title: T24-si-circSLC38A1-3 CUT&Tag

data_processing:
Library strategy: CUT-Tag-Seq
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. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome. Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
Peaks were annotated by using homer's annotatePeaks.pl.
Count the results of the annotations and plot the distribution results using R.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

extract_protocol: To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

treatment_protocol: Cells were treated with a control scramble (scr) siRNA or a siRNA that specifically knock down the expression of circSLC38A1.48h after transfection, cells were harvested and pre-treated with ConA-beads.Then we use digitonin to increase the permeability of the T24 cell membrane. Added anti-ILF3 binds to the target chromatin protein between nucleosomes in the genome, and the excess was washed away. A second antibody was added to tether pA-Tn5 transposome at antibody-bound sites. After washing away excess transposome, addition of Mg++ activates the transposome and integrates adapters at chromatin protein binding sites. After DNA purification genomic fragments with adapters at both ends are enriched by PCR. Then sequencing was performed and target genes were analyzed.

tag: antibody


title: MCOHS_14

status: Public on Oct 01 2022

type: SRA

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

library_source: genomic

data_processing:
library strategy: 16S rDNA seq
Illumina HiSeq software used for basecalling.
Take the method of removing low quality by window, the specific operation is as follows: set a window of 25 bp, if the average quality value of the window is less than 20, the back-end bases will be truncated from the window; the read length after truncation is lower than the original read length For 75%, remove the entire sequence.
Remove linker contamination of reads (default adapter sequence and read sequence have an overlap of 15 bp, set to 15 bp, and allow the number of mismatches to be 3);
Remove reads containing N;Remove low-complexity reads (default reads with continuous base length ≥10 are low-complexity reads) finally, get the Cleandata
Splice the reads into tags through the overlap relationship between the reads; cluster the tags into OTUs and compare them with the database, and annotate species; based on the OTU and annotation results, perform sample species complexity analysis, analysis of species differences between groups, and association analysis. Model prediction, etc.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression

molecule: genomic DNA

organism: Mus musculus

source_name: colon

extract_protocol:
COLON were removed, than quikly removed the contents and frozen in the luquid nitrogen, and extract the total DNA to analyze the microbial diversity
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

tag: strain

value: ICR

tag: tissue

value: colon

tag: age

value: 10 weeks

tag: treatment

value: High fat diet & STZ


title: consi3

city: Hangzhou

first: Wenqi

last: Diao

state: Zhejiang

address: 88 JieFang Road

department: Department of Respiratory and Critical Care Medicine

institute: Second Affiliated Hospital of Zhejiang University School of Medicine

description: control-siRNA HBE-rep-3

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing sequencing adapter;
removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%
removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to reference genome (GRCh38) using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_exp.csv: Expression level of gene was calculated by RSEM (v1.2.12).

molecule: total RNA

organism: Homo sapiens

source_name: control-siRNA HBE-3

growth_protocol: HBE cells were purchased from American Type Culture Collection (CRL-2741), and were cultured in RPMI 1640 (Gibco, C11875500BT) with 10% FBS (Gibco, 10082147) and 1% penicillin-streptomycin (Beyotime Biotechnology) in 5% CO2 at 37 ̊C.

extract_protocol:
HBE cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80℃ under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The siRNA transfection was performed with the transfection reagent (GenMute™ siRNA Transfection Reagent, SignaGen Laboratories) following the manufacturer’s protocol. Briefly, 5×10^4 cells were placed in each well of 6-well plates for 18 h prior to transfection. The siRNA in 1 ml growth medium were incubated with HBE cells for 5 h. The transfection medium was removed and replaced with 2ml fresh growth medium.

tag: cell type

value: human bronchial epithelial (HBE) cell line

tag: sirna

value: control


title: consi2

description: control-siRNA HBE-rep-2

source_name: control-siRNA HBE-2


title: ES_ChIL100C_S2P_3

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

data_processing:
Library strategy: ChIL-seq
The mouse reference genome and annotations were downloaded from Ensembl (version GRCm38.dna.primary_assembly.fa and GRCm38.101.gtf).
Paired-end sequencing reads were trimmed using cutadapt (version 3.4) with parameters -a CTGTCTCTTATA -A CTGTCTCTTATA --pair-filter=any --minimum-length=20.
Trimmed reads were mapped to the reference genome using bowtie2 (version 2.3.5) with parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 500.
Aligned reads were filtered by quality using samtools (version 1.3) with parameter -q 12. Read pairs were read in to R (version 3.6.3) using readGAlignmentPairs from the GenomicAlignment package (version 1.22.0) and fragments were filtered for fragments that have both unique start and end positions.
Coverage vectors were created using the coverage function from GenomicRanges package (version 1.38.0) and were normalized by the number of fragments and multiplied by a million. Normalized coverage were exported as bigwig files using the rtracklayer package (version 1.46.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig files of normalized coverage

source_name: mES-cells

extract_protocol:
ChIL-seq was performed following a modified protocol of the original ChIL-seq (PMID: 30532068). For ES cells, 100 or 1000 cells were plated on gelatin coated 96-well plates and let to attach for 16h in culture. Cells were then fixed with 1% formaldehyde in DMEM for 5 min and permeabilized with 1% Triton X-100 in PBS for 20min. Embryos were fixed using the same procedure. Samples were incubated in 2% BSA in PBS with anti-Pol II Ser5P (Abcam, ab5131) or anti-Pol II Ser2P (Abcam, ab5095) at 2μg/ml for 6h at room temperature, washed three times in 0.5% BSA in PBS and then incubated at 4 °C overnight in 2% BSA in PBS containing 500mM NaCl and the ChIL probe at 2μg/ml. After washing in PBS for ES-cells or PBS containing 0.1% BSA for embryos, samples were incubated in 50 µl Tn5 solution (50mM HEPES-KOH, pH 7.2, 0.1M NaCl, 0.1mM EDTA, 1mM dithiothreitol, 0.1% Triton X-100 and 10% glycerol) containing 0.5µl HActive™ Tn5 transposase (Glow Biologics, GBRP-TN5) for 10min at room temperature. Tn5-MEDS-B oligo (2 µM) was then added at 0.5 µl per well in 1× dialysis buffer (50mM HEPES-KOH, pH 7.2, 0.1M NaCl, 0.1mM EDTA, 1mM dithiothreitol, 0.1% Triton X-100 and 10% glycerol) and incubated for 60min at room temperature. Samples were then washed in 1× dialysis buffer and three times in PBS for ES-cells or PBS containing 0.1% BSA for embryos, incubated in 100 µl 1× TAPS-DMF buffer (10mM TAPS-NaOH, pH 8.5, 5mM MgCl2 and 10% N,N-dimethylformamide) for 1h at 37 °C, and washed at three times in PBS for ES-cells or PBS containing 0.1% BSA for embryos. To stop the Tn5 reaction, cells were incubated in 100 µl 0.2% SDS for 10min at room temperature or embryos were incubated in 0.1% BSA/PBS containing 50mM EDTA at 50 °C for 30 min. After washing at three times in PBS for ES-cells or PBS containing 0.1% BSA for embryos, samples were incubated in 50 µl reaction mixture (200U T4 DNA ligase, NEB, and 1.5U T4 DNA polymerase, NEB, in 1× T4 DNA ligase reaction buffer containing 0.1 mM dNTP) for 30min at room temperature. After discarding the solution, for ES cells, 100µl 0.2% SDS were added to remove DNA-bound enzymes, followed by incubation for 10min at room temperature and three washes in PBS. For embryos, 0.1% BSA/PBS containing 50mM EDTA was added for 30 min at 50 °C, and then washed at three times in 0.1% BSA/PBS. In situ transcription was then carried out using T7 RNA polymerase (800U per well; NEB) for 20h at 37 °C. The samples were treated with DNase I (2.5U per well; Thermo) for 30min at 37 °C and RNA was extracted using a Qiagen MinElute Cleanup kit.
Purified RNA was reverse-transcribed with SMARTScribe reverse transcriptase (Takara) following the manufacturer’s instructions and the resulting cDNA was amplified by Prime star GXL (Takara) by 14 cycles for 1000 cells with anti-Pol II Ser5P antibody, 15 cycles for 1000 cells with anti-Pol II Ser2P antibody, 16 cycles for 100 cells or embryos with anti-Ser5P antibody, or 17 cycles for 100 cells or embryos with anti-Ser2P antibody. After amplification, small fragments (<150bp) were removed using Gene read Size selection kit (Qiagen) and large size of fragments (>600bp) were removed using AMPure XP beads (Beckman Coulter). The amplified DNA was purified using AMPure XP beads and the quality of the libraries was assessed using a Bioanalyzer 2100 (Agilent Technologies). Samples were paired-end sequenced at PE150 on an Illumina NovaSeq 6000 platform

tag: protocol

value: ChIL-seq

tag: assay

value: S2P (Abcam, ab5095)


title: ES_ChIP_IgG_2

data_processing:
The mouse reference genome and annotations were downloaded from Ensembl (version GRCm38.dna.primary_assembly.fa and GRCm38.101.gtf).
Paired-end sequencing reads were trimmed using cutadapt (version 3.4) with parameters -a CTGTCTCTTATA -A CTGTCTCTTATA --pair-filter=any --minimum-length=20.
Trimmed reads were mapped to the reference genome using bowtie2 (version 2.3.5) with parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 500.
Aligned reads were filtered by quality using samtools (version 1.3) with parameter -q 12. Read pairs were read in to R (version 3.6.3) using readGAlignmentPairs from the GenomicAlignment package (version 1.22.0) and fragments were filtered for fragments that have both unique start and end positions.
Coverage vectors were created using the coverage function from GenomicRanges package (version 1.38.0) and were normalized by the number of fragments and multiplied by a million. Normalized coverage were exported as bigwig files using the rtracklayer package (version 1.46.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig files of normalized coverage

extract_protocol:
ES cells were fixed with 1% formaldehyde in DMEM at 37 °C for 10 min, neutralized in DMEM containing 125 mM glycine at room temperature for 5 min and washed with PBS three times. Fixed cells were collected with 2ml soft lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA and 0.1% NP-40 10% Glycerol) and centrifuged at 3000 rpm for 15 min. The cell pellet was resuspended in 100µl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), and sonicated. Soluble chromatin was diluted in 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167mM NaCl) and incubated with 2µg anti-Pol II Ser5P (Abcam, ab5131), anti-Pol II Ser2P (Abcam, ab5095) antibodies or IgG at 4 °C overnight. Bound chromatin was purified on magnetic beads after washings in low salt buffer (20 mM Tris-HCl, pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), high salt buffer (20 mM Tris-HCl, pH 8.0 ,2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1% Triton X-100) and LiCl buffer (250 mM LiCl, 1% NP-40, 1% sodium deoxycholate). Chromatin was eluted in 1% SDS, 100mM NaHCO3 at 65 °C, reverse-crosslinked and was purified by phenol-chloroform extraction.
ChIP–seq libraries were prepared using a NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and the library quality was assessed using a 2100 Bioanalyzer (Agilent). Samples were paired-end sequenced at PE150 on an Illumina Hiseq 4000.

value: ChIP-seq

value: IgG


title: T24-si-circSLC38A1-2 CUT&Tag

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

source_name: Human bladder cancer cells

tag: cell line

value: Human bladder cancer cells

value: si-circSCL38A1 transfection


title: consi1

description: control-siRNA HBE-rep-1

source_name: control-siRNA HBE-1


title: ES_ChIP_IgG_1


title: MCOHS_11


title: MCOHS_9


title: cgassi3

description: cgas-siRNA treated HBE-rep-3

source_name: cgas-siRNA treated HBE-3

value: cGas


title: T24-si-circSLC38A1-1 CUT&Tag


title: ES_ChIL100C_S2P_2


title: ES_ChIL100C_S2P_1


title: cgassi2

description: cgas-siRNA treated HBE-rep-2

source_name: cgas-siRNA treated HBE-2


title: MCOHS_7


title: ES_ChIL100C_IgG_3


title: T24-si-NC-2 CUT&Tag

value: control scramble siRNA transfection


title: T24-si-NC-1 CUT&Tag


title: MCOHS_2


title: ES_ChIL100C_IgG_2


title: cgassi1

description: cgas-siRNA treated HBE-rep-1

source_name: cgas-siRNA treated HBE-1


title: MCOcon_12


title: ES_ChIL100C_IgG_1


title: bm-MPC_Control growth media_48hrs_rep1

type: RNA

city: London

first: Jina

last: Kum

state: ON

address: 1151 Richmond Street

country: Canada

institute: Western University

description: Control media

hyb_protocol: 5.5 ug cDNA is fragmented and labelled, and a volume that should be equivalent to 2.3 ug of fragmented and labelled ss-cDNA is hybridized to the Clariom S Human Array. The GeneChip Fluidics Station 450 is used to stain and wash the arrays.

scan_protocol: Scanning is performed on the GeneChip Scanner 3000.

data_processing:
SST-RMA gene-level probeset summary with standard settings of the Thermo Fisher Scientific Transcriptome Analysis Console (TAC) software.
Normalized data matrix contains: TAC (4.0.2.15) Tukey biweight average of the expression levels of the probe selection region/junction probeset for samples from condition.

label: Biotin

source_name: Human bm-MPCs, control growth media, 48 hours

label_protocol: 100 ng input RNA to cRNA to cDNA. Samples are processed using the Applied Biosystems WTPlus reagent kit.

growth_protocol: Human mesenchymal progenitor cells derived from bone marrow mononuclear cells were seeded on tissue culture plates in low glucose Dulbecco’s Modified Eagle Medium, supplemented with 10% fetal bovine serum and 1X PSF.

extract_protocol: Total RNA was isolated using RNeasy Mini Plus Kit (Qiagen)

treatment_protocol: To induce adipogenic differentiation, bm-MPCs were plated at a density of 40,000 cells/cm^2.  The next day, cells were exposed to adipogenesis-inducing media (ADP) for 48 hours.

value: Bone marrow

value: bone marrow-derived mesenchymal progenitor cells

value: Control media


title: MCOcon_11

value: ICR


title: SSc

city: Serdang

first: Siti Nor Ani

last: Azaman

state: Selangor

address: Jalan UPM

country: Malaysia

institute: Universiti Putra Malaysia

description: small RNA

data_processing:
CLC genomic workbench 7.0
Illumina adapter sequences and sequences tags of length less than 17 and more than 27 were removed
miRNA sequences were aligned to miRNA database (miRBase-21)
Statistical analysis: EDGE test, t-test and Baggerley's test
Genome_build: miRBase-21
Supplementary_files_format_and_content: Excel files xlsx containing expression values  and statistical analysis of nomal and stress C. sorokiniana and C. zofingiensis analysed using CLC genomic workbench
OmiRas (tools.genxpro.net/omiras)
Illumina adapter sequences and sequences tags of length less than 17 and more than 27 were removed
miRNA sequences were mapped to Arabidopsis thaliana genome reference sequence (TAIR9) and miRBase-21
Differential expression analysis using DESeq
Genome_build: TAIR9 and miRBase-21
Supplementary_files_format_and_content: Excel files xlsx containing expression values  and statistical analysis of nomal and stress C. sorokiniana and C. zofingiensis analysed using OmiRas

organism: Chlorella sorokiniana

source_name: C. sorokiniana stress sample (replicate 3)

growth_protocol: The cells were first cultivated in Bold’s Basal Medium (BBM) at 27°C under continuous light at a light intensity about 10 µmol photons m-1 s-1 with a shaking speed of 30 rpm.

extract_protocol:
Total RNA was extracted using TRIzol method.
RNA libraries were prepared for sequencing using standard Illumina protocols
NEBNext Multiplex Small RNA Library Prep for Illumina

treatment_protocol: stress was induced at mid log phase of culture by increasing the light intensity than the normal condition (100 µmol photons m-1 s-1) and the addition of 2% of glucose


title: SSa

description: small RNA

source_name: C. sorokiniana stress sample (replicate 1)


title: MCOcon_8

value: colon


title: HEK293T_PRP5-KD_rep2

first: Xiaofeng

last: Zhang

address: Westlake University

institute: Westlake University

data_processing:
Sequencing reads were mapped to human hg19 genome index with STAR (v2.7.7a) (10.1093/bioinformatics/bts635) with parameter settings --outSAMattributes NH HI AS nM NM MD jM jI MC XS --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --twopassMode Basic.
The STAR index files were generated with hg19 genome sequence and Gencode (10.1101/gr.135350.111) annotation file (Ensembl 88 GRCh37).
The generated bam files by STAR then been sorted with samtools (v1.3.1) (10.1093/bioinformatics/btp352).
Alternative splicing analysis was carried out with JuncBASE (v0.6) (10.1101/gr.108662.110) according to the description of the manual. The significantly differential alternative splicing events were defined as those with |ΔPSI|>10 and P-value<0.05.
Genome_build: hg19
Supplementary_files_format_and_content: High confidence collapsed splice junctions in tab-delimited format generated by STAR (v2.7.7a) (10.1093/bioinformatics/bts635).  Nine columns: chromosome, first base of the intron (1-based), last base of the intron (1-based), strand (0: undefined, 1: +, 2: -), intron motif: 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT, 0: unannotated, 1: annotated in the splice junctions database, number of uniquely mapping reads crossing the junction, number of multi-mapping reads crossing the junction, maximum spliced alignment overhang.

growth_protocol: HEK293T cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) , 100 U/mL penicillin, and 100 μg/mL streptomycin at 37 °C in a 5% CO2 incubator.

extract_protocol:
After 48h transfection, cells were washed with PBS, then extract the total RNA using TRIzol reagent.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-01/02) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform (Novaseq 6000 S4) and 150 bp paired-end reads were generated.

treatment_protocol: HEK293T cells were seeded in 6-well plates (40-50% confluence) 24h before transfection. A final siRNA concentration of 30 nm was obtained using Lipofectamine 2000 Reagent.

value: Kidney

value: treated with PRP5 siRNA for 48h

tag: genotype

value: PRP5 knockdown


title: HEK293T_PRP5-KD_rep3


title: ES_ChIL1000C_S5P_3

value: S5P (Abcam, ab5131)


title: MCOcon_10

value: 10 weeks

value: control


title: SSb

description: small RNA

source_name: C. sorokiniana stress sample (replicate 2)


title: NSc

description: small RNA

source_name: C. sorokiniana normal sample (replicate 3)


title: ES_ChIL1000C_S5P_2

value: ChIL-seq


title: MCOcon_7


title: HEK293T_Negative control_rep3

source_name: HEK293T_Negative control

value: treated with negative control siRNA for 48h


title: T24-si-NC-3 CUT&Tag

value: Human bladder cancer cells


title: NSb

description: small RNA

source_name: C. sorokiniana normal sample (replicate 2)


title: ES_ChIL1000C_S2P_3

value: S2P (Abcam, ab5095)


title: ES_ChIL1000C_S5P_1


title: MCOcon_5


title: HEK293T_Negative control_rep2


title: NSa

description: small RNA

source_name: C. sorokiniana normal sample (replicate 1)


title: ES_ChIL1000C_S2P_2


title: MCOcon_4

source_name: colon


title: HEK293T_Negative control_rep1


title: MCOcon_3


title: L1714-Haloferax_volcanii_standing_NOMe_Rep2

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

country: USA

institute: STANFORD UNIVERSITY

data_processing:
read alignment, ATAC-seq and KAS-seq data: Bowtie 1.0.1
read alignment, NOMe-seq/dSMF data: bwameth
bigWig file generation: custom code
Assembly: Haloferax volcanii DS2 haloVolc1
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for KAS-seq and ATAC-seq datasets, bedGraph of methylation percentage for NOMe/SMF datasets
Library strategy: NOME

organism: Haloferax volcanii DS2

growth_protocol: H. volcanii cells were obtained from the DSMZ German Collection of Microorganisms and Cell Cultures GmbH (Cat # 3757), and cultured in Halobacterium media, prepared as follows: 7.50 g casamino acids, 10.00 g yeast extract, 3.00 g sodium citrate, 2.00 g KCl, 20.00 g MgSO4 X 7 H2O, 0.05 g FeSO4 X 7 H2O, 0.20 mg MnSO4 x H2O, and 250.00 g NaCl were mixed with distilled water in a total volume of 1 L. Media was then autoclaved and allowed to cool. H. volcanii was typically grown at 42C, except for where otherwise indicated. Cultures were stored at room temperature when not actively growing.

extract_protocol:
Cells were fixed by adding 37% formaldehyde (Sigma) at a final concentration of 1% and incubating for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M Glycine at a final concentration of 0.25 M. Cells were subsequently centrifuged at 10,000 g for 2 minutes, washed once in 1x PBS, and centrifuged again at 10,000 g for 2 minutes. Fixed cells were resuspended in 100 uL M.CviPI Reaction Buffer (50 mM Tris-HCl pH 8.5, 50 mM NaCl, 10 mM DTT), then treated with M.CviPI by adding 200 U of M.CviPI (NEB), SAM at 0.6 mM and sucrose at 300 mM, and incubating at 30C for 20 minutes. After this incubation, 128 pmol SAM and another 100 U of enzyme were added, and a further incubation at 30C for 20 min was carried out. For dSMF experiments, M.SssI treatment followed immediately, by adding 60 U of M.SssI (NEB), 128 pmol SAM, MgCl2 at 10 mM and incubation at 30C for 20 min. The reaction was stopped by adding an equal volume of Stop Buffer (20 mM Tris-HCl pH 8.5, 600 mM NaCl, 1% SDS, 10 mM EDTA). Crosslinks were reversed overnight at 65C, and DNA was isolated using the MinElute PCR Purification Kit (Qiagen, Cat \# 28006).
Enzymatically labeled DNA was then sheared on a Covaris E220, and converted into sequencing libraries following the EM-seq protocol, using the NEBNext Enzymatic Methyl-seq Kit (NEB, Cat \# E7120L).

tag: condition


title: L1713-Haloferax_volcanii_standing_NOMe_Rep1


title: GM-CSF-activated_blood_DC-polarized_CD4_T_cells

city: Paris

first: Melissa

last: Saichi

address: 1 avenue Claude Vellefaux

country: France

institute: Human Immunology Pathophysiology Immunotherapy (HIPI)- Inserm

description: polarized CD+Tcells with GM-CSF_Activated DC

data_processing:
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v3.1.0)
Fastq were aligned on Grch38 reference genome
Bam files and filtered expression matrices were generated using “cellranger_count”
All expression matrices were loaded into R 4.0.0 using “Read10X” function from Seurat library (3.1.5)
Seurat suite was used to perform downstream analyses
Genome_build: Grch38
Supplementary_files_format_and_content: Processed files are raw count UMI matrices (including the matrix (.mtx), cell barcodes (barcodes.tsv) and gene names (genes.tsv)  which are given by Cellranger pipeline (LPS_activated_blood_DCpolarized_CD4_T_cells_RAW_matrix.mtx, GM-CSF_activated_blood_DCpolarized_CD4_T_cells_RAW_matrix.mtx and  Day_0_Naive_CD4_T_cells_RAW_matrix.mtx)  and  Seurat objects with the original uncorrected matrix, in the "RNA" assay ( GMCSF_activated_blood_DCpolarized_CD4_T_cells_SeuratObject.Rds, LPS_activated_blood_DCpolarized_CD4_T_cells_SeuratObject.Rds, Day_0_Naive_CD4_T_cells_SeuratObject.Rds)

source_name: Activated CD4+Tcells

extract_protocol:
PolyA RNA
RNA from all the samples was extracted according to the Single Cell 3' Reagent Kits V2

treatment_protocol: PBMC were isolated by centrifugation on a density gradient (Lymphoprep, StemCell Technologies). Human blood primary DC were purified according to an established protocol (Alculumbre and Pattarini, 2016). In brief, after FICOLL (GE Healthcare and Lymphoprep StemCell) gradient centrifugation, total PBMC were enriched in DC using the EasySep Human Pan-DC Pre-Enrichment kit (StemCell Technologies). Enriched DC were sorted to obtain 98% purity on an MoFloAstrios Cell Sorting (Beckman Coulter) or FACS ARIA III (BD Technologies), as Lineage (CD3, CD14, CD16, CD56, CD20 and CD19)- (Miltenyi Biotech), CD4+ (Biolegend), CD11c+ (BioLegend), CD1c+ (eBioscience).   DC were cultured in RPMI 1640 Medium Gluta-MAX (Life Technologies) containing 10% Fetal Calf Serum (Hyclone), 100 U/ml Penicillin/Streptomycin (Gibco), MEM Non-Essential Amino Acids (Gibco), and 1 mM NA pyruvate (GIB CO). DC were cultured at 106 cells/ml in flat bottom plates for 24h or 48h in the presence of 50 ng/ml rhGM-CSF (Prospec) (where differently specified) or 100 ng/ml ultrapure LPS (InvivoGen).  For co-culture, activated-DC were washed twice in PBS 1X and put in culture with allogeneic naive CD4+ T cells (104 DC and 5x104 T) in X-VIVO 15 medium (LONZA) for the indicated time. For co-culture, CD4+ T cells were freshly purified from PBMC the day after DC purification or 2 days later depending on the experimental condition. Coupling exclusively a single DC donor with a single CD4+ T cell donor was used to perform each co-culture experiment. DC were stimulated either with rhGM-CSF or LPS for 24h to activate total cells or only with rhGM-CSF for 48h/72h to induce the emergence of two different sub-populations. After 2 days of activation, sub-populations of DC were electronically sorted based on the expression of ICOS-L and CD40 (ARIA III, BD). Total activated DC or both sub-types of GM-CSF-activated DC as well as LPS-activated DC and Medium-activated DC, were put in co-culture with allogeneic naïve CD4+ T cells with exactly the same ratio as mentioned before.

tag: co-culture condition

tag: dataset name

value: Blood


title: HEK293T_PRP5-KD_rep1


title: MCOcon_2


title: MCOcon_1


title: MCOA10_10


title: ES_ChIL1000C_IgG_3

value: IgG


title: L1712-Haloferax_volcanii_stationary_NOMe_Rep2


title: Day_0_Naive_CD4_T_cells

description: naive CD4+Tcells


title: LPS-activated_blood_DC-polarized_CD4_T_cells

description: polarized CD+Tcells  with LPS-Activated DC


title: ES_ChIL1000C_IgG_1


title: L1710-Haloferax_volcanii_exponential_dSMF

data_processing:
read alignment, ATAC-seq and KAS-seq data: Bowtie 1.0.1
read alignment, NOMe-seq/dSMF data: bwameth
bigWig file generation: custom code
Assembly: Haloferax volcanii DS2 haloVolc1
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for KAS-seq and ATAC-seq datasets, bedGraph of methylation percentage for NOMe/SMF datasets
Library strategy: dSMF


title: MCOA10_9


title: 8C_S5P_3

source_name: 8-cell embryo


title: 8C_S5P_2


title: dopamine-Metformin2

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Transcript abundances was estimated in Fragments Per Kilobase of exon per Million mapped reads (FPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file storing expression FPKM values

source_name: hPSC-derived DA neurons

growth_protocol: mDA differentiation were performed using H9 hESCs.  hESCs were grown on VTN-N (Thermo Fisher Scientific)-coated 6-well plates in E8-essential medium. Cells were maintained at 37℃, 5% CO2.

extract_protocol:
For RNA analysis cells were lysed in TRIzol (Invitrogen).
Libraries were prepared using Illumina TruSeq stranded mRNA Sample Preparation kit.

treatment_protocol: SARS-CoV-2 infections of hPSC-derived DA neurons were performed in the culture media at the indicated MOIs at 37°C. At the indicate hpi, cells were washed three times with PBS.

value: hPSC-derived DA neurons

tag: virus

value: SARS-CoV-2 infect

tag: chemical

value: 50mM Metformin


title: L1709-Haloferax_volcanii_exponential_NOMe


title: dopamine-Metformin3


title: dopamine-Metformin1


title: MCOA10_8

value: ICR


title: 8C_S5P_1


title: ES_ChIL1000C_S2P_1

source_name: mES-cells


title: MCOA10_7

value: colon


title: 210202432

city: Beijing

first: Dong

last: Yan

state: Beijing

address: 82th South Xinhua Road, Tongzhou District

department: Oncology Department

institute: Beijing Luhe Hospital,Capital Medical University

hyb_protocol: Reporter and Capture probes against genes  of interest were prepared as previously described by Geiss et al. (2008; PMID: 18278033). Data were collected and analyszed using the nCounter Digtal Analyzer.

scan_protocol: According to the manufacturer's instructions (NanoStrings Technologies, Seattle, WA)

data_processing: The nSolver Analysis Software (NanoString Technologies) was used for the extraction of raw RNA data and for checking the quality of the data. Using the positive control data, a generalized linear model was fitted with 8 negative and 6 positive controls, where the counts for each positive control follow a Poisson's distribubtion with the mean modeled as a linear function of concentration. Each sample was then normalized to the median slope and intercept of all samples and log2 transformed. Using the transformed data pf all genes, a Bland-Altman plot was generated for each sample to compare the sample to the average of all samples. A loess curve was fitted for each Bland-Altman plot to globally normalize the transformed data as described in our recent publication. A two sample t-statistical was performed on each RNA, and the RNA was filtered based on the folloeing three criteria:(a) p-value ≤ 0.08; (b) the log2 fold change between PD and control is greater than 0.263 in absolute value, equivalent to 20% change; and (c) the mean of the log2 transformed gege expression for one of the two groups is at least 5.Gene expression was measured using the nCounter platform (NanoString Technologies, Seattle, WA), and transcriptome analysis was based on the 289-immuno-gene panel. This panel allows the simultaneous analysis of 289 genes involved in the immune response in cancer. For each sample, quality control indicators, including the Imaging QC, Binding Density QC, Positive Control Linearity QC, Positive Control Limit of Detection QC, positive normalization factor, and content normalization factor, were then calculated. Samples qualified for quality control were included in the subsequent analysis. The raw data of each sample and gene were standardized against the internal External RNA Controls Consortium controls to eliminate technical variability in the assay, and then, counts were normalized to the geometric mean of endogenous housekeeping genes, followed by log2 transformation.

label: Biotin & color-coded tag

source_name: Colorectal Cancer

label_protocol: Using 225 ng total RNA, 289 gene transcripts levels were assayed using Nanostring nCounter assay kits by direct digital detection following the manufacturer's guidelines (NanoString Technologies, Seattle, WA).

extract_protocol: Human FFPE tissues from colorectal cancer patients were obtained from the Beijing Luhe Hospital. Tatal RNA was extracted using the RNA isolation kit, following the manufacturer's instructions (Ambion).

value: rectum

tag: ras mutation

value: KRAS

tag: prognosis

value: Worse

tag: pfs/m

tag: metastasis

value: noCRCPM

tag: gender

value: Male


title: 8C_S2P_3


title: dopamine-imatinib2

value: 10mM imatinib


title: MCOA10_6

tag: strain

tag: tissue

tag: age

value: 10 weeks

tag: treatment


title: L1711-Haloferax_volcanii_stationary_NOMe_Rep1


title: 210202431

value: CRCPM

value: Female


title: ES_ChIL1000C_IgG_2

tag: protocol

value: ChIL-seq

tag: assay


title: 8C_S2P_2

value: S2P (Abcam, ab5095)


title: MCOA10_5


title: dopamine-imatinib1

tag: cell type


title: MCOA10_4


title: dopamine-Riluzole3

value: 10mM Riluzole


title: 8C_IgG_3

value: IgG


title: dopamine-Riluzole2

value: hPSC-derived DA neurons

value: SARS-CoV-2 infect


title: 8C_S2P_1


title: MCOA10_3

value: ICR

value: AOS 10mg/kg


title: MCOA10_2

value: colon


title: 210202430

value: right colon

value: KRAS


title: 210202428

value: left colon

value: KRAS/NRAS

value: Worse


title: 210202427

value: Male


title: 8C_IgG_2


title: dopamine-Riluzole1


title: 8C_IgG_1


title: dopamine-imatinib3

value: 10mM imatinib


title: 210202420


title: 210202422

value: rectum

value: CRCPM

value: Female


title: MCOA10_1

value: 10 weeks


title: dopamine-DMSO3

value: DMSO


title: 2C_S5P_DRB_3

source_name: 2-cell embryo

value: ChIL-seq

value: S5P (Abcam, ab5131)

value: DRB


title: MCHSCF_20

source_name: cecum

extract_protocol:
CECUM were removed, than quikly removed the contents and frozen in the luquid nitrogen, and extract the total DNA to analyze the microbial diversity
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

value: ICR

value: cecum

value: High fat diet & STZ+control-FMT


title: 210202417

value: KRAS


title: dopamine-DMSO2

value: hPSC-derived DA neurons

value: SARS-CoV-2 infect


title: MCHSCF_18


title: dopamine-DMSO1


title: 2C_S5P_DRB_2


title: 2C_S5P_DRB_1


title: dpamine-neuron-48h-mock-3

value: Mock


title: 210202325

value: left colon

value: Worse

value: Male


title: 210202316

value: rectum

value: Better

value: noCRCPM


title: MCHSCF_11

value: 10 weeks


title: dpamine-neuron-48h-mock-2


title: 2C_S5P_3

value: ChIL-seq


title: dpamine-neuron-48h-mock-1


title: 210202309


title: 2C_S5P_2

value: S5P (Abcam, ab5131)


title: 210202283


title: 2C_S5P_1


title: MCHSCF_10


title: MCHSCF_7


title: dpamine-neuron-48h-H-2


title: MCHSCF_5


title: 2C_S2P_3

value: S2P (Abcam, ab5095)


title: 210202260

value: right colon

value: NRAS


title: dpamine-neuron-48h-H-3


title: 210202270

value: Female


title: MCHSCF_4

value: ICR

value: cecum

value: High fat diet & STZ+control-FMT


title: 2C_S2P_2


title: dpamine-neuron-48h-H-1

value: hPSC-derived DA neurons

value: SARS-CoV-2 infect


title: MCHSCF_13


title: 2C_S2P_1


title: MCHSCF_2


title: 210202242

value: KRAS


title: 2C_IgG_3

value: IgG


title: 210202236

value: rectum

value: Male


title: Treatment_3_post

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description:
Sample 11
processed data file: counts_table.csv
processed data file: normcounts.csv

data_processing:
Demultiplex with Casava.
Alignment with Hisat2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: counts_table.csv: Comma-separated text file includes counts table.
Supplementary_files_format_and_content: normcounts.csv: Comma-separated text file includes normalised counts from DESEq2.

source_name: Kidney

extract_protocol:
Pure link RNA mini kit.
KAPA stranded RNASeq kit.

value: Kidney

value: tPA

tag: timepoint

value: Cold Storage


title: Control_3_pre

description:
Sample 10
processed data file: counts_table.csv
processed data file: normcounts.csv

value: Post perfusion


title: Treatment_3_pre

description:
Sample 12
processed data file: counts_table.csv
processed data file: normcounts.csv


title: 210109718

value: left colon

value: Worse

value: CRCPM


title: MCHSAF_17

value: 10 weeks

value: High fat diet & STZ+AOS10mg/kg-FMT


title: 210109709

value: NRAS

value: Female


title: Treatment_2_pre

description:
Sample 8
processed data file: counts_table.csv
processed data file: normcounts.csv


title: 210202244

value: Better


title: 210109705

value: noCRCPM


title: MCHSAF_18

value: ICR

value: cecum


title: Treatment_2_post

description:
Sample 7
processed data file: counts_table.csv
processed data file: normcounts.csv


title: MCHSAF_15


title: Zy_S5P_2

source_name: zygote

value: ChIL-seq

value: S5P (Abcam, ab5131)


title: 210109692

value: rectum

value: KRAS

value: Male


title: Zy_S5P_3


title: T156_43_testis

city: Bloomington

first: Kimberly

middle: A

last: Rosvall

state: IN

address: Dept of Biology, Indiana Univ., 1001 E. 3rd St, Jordan Hall

institute: Indiana University

data_processing:
Illumina Casava software used for basecalling.
Adapters and low quality bases were trimmed using Trimmomatic (version 0.36) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17
Reads were mapped to the Zebra finch, taeGut3.2.4, using Hisat2 (version 2.1.0)
Genes were quantified using featureCounts (version 1.6.4) with parameters “-O -M --primary -p --largestOverlap  -B -s 2” and taeGut3.2.4.98 as the annotation.
Genome_build: taeGut3.2.4
Supplementary_files_format_and_content: tab-delimited file of raw gene counts for each tissue

organism: Taeniopygia guttata

source_name: testis

extract_protocol:
Brains were frozen on dry ice and macrodissected into functional regions. Total RNA was extracted from each sample using Trizol (Invitrogen, Carlsbad, CA).
Total RNA was used for cDNA library construction using a TruSeq Stranded mRNA kit (Illumina) following the kit protocol.

treatment_protocol: 5 hours at air temperature either above (Ta = 43°C), within  (Ta = 35°C), or below thermoneutral zone (Ta = 27°C)

tag: temperature treatment

value: gonad

tag: developmental stage

value: adult

tag: Sex

value: male


title: Control_3_post

description:
Sample 9
processed data file: counts_table.csv
processed data file: normcounts.csv

value: Kidney

value: Cold Storage


title: MCHSAF_14

value: 10 weeks

value: High fat diet & STZ+AOS10mg/kg-FMT


title: T153_43_testis


title: Zy_S5P_1


title: Control_2_pre

description:
Sample 6
processed data file: counts_table.csv
processed data file: normcounts.csv

value: Post perfusion


title: MCHSCF_1

value: High fat diet & STZ+control-FMT


title: MCHSAF_7


title: Control_2_post

description:
Sample 5
processed data file: counts_table.csv
processed data file: normcounts.csv


title: MCHSAF_20


title: 2C_IgG_2

value: IgG


title: T152_43_testis


title: MCHSAF_6

value: ICR


title: 2C_IgG_1


title: Treatment_1_pre

description:
Sample 4
processed data file: counts_table.csv
processed data file: normcounts.csv

value: tPA


title: T144_43_testis


title: MCHSAF_4

value: cecum


title: T141_43_testis


title: T136_43_testis


title: Zy_IgG_2

value: ChIL-seq


title: MCHSAF_3


title: Zy_S2P_1

value: S2P (Abcam, ab5095)


title: MCHSAF_1


title: Control_1_post

description:
Sample 1
processed data file: counts_table.csv
processed data file: normcounts.csv


title: Control_1_pre

description:
Sample 2
processed data file: counts_table.csv
processed data file: normcounts.csv


title: Zy_IgG_3


title: MCHSA10_10

value: High fat diet & STZ+AOS10mg/kg


title: L1691-Haloferax_volcanii_standing

data_processing:
read alignment, ATAC-seq and KAS-seq data: Bowtie 1.0.1
read alignment, NOMe-seq/dSMF data: bwameth
bigWig file generation: custom code
Assembly: Haloferax volcanii DS2 haloVolc1
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for KAS-seq and ATAC-seq datasets, bedGraph of methylation percentage for NOMe/SMF datasets
Library strategy: KAS

extract_protocol:
A 500-mM N3-kethoxal solution was brought to 37C, then added to 2 mL of culture at a final concentration of 5 uM. Cells were then incubated for 5 minutes at 37C in a ThermoMixer at 1000 rpm. Cells were then pelleted by centrifugation at 10,000 g for 1 minute, resuspended in 200 uL 1x PBS buffer, and DNA was immediately isolated using the Monarch Genomic DNA Purification Kit (NEB, Cat \# T3010S), with the modification that elution was carried out with 50 uL 25 mM K3BO3 solution (pH 7.0).
The click reaction was carried out by combining 87.5 uL purified and sheared DNA, 2.5 uL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma 760749), and 10 uL 10x PBS in a final volume of 100 uL. The reaction was incubated at 37C for 90 minutes. DNA was purified using AMPure XP beads (50 uL for a 100 uL reaction or 100 uL for a 200 uL reaction), beads were washed on a magnetic stand twice with 80% EtOH, and eluted in 130 uL 25mM K3BO3. Purified DNA was then sheared on a Covaris E220 instrument down to ~150-400 bp size. For streptavidin pulldown of biotin-labeled DNA, 10 uL of 10 mg/mL Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) were separated on a magnetic stand, then washed with 300 uL of 1x TWB (Tween Washing Buffer; 5 mM Tris-HCl pH 7.5; 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20). The beads were resuspended in 300 uL of 2x Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA; 2 M NaCl), the sonicated DNA was added (diluted to a final volume of 300 uL if necessary), and the beads were incubated for >=15 minutes at room temperature on a rotator. After separation on a magnetic stand, the beads were washed with 300 uL of 1x TWB, and heated at 55C in a Thermomixer with shaking for 2 minutes. After removal of the supernatant on a magnetic stand, the TWB wash and 55C incubation were repeated. Final libraries were prepared on beads using the NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645) as follows. End repair was carried out by resuspending beads in 50 uL 1x EB buffer, and adding 3 uL NEB Ultra End Repair Enzyme and 7 uL NEB Ultra End Repair Enzyme, followed by incubation at 20C for 30 minutes (in a Thermomixer, with shaking at 1,000 rpm) and then at 65C for 30 minutes.  Adapters were ligated to DNA fragments by adding 30 uL Blunt Ligation mix, 1 uL Ligation Enhancer and 2.5 uL NEB Adapter, incubating at 20C for 20 minutes, adding 3 uL USER enzyme, and incubating at 37C for 15 minutes (in a Thermomixer, with shaking at 1,000 rpm) . Beads were then separated on a magnetic stand, and washed with 300 uL TWB for 2 minutes at 55C, 1000 rpm in a Thermomixer. After separation on a magnetic stand, beads were washed in 100 uL 0.1 x TE buffer, then resuspended in 15 uL 0.1 x TE buffer, and heated at 98C for 10 minutes. For PCR, 5 uL of each of the i5 and i7 NEB Next sequencing adapters were added together with 25 uL 2x NEB Ultra PCR Mater Mix. PCR was carried out with a 98C incubation for 30 seconds and 12 cycles of 98C for 10 seconds, 65C for 30 seconds, and 72C for 1 minute, followed by incubation at 72C for 5 minutes. Beads were separated on a magnetic stand, and the supernatant was cleaned up using 1.8x AMPure XP beads. Libraries were sequenced in a paired-end format on a Illumina NextSeq instrument using NextSeq 500/550 high output kits (2x36 cycles).

tag: condition


title: Mouse kidney scRNA-seq

city: New Haven

first: Haikuo

last: Li

state: CT

address: 55 Prospect St

institute: Washington University in St. Louis

description: A mixture of 24 kidney samples

data_processing:
i5/i7 demultiplexing
Barcode aligning
Adapter clipping
Genome mapping
Gene counting
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table (cell-by-gene)

source_name: Male mouse left kidney

extract_protocol:
For each sample mentioned above, nuclei were extracted from the kidney tissue, fixed and snap-frozen. We generated a sci-RNA-seq3 (current version of sci-RNA-seq) library based on a previously demonstrated protocol, including nuclei permeabilization, three-level combinatorial indexing composed of reverse transcription (RT), hairpin ligation and indexed PCR, and library purification.
Libraries were preparedusing the current protocol of sci-RNA-seq3.

value: left kidney

tag: surgery

value: multiplexed sample:No surgery; uni-IRI; or UUO

value: 8-9 weeks old


title: Zy_IgG_1


title: Zy_S2P_3


title: T135_43_testis

value: gonad

value: adult

value: male


title: MCHSA10_9

value: 10 weeks


title: Podocyte Fraction Kidney Digest AGED PD1 Control Ab: 26221 Male

city: Box

first: Stuart

last: Shankland

state: WA

address: 1959 NE Pacific Avenue

department: Nephrology

institute: University of Washington, Seattle

data_processing:
Raw reads from fastq files were aligned to mm10 using the HISAT2 aligner
Gene-level read counts were obtained using featureCounts using Ensembl GRCm38 gene annotations.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file of gene-level read counts for each sample.

source_name: Podocytes

growth_protocol: 21 month-old male C57BL/6J mice (~ 70 year-old humans) were randomized into two groups: (1) anti-PD-1 antibody-injected group (n=12) that received weekly IP injections of InVivoMAb anti-mouse PD-1 antibody (RMP1-14, Bio X Cell, Lebanon, NH) at 12 mg/kg for 8 weeks; (2) aged-matched control mice (n=7) that received weekly IP injections of the isotype control IgG2A antibody (2A3, Bio X Cell, Lebanon, NH) at 12 mg/kg for 8 weeks. A third group of young uninjected C57BL/6J mice aged 4 months (n=9) were used as a non-aged comparison. Animals were weighed weekly; spot urines were collected prior to injections, and albumin was measured by radial immunodiffusion assay (RID) at 4 and 8 weeks.(31) Blood Urea Nitrogen was measured at baseline, week 4 and at sacrifice, with a colorimetric Urea Assay Kit (Abcam, Cambridge, United Kingdom).

extract_protocol:
mRNA was isolated using the RNeasy Mini Kit (Qiagen, Germantown, MD) as per the manufacturer’s instructions.
Library generation and bulk next-generation mRNA sequencing was performed by Psomagen, Inc. (Rockville, MD, USA) using TruSeq RNA Library Prep Kits (Illumina, San Diego, CA, USA) and the Illumina platform

treatment_protocol: The podocyte fraction was MACS-sorted as the following. Kidney tissue (w/o the kidney capsule and surrounding fat) was placed into ice cold RPMI 1640 medium, (w/o L-glutamine and phenol red, GE Healthcare Bio-Sciences, Pittsburgh, PA). After removal of the medulla the remaining cortex was minced into fine pieces and digested in 0.2 mg/ml Liberase™ TL (Sigma-Aldrich, St. Louis, MO), 100 U/ml DNAse I (Sigma-Aldrich, St. Louis, MO) in RPMI 1640 medium (w/o L-glutamine and phenol red) by shaking at 37oC for 30 minutes. The digest was passed through an 18G needle (Becton Dickenson, Franklin Lakes, NJ) 10 times and enzymes were inactivated by adding 5 ml of RPMI 1640 medium (w/o L-glutamine and phenol red) supplemented with 1 mM sodium pyruvate (ThermoFisher Scientific, Waltham, MA), 9% Nu-Serum™ IV Growth Medium Supplement (Corning Incorporated - Life Sciences, Durham, NC) and 100U/ml Penicillin-Streptomycin (ThermoFisher Scientific, Waltham, MA). The cell suspension was passed through a 100 µm and a 40 µm cell strainer (BD Biosciences, San Jose, CA) and pelleted by centrifugation at 200G at 4oC for 5 minutes. Cells were were resuspended in media containing two rabbit anti-Nephrin antibodies (36) (1:100, Abcam, Cambridge, MA). After 1 hour at 4oC cells were pelleted, washed in media and incubated with anti-rabbit microbeads (Miltenyi Biotec, Auburn, CA) along with Alexa Fluor 594-conjugated AffiniPure Donkey Anti-Rabbit IgG 1:200 (in order to visualize binding of the Nephrin antibodies to the podocytes) for 30 minutes at 4oC. Cells were pelleted and washed in PBS with 0.5% BSA and 2mM EDTA and applied to MACS LS columns (Miltenyi Biotec, Auburn, CA) to gently separate microbead-bound podocytes from the other kidney cells. Cells not retained by the magnetic field were collected, pelleted and designated non-podocyte (NP) fractions. LS columns were removed from the magnetic field then washed with PBS with 0.5% BSA and 2mM EDTA and podocytes were collected. A small aliquot of each fraction imaged using an EVOS FL Cell Imaging System to verify podocyte isolation, based on the presence of Nephrin antibody. Additionally, qRT-PCR for a panel of podocyte genes was performed in both podocyte and non-podocyte fractions to confirm cell type identity. Only fractions with significant podocyte expression or absence thereof were moved along for subsequent analysis as podocytes or non-podocytes, respectively.

value: Male

value: Aged (21-month-old)

value: PD1 control antibody


title: Zy_S2P_2


title: T157_35_testis


title: T158_35_testis


title: MCHSA10_8

data_processing:
library strategy: 16S rDNA seq
Illumina HiSeq software used for basecalling.
Take the method of removing low quality by window, the specific operation is as follows: set a window of 25 bp, if the average quality value of the window is less than 20, the back-end bases will be truncated from the window; the read length after truncation is lower than the original read length For 75%, remove the entire sequence.
Remove linker contamination of reads (default adapter sequence and read sequence have an overlap of 15 bp, set to 15 bp, and allow the number of mismatches to be 3);
Remove reads containing N;Remove low-complexity reads (default reads with continuous base length ≥10 are low-complexity reads) finally, get the Cleandata
Splice the reads into tags through the overlap relationship between the reads; cluster the tags into OTUs and compare them with the database, and annotate species; based on the OTU and annotation results, perform sample species complexity analysis, analysis of species differences between groups, and association analysis. Model prediction, etc.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression


title: T154_35_testis


title: MCHSA10_7


title: L1689-Haloferax_volcanii_stationary


title: Podocyte Fraction Kidney Digest AGED PD1 Control Ab: 26219 Male


title: L1690-Haloferax_volcanii_standing


title: Treatment_1_post

description:
Sample 3
processed data file: counts_table.csv
processed data file: normcounts.csv

value: Kidney

value: Cold Storage


title: Podocyte Fraction Kidney Digest AGED PD1 Control Ab: 26218 Male


title: T146_35_testis


title: L1688-Haloferax_volcanii_stationary


title: MCHSA10_5

value: ICR


title: L1686-Haloferax_volcanii_exponential


title: MCHSA10_4

value: cecum


title: T140_35_testis


title: L1687-Haloferax_volcanii_stationary


title: T139_35_testis


title: Podocyte Fraction Kidney Digest AGED PD1 Control Ab: 26215 Male


title: L1684-Haloferax_volcanii_exponential


title: L1685-Haloferax_volcanii_exponential


title: T137_35_testis


title: MCHSA10_3


title: MCHSA10_2


title: L1671-Haloferax_volcanii_standing_ATAC_1pFA_rep3

data_processing:
read alignment, ATAC-seq and KAS-seq data: Bowtie 1.0.1
read alignment, NOMe-seq/dSMF data: bwameth
bigWig file generation: custom code
Assembly: Haloferax volcanii DS2 haloVolc1
Supplementary files format and content: bedGraph of read coverage, normalized to RPM for KAS-seq and ATAC-seq datasets, bedGraph of methylation percentage for NOMe/SMF datasets

extract_protocol:
Cells were fixed by adding 37% formaldehyde (Sigma) at a final concentration of 1% and incubating for 15 minutes at room temperature. Formaldehyde was then quenched using 2.5 M Glycine at a final concentration of 0.25 M. Cells were subsequently centrifuged at 10,000 g for 2 minutes, washed once in 1x PBS, and centrifuged again at 10,000 g for 2 minutes. Transposition was carried out as above for 15 minutes. The reaction was stopped with the addition of 150 uL IP Elution Buffer (1% SDS, 0.1M NaHCO3) and 2 uL Proteinase K (Promega, Cat # MC5005), then incubated at 65C overnight to reverse crosslinks. DNA was isolated by adding and equal volume of 25:24:1 phenol:chloroform:isoamyl solution, vortexing and centrifuging for 3 minutes at 14,000 rpm, then purifying the top aqueous phase using the MinElute PCR Purification Kit, eluting in 10 uL EB buffer.
Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and PCR amplified for 10 cycles using the usual ATAC-seq settings. Libraries were purified using the MinElute kit, then sequenced on a Illumina NextSeq 550 instrument as 2x36mers.


title: MCHS_19

value: High fat diet & STZ


title: L1668-Haloferax_volcanii_stationary_ATAC_1pFA_rep3


title: MCHSA10_1


title: T147_35_testis


title: T159_27_testis


title: T155_27_testis


title: T151_27_testis


title: L1670-Haloferax_volcanii_standing_ATAC_1pFA_rep2


title: L1666-Haloferax_volcanii_stationary_ATAC_1pFA_rep1


title: MCHS_18


title: Podocyte Fraction Kidney Digest AGED PD1 Ab 47 days: 26109 Male

value: Anti-PD1 antibody


title: T148_27_testis


title: L1667-Haloferax_volcanii_stationary_ATAC_1pFA_rep2


title: Podocyte Fraction Kidney Digest AGED PD1 Ab 47 days: 26108 Male


title: MCHS_16


title: T149_27_testis


title: MCHS_17


title: Podocyte Fraction Kidney Digest AGED PD1 Ab 47 days: 26111 Male


title: MCHSA10_6

value: High fat diet & STZ+AOS10mg/kg


title: MCHS_15


title: Podocyte Fraction Kidney Digest (25862 4-Month-Old Male)

value: Young (4-month-old)


title: T142_27_testis

value: brain


title: Podocyte Fraction Kidney Digest (25857 4-Month-Old Male)


title: Podocyte Fraction Kidney Digest (25856 4-Month-Old Male)


title: L1663-Haloferax_volcanii_exponential_ATAC_1pFA_rep1


title: T145_27_testis


title: Podocyte Fraction Kidney Digest AGED PD1 Control Ab: 26217 Male


title: L1665-Haloferax_volcanii_exponential_ATAC_1pFA_rep3


title: Podocyte Fraction Kidney Digest AGED PD1 Ab 47 days: 26110 Male


title: Podocyte Fraction Kidney Digest AGED PD1 Ab 47 days: 26107 Male


title: Podocyte Fraction Kidney Digest (25854 4-Month-Old Male)


title: MCHS_14


title: Podocyte Fraction Kidney Digest (25853 4-Month-Old Male)


title: L1539-standing_rep2-ATAC-1uL-1pFA


title: MCHS_11


title: T156_43_PTR

source_name: posterior telencephalon


title: T153_43_PTR


title: L1538-standing_rep1-ATAC-1uL-1pFA


title: MCHS_7


title: L1533-Haloferax_volcanii_4C_rep2-KAS


title: L1532-Haloferax_volcanii_4C_rep1-KAS


title: T144_43_PTR


title: MDX5cv-4

city: Birmingham

first: Matthew

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

data_processing:
Raw data QC was evaluated with FastQC, and removal of Illumina adapters was perfromed with Trim_Galore! (v.0.6.4) [`--2colour 20` enabled]
Trimmed reads were re-evaluated with FastQC, and reads were mapped to the GENCODE mouse mm10 primary assembly reference (M25) with STAR (v.2.6.0c, `--twopassMode Basic --outSAMattributes NH HI AS nM NM MD --outSAMtype BAM SortedByCoordinate` enabled)
BAM files were indexed with SAMtools (v.1.9) and QC on BAM files was performed with RseQC (v3.0.1). QCs included checks for genebody coverage, inner distance quantification, infer experiment (to check that read orientation matched expected) and read distribution quantification
Raw read counts were generated with featureCounts (rsubread v1.32.2, r-base 3.5.1. Reads were reversly stranded, `strandSpecific=2`. GENCODE M25 GTF was used in this step). Logs were compiled with MultiQC (v1.6)
Read normalization and differential gene expression were performed with DESeq2 (v.1.26.0 in R version 3.6.2). Fold changes were shrunken with apeglm (v1.8.0). gprofiler2 was utilized to conduct GO enrichment analysis
Genome_build: mm10 (GENCODE M25)
Supplementary_files_format_and_content: Tab delimited file which contains the normalized gene-level counts for each biological sample.

source_name: Skeletal Muscle (Tibialis Anterior)

extract_protocol:
Tibialis anterior muscles were harvested from 6 month mice. RNA was isolated using Trizol.
Truseq Stranded Total RNA H/M/R Prep Kit (thus reversely stranded)

value: C57/Bl6 Strain

tag: genotype

value: mdx5cv (DMD mouse model)

value: 6 months old


title: MCHS_2


title: T141_43_PTR

value: adult

value: male


title: MDX5cv-2


title: L1531-Haloferax_volcanii_23C_rep2-KAS


title: MDX5cv-3


title: T138_43_PTR


title: MCcon_12

value: 10 weeks

value: control


title: MDX5cv-1


title: L1529-Haloferax_volcanii_37C_rep2-KAS


title: T136_43_PTR


title: B6 WT-4

value: Wild type (WT)


title: B6 WT-3


title: MCcon_10


title: L1528-Haloferax_volcanii_37C_rep1-KAS


title: MCHS_9


title: T135_43_PTR


title: B6 WT-1


title: T158_35_PTR


title: T152_43_PTR


title: L1527-Haloferax_volcanii_42C_rep2-KAS


title: B6 WT-2


title: MCcon_8


title: T157_35_PTR


title: L1530-Haloferax_volcanii_23C_rep1-KAS


title: 5EnPGC1H3K27Ac2

city: Kyoto

first: Madhu

last: Malinee

state: Kyoto

address: Kitashirakawa-Oiwakecho,

department: Graduate School of Science

country: Japan

institute: Kyoto University

data_processing:
Data were trimmed using Trimmomatic (version 0.38) that trim and crop the Illumina (fastq) data as well as remove adapters.
Trimmed reads were further mapped using Bowtie (version 1.1.2) which aligns short DNA sequences to the reference genome at a rate of over 25 million 35-bp reads per hour.
Mapped data were further checked for duplicates, if any and removed using Picard (version 0.118)
After removing duplicates, reads were further peak called using MACS2 (version 2.2.2.20160309)
Peak annotation were given using ChIPseeker (version 11.16.1)
Genome_build: mm10
Supplementary_files_format_and_content: bed file for  Peak calling  of  samples

source_name: CD8+ T cells

extract_protocol:
Treated cells were cross-linked followed by ChIP using ChIP-IT PBMC kit following manufacturer’s protocol (Active Motif, Catalog#53042).
TruSeq ChIP Sample Preparation Guide 15023092 Rev. B

treatment_protocol: Murine primary CD8+ T cells purifed from lymph node and spleen of mice; Further CD8+ T cells were given TCR stimulation with anti-CD3 and anti-CD28 mAbs and treated with PIPs for 48 hours.

value: CD8+ T cells

value: PIPs EnPGC-1

tag: chip antibody

value: H3K27Ac (Abcam, Catalog# ab4729)


title: T154_35_PTR


title: L1526-Haloferax_volcanii_42C_rep1-KAS


title: MCcon_5

first: Yong

last: Zhao

address: 700 Changcheng Road

institute: Qingdao Agricultural University

value: ICR

value: cecum


title: MCcon_9


title: T147_35_PTR


title: MCcon_11


title: T146_35_PTR


title: 4DMSO_H3K27Ac2

value: DMSO


title: MCcon_4


title: 4DMSO_H3K27Ac1


title: MCcon_3


title: L1525-Haloferax_volcanii_standing_rep2-KAS


title: L1524-Haloferax_volcanii_standing_rep1-KAS


title: MCcon_2


title: L1212-Haloferax-KAS-standing_culture


title: T140_35_PTR


title: SZc

description: small RNA

organism: Chromochloris zofingiensis

source_name: C. zofingiensis stress sample (replicate 3)


title: MCcon_1


title: T139_35_PTR


title: SZb

description: small RNA

source_name: C. zofingiensis stress sample (replicate 2)


title: 3DMSO-IgG_1

value: Rabbit pAb (Abcam, Catalog#ab37415)


title: MCA10_10


title: SZa

description: small RNA

source_name: C. zofingiensis stress sample (replicate 1)


title: T137_35_PTR


title: 2EnPGC-1_Input


title: 5EnPGC1H3K27Ac1


title: MCA10_8


title: 1DMSO_input


title: NZc

description: small RNA

source_name: C. zofingiensis normal sample (replicate 3)


title: NZb

description: small RNA

source_name: C. zofingiensis normal sample (replicate 2)


title: T155_27_PTR


title: MCA10_9


title: MCA10_7


title: NZa

description: small RNA

source_name: C. zofingiensis normal sample (replicate 1)


title: CD8+ T SGC-CBP30_1

data_processing:
Trimmed reads are mapped to reference genome with HISAT2. After the read mapping, Stringtie was used for transcript assembly.
Performed read counting per gene and used gene count matrix for differential expression analysis with DESeq2.
For differential expression analysis, known batches as “-1” and “–2” were included for samples sequenced at two different times using same schedule.
Unknown batch variables were predicted with sva package and one variable was identified which was included as well.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files rlog count for Samples ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA were purified using RNeasy mini kit (QIAGEN);
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E was used with 1 ug of total RNA for the construction of sequencing libraries.


title: MCA10_6


title: MCA10_5


title: T149_27_PTR


title: MCA10_4


title: T151_27_PTR


title: T148_27_PTR


title: CD8+ T Ctrl PIP-1


title: 3DMSO-IgG_2


title: T145_27_PTR


title: CD8+ T EnPGC-1_2


title: MCA10_3

value: AOS 10mg/kg


title: T143_27_PTR

value: brain


title: T159_27_PTR


title: CD8+ T EnPGC-1_1


title: MCA10_2


title: T142_27_PTR


title: MCA10_1


title: CD8+ T DMSO-1


title: small intestine scRNA-seq from control ileum

city: Boston

first: Isaac

last: Chiu

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard medical school

description:
inDrops
Nav1.8_DTA_Ileum_cluster_de_markers_LR.xlsx
DE_Genes_Nav1.8_DTA_Ileum_perCellType(DESeq2).xlsx

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger, and Cell Ranger count QC summary report identified between 12,000-14,000 single cells in the samples.
Briefly, the data were loaded into R and analyzed using Seurat. After quality control and normalization, cells were clustered using FindClusters() function from the R package Seurat. To annotate the cell types of each cluster, FindAllMarkers() was run with the option “test.use = LR”, which identifies marker genes by comparing expression of each gene in a cluster against its expression in the rest of the cells using a logistic regression test. Only genes significantly and strongly up-regulated in the cluster were considered as potential markers. Potential markers were then intersected with canonical markers from the literature for intestinal epithelial cells, and the results were used to annotate the clusters (Nav1.8_DTA_Ileum_cluster_de_markers_LR.xlsx)
To test whether genes were statistically differentially expressed (DE) between mouse models within specific cell types, a negative binomial generalized linear model in the DESeq2 (v.1.30.1) R package was used via the Seurat wrapper function FindMarkers() with option ?test.use=DESeq2?. For each cell type being tested, the input consisted of the subset of the count matrix containing the cells annotated by that cell type. Size factors and dispersions were estimated prior to fitting the model. Wald statistics were used to determine the significance and the LFC of the fit for each gene. Benjamini-Hochberg method was used to control the false discovery rate (FDR) (DE_Genes_Nav1.8_DTA_Ileum_perCellType(DESeq2).xlsx).
Assembly: mm10
Supplementary files format and content: Nav1.8_DTA_Ileum_cluster_de_markers_LR.xlsx
Supplementary files format and content: DE_Genes_Nav1.8_DTA_Ileum_perCellType(DESeq2).xlsx

organism: Mus

source_name: Ileum

extract_protocol:
Briefly, distal ileum was collected from euthanized mice and flushed with ice cold PBS. Ileums were cut into 0.5cm pieces and incubated on ice for 5 min in 10 mL of PBS containing 5 mM EDTA and 1 mM DTT. After shaking, the intestinal pieces were incubated at 37 ºC for 10 minutes in PBS containing 5 mM EDTA and 2% FBS. After vigorous shaking, the wash containing crypts was collected. This step was performed three times in total for colonic pieces and two times for ileal pieces with the epithelial fraction collected at the end of each wash. The crypt cells were pelleted and digested with 10 ml HBSS containing 8 mg Dispase II (Sigma) for 10 minutes at 37 ºC. Single epithelial cells were collected in PBS containing 2% FBS for flow cytometry staining and sorting.
scRNA-seq of ileal epithelial cells isolated from Nav1.8DTA (three mice pooled together) and their littermate control (three mice pooled together) mice was performed using inDrops single cell sequencing following the user guide. Briefly, cells were encapsulated in droplets following a previously described protocol (Klein et al., 2015; Zilionis et al., 2017), with the following modifications in the primer sequences. RT primers on hydrogel beads-  5’CGATTGATCAACGTAATACGACTCACTATAGGGTGTCGGGTGCAG [bc1,8nt] GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG[bc2,8nt]NNNNNNTTTTTTTTTTTTTTTTTTTV- 3’ PCR primer sequences (steps 157 and 160 in the library prep protocol in (Zilionis et al., 2017))-5’-AATGATACGGCGACCACCGAGATCTACACXXXXXXXXTCGTCGGCAGCGTC-3’, where XXXXXX is an index sequence for multiplexing libraries. 5’- CAAGCAGAAGACGGCATACGAGATGGGTGTCGGGTGCAG-3’ With these modifications in the primer sequences, custom sequencing primers are no longer required. The library prep protocol used here was based on Smart-seq2 (Picelli et al., 2014) with modifications. The workflow of the library preparation can be summarized as follows: Reverse transcription with Maxima H minus RTase at 50°C for 60 min -> cleanup with SILANE beads -> template switching reaction with Maxima H minus RTase -> SPRI purification -> cDNA amplification -> SPRI purification -> DNA fragmentation, end repair and A-tailing -> adapter ligation -> SPRI purification -> library enrichment PCR -> double-sided SPRI purification. Referring to the detailed protocol in (Picelli et al., 2014), the following modifications were made to the protocol: Reverse transcription and template-switching were decoupled, where reverse transcription occurred within the droplet, while template-switching was not. cDNA was fragmented enzymatically here followed by adapter ligation, as opposed to tagmentation in (Picelli et al., 2014). Sequence of the adapters are as follows- 5’-CTGTCTCTTATACACATCTGACGCTGCCGACGA- 3’ (with 5’ phosphorylation). 5’-AGATGTGTATAAGAGACAG*T- 3’ (with phosphorothioate bond on the 3’ terminal nucleotide). The barcoded library was sequenced following the manufacture's instructions.

value: Ileum

value: Epithelial cells

value: Baseline


title: CD8+ T SGC-CBP30_2


title: CD8+ T Ctrl PIP-2


title: CD8+ T DMSO-2


title: SKI3 Sm Rep#2

city: La Plata

first: Soledad

last: Traubenik

state: Buenos Aires

department: Ciencias Biologicas

country: Argentina

institute: Universidad Nacional de La Plata

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_SKI3_SmR2_S8

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina reads were aligned to the M. truncatula genome (Mtv4.0) using Tophat 2 (Kim et al., 2013, Genome Biol. 14, R36)
Peaks were detected with the “Findpeaks” function of the HOMER package (Heinz et al., 2010, Molecular cell 38(4)) with the parameters “-regionRes 1”, “-minDist 150” and “-region”
Reads in the peaks were quantified in each replicate using the “summarizeOverlaps” function of the GenomicRanges R package (Lawrence et al. , 2013, PLoS Computational Biology, 9).
The counts for peaks and cut-sites were statistically evaluated using DESeq2.
Genome_build: Mtv4.0
Supplementary_files_format_and_content: GMUCT 2.0 Differentially accumulated peaks. Peaks were detected using HOMER package.
Supplementary_files_format_and_content: GMUCT 2.0 miRNA targets detected. Peaks were detected using HOMER package.

molecule: polyA RNA

organism: Medicago truncatula

source_name: SKI3 RNAi roots inoculated with S. meliloti 1021

growth_protocol: Transgenic roots were generated by Agrobacterium rhizogenes-mediated transformation as previously described (Boisson-Dernier et al., 2001, Mol. Plant Microbe Interact. 14) using GUS RNAi or SKI3 RNAi constructs. Plants withdeveloped hairy roots were transferred to slanted boxes containing Fahraeus media free of nitrogen. Seedlings were grown at 25°C with a long-day period (16-h day/8-h night cycle) and 50% humidity.

extract_protocol:
RNA was extracted with Trizol
30 µg of RNA from each condition were used for generation of GMUCT libraries following the protocol described by Willmann et al., 2014, Methods 67, with modifcations. Briefly, kits were replaced by commercially available supplies; Poly-A RNA was purified with oligodT-magnetic beads. RNA 5’ Adapter (RA5) was phosphorylated using T4 Polynucleotide Kinase (Thermo Scientific). 3' adapter and PCR primers from BrAD-seq (Townsley et. al., 2015, Front. Plant Sci. 6) were used.  KAPA HiFi DNA Polymerase (Kapa Biosystems) was used for amplification. PCR fragments were purified using AMPure XP beads (Beckman Coulter Genomics).
GMUCT 2.0-seq Degradome-Seq

treatment_protocol: Roots were inoculated with 10 ml of a 1:1000 dilution of S. meliloti 1021 (Meade and Signer, 1977, Proc. Natl. Acad. Sci. U. S. A. 74) culture grown in liquid TY media until OD600 reached 0.8 or with 10 ml of water as a control (mock treatment). Tissue was collected at 48 horus post-inoculation.

tag: genotype/variation

value: SKI3 RNAi

value: S. meliloti 1021

tag: tag

value: GMUCT 2.0 RNA

tag: molecule subtype

value: polyA/uncapped RNA


title: LLC cells, radiation+MEKi, rep3

city: jinan

first: yawen

last: zheng

address: jiefang road,No105

institute: jinan central hospital

data_processing:
In this project, we sequence 12 samples used DNBSEQ platform, averagely generating about 6.39G Gb bases per sample. The average mapping ratio with reference genome is 93.97%, the average mapping ratio with gene is 78.16%; 18147 genes were identified.
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: matrix table with RPKM values for  every gene and every sample

source_name: colon cancer

growth_protocol: Freshly isolated tumor tissues were cleaned using PBS. Tissue blocks (50 mm3) were cut to avoid the necrotic site, and three tumor tissues from different mice were analyzed for each group. Tissues were placed in TRIzol, stored at −80 °C, and transported to BGI for gene sequencing using dry ice. Sequencing was started after samples passed quality control.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: In total, 3 × 105 CT26 or LLC cells were subcutaneously injected into the right flank of BALB/c or C57BL/6 mice. When the tumor volume reached 50–75 cm3, the mice were randomly assigned to the following four groups: Control, drug (MEK inhibitor or AMG510), RT, and drug + RT. Each group contained six or seven mice. Mice in the MEKi and MEKi + RT groups were administered trametinib (1 mg/kg) via oral gavage daily, mice in the AMG510 and AMG510 + RT groups were administered sotorasib (3 mg/kg) via oral gavage daily, and the others were administered the solvent (corn oil) via oral gavage at the same time. After 2 days of oral gavage, the mice in the RT and combined therapy groups received radiation (8 Gy/1F).

tag: tissue

value: colon cancer

tag: cell line

value: LLC

value: lung cancer cell

value: WT

value: trametinib 1mg/Kg+8Gy/1f


title: SKI3 Sm Rep#3

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_SKI_3_SmR3_S12

tag: treatment


title: LLC cells, radiation+MEKi, rep2


title: SKI3 Sm Rep#1

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_SKI3_SmR1_S4


title: Sh_D1N_Gn: non-D1R expressing, non-virus infected, AAV5-ZacF-U6-luczsGreen-shShank3

city: Lausanne

first: Elia

last: Magrinelli

state: Canto Vaud

address: Rue du Bugnon 9

department: Department of Neuroscience

country: Switzerland

institute: University of Lausanne

data_processing:
RNAseq reads were aligned to the GRCm38 genome assembly using STAR aligner
The number of reads per transcript was calculated with the open-source HTSeq Python library
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files containing count table for every replicated sample per condition

source_name: Nucleus Accumbens cells

extract_protocol:
Nucleus Accumbens were removed, cells were dissociated using papain incubation and FACsorted to obtain the 4 types of cells per experiment used in the analysis. To prepare cDNA libraries, collected frozen cells were processed using a Quiagen RNeasy kit (Qiagen, #74034) to extract RNA
cDNA libraries were prepared for sequencing using standard Illumina protocols using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 in 100 pairbase length fragments for a minimum of 1 million reads per sample.

tag: strain

value: C57Bl/6j, D1R:Cre

tag: age

tag: phenotype

value: D1n - D1R non-expressing

tag: viral infection

value: Gn - non-infected

tag: virus type

value: sh - AAV5-ZacF-U6-luczsGreen-shShank3


title: Sh_D1p_Gn: D1R expressing, non-virus infected, AAV5-ZacF-U6-luczsGreen-shShank3

value: D1p - D1R expressing


title: Sh_D1n_Gp: non-D1R expressing, virus infected, AAV5-ZacF-U6-luczsGreen-shShank3

value: Gp - infected


title: LLC cells, radiation, rep3

tag: cell type


title: Sh_D1p_Gp: D1R expressing, virus infected, AAV5-ZacF-U6-luczsGreen-shShank3


title: small intestine scRNA-seq from nociceptor knockout ileum

value: Ileum

value: Epithelial cells


title: LLC cells, radiation, rep2


title: SKI3 Mock Rep#2

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_SKI3_MockR2_S7

source_name: SKI3 RNAi roots inoculated with water

value: SKI3 RNAi

value: water


title: LLC cells, radiation+MEKi, rep1


title: Scr_D1n_Gn: non-D1R expressing, non-virus infected, AAV1-GFP-U6-scrmbshRNA

value: scr - AAV1-GFP-U6-scrmbshRNA


title: SKI3 Mock Rep#1

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_SKI3_MockR1_S3

value: GMUCT 2.0 RNA

value: polyA/uncapped RNA


title: LLC cells, radiation, rep1

value: colon cancer

value: LLC


title: Scr_D1p_Gn: D1R expressing, non-virus infected, AAV1-GFP-U6-scrmbshRNA


title: Gus Sm Rep#3

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_Gus_SmR3_S10

source_name: Gus RNAi roots inoculated with S. meliloti 1021

value: Gus RNAi

value: S. meliloti 1021


title: LLC cells, control, rep3

value: lung cancer cell

value: WT

value: control


title: Scr_D1n_Gp: non-D1R expressing, virus infected, AAV1-GFP-U6-scrmbshRNA

value: C57Bl/6j, D1R:Cre

value: D1n - D1R non-expressing


title: Gus Sm Rep#2

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_Gus_SmR2_S6


title: Scr_D1p_Gp: D1R expressing, virus infected, AAV1-GFP-U6-scrmbshRNA

value: D1p - D1R expressing

value: Gp - infected


title: LLC cells, control, rep2


title: SKI3 Mock Rep#3

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_SKI3_MockR3_S11


title: Gus Sm Rep#1

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_Gus_SmR1_S2


title: mouse rep3

city: Dublin

first: vikrant

last: singh

state: Ireland

address: 31 York Street

country: Ireland

institute: Royal college of Surgeons in Ireland

description: Total RNA containing micro-RNA

data_processing:
The quality of all the sample were analysed and assured that all sample have Q-score more than 30.
The fastq file were processed by the mapper and quantification module miRDEEP2 ver 2.0.0.7 (PMID: 18392026 ) for miRNA expression profiling.
The processed reads were further mapped to the known miRNA for mouse and rat by using MIRBASE version 21 (http://www.mirbase.org) and miRNA read counts were obtained for all the samples.
Supplementary_files_format_and_content: Processed data contains read count and are in tabular format

source_name: Retina

extract_protocol:
The enucleated rat eyes were harvested and stored in the RNAlater (Qiagen), and retinas were dissected immediately under a dissection microscope. Total RNAs and miRNAs were isolated from the dissected retina by using a miRNeasy mini kit (Qiagen, Hilden, Germany). One microgram of miRNA samples in triplicate was prepared as per the manufacturers’ instructions (Illumina Inc. San Diego, CA, USA). The libraries of cDNA from the biological samples in triplicate were sequenced by using an Illumina Hiseq-2500 RNA-seq platform as 50 bp single-end chemistry.
miRNA libraries were prepared for sequencing using a standard Illumina protocols

value: Retina

value: 9 weeks

value: Wild type


title: LLC cells, MEKi, rep3

value: trametinib 1mg/Kg


title: LLC cells, control, rep1


title: SAS-R after 10Gy IR 3h

city: Kumamoto

first: Ryoji

last: Yoshida

state: Kumamoto

address: Honjo 1-1-1, Chu-o-ku

department: Oral and Maxillofacial Surgery

institute: Kumamoto University

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

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

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

source_name: SAS_R, 3hr_after_2Gyx5_days

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

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

value: squamous cell carcinoma

value: SAS-R


title: SAS-R after 10Gy IR 6h

source_name: SAS_R, 6hr_after_2Gyx5_days


title: mouse rep2

description: Total RNA containing micro-RNA


title: Gus Mock Rep#3

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_Gus_MockR3_S9

source_name: Gus RNAi roots inoculated with water

value: water

value: GMUCT 2.0 RNA

value: polyA/uncapped RNA


title: SAS-R after 10Gy IR 12h

source_name: SAS_R, 12hr_after_2Gyx5_days


title: Gus Mock Rep#2

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_Gus_MockR2_S5

value: Gus RNAi


title: LLC cells, MEKi, rep2

value: colon cancer

value: LLC

value: lung cancer cell


title: mouse rep1

description: Total RNA containing micro-RNA


title: Gus Mock Rep#1

description:
polyA from uncapped RNA purified with oligodT-magnetic beads
GMUCT_Gus_MockR1_S1


title: LLC cells, MEKi, rep1

value: WT


title: SAS after 10Gy IR 12h

source_name: SAS_WT, 12hr_after_2Gyx5_days

value: SAS


title: protein A and protein G control

status: Public on Sep 30 2022

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

description: bigWig: chr1-20,X

data_processing:
Paired end reads (R1 and R2 FASTQ files) were treated as single reads
R1 and R2 reads were cleaned using fastp application (github..com/OpenGene/fastp.git) . Reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3
Peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
Peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
Bedgraph files were converted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromosome fragments
Genome_build: macFas5 (June 2013), Accession GCA_000364345.1 , NCBI Assembly 704988.
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

organism: Macaca fascicularis

source_name: dissected testis

extract_protocol:
Testis fractionation: Testis samples were placed on ice and cut into pieces with sterile scalpel. Homogenates were individually filtered through two mesh wire gauzes to remove large pieces of tissue fragments and the cells of stroma. Cells in filtered homogenates were extensively washed with cold PBS and fixed with 1% EM-grade formaldehyde/PBS for 15 min. Crosslinking was quenched with glycine (0.125M final concentration). Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrees C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina HiSeq system with Illumina-provided protocols for paired-end sequencing.

value: testis

value: male germline cells

tag: antibody

value: Dynabeads Protein A and protein G


title: SAS-R non-IR

source_name: SAS_R, Non_IR


title: SAS after 10Gy IR 3h

source_name: SAS_WT, 3hr_after_2Gyx5_days


title: SAS after 10Gy IR 6h

source_name: SAS_WT, 6hr_after_2Gyx5_days


title: SAS-R after 10Gy IR 1h

source_name: SAS_R, 1hr_after_2Gyx5_days


title: STAG3_SMC1B_RAD21L_c2: 3x RAD21L transgene clone 2

description: infected with rtTA, Tet-On-STAG3, Tet-On-SMC1beta, and Tet-On-RAD21L lentiviruses

data_processing:
the original image data was transferred into sequence data via base calling, producing raw reads and saved as FASTQ files.
reads trimmed of adapters and  low quality reads using Trim Galore v 0.5.0
clean FASTQ files  generated.
gene counts  calculated using RSEM v1.2.22, using rsem-calculate-expression with --bowtie2, --bowtie2-sensisitvity-level very_sensitive
reads  aligned to hg38 assembly indexed with version 81 Ensembl GTF
pairwise differential expression values, PCA plots and MA plots generated using DESeq2 v1.24 in R v3.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: (1) BigWig files from individual reads showing the RNA-seq signal genome-wide. (2) csv matrix  DLD1_joined_RNA_expression.txt, with fields: ensg, gene_symbol, log2FoldChange, padj, and raw read counts.

source_name: colon epithelium

growth_protocol: DLD-1 cells and stably infected derivatives were grown in IMDM with 10% or 20% Tet-On certified FBS. Cells infected with lentivirus stock were selected for 4 weeks or more in media supplemented with 600µg/ml G418, 300 µg/ml zeocin, 1 µg/ml puromycin, or 200 µg/ml hygromycin B, dependent on the vector's marker, followed by the selection of individual clones.

extract_protocol:
trizol, DNase I, oligo-dT beads enrichment, fragmentation with average size 200nt
cDNA libraries were prepared for sequencing using standard protocols, including: first strand synthesis using random hexamer primers, purification of dsDNA with magnetic beads, end repai, addition of single adenine to the 3' termini, sequencing adaptor ligation, and PCR amplification.

treatment_protocol: For RNA-seq experiments, stable Tet-On transgenic DLD-1 cells and the control replicates were plated at 40% to 50% confluence in 10 cm plates, and induced by 200 ng/ml of doxycycline for 72 hours

value: immortalized tumor cells DLD-1

tag: disease

value: colorectal adenocarcinoma

tag: transgene


title: CENP-A ChIP Monkey 5

description: bigWig: chr1-20,X

value: Abcam, anti-CENP-A ab13939


title: STAG3_SMC1B_REC8_p1: 3x REC8 transgene population 1

description: infected with rtTA, Tet-On-STAG3, Tet-On-SMC1beta, and Tet-On-REC8 lentiviruses


title: STAG3_SMC1B_RAD21L_p1: 3x RAD21L transgene population 1

value: rtTA, Tet-On-STAG3, Tet-On-SMC1beta, and Tet-On-RAD21L lentiviruses


title: STAG3_SMC1B_REC8_c3: 3x REC8 transgene clone 3

value: rtTA, Tet-On-STAG3, Tet-On-SMC1beta, and Tet-On-REC8 lentiviruses


title: STAG3_SMC1B_p3: 2x transgene population 3

description: infected with rtTA, Tet-On-STAG3, and Tet-On-SMC1beta lentiviruses


title: STAG3_SMC1B_REC8_c2: 3x REC8 transgene clone 2


title: Normal_p3: control population 3

description: parent cell line


title: Normal_p2: control population 2

description: parent cell line


title: Normal_p1: control population 1

description: parent cell line


title: SAS non-IR

source_name: SAS_WT, Non_IR

value: squamous cell carcinoma


title: STAG3_SMC1B_p2: 2x transgene population 2

value: rtTA, Tet-On-STAG3, and Tet-On-SMC1beta lentiviruses


title: 5KO,DS,HiC,rep1

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

data_processing:
Hi-C data processing was done by using Docker for 4DN Hi-C pipeline (v43, https://github.com/4dn-dcic/docker-4dn-hic). The pipeline includes alignment (using the mouse genome, mm10) and filtering steps.
After filtering valid Hi-C alignments, .hic format Hi-C matrix files were generated by Juicer Tools
Assembly: mm10
Supplementary files format and content: hic

extract_protocol: Hi-C experiments were performed based on DpnII enzyme (4-bps cutter) using 2×106 fixed cells. Hi-C libraries were subject to paired-end sequencing (150 base pair (bp) read length) using HiSeq X Ten. Detailed protocol for HiC-seq library preparation is available at Protocols.io (https://www.protocols.io/view/iconhi-c-protocol-ver-1-0-4mjgu4n).

value: iMEFs

tag: genotype


title: 5KO,DS,HiC,rep2


title: 5KO,DMSO,HiC,rep1

value: DMSO


title: WT,DS,HiC,rep1


title: 5KO,DMSO,HiC,rep2


title: STAG3_SMC1B_RAD21L_c1: 3x RAD21L transgene clone 1


title: WT,DMSO,HiC,rep2


title: WT,DMSO,HiC,rep1


title: ATAC-seq biol. repl.2 DLD1-control

data_processing:
the original image data was transferred into sequence data via base calling, producing raw reads and saved as FASTQ files.
clean FASTQ files were generated, i.e. reads trimmed of adapters and  low quality reads using fastp software (PMID: 30423086)
paired end reads (R1 and R2 FASTQ files) were aligned to human genome as paired reads using bowtie2 software (PMID: 22388286) with parameters: --very-sensitive -k 5  -X 1000 -x hg38
peaks were identified by Genrich v.0.6.1 (github.com/jsh58/Genrich), in ATAC-seq mode. The resulting tag density files were used for differential analyses. Bedgraph files were converted to bigWig files using bedGraphToBigWig script (ucsC utilities)
ATAC-seq peak annotations were done with GeneHancer (PMID: 28605766)
Assembly: hg38 (GRCh38.p12, NCBI Assembly ID: 5800238)
Supplementary files format and content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

extract_protocol:
~50,000 cells form each replicate and conditions were washed in PBS and then re-suspended in nuclei lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). The crude nuclear pellet was re-suspended directly in Tn5 reaction mix (10 µl of 5X TTBL, µl TTE Mix V50, and 35 µl of RNase/DNase free H2O) using TruePrepTM DNA Library Prep Kit V2 for Illumina® TD501 from VAZYME). The reactions mix were then incubated at 37 oC for 30 min, and kept on ice. The DNA was purified in 20 µl of 10 mM Tris, pH8 using MiniElute KIT (Qiagen).
DNA was amplified for an initial 5 cycles using the full eluate of transposed DNA, 2.5 µl of customized Nextera universal primer, 2.5 µl of customized Nextera barcoded primer and 25 µl of NEBNext High-Fidelity 2x PCR Master Mix (NEB). In the meantime, qPCR was set up in a total volume of 15 µl to determine the optimal PCR cycles for libraries amplifications. For each reaction, the number of PCR cycles that were added, were calculated from the plot of Rn vs. Cycle that corresponded to ¼ of maximum fluorescent intensity. Size selection of DNA was performed to eliminate the bulk of primer-dimer artifacts after libraries amplifications as described (PMID: 32913232). Namely,libraries were size selected by adding 1.3x volume of Agencourt AMPure XP magnetic beads (Beckman Coulter) to each PCR reaction, and eluted in 23 µl of 10 mM Tris, pH 8, after which, they  were quantified by Qubit using Quant-iT™ PicoGreen™ dsDNA Assay Kit, and sent for sequencing.  Libraries qualities were determined with The Agilent 2200 TapeStation system.

treatment_protocol: For ATAC-seq experiments, stable Tet-On transgenic cells and the control replicates were plated at 40% to 50% confluence in 10 cm plates, and induced by 200 ng/ml of doxycycline for 72 hours. ATAC-seq was carried out as described  (PMID: 25559105) with minor modifications.

value: colon epithelium

value: epithelial tumor cells

tag: disease state

tag: clone

value: control

value: Dox-induced


title: STAG3_SMC1B_p1: 2x transgene population 1


title: SAS after 10Gy IR 1h

source_name: SAS_WT, 1hr_after_2Gyx5_days

value: SAS


title: ATAC-seq  biol. repl. 2 DLD1/SMC1B-STAG3-RAD21L


title: WT,DS,HiC,rep2

value: WT


title: ChIP-2 STAG3 DLD-1/REC8+STAG3+SMC1B

description: bigWig: chr1-22,X,Y

data_processing:
the original image data was transferred into sequence data via base calling, producing raw reads and saved as FASTQ files.
reads trimmed of adapters and  low quality reads using fastp (doi.org/10.1093/bioinformatics/bty560)
clean FASTQ files  generated.
paired end reads (R1 and R2 FASTQ files) were treated as single reads. R1 and R2 reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3
peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
bedgraph files were converted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromsome fragments
Genome_build: hg38 (GRCh38.p12, NCBI Assembly ID: 5800238)
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

growth_protocol: K562, hTERT RPE-1, or DLD-1 cells and stably infected derivatives were grown in IMDM with 10% or 20% Tet-On certified FBS. Cells infected with lentivirus stock were selected for 4 weeks or more in media supplemented with 600µg/ml G418, 300 µg/ml zeocin, 1 µg/ml puromycin, or 200 µg/ml hygromycin B, dependent on the vector's marker, followed by the selection of individual clones.

extract_protocol:
Cells were fixed at 1% formaldehyde for 10 min at room temperature and quenched with 0.125 mM glycine for 5 min. For some experiments a dual crosslinking was used, by incubating the cells in 1.5 mM ethylene glycol bis(succinimidyl succinate) (EGS) (Sigma) in PBS for 45 min at RT under gentle shaking. Then, 1% formaldehyde was added and the incubation left to proceed for 20 min, after which the fixation was quenched with 0.125 mM glycine for 5 min at RT. Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrees C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), and the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina system with Illumina-provided protocols for paired-end sequencing

treatment_protocol: For ChIP-seq experiments, stable Tet-On transgenic cells and the control replicates were plated at 40% to 50% confluence in 10 cm plates, and induced by 200 ng/ml of doxycycline for 72 hours

value: epithelial tumor cells DLD-1

tag: chip antibody

value: custom rabbit polyclonal anti-STAG3


title: ChIP-2 STAG3 DLD-1/RAD21L+STAG3+SMC1B

description: bigWig: chr1-22,X,Y


title: ChIP-1 STAG3 DLD-1/REC8+STAG3+SMC1B

description: bigWig: chr1-22,X,Y


title: ChIP-1 RAD21L DLD-1/RAD21L+STAG3+SMC1B

description: bigWig: chr1-22,X,Y

value: custom goat polyclonal anti-RAD21L


title: ChIP-2 SMC1B DLD-1/REC8+STAG3+SMC1B

description: bigWig: chr1-22,X,Y

value: colorectal adenocarcinoma

value: custom rabbit polyclonal anti-SMC1B


title: ChIP-2 RAD21L DLD-1/RAD21L+STAG3+SMC1B

description: bigWig: chr1-22,X,Y

value: custom rabbit polyclonal anti-RAD21L


title: ChIP-2 SMC1B DLD-1/RAD21L+STAG3+SMC1B

description: bigWig: chr1-22,X,Y


title: ChIP-1 SMC1B DLD-1/REC8+STAG3+SMC1B

description: bigWig: chr1-22,X,Y


title: ATAC-seq biol. repl. 1 DLD1/SMC1B-STAG3-RAD21L


title: ChIP-2 SMC3 DLD-1/REC8+STAG3+SMC1B

description: bigWig: chr1-22,X,Y

value: rabbit polyclonal anti-SMC3, Abcam ab9263


title: ChIP-2 SMC3 DLD-1/RAD21L+STAG3+SMC1B

description: bigWig: chr1-22,X,Y


title: ChIP-2 REC8 DLD-1/REC8+STAG3+SMC1B

description: bigWig: chr1-22,X,Y

value: custom rabbit polyclonal anti-REC8


title: ChIP-1 SMC3 DLD-1/REC8+STAG3+SMC1B

description: bigWig: chr1-22,X,Y


title: ChIP-1 STAG3 DLD-1/RAD21L+STAG3+SMC1B

description: bigWig: chr1-22,X,Y


title: ChIP-1 SMC3 DLD-1

description: bigWig: chr1-22,X,Y


title: ChIP-2 CTCF DLD-1

description: bigWig: chr1-22,X,Y

value: rabbit monoclonal anti-CTCF, Cell Signalling, D31H2 and D1A7


title: ChIP-1 REC8 DLD-1/REC8+STAG3+SMC1B

description: bigWig: chr1-22,X,Y


title: ChIP STAG3 DLD-1/STAG3

description: bigWig: chr1-22,X,Y


title: ChIP-2 SMC3 DLD-1

description: bigWig: chr1-22,X,Y


title: ATAC-seq biol. repl.1 DLD1-control


title: ChIP-1 CTCF DLD-1

description: bigWig: chr1-22,X,Y


title: ChIP-1 STAG3 K562/STAG3

description: bigWig: chr1-22,X

source_name: bone marrow

value: lymphoblast  tumor cells K-562

value: chronic myelogenous leukemia