Cells were harvested with trypinization, and cell suspension was prepared to count cell numbers. Total RNA was extracted by using TRIZOL.
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion

treatment_protocol: Healthy cells in growing condition in 10cm culture dishes were used without any treatment.

value: Triple Negative Breast Cancer, Basal B

tag: passages


title: MDA-MB-453

value: HER2 amplified


title: ZR-75-1

value: Estrogen Receptor positive


title: T47D


title: MDA-MB-468

value: Triple Negative Breast Cancer, Basal A


title: MDA-MB-231


title: HCC38


title: CR27 24h BS1

tag: time


title: Hs578T


title: HCC1954


title: HCC1937


title: HCC1500


title: CR27 24h CL2


title: CR27 24h CL1


title: CR27 24h CTRL


title: BT474

value: Estrogen Receptor positive, HER2 amplified


title: BT20


title: pCHiC_CD4

description:
Promoter Capture Hi-C library, data for all CD4 samples
chicdiff_CD4vsCD14.csv.gz

value: Primary CD4 T cells


title: CR27 6h CB2


title: MCF7


title: AU565


title: CR27 6h BS2


title: CR27 6h CB1


title: CR27 24h BS2


title: CR27 6h BS1


title: IL-15 KO replicate 4

city: Toulouse

first: Joost

last: Van Meerwijk

state: HG

address: CHU Purpan BP 3028

department: CPTP U1043

country: France

institute: INSERM

data_processing:
High quality selection with pRESTO-FilterSeq
Indexing and annotation UMI pRESTO-MaskPrimers and PairSeq
Construction concensus pRESTO-BuildConsensus
Aligned F and R pRESTO-AssemblePairs
Aligment to TCR end table export MiXCR-align-assemble-exportClones
Genome_build: mm10
Supplementary_files_format_and_content: Number of UMI and VJ segments, Delimited tab text

source_name: Thymic regulatory T cells

growth_protocol: Sorting

extract_protocol:
RNA was extracted by Nucleospin RNA XS (Macherey-Nagel)
Libraries for TCR-sequencing (TCR-seq), the cDNA synthesis and library preparation were performed as previously described (Feng et al., 2015), and was adjusted to our different conditions.) the RNA had a high quality (RIN>8.5)
TCR-seq

value: Thymic regulatory T cells

tag: sorting

tag: strain/genotype

value: Rag2-Gfp Foxp3-Thy1a Kaa Tcrb-transgenic Tcra+/null  Il15null B6

value: 3 weeks


title: CR27 6h CL1


title: CR27 6h CL2


title: CR26 24h CB2


title: IL-15 KO replicate 3


title: IL-15 KO replicate 1


title: IL-2 KO replicate 2

value: Rag2-Gfp Foxp3-Thy1a Kaa Tcrb-transgenic Tcra+/null  Il2null B6


title: IL-15 KO replicate 2


title: CR26 24h BS1

value: Chondrocytes


title: IL-2 KO replicate 3


title: CR27 6h CTRL


title: CR26 24h CB1


title: CR26 24h BS2


title: Wild type replicate 3

value: Rag2-Gfp Foxp3-Thy1a Kaa Tcrb-transgenic Tcra+/null  wt B6


title: CR26 24h CTRL


title: IL-2 KO replicate 1


title: Wild type replicate 4


title: Male aged Rep 2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “-r 100 -N 2 --b2-very-sensitive --library-type fr-firststrand --b2-L 25” with gene annotation from Ensembl version 67
Gene-based read count was obtained using htseq-count function from HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

molecule: polyA RNA

source_name: bone endothelial cells

extract_protocol:
Bone endothelial cells were purified using endomucin expression  and sorted directly into lysis buffer of the RNeasy Plus Micro Kit (QIAGEN). Total RNA was isolated as per the manufacturer’s guidelines.
RNA quality was checked using a 2100 BioAnalyzer (Agilent), and libraries were prepared with TruSeq Total RNA Library Preparation Kit (Illumina) following the manufacturer’s guidelines. Sequencing of libraries was carried out at the LMS Genomics Facility on an Illumina HiSeq 2500 platform with 100-nucleotide-length paired-end reads.

value: freshly isolated from tibia

value: bone endothelial cells

value: 65 weeks

value: M

tag: strain


title: Wild type replicate 1


title: CR26 24h CL2


title: CR26 6h CB2


title: Wild type replicate 2


title: CR26 6h BS2


title: IL-2 KO replicate 4


title: CR26 6h CB1


title: CR26 6h BS1


title: CR26 24h CL1


title: Male aged Rep 3


title: Male aged Rep 1


title: Female aged Rep 3

value: F


title: Female aged Rep 2


title: Male young Rep 3

value: 2 weeks


title: CR26 6h CL2


title: Female aged Rep 1


title: CR25 24h CB1


title: CR26 6h CTRL


title: Male young Rep 2


title: Female young Rep 3


title: Male young Rep 1


title: CR26 6h CL1


title: CR25 24h CB2


title: Female young Rep 1


title: CR25 24h BS1


title: CR25 24h CL1


title: Female young Rep 2


title: CR25 6h CB1


title: CR25 24h CL2


title: CR25 24h BS2


title: CR25 6h CL2


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 11

city: Toronto

first: Chi Kin

last: Wong

address: 600 University Avenue

country: Canada

institute: LTRI

data_processing:
Raw reads were trimmed and filtered by Cutadapt and Trimmomatic
Trimmed reads were mapped to the Silva database for taxonomy assignment using DADA2
The abundance table generated was analyzed using phylosesq
Differential abundance analysis was performed using DESeq2 and LEfSe, and functional abundance analysis was performed using PICRUSt2
Assembly: NA
Supplementary files format and content: An abundance table stored in seqtab_nochim_transposed_DD9-52_v34.csv
Library strategy: 16s rRNA-seq

organism: feces metagenome

source_name: Fecal pellet

extract_protocol:
Fecal pellets with lyzed guanidine thiocyanate-EDTA-lauryl sarkosine buffer followed by phenol-chloroform extraction to precipitate gDNA.
V3 and V4 regions of the 16s rRNA gene were amplified using primers spanning the regions and containing barcodes and adapters.
Targeted DNA libraries

treatment_protocol: Control or Glp1rTcell-/- mice were fed a high-fat diet for 12 weeks followed by one more week of HFD with or without semaglutide treatment (10 ug/kg). The first fecal pellet most distal in the colon was collected from each mouse and snap frozen in liquid nitrogen.

value: Fecal pellet

tag: genotype

tag: diet

value: HFD

tag: treatment

value: Vehicle-treated


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 9

value: Semaglutide-treated


title: CR25 24h CTRL

tag: cell type


title: CR25 6h CB2


title: CR25 6h CTRL


title: CR25 6h CL1


title: CR24 24h BS2


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 8


title: CR24 24h CB1


title: CR24 24h BS1


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 9


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 6


title: CR24 24h CB2


title: CR24 24h CL2


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 8


title: CR25 6h BS1


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 7


title: CR24 24h CL1


title: CR24 24h CTRL


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 9


title: 64-Neck

city: Taipei

first: Chih-Hung

last: Chung

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Reads were trimmed and clipped for quality control in AfterQC v0.9.7.
Read quality was checked for each sample using FastQC v0.11.7.
High-quality reads were then imported into STAR v2.6.1a for alignment into BAM files.
BAM files were imported into the RSEM v1.3.1 for expected counts, FPKM and TPM estimation.
Expected counts table was extracted from each RSEM output .gene.results file.
Expected counts table was imported into the DESeq2 v1.26.0 for rlog transformation.
Genome_build: hg38, GRCh38.94
Supplementary_files_format_and_content: Tab-delimited text file for expected counts of each sample.  Tab-delimited text file for FPKM of each sample.  Tab-delimited text file for TPM of each sample.  Tab-delimited text file for rlog of each sample.

source_name: Lymph node metastatic tumor

extract_protocol:
The samples were frozen in the RNALater buffer and stored at -80oC. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction
Sample Prep. Kit : QIAseq FastSelect RNA Removal Kit_Human Cyto & Mito rRNA + Illumina TruSeq Stranded mRNA Sample Prep Kit + limited cycles of PCR by KAPA HiFi Polymerase

treatment_protocol: We collected matched pairs of primary tumor (invasive front region 0.3-0.5cm and inner-tumor region) , lymph node metastatic tumor region and adjacent normal tissue from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH), according to the current TVGH-IACUC regulations. IRB approval number : 2017-05-013AC.

tag: disease state

value: HNSCC Patient

value: Lymph node metastatic tumor

tag: unique patient number (upn)


title: 69-Neck


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 9


title: 65-IT

source_name: Primary Tumor (Inner site)

value: Primary Tumor (Inner site)


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 8


title: CR24 6h CB2

tag: patient

tag: cl treatment


title: 69-N

source_name: adjacent normal tissue

value: adjacent normal tissue


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 7

tag: tissue


title: 69-VT

source_name: Primary Tumor (Invasive front)

value: Primary Tumor (Invasive front)


title: CR24 6h CB1

value: Chondrocytes

tag: bs treatment


title: CR24 6h BS2


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 8


title: 64-Neck-2


title: 65-N


title: 65-VT


title: 64-VT


title: 64-IT


title: CR24 6h BS1


title: 64-N


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 7


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 5


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 6


title: 45dpi_Spatial

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

institute: University of Manchester

description: Spatial transcriptome

data_processing:
For FASTQ generation and alignments, illumina basecall files (*.bcl) were converted to FASTQs using bcl2fastq
Gene counts were generated using CellRanger for single cell RNAseq (v.6.0.0) or SpaceRanger for spatial transcriptomics (v.1.2.2)
Mapping strategy was conducted on CellRanger or SpaceRanger against a combined Mus musculus (mm10) and Trypanosoma brucei (TREU927) transcriptome reference
After alignment, reads were grouped based on barcode sequences and demultiplexed using the Unique Molecular Identifiers (UMIs)
Assembly: mm10 + TREU927
Supplementary files format and content: .h5 files were generated as outputs from CellRanger or SpaceRanger. The filter matrices can be used for downstream analysis using the scripts available on https://zenodo.org/record/6387555#.Yksy3y8w1nk
Library strategy: Spatial transcriptomics

growth_protocol: 6-8 weeks old mice were infected (i.p.) with 2,000 Trypanosoma brucei brucei strain Antat 1.1E. Mouse hypothalami from naïve and infected mice were harvested for scRNAseq analysis. Coronal brain sections were flash-frozen in OCT for spatial transcriptomics analysis

extract_protocol:
Single cell suspensions were obtained from murine hypothalami using enzymatic dissociation, followed by library preparation using the 10X Chromium platform. Coronal brain sections were flash-frozen in OCT, and cryo-sections (5 um) were used for tissue analysis using the 10X Visium platform.
Illumina compatible, RNA libraries were prepared with the 10X Chromium technolgy

treatment_protocol: Two biological replicates per time point (naïve, 25- and 45 days post-infection) for single cell transcriptomics. One biological replicate for spatial transcriptomics

value: Female

tag: age

value: 6-8 weeks old

value: Brain (forebrain coronal section)

value: 45 days post-infection


title: CR24 6h CL2


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 7


title: CR24 6h CL1


title: 63-IT


title: 25dpi_Spatial

description: Spatial transcriptome

tag: Sex

value: 25 days post-infection


title: 63-VT


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 5


title: Naïve_Spatial

description: Spatial transcriptome

value: Naive


title: 63-N


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 6


title: CR24 6h CTRL


title: lepbibl54 M. marinum 3

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description:
150 nucleotides
Ding_Lepb--Mm vs ++Mm_DEseq.xlsx, Ding_Lepb--Mm vs lepb--pvp_DEseq.xlsx
HFK57DSXY_104090-002-012

data_processing:
Sequencing data of zebrafish larvae were aligned and mapped to the zebrafish genome GRCz11 using CLC Genomics, and differential gene expression was analyzed using DESeq2 v1.21.1.
Gene Ontology (GO) term enrichment and KEGG pathway analysis were performed in DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Assembly: the zebrafish genome GRCz11
Supplementary files format and content: tab-delimited text files include normalized read values per million for each Sample

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://zfin.org).

extract_protocol:
Zebrafish larvae from lepb+ and lepbibl54 infected and control groups (15 pooled larvae/replicate, n=3) were resuspended and crushed in 0.5 ml of TRIzol Reagent.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was used to process the samples. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation of the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with Fragment Analyzer.

treatment_protocol: M. marinum infection

value: lepb mutation

value: whole embryos

value: 5 days post fertilization


title: CR23 24h CB2


title: 61-IT


title: CR23 24h CB1


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 4

value: Fecal pellet

value: HFD


title: 61-VT

value: HNSCC Patient


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 4

value: Vehicle-treated


title: lepbibl54 M. marinum 1

description:
150 nucleotides
Ding_Lepb--Mm vs ++Mm_DEseq.xlsx, Ding_Lepb--Mm vs lepb--pvp_DEseq.xlsx
HFK57DSXY_104090-002-010


title: lepbibl54 M. marinum 2

description:
150 nucleotides
Ding_Lepb--Mm vs ++Mm_DEseq.xlsx, Ding_Lepb--Mm vs lepb--pvp_DEseq.xlsx
HFK57DSXY_104090-002-011


title: 61-N


title: CR23 24h BS2


title: lepbibl54 pvp 40 4

description:
150 nucleotides
Ding_Lepb--pvp vs lepb++ pvp_DEseq.xlsx, Ding_Lepb--Mm vs lepb--pvp_DEseq.xlsx
HTHCLDMXX_104090-002-029RR


title: lepbibl54 pvp 40 3

description:
150 nucleotides
Ding_Lepb--pvp vs lepb++ pvp_DEseq.xlsx, Ding_Lepb--Mm vs lepb--pvp_DEseq.xlsx
HFK57DSXY_104090-002-009


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 5

value: Semaglutide-treated


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 5


title: lepbibl54 pvp 40 2

description:
150 nucleotides
Ding_Lepb--pvp vs lepb++ pvp_DEseq.xlsx, Ding_Lepb--Mm vs lepb--pvp_DEseq.xlsx
HFK57DSXY_104090-002-008


title: 59-VT


title: CR23 24h CL1


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 4


title: lepbibl54 pvp 40 1

description:
150 nucleotides
Ding_Lepb--pvp vs lepb++ pvp_DEseq.xlsx, Ding_Lepb--Mm vs lepb--pvp_DEseq.xlsx
HTHCLDMXX_104090-002-007


title: 59-N

value: adjacent normal tissue


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 6


title: 54-VT

value: Primary Tumor (Invasive front)


title: CR23 6h CB2

value: Chondrocytes


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 3


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 3


title: lepb+  M. marinum 3

description:
150 nucleotides
Ding_Lepb++Mm vs lepb++ pvp_DEseq.xlsx, Ding_Lepb--Mm vs ++Mm_DEseq.xlsx
HFK57DSXY_104090-002-006

value: wild type


title: lepb+  M. marinum 2

description:
150 nucleotides
Ding_Lepb++Mm vs lepb++ pvp_DEseq.xlsx, Ding_Lepb--Mm vs ++Mm_DEseq.xlsx
HTHCLDMXX_104090-002-005RR


title: 54-N


title: lepb+  M. marinum 1

description:
150 nucleotides
Ding_Lepb++Mm vs lepb++ pvp_DEseq.xlsx, Ding_Lepb--Mm vs ++Mm_DEseq.xlsx
HFK57DSXY_104090-002-004


title: CR23 6h CB1


title: CR23 24h BS1


title: CR23 6h BS1


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 4


title: CR23 24h CL2


title: lepb+ pvp 40 3

description:
150 nucleotides
Ding_Lepb++Mm vs lepb++ pvp_Deseq.xlsx, Ding_Lepb--pvp vs lepb++ pvp_Deseq.xlsx
HTHCLDMXX_104090-002-002RR


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 3


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 3


title: lepb+ pvp 40 2

description:
150 nucleotides
Ding_Lepb++Mm vs lepb++ pvp_Deseq.xlsx, Ding_Lepb--pvp vs lepb++ pvp_Deseq.xlsx
HFK57DSXY_104090-001-025


title: CR23 6h CL2


title: CR23 24h CTRL


title: 47-N


title: lepb+ pvp 40 1

description:
150 nucleotides
Ding_Lepb++Mm vs lepb++ pvp_Deseq.xlsx, Ding_Lepb--pvp vs lepb++ pvp_Deseq.xlsx
HFK57DSXY_104090-001-003


title: CR23 6h CL1


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 2


title: MTZ treated zebrafish larval kiney hematopoietic cells rep3

city: Chongqing

first: jiangyong

last: he

address: Tiansheng Li Street of Beibei District

institute: southwest university

description: Labeled coro1a-Dendra2+ cells from zebrafish larval kidney tissue

data_processing:
Illumina NovaSeq 6000 software used for basecalling. Raw reads used FASTP for quality control to filter low quality data. Then the clean reads were aligned to the GRCz119 genome assembly using HISAT2
Genome_build: GRCz11

source_name: kidney hematopoietic cells

extract_protocol:
The cells in the 3.5 dpt kidney of DMSO or MTZ groups were labeled by red color via irradiating Tg(coro1a:DenNTR) transgenic larvae by a 405-nm laser in an LSM880 confocal microscope for 30 seconds. After photoconversion, approximately eighty zebrafish larvae were collected, mixed, dissected, and homogenized in 1 ml 0.5% trypsin at 4 °C. The homogenized cell suspension was centrifuged at 1000x g at 4 °C for 5 minutes. Then, the supernatant was removed and the cell pellet was re-suspended in PBS, followed by cell sorting using flow cytometry (Moflo XDP, Beckman).
A cDNA library was generated from fifty red Dendra2+ cells by using the Smart-seq2 protocol.

value: WT

value: kidney

value: 3.5 dpt/9 dpf


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 2


title: CR23 6h BS2


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 10


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 2


title: MTZ treated zebrafish larval kiney hematopoietic cells rep2


title: 47-VT


title: CR23 6h CTRL


title: CR20 24h CB1


title: 44-N


title: 44-VT


title: CR20 24h CB2


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell+/+ mice, 1


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 2


title: DMSO treated zebrafish larval kiney hematopoietic cells rep3


title: MTZ treated zebrafish larval kiney hematopoietic cells rep1


title: CR20 24h BS2


title: 28-Neck

value: Lymph node metastatic tumor


title: DMSO treated zebrafish larval kiney hematopoietic cells rep1


title: 28-N


title: DMSO treated zebrafish larval kiney hematopoietic cells rep2


title: 28-IT

value: Primary Tumor (Inner site)


title: CR20 24h BS1


title: Fecal pellet DNA from vehicle-treated Glp1rTcell-/- mice, 1


title: CR20 24h CL2


title: CR20 24h CL1


title: Fecal pellet DNA from chow-fed mice, 6

value: Chow control


title: 44-IT


title: Fecal pellet DNA from vehicle-treated Glp1rTcell+/+ mice, 1


title: 26-Neck


title: CR20 24h CTRL


title: Fecal pellet DNA from semaglutide-treated Glp1rTcell-/- mice, 1


title: CR20 6h CB2


title: Fecal pellet DNA from chow-fed mice, 5


title: Input replicate 6

city: Barcelona

first: Estefania

last: Mancini

state: Barcelona

address: C/ Dr. Aiguader, 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Centre for Genomic Regulation

data_processing:
Base-calling was done using Illumina bcl2fastq program
Mapping was performed with STAR to Drosophila melanogaster ENSEMBL genome release 87
Reads count per gene was done with HTSeq
Genome_build: BDGP release 6 + ISO1 MT/dm6 assembly
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: Early embryos

growth_protocol: Large scale collections of staged 90 min embryos were obtained and processed as described in Coll et al. (2010). Egg-laying trays were exchanged three times for embryo synchronization, and 90 min embryos collected thereafter.

extract_protocol:
RNA was extracted using TRIZOL. RNA quality was monitored in a Bioanalyzer.
Ribo-depleted RNA
Illumina True-seq libraries were prepared using Ribo-zero kit and subjected to HiSeq 50 bp single-end sequencing

treatment_protocol: Embryos were washed twice in EW buffer (0.7% NaCl, 0.04% TritonX‐100), dechorionated in bleach (1:3 in EW buffer) for 2-3 min, and washed several times with milliQ water. Dechorionated embryos were then washed once with cold DEI buffer (10 mM HEPES pH 7.4, 5 mM DTT and 1x complete protease inhibitor from Roche) followed by homogenization in 1-2 embryo volumes of DEI buffer on ice. The homogenate was centrifuged at 10,000g for 10 min at 4°C. The intermediate cytosolic fraction was carefully collected, avoiding the upper lipid layer and the pellet. Glycerol was added to 10%, and extracts aliquoted, snap frozen and stored at -80°C. Extracts were submitted to RNA-immunoprecipitation: protein-A Dynabeads (Invitrogen) containing affinity purified anti-Dicer-2 antibody to their maximum binding capacity (2.4 µg antibody per 10 µl beads) were prepared by washing beads with 10 volumes of IPP 500 buffer (20 mM HEPES, 500 mM NaCl, 1.5 mM MgCl2, 0.5 mM DTT and 0.05 % NP-40) followed by incubation with anti-Dicer-2 antibody for 30 min at room temperature. Antibody-bound beads were washed twice with 10 vol of IPP 500 and IPP containing 150 mM NaCl (IPP 150). A similar procedure was followed to obtain beads with IgG used as negative control.   Embryo extracts were pre-cleared with empty beads equilibrated in IPP 150 for 30 min at 4°C in the presence of 1x complete protease inhibitor cocktail (Roche). Pre-cleared extracts (300-500 µg) were then added to 60 µl of antibody-bound beads in a final volume of 780 µl of IPP 150, and incubated at 4°C for 4h on a rotating wheel. Following IP, beads were pelleted, washed four times with 5 vol of IPP 150.

tag: developmental stage

value: 90 minute embryos

tag: rip antibody


title: Input replicate 4


title: CR20 6h CB1

tag: time


title: Fecal pellet DNA from chow-fed mice, 2


title: Input replicate 1


title: Fecal pellet DNA from chow-fed mice, 3


title: IgG IP replicate 6

value: IgG antibody


title: 26-IT


title: Fecal pellet DNA from chow-fed mice, 1

value: Fecal pellet


title: IgG IP replicate 5


title: CR20 6h BS1


title: 26-N


title: CR20 6h CL2


title: 26-VT


title: 23-N


title: SCC59A_LINC00094_siRNA

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

data_processing:
The samples were sequenced with the HiSeq3000 instrument using single-end sequencing with 50bp read length. All sample libraries were pooled in one sequencing lane.
The reads obtained from the instrument were base called using instrument manufacturer’s Bcl2fastq2 version 2.17 base calling software and aligned against the human reference genome (GRCh37 assembly).
The reads were aligned against the reference genome using Star version 2.5.2b. Then the reads were associated with known genes and the number of reads associated with each gene was counted using subreads package (v. 1.5.1).
The counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package (R version 3.3, Bioconductor version 3.3).
Assembly: GRCh37
Supplementary files format and content: For statistical testing the data were further log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalized counts are represented as RPKM values.

source_name: Cutaneous squamous cell carcinoma 59A

growth_protocol: cSCC cells were cultured and incubated at 37C.

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile RNAse-free water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
RNA libraries were prepared for sequencing using  Illumina TruSeq Stranded total RNA Sample Preparation Kit according to the manufacturer's instructions.

treatment_protocol: cSCC cell lysates were harvested 72 hours after siRNA-treatment and serum-starvated 24 hours before harvesting.

value: Cutaneous SCC

tag: source

value: Derived from cSCC tumors

tag: metastasis status

value: Metastatic cSCC cells

value: LINC00094 siRNA


title: Input replicate 5


title: CR20 6h CL1


title: Input replicate 2_3


title: Fecal pellet DNA from chow-fed mice, 4

tag: strain


title: IgG IP replicate 3


title: SCC59A_ctr_siRNA

value: Negative control siRNA


title: 22-VT

value: HNSCC Patient

value: Primary Tumor (Invasive front)


title: CR20 6h CTRL

value: Chondrocytes


title: SCC12A_LINC00094_siRNA

source_name: Cutaneous squamous cell carcinoma 12A

value: Primary cSCC cells


title: IgG IP replicate 2


title: CR20 6h BS2


title: CR19 24h CB2


title: 20-Neck


title: 22-N

value: adjacent normal tissue


title: SCC12A_ctr_siRNA


title: CR19 24h CB1


title: IgG IP replicate 4


title: 20-IT


title: IgG IP replicate 1


title: Dicer2 IP replicate 6

value: Dicer-2 antibody


title: SCC7_LINC00094_siRNA

source_name: Cutaneous squamous cell carcinoma 7


title: Dicer2 IP replicate 5


title: CR19 24h BS1

source_name: Chondrocytes


title: 20-VT


title: SCC7_ctr_siRNA


title: 16-Neck

value: Lymph node metastatic tumor


title: Dicer2 IP replicate 4


title: mutant zebrafish-3

city: Wuhan

first: Shan

last: Zhong

address: Donghu Road 185

institute: Wuhan University

data_processing:
Data were filtered using Trimmomatic version 0.36.
RNA-seq reads were aligned to the Danio rerio genome (GRCz11)assembly using STAR version 2.7.
Counts were calculated using featureCounts v1.5.2.
Assembly: z11
Supplementary files format and content: tab-delimited text files include raw counts of each gene for each Sample.

source_name: liver

growth_protocol: The WT and mutant zebrafish were cultured at a constant water temperature of 28°C, the pH value of the water quality maintained by the culture equipment was 7.0-8.0, the salinity control range was 0.25-0.75‰, and the dissolved oxygen was maintained at or not lower than 6.0 mg/L. The nitrate concentration does not exceed 200 ppm.

extract_protocol: Total RNA was extracted from zebrafish liver tissue using the RNA extraction kit produced by Nanjing Novizan Biotechnology Co., Ltd.

treatment_protocol: Obtaining scd mutant zebrafish using Crispr Cas9 knockout technology

value: liver

tag: genotype

value: scd knock out


title: CR19 24h CL2


title: mutant zebrafish-2


title: CR19 24h CL1


title: 16-N


title: mutant zebrafish-1


title: Dicer2 IP replicate 3

value: 90 minute embryos


title: Dicer2 IP replicate 2


title: WT zebrafish-3

value: WT


title: 13-IT

value: Primary Tumor (Inner site)


title: CR19 6h CB2


title: 13-N


title: CR19 6h CB1


title: CR19 24h BS2


title: 20-N


title: CR19 6h BS2


title: WT zebrafish-1


title: 6-VT


title: PCDH_S107_L004

city: Hefei

first: yang

last: xia

state: Anhui

address: Sanlian

institute: Anhui medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: DMEM medium mixed with 10% fetal bovine serum

extract_protocol:
Retinas 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 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Using TRIzol reagent

value: Colon

tag: treatment

value: Control


title: 6-N

tag: cell type


title: 58-VT

tag: disease state


title: CR19 6h CL2


title: VAT_NLRP3_KO_old_2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
DESeq2_norm_old_young_VAT.txt
B56

data_processing:
Illumina Casava1.82 software used for basecalling and demultiplexing.
After demultiplexing, raw reads were pseudoaligned to the murine transcriptome (mm10, GENCODE general assembly release vM16) using Kallisto with default settings
Based on the pseudoalignment estimated by Kallisto, transcript levels were quantified and counts were imported into R using tximport. Transcript information was summarized on gene-level. We imported the resulting dataset and performed the downstream analysis using the DESeq2 pipeline.
Genome_build: mm10
Genome_build: transcriptome build: mm10, GENCODE general assembly release vM16
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome

source_name: visceral adipose

extract_protocol:
Batch1 :  Cells were stored in Trizol and extracted using Qiagen mini kit according to recommendations from manufacture;    Batch2:  Cells were sorted into RLT buffer and extracted using Qiagen mini kit according to recommendations from manufacture
mRNA is purified from approximately 500pg-1ng of total RNA using the Clontech SMARTer Ultra Low V4 RNA Kit.  The kit utilizes an oligo(dT) primer, which primes the first-strand synthesis reaction.  SPRI beads are used to selectively bind first-strand cDNA.   ss cDNA is then amplified by LD PCR to make ds cDNA and is again purified using SPRI beads.  During amplification the poly A sequence serves as the universal priming site for end-to-end cDNA amplification.  Thus, cDNA without these sequences, such as prematurely terminated cDNAs, containing genomic DNA, or cDNA transcribed from Poly A minus RNA, are not exponentially amplified.  The beads are then washed with 80% ethanol and eluted in purification buffer.  The full-length cDNAs are then sheared using the Covaris, which results in 200-500bp DNA fragments.  The fragmented cDNA library is then end-repaired, A-tailed, and adapters are ligated. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

value: old

value: visceral adipose

value: B cells

tag: cohort


title: CR19 24h CTRL

tag: patient


title: MCF10A dosage effect

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

data_processing:
cellranger ranger2.1.1  used for processing and mapping the raw sequnce reads
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mammary epithelium

extract_protocol:
MCF10A cells were first labelled with Perturb-seq vectors without sgRNA expression using guide barcodes (GBCs) that were originally used to identify sgRNAs. Barcoded MCF10A cells were then treated with different dosages of TGF-β for 14 days and single cells were prepared and mixed at a concentration of approximately 1,000 cell/μL in ice-cold PBS.
RNA-Seq library was prepared using 10x Chromium Single Cell 3' –end Reagent Kits User Guide (v2 Chemistry)
Libraries were sequenced using paired-end sequencing (26bp Read 1 and 98bp Read 2) with a single sample index (8bp) on the Illumina HiSeq 2500

value: Mammary epithelium

tag: cell line

value: Normal human mammary epithelial cell

value: stimulated with TGFbeta  at concentrations of 0, 12.5, 25, 50, 100, 200, 400, 800 pM for 14 days


title: 2-IT

value: HNSCC Patient

tag: unique patient number (upn)


title: VAT_NLRP3_KO_old_3

description:
DESeq2_norm_old_young_VAT.txt
B57

tag: tissue


title: 2-N

value: adjacent normal tissue


title: VAT_WT_old_2

description:
DESeq2_norm_old_young_VAT.txt
B54

tag: age


title: Spleen_NLRP3_KO_old_4

description:
DESeq2_norm_old_young_VAT.txt
B47

source_name: spleen

value: spleen


title: 58-IT


title: PCDH_FIT_S108_L004

value: treated with overexpres FIT


title: Dicer2 IP replicate 1

value: Dicer-2 antibody


title: CR19 6h CL1

value: Chondrocytes

tag: cl treatment

tag: bs treatment


title: 58-N


title: CR19 6h CTRL


title: WT zebrafish-2

value: liver


title: 1-IT


title: 6-IT


title: Spleen_NLRP3_KO_old_3

description:
DESeq2_norm_old_young_VAT.txt
B46


title: 1-VT

value: Primary Tumor (Invasive front)


title: CR18 24h CB2


title: 56-Neck

value: Lymph node metastatic tumor


title: 56-VT


title: CR19 6h BS1


title: CR18 24h CB1


title: Spleen_NLRP3_KO_old_2

description:
DESeq2_norm_old_young_VAT.txt
B45


title: 1-N


title: CR18 24h BS2


title: 56-IT

value: Primary Tumor (Inner site)


title: 56-N


title: Spleen_NLRP3_KO_old_1

description:
DESeq2_norm_old_young_VAT.txt
B44


title: Spleen_WT_old_4

description:
DESeq2_norm_old_young_VAT.txt
B43

value: WT


title: Tag-seq_Human_rep2

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

description: Mitochondrial RNA

data_processing:
Adapter trimming was performed by cutadapt 1.18
Cappable-seq and TagRNA-seq reads were aligned to human genome using Hisat2
5'-end coordinates were extracted using samtools and bedtools
TSS (transcription start sites) counts (from Cappable-seq) and TSS+PSS(processing starting sites) counts (from TagRNA-seq) were normalized to total mitochondrial reads
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalized Cappable-seq and TagRNA-seq bedgraph files

source_name: HeLa cell

extract_protocol:
Mitochondria isolation from mouse heart was performed as described previously (PMID: 31588022). For Hela cells, cells at about 80% confluence were harvested, and spin down at 500g for 3min at 4°C, washed once with cold PBS. Cell pellet was resuspended in 1 ml of lysis buffer (20mM Tris-Cl pH7.6, 220mM mannitol, 70mM sucrose, 1mM EDTA, 1xprotease inhibitor, 1mg/ml BSA) and incubated on ice for 15 min, then transferred to glass Dounce homogenizer (1 ml), the cells were broken by 20-25 strokes, followed by centrifugation at 1200g for 3 min at 4°C. The supernatant was transferred to a new Eppendorf tube and spin at 14,000g for 3 min at 4°C to pellet the crude mitochondria. Mitochondrial RNA was prepared from crude mitochondria by Trizol extraction following manufacture’s instructions, after ethanol precipitation, the RNA was dissolved in nuclease-free water and treated with RNase-free Dnase I (Thermol) at 37°C for 20 min, followed by purification with Quick RNA Micro prep column (Zymo Research).
Library construction was performed by Vertis Biotechnologie (Freising, Germany)

treatment_protocol: HeLa cells were grown at 37°C, 5% CO2 in DMEM GlutaMAX™supplemented with 10% fetal bovine serum (FBS)

value: HeLa


title: CR25 6h BS2

first: Christelle

last: Sanchez

address: Quai G. Kurth 45

institute: ULiege

data_processing:
Raw data were demultiplexed into individual libraries. After filtering out reads mapping to rRNA, tRNA, mitochondrial RNA, and other contaminants (e.g., adapters, etc.) using bowtie2
Assembly: GRCh38
Supplementary files format and content: reads were aligned onto the human reference genome (GRCh38 and Ensembl 105 annotation) and quantified with Star to give the Counts file.

extract_protocol:
18 beads were pooled, degelified in 0,1M cold citrate and cells were homogenized in 600 µl RTL lysis buffer (Qiagen) then extract using Rneasy mini kit from Qiagen according to the manufacturer's instructions. Dnase step were performed during extraction. Samples were eluted in 30 µl RNase free H2O
0,1 µg of RNA from each culture condition was used for this analysis. Libraries were prepared with the Illumina Truseq stranded mRNA sample prep kit according to the manufacturer's instructions


title: Spleen_WT_old_3

description:
DESeq2_norm_old_young_VAT.txt
B42

value: old


title: Spleen_WT_old_2

description:
DESeq2_norm_old_young_VAT.txt
B41

value: B cells


title: CR18 24h CL1


title: Cap-seq_Human_rep2

description: Mitochondrial RNA


title: Spleen_WT_old_1

description:
DESeq2_norm_old_young_VAT.txt
B40


title: CR18 24h CTRL


title: CR18 24h BS1


title: Cap-seq_Human_rep1

description: Mitochondrial RNA


title: Cap-seq_Human_siSSBP1_rep2

description: Mitochondrial RNA

data_processing:
Adapter trimming was performed by cutadapt 1.18
Cappable-seq reads were aligned to human or mouse genome using bowtie2
5'-end coordinates were extracted using samtools and bedtools
TSS (transcription start sites) counts were normalized to total mitochondrial reads
Relative Log2 fold changes across a 25 bp window were calculated using normalized TSS from biological repeats plus a pseudocount of one in HeLa cells (siSSBP1 vs siCtrl) or in mouse heart( L/L, cre vs L/L)  with bigwigCompare v3.1.3
Genome_build: GRCm38 or GRCh38
Supplementary_files_format_and_content: Normalized TSS bedgraph file

source_name: Hela cell

growth_protocol: All mice maintaining an inbred C57BL/6N nuclear background were housed in a 12-hour light/dark cycle at 21°C and fed ad libitum on a standard mouse food (ssniff RM-H Low-Phytoestrogen). The health status of the animals is specific pathogen free according to the Federation of the European Laboratory Animal Science Association (FELASA) recommendations.

extract_protocol:
Mitochondria isolation from mouse heart was performed as described previously (PMID: 31588022). For Hela cells, cells at about 80% confluence were harvested, and spin down at 500g for 3min at 4°C, washed once with cold PBS. Cell pellet was resuspended in 1 ml of lysis buffer (20mM Tris-Cl pH7.6, 220mM mannitol, 70mM sucrose, 1mM EDTA, 1xprotease inhibitor, 1mg/ml BSA) and incubated on ice for 15 min, then transferred to glass Dounce homogenizer (1 ml), the cells were broken by 20-25 strokes, followed by centrifugation at 1200g for 3 min at 4°C. The supernatant was transferred to a new Eppendorf tube and spin at 14,000g for 3 min at 4°C to pellet the crude mitochondria. Mitochondrial RNA was prepared from crude mitochondria by Trizol extraction following manufacture’s instructions, after ethanol precipitation, the RNA was dissolved in nuclease-free water and treated with RNase-free Dnase I (Thermol) at 37°C for 20 min, followed by purification with Quick RNA Micro prep column (Zymo Research).
Library construction was performed by Vertis Biotechnologie (Freising, Germany)
Cappable-seq

treatment_protocol: HeLa cells were grown at 37°C, 5% CO2 in DMEM GlutaMAX™supplemented with 10% fetal bovine serum (FBS). For siRNA transfections, HeLa cells were reverse transfected with 10 nM of indicated siRNA using Lipofectamine RNAiMAX. Experiments were performed at 72 hours after transfection.

value: 3 days


title: VAT_NLRP3_KO_old_1

description:
DESeq2_norm_old_young_VAT.txt
B34

value: visceral adipose


title: yeast cells, H10423 rep3

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description:
salmon.merged.gene_counts.rds
SupplementalFileRNA.csv

data_processing:
Nextflow nf-core rna-seq pipeline was used to process the fastq files (doi: 10.5281/zenodo.1400710) with the   --save_reference --trim_nextseq --remove_ribo_rna options.
The pipeline uses Trim Galore! for trimming and quality control.
The pipeline uses the STAR aligner to map reads.
The pipeline uses salmon to quantify the reads.
DESeq2 was used for differential expression analysis.
Genome_build: NCBI assembly ASM205788v1,  SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: salmon.merged.gene_counts.rds (Output of salmon quantification, R object)
Supplementary_files_format_and_content: SupplementalFileRNA.csv (DESeq2 output)

source_name: yeast cells

growth_protocol: Cells were grown in YPD for 24 hours at room temperature and then were transferred to BYTA (1% yeast extract, 2% bactotryptone, 1% potassium acetate, 50mM potassium phtalate) media at OD600 = 0.3. After growing at 30C for ~16.5 hours, cells were washed twice with water and resuspended in SPO (0.3% potassium acetate) media at OD600 = 1.9. Then the cultures were incubated at 30C.

extract_protocol:
1.5 ml of meiotic culture was collected for each sample. RNeasy Mini Kit (Qiagen) was used for total RNA extraction following the kit`s instructions for mechanical extraction.  We assesed the quality of RNAs with Tapestation 2200. We started with 1.2 µg of total RNA for library preparation. polyA enrichment was perfomed using Sera-Mag oligo(dt) Magnetic particles (Sigma-Aldrich).
cDNA synthesis was achieved in similar manner to as in (Parkhomchuk et al., 2009).  Libraries were prepared using Illumuna TruSeq adapters, and quantified by qPCR. Libraries were sequenced at NYU Genome Center with NextSeq 500 to produce pair-ended 75 bp reads.

tag: cell stage

value: meiosis


title: yeast cells, H10423 rep1


title: yeast cells, H10423 rep2


title: yeast cells, H10355 rep3


title: VAT_WT_old_1

description:
DESeq2_norm_old_young_VAT.txt
B30


title: Cap-seq_Human_siSSBP1_rep1

description: Mitochondrial RNA


title: CR18 6h CB1

city: Liège

tag: time


title: yeast cells, H10355 rep2


title: VAT_WT_young_3

description:
DESeq2_norm_old_young_VAT.txt
B29

value: young


title: Tag-seq_Human_rep1

description: Mitochondrial RNA


title: CR18 6h CB2


title: CR18 24h CL2


title: yeast cells, H10355 rep1


title: VAT_WT_young_2

description:
DESeq2_norm_old_young_VAT.txt
B28


title: Cap-seq_Human_siCtrl_rep2

description: Mitochondrial RNA


title: Patient10_CD14_RNA

city: Manchester

first: chenfu

last: shi

address: AV Hill Building, Upper Brook Street, room 1.023

institute: the university of manchester

description: RNA-seq library generated using Quant-seq

data_processing:
pCHiC sequencing data was filtered and the adapters were removed using fastp v0.19.4
pCHiC mapping was performed using HICUP 0.7.4 on hg38 genome. CHICAGO 1.13.1 was used to identify significant interactions
RNA-seq sequencing data was filtered and the adapters were removed using fastp v0.19.4
RNA-seq reads were mapped using STAR v2.7.3a on hg38 gencode v32 annotation
RNA-seq counts were generated using Htseq
Assembly: hg38
Supplementary files format and content: .RDs files contain chicago classes containing data for the specified samples
Supplementary files format and content: washU_track.txt.gz files contain the longrage interaction files for washu browser
Supplementary files format and content: csv.gz files contain the data from the differential interaction analysis from chicdiff
Supplementary files format and content: .count file contain the counts from the RNA-seq

source_name: Primary CD14 Monocytes

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from blood using Ficoll density gradient centrifugation. EasySep Human CD14+ Positive selection kit (StemCell Technologies, ref:17858) was used to isolate CD14+ cells from PBMCs and, subsequently, Easysep CD4+ T cell isolation kit (StemCell Technologies, ref:17952) was used to isolate CD4+ T cells from the remaining PBMCs, according to the manufacturer’s instructions.
pCHiC: 5-10 million isolated CD4+ T cells and CD14+ monocytes were crosslinked for 10 min in 1% formaldehyde and agitated at room temperature, the reaction was then quenched with ice cold 0.125 M glycine for 5 min. Crosslinked cells were washed in ice-cold PBS, and the supernatant was discarded, the pellets were then stored at -80ºC.  Each Hi-C library was prepared from fixed cells following the Arima HiC kit (Arima Genomics) and the KAPA HyperPrep kit (KAPA Biosystems) following the manufacturer’s protocol. Briefly, crosslinked cells were lysed, and DNA was digested by two different restriction enzymes, and ligated.  The ligated DNA was reverse-crosslinked and fragmented by sonication (Covaris S220), followed by DNA size selection, biotin enrichment, adaptor ligation, and final library amplification. A quality control step to determine the number of PCR cycles needed for library amplification was performed for each library using the NEBNext Library Quant kit (NEBNext, ref: E7630). Final quality and quantity were assessed by Bioanalyzer 2100 (Agilent) and Qubit (Thermo Fisher).  Hi-C samples were then hybridized with the SureSelect custom capture library by following Agilent SureSelectXT HS reagents (ref: G9702A, G9496A) and protocols (ref: G9702-9000). Briefly, target regions are hybridized with designed probes, followed by capture enrichment of these regions through streptavidin pulldown using Dynabeads MyOne Streptavidin T1 (ThermoFisher, ref: 65601). Post-capture amplification was carried out using nine PCR cycles. Final quality and quantity were assessed by Bioanalyzer 2100 (Agilent) and Qubit (Thermo Fisher).   RNA: A total of 0.5 million purified cells was resuspended in 700 uL Qiazol lysis reagent (QIAGEN, ref: 79306) to isolate RNA, then 140 uL of chloroform was added. After centrifugation at 12000 x g for 15 min, approximately 350 uL of the upper layer containing the RNA was transferred and mixed with 525 uL of 100% ethanol. RNA isolation was continued from this point using the RNeasy microkit (QIAGEN, ref: 74004) reagents and protocol. Final quantity was assessed by Qubit (Thermo Fisher). Libraries for RNA-seq were prepared using Illumina Truseq Stranded Total RNA reagents and protocol, except for Control 1 CD4+ and CD14+ samples, for which library preparation failed. Library quality and quantity was assessed by Bioanalyzer. The 28 libraries generated were sequenced using three lanes on Illumina HiSeq4000, generating 75 bp paired-end reads, and leading to an average of 30 million reads per sample (Genomics Facility, University of Manchester).

tag: disease

value: Systemic sclerosis

value: Primary CD14 Monocytes