title: CD40L_FasL_QVD replicate 3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt file including raw read count per gene for each sample

source_name: peripheral blood

growth_protocol: Human CD19+ CD27- B cells were isolated magnetically from peripheral blood of healthy donors.

extract_protocol:
RNA was isolated using the RNAeasy Mini Kit (Qiagen) according to manufacturer's instructions. On-column Dnase I treatment was performed during RNA extraction.
Barcoded RNA-sequencing libraries were prepared from 100 ng total RNA using the Illumina TruSeq RNA Sample Preparation v2 Kit (Illumina) implemented on the liquid handling robot Beckman FXP2

treatment_protocol: Isolated B cells were stimulated with CD40L overnight or left unstimulated. CD40L-stimulated B cells were treated then with FasL or FasL+Q-VD for 4h.

value: CD19+ CD27- B cells

value: peripheral blood

value: healthy donor

tag: agent

value: CD40L+ FasL+Q-VD(4h)


title: MDA468_24h_DMSO_b

status: Public on Mar 07 2024

type: SRA

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: count matrix for combinations - MDA468 24h.csv

library_source: transcriptomic

data_processing:
Libraries were sequenced by the Illumina Novaseq 6000 using SP mode 100 cycles kit (Illumina)
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154))
Reads were trimmed using cutadapt (DOI:10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
The remaining reads were mapped to the genome (hg38) using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Assembly: hg38
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were maintained in RPMI medium supplemented with 10% FBS, 1% Penicillin-Streptomycin solution.

extract_protocol:
RNA was extracted using TRI reagent (Sigma), following standard extraction protocol.
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

treatment_protocol: Treatment was performed in low cell density (~50% confluency). Treatment with single reagents (JQ1, BTZ, erastin, RSL3) was done in the indicated concentrations and time points. Treatment with the JQ1 + BTZ combinations was done by diluting the components in growth medium, followed by 2-3 minutes of vortexing. The combination was added immediatly to the cells. DMSO concentrations were equalized in all treatments.

tag: cell line

tag: cell type

value: triple negative breast cancer line

tag: genotype

value: WT

tag: treatment

value: DMSO

tag: concentration

tag: time

value: 24 hr


title: MDA468_24h_B3_b

value: BTZ

value: 3 nM


title: CD40L_FasL replicate 3

country: Germany

tag: tissue

value: CD40L+ FasL(4h)


title: LNCAP_250_3

type: genomic

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

description: transformed prostate cancer cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing:
All arrays were processed and normalised using the Sesame pipeline (Zhou et al. 2018) with functions inferInfiniumIChannel(), dyeBiasNL(), pOOBAH() and noob() with default arguments.
Normalised beta values from sesame::getBetas().
Unmethylated and methylated signal intensities are taken from the “UR” and “UG” columns respectively from the sample SigDF object

label: Cy5 and Cy3

molecule: genomic DNA

source_name: LNCaP cells

label_protocol: Standard Illumina Protocol

growth_protocol: LNCaP prostate cancer cells were cultured as described in PMID 11850822. Normal prostate epithelial cells (PrEC) were cultured according to the manufacturer’s instructions in prostate epithelial growth medium (PrEGM, catalogue no. CC-3166; Cambrex Bio Science) as described in PMID 20173741. MCF7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF7 (TAMR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10－7 M) (TAM). Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge. MCF7 and TAMR cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.

extract_protocol: For the LNCaP, PrEC, TAMR and MCF7 cells and PDX samples genomic DNA was isolated using the QIAamp DNA Mini kit (Qiagen). For the prostate tumour samples fresh-frozen tissue cores (10x5mm) were retrieved, and matched H&E slides reviewed by a specialist pathologist to identify areas of tumour. Regions of high tumour content were microdissected from the core and DNA extracted using the Qiagen AllPrep kit (Qiagen).

treatment_protocol: For the breast cancer PDX model mice were randomly assigned to treatment groups and treated  with either a vehicle (0.5mg/kg PBS) or Decitabine (0.5mg/kg DAC) and treated until ethical end-point. For the TAMR cell experiments cells were treated daily with Decitabine (100 nM) for 7 consecutive days and harvested at day 7 (“Decitabine Day 7”). Control cells were cultured for a total of 11 days in normal media and harvested for “Control”. For the “Decitabine Recovery” samples, cells were treated daily with Decitabine (100nM) for 7 consecutive days, after which fresh media was added; cells were cultured for 28 additional days and harvested on day 35.

value: Cell line


title: LNCAP_125_3

description: transformed prostate cancer cell line


title: Stromal cell Durvalumab treated replicate 2

city: Silver Spring

first: Carole

last: Sourbier

state: MD

address: 10903 New Hampshire Ave

department: CBER

country: USA

institute: FDA

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed for quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Homo sapiens sequence/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: Stromal cells

extract_protocol:
Total RNA was isolated from cultured cells according to the QIAGEN RNeasy mini kit protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Sample prep kit.

value: Fibroblast

value: Durvalumab


title: MDA468_24h_B3_a


title: CD40L replicate 3


title: SYN_15917

description: prostate tumour

source_name: Prostate tumour

value: Prostate tumour


title: Stromal cell Durvalumab treated replicate 1


title: MDA468_24h_B2_b

value: 2 nM


title: TAMR_Decitabine_Recovery_1

description: Tamoxifen-resistant MCF7, Decitabine Recovery Day 28

source_name: TAMR cells

value: Decitabine Recovery Day 28


title: Stromal cell Atezolizumab treated replicate 3

value: Atezolizumab


title: MDA468_24h_B2_a


title: PREC_125_3

description: primary cell culture of prostate epithelial cells

source_name: PrEC cells


title: CD40L_FasL_QVD replicate 2

value: CD19+ CD27- B cells

value: peripheral blood


title: PREC_250_3


title: Stromal cell Atezolizumab treated replicate 2


title: MDA468_6h_JB6_b

description: count matrix for combinations - MDA468 6hr.csv

value: JQ1 + BTZ

value: 6 hr


title: TAMR_Decitabine_Recovery_2


title: LNCAP_500_3

description: transformed prostate cancer cell line


title: DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 4-9hr ICRF-193 R2

city: Worcester

first: Job

last: Dekker

state: MA

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School/HHMI

library_source: genomic

data_processing:
Fastq files were mapped to the hg38 genome using the distiller pipeline (github.com/mirnylab/distiller-nf). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019). Reads were filtered for mapping quality (>Mapq30), and read normalized within each experiment. Multiresolution cooler files with iterative correction were made for both individual replicates and combined replicates.
Multiresolution cooler files (multires.cool) containing high quality (Mapq>30) read normalized pairwise interactions for separate replicates and combined replicates.
Assembly: hg38

source_name: uterine/cervical adenocarcinoma cell line

growth_protocol: HeLa-S3 cells were cultured in glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin.

extract_protocol:
For each Hi-C library, approximately 1-5 million cells were used as input. Cells were crosslinked for 10 minutes at room temperature in a final concentration of 1% formaldehyde. Glycine was added to quench crosslinking. Cell pellets were frozen at -80C until PI staining and cell sorting, then were again frozen and stored at -80C until Hi-C library generation.
Hi-C was performed as described in Belagzhal et al, 2017, Methods. Restriction enzyme: DpnII

treatment_protocol: Cells were arrested in mitosis using 24hr Thymidine treatment, 3hr release, and 12hr Nocodazole, then released into G1. 30uM ICRF-193 was added at t4hr, and cells were fixed at t9hr. G1 cells were isolated by FACS.

value: HeLa-S3 (CCL-2.2)


title: TAMR

description: Tamoxifen-resistant MCF7


title: MDA468_6h_JB6_a

value: triple negative breast cancer line

value: WT


title: CD40L replicate 2

value: healthy donor


title: Stromal cell Atezolizumab treated replicate 1


title: PREC_500_3


title: Stromal cell Avelumab treated replicate 3

value: Avelumab


title: TAMR_Control_1

description: Tamoxifen-resistant MCF7, Control

value: Control


title: TAMR_Decitabine_Day7_1

description: Tamoxifen-resistant MCF7, Decitabine Day 7

value: Cell line

value: Decitabine Day 7


title: Stromal cell Avelumab treated replicate 2

value: Fibroblast


title: MDA468_6h_JB3_a


title: CD40L_FasL_QVD replicate 1

value: CD40L+ FasL+Q-VD(4h)


title: Stromal cell Avelumab treated replicate 1


title: MDA468_6h_JB2_b


title: CD40L_FasL replicate 1

value: CD40L+ FasL(4h)


title: Stromal cell treated as Vehicle replicate 3


title: TAMR_Decitabine_Day7_2


title: MDA468_6h_JB2_a


title: MCF7

description: MCF7 breast cancer cells

source_name: MCF7 cells


title: SYN_16599

description: prostate tumour

value: Prostate tumour


title: CD40L replicate 1


title: CD40L_FasL replicate 2


title: MDA468_6h_JB3_b


title: MDA468_6h_J_b


title: vein blood, CON, CON_9

city: Wuhan

first: Xuan

last: Xiao

state: Hubei

address: Yellow Crane Tower Street

country: China

institute: Wuhan University

data_processing:
The prepared DNA libraries were validated for quality control purposes. The libraries were then pooled together and sequenced using an Illumina sequencing platform to generate paired-end reads of 150 base pairs in length.
The raw RNA sequencing data was processed and analyzed using standard bioinformatics tools and methods to generate counts for each gene/feature.
Assembly: human GRCh38.102
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: vein blood

extract_protocol:
Blood samples were collected from patients and processed to isolate specific components. The isolated samples were preserved using established methods and stored frozen until needed for further analysis.
RNA libraries for RNA-seq were prepared using ABclonal Whole RNA-seq Library Prep kit following manufacture's protocols

value: vein blood

value: peripheral blood mononuclear cell

tag: group

value: control


title: MDA468_6h_J_a


title: Control replicate 2

value: CD19+ CD27- B cells

value: peripheral blood

value: unstimulated


title: WT, Colonic epithelium, Input

city: Shanghai

first: Wei

last: Gu

state: Shanghai

address: 51 Rijing Road

department: Beigene Institute

institute: Beigene

data_processing:
All reads were trimmed with trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and subjected to quality control with FastQC before and after adapter trimming.
Bowtie2 (Langmead and Salzberg, 2012)(version 2.4.1) was used to align the two independent ChIP-Seq analyses to the mouse (mm10) genome with default parameters.
Peaks were called using callpeak function in the MACS2 package with the following parameters (callpeak -t ChIPfile.bam -c Inputfile.bam --format Paired-end BAM --gsize M.musculs(1.87e9) -m 10 30 -q 0.001-bw 300); bigwigs made using bamCoverage function in the deeptools v3.4.3 with following the parameters (bamCoverage --binSize 25 -p 4 --normalizeUsing RPKM --extendReads $fragLength -b Chip.bam  -o ChIP.bw)
Supplementary files format and content: Bigwig
Supplementary files format and content: Bed

organism: Mus musculus

source_name: Colon

growth_protocol: Colonic epithelial tissues were collected by the EDTA method 30 days after tamoxifen injection and cross-linked with 1% formaldehye.

extract_protocol: Libraries were prepared using the ThruPLEX DNA-Seq Kit (Rubicon Genomics, R400427). All final libraries were size selected (200-800 bp) by AMPure XP beads (Beckman, A63880) and loaded for sequencing.

treatment_protocol: Pelleted cross-linked cells were resupended in 130 µl lysis buffer (50 mM Tris-HCl, 0.1% SDS, 10 mM EDTA and 1x Roche EDTA-free protease inhibitor) and sonicated ain a Covaris E210 sonicator at 4oC for 50 min with 5 min on/off cycles to obtain 200bp to 800bp chromatin fragments. Diluted lysates were incubated with anti-H3K27Ac antibodies at 4 °C overnight and were additionally incubated with 30 µl protein A/G magnetic beads. ChIPed DNA was purified with a MinElute purification kit.

value: Colon

value: Epithelium cells

tag: antibody


title: MDA468_6h_DMSO_b

value: triple negative breast cancer line

value: WT

value: DMSO

value: 6 hr


title: Stromal cell Durvalumab treated replicate_3

value: Durvalumab


title: Stromal cell treated as Vehicle replicate 1

value: Fibroblast


title: Control replicate 3

value: healthy donor


title: WT, Colonic epithelium, H3K27Ac-ChIP, Biological Repicate 2


title: vein blood, CON, CON_8


title: vein blood, CON, CON_7


title: Stromal cell Durvalumab treated replicate_2


title: WT, Colonic epithelium, H3K27Ac-ChIP, Biological Repicate 1


title: vein blood, CON, CON_6


title: MDA468_6h_B6_b

value: BTZ

value: 6 nM


title: MTA2KO, Colonic epithelium, H3K27Ac-ChIP, Biological Repicate 2


title: Stromal cell Atezolizumab treated replicate_3

value: Atezolizumab


title: vein blood, CON, CON_5

value: vein blood

value: peripheral blood mononuclear cell


title: Stromal cell Durvalumab treated replicate_1


title: TAMR_Control_2

description: Tamoxifen-resistant MCF7, Control

value: Cell line

value: Control


title: MDA468_6h_B6_a


title: vein blood, CON, CON_4

value: control


title: LNCAP_125_2

description: transformed prostate cancer cell line


title: Stromal cell treated as Vehicle replicate 2


title: SYN_5656

description: prostate tumour

value: Prostate tumour


title: LNCAP_500_2

description: transformed prostate cancer cell line


title: Stromal cell Atezolizumab treated replicate_2


title: vein blood, CON, CON_3


title: MDA468_6h_B3_a

value: 3 nM


title: Stromal cell Atezolizumab treated replicate_1


title: Input of MTA2KO colonic epithelium

description: Input

data_processing:
All reads were trimmed with trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and subjected to quality control with FastQC before and after adapter trimming.
Bowtie2 (Langmead and Salzberg, 2012) was used to align the two independent ChIP-Seq analyses to the mouse (mm10) genome with default parameters.
Aligned ChIP-Seq data in SAM format were transformed to BAM files and non-uniquely mapped reads were filtered-out.
Duplicate alignments were then marked and removed using Sambamba.
The merge function in samtools was used to merge the BAM files of different replicates and filter out non-uniquely mapped reads.
Deeptools bamCoverage (duplicate reads ignored, RPKM normalized) was used to generate bigWig files from BAM files.
Assembly: Mouse mm10
Supplementary files format and content: Bigwig files for visualization of TFs genomic binding peaks.

source_name: Intestine epithelium

extract_protocol:
50 µl of pelleted cross-linked cells were resuspended in 350 µl sarkosyl lysis buffer (0.25% sarkosyl, 1 mM DTT and protease inhibitor in RIPA buffer) and sonicated at 15% amplification by a tip sonicator (Qsonica, Q125) to obtain 200bp to 800bp chromatin fragments. Diluted lysates were incubated with TFs antibodies at 4°C overnight and were additionally incubated with 30 µl protein A/G magnetic beads. ChIPed DNA was purified with a MinElute purification kit.
Libraries were prepared using the ThruPLEX DNA-Seq Kit
Exactly followed the protocol from Takara bio, R400428. All final libraries were size selected (200-800 bp) by AMPure XP beads (Beckman, A63880) and loaded for sequencing.

treatment_protocol: Epithilal tissues were collected by the EDTA method 30 days after tamoxifen injection and cross-linked with 2mM DSG and 1% formaldehye.

tag: genotyping

value: MTA2 KO

tag: intestine part

value: Colon


title: PREC_125_2


title: Input of wild type colonic epithelium

description: Input

value: Wild Type


title: HNF4A_ChIP in MTA2KO colonic epithelium


title: Stromal cell Avelumab treated replicate_3

value: Avelumab


title: vein blood, CON, CON_1


title: Control replicate 1

value: CD19+ CD27- B cells

value: peripheral blood

value: unstimulated


title: LNCAP_250_2

description: transformed prostate cancer cell line


title: Stromal cell Avelumab treated replicate_2

value: Fibroblast


title: MDA468_6h_B2_a

value: triple negative breast cancer line

value: WT

value: BTZ

value: 2 nM

value: 6 hr


title: HNF4A_ChIP in wild type colonic epithelium


title: PREC_250_2

value: Cell line


title: MTA2KO, Colonic epithelium, H3K27Ac-ChIP, Biological Repicate 1

value: Epithelium cells


title: vein blood, CRAO, CRAO_V9

value: vein blood

value: peripheral blood mononuclear cell


title: HCC70_RSL3_b

description: count matrix for ferroptosis inducers - MDA468 and HCC70.csv

value: 4 hr


title: SATB2_ChIP in MTA2KO colonic epithelium

value: MTA2 KO

value: Colon


title: vein blood, CRAO, CRAO_V8


title: Stromal cell treated as Vehicle replicate_3


title: HCC70_RSL3_a


title: MDA468_6h_DMSO_a

value: DMSO


title: vein blood, CRAO, CRAO_V7


title: Stromal cell Avelumab treated replicate_1

value: Avelumab


title: Stromal cell treated as Vehicle replicate_2


title: HCC70_Erastin_b

value: Erastin

value: 1 μM

value: 9 hr


title: MDA468_6h_B3_b

value: triple negative breast cancer line

value: 3 nM


title: MTA2_ChIP in Satb2KO colonic epithelium rep 2

value: SATB2 KO


title: vein blood, CRAO, CRAO_V6


title: SATB2_ChIP in wild type colonic epithelium

value: Wild Type


title: vein blood, CRAO, CRAO_V5


title: Stromal cell treated as Vehicle replicate_1

value: Fibroblast


title: Bone marrow cell Nivolumab treated replicate 3

source_name: Bone marrow cells

value: Nivolumab


title: MDA468_6h_B2_b

value: WT

value: BTZ

value: 2 nM

value: 6 hr


title: vein blood, CON, CON_2

value: vein blood

value: peripheral blood mononuclear cell

value: control


title: vein blood, CRAO, CRAO_V4


title: HCC70_DMSO_a

value: DMSO


title: MTA2_ChIP in wild type colonic epithelium rep 2

value: Colon


title: MTA2_ChIP in Satb2KO colonic epithelium rep 1


title: SYN_10651

description: prostate tumour

value: Prostate tumour


title: HCC70_Erastin_a

value: Erastin

value: 1 μM

value: 9 hr


title: Bone marrow cell Nivolumab treated replicate 1


title: PREC_500_2

value: Cell line


title: Bone marrow cell Nivolumab treated replicate 2


title: vein blood, CRAO, CRAO_V3


title: MTA2_ChIP in wild type colonic epithelium rep 1

value: Wild Type


title: SYN_12543

description: prostate tumour


title: vein blood, CRAO, CRAO_V2


title: Bone marrow cell treated as Vehicle for Nivolumab treated replicate 3

value: Fibroblast


title: Chlamydomonas, Control  24 hours, rep5

city: Mountain View

first: Josep

middle: Vilarrasa

last: Blasi

state: CA

address: 787 corto street

institute: Aetna

data_processing:
RNA-seq reads were aligned using BWA to the Chlamydomonas reference genome 5.6
DESeq2 package was used to call transcripts as differentially expressed at a false-discovery-rate (Benjamini-Hochberg method) FC > 2, (FDR < 0.01)
Assembly: Chlamydomonas reference genome 5.6
Supplementary files format and content: tab-limited text files, including raw counts fr each gene

organism: Chlamydomonas reinhardtii

source_name: Vegetative, haploid, Cells

growth_protocol: RNA-seq samples: prior to sample collection wild-type strains (CMJ030/CC-4533) were refreshed in solid media and inoculated in liquid media, Tris-Acetate-Phosphate (TAP) with modified trace elements 95 at 22 ºC in low continuous light (100 μmol photons m-2 s-1). After 2 passages in liquid media (~6 doublings/passage), cells growing in early-mid exponential phase (~2E+06 cells/ml) were used for inoculation. Once cultures reached early-mid exponential phase (~2E+06 cells/ml) different osmolyte concentrations were inoculated, 100 mM NaCl (Sigma) and 300 mM mannitol using 1 liter Erlenmeyer flasks and grown with mild agitation (~150 rpm), 22 ºC and low continuous light

extract_protocol:
RNA extraction was performed using Direct-zol RNA miniprep kit (R2050) following manufacturer's instructions including in-column DNase I treatment prior RNA washing and elution steps
RNA-seq libraries were made using the Kapa mRNA HyperPrep kit (Roche, KK8540) following manufacturer’s protocols. Libraries were pooled based on fragment analyzer concentration
Libraries were pooled based on fragment analyzer concentrations

value: Vegetative, haploid, Cells

value: Wild-type

value: Control

tag: time point

value: 24 hours


title: Chlamydomonas, NaCl , 24 hours, rep3

treatment_protocol: Once cultures reached early-mid exponential phase (~2E+06 cells/ml) different osmolyte concentrations were inoculated, 100 mM NaCl (Sigma) and 300 mM mannitol using 1 liter Erlenmeyer flasks and grown with mild agitation (~150 rpm), 22 ºC and low continuous light

value: NaCl


title: Bone marrow cell treated as Vehicle for Nivolumab treated replicate 2


title: HCC70_24h_JB3_b

description: count matrix for combinations - HCC70 24h.csv

value: triple negative breast cancer line

value: WT

value: JQ1 + BTZ

value: 24 hr


title: vein blood, CRAO, CRAO_V1

value: vein blood

value: peripheral blood mononuclear cell


title: LNCAP_250_1

description: transformed prostate cancer cell line


title: Chlamydomonas, Mannitol, 24 hours, rep3

value: Mannitol


title: HCC70_24h_JB6_a


title: Bone marrow cell treated as Vehicle for Nivolumab treated replicate 1


title: arterial blood, CRAO, CRAO_A7

source_name: arterial blood

value: arterial blood


title: HCC70_24h_JB3_a


title: Chlamydomonas, NaCl, 6 hours, rep3

value: 6 hours


title: HCC70_24h_JB2_b


title: arterial blood, CRAO, CRAO_A6


title: Chlamydomonas, Mannitol, 6 hours, rep3


title: Bone marrow cell Pembrolizumab treated replicate 3

value: Pembrolizumab


title: Bone marrow cell Pembrolizumab treated replicate 2


title: HCC70_24h_JB2_a


title: arterial blood, CRAO, CRAO_A5


title: PREC_250_1

value: Cell line


title: arterial blood, CRAO, CRAO_A4


title: Bone marrow cell Pembrolizumab treated replicate 1

value: Fibroblast


title: arterial blood, CRAO, CRAO_A3


title: Bone marrow cell treated as Vehicle for Pembrolizumab treated replicate 3


title: HCC70_24h_J_a


title: Chlamydomonas, NaCl, 4 hours, rep3

value: Vegetative, haploid, Cells

value: 4 hours


title: arterial blood, CRAO, CRAO_A2


title: Bone marrow cell treated as Vehicle for Pembrolizumab treated replicate 2


title: Bone marrow cell treated as Vehicle for Pembrolizumab treated replicate 1


title: Chlamydomonas, NaCl, 60 min, rep3

value: Wild-type

value: 60 min


title: HCC70_24h_DMSO_a

value: DMSO


title: PREC_500_1


title: Infected macrophages with BM16M vs infected macrophages with BMLVM31 4 h p.i.

type: RNA

city: Mexico City

first: Cloé

last: Queijeiro-Barroso

state: Mexico City

address: Av Universidad 3000

department: FMVZ/Microbiología

country: Mexico

institute: Universidad Nacional Autónoma de México

description: Human macrophages diferenciated with PMA for 72 h, from THP1 human cell line, infected with Brucella melitensis 16M for 2 h and BM 1LVM31 for 2 h.

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature

scan_protocol: Images of the microarrays were acquired and quantified in a GenPix 4100 (Molecular devises) using the Array Pro Analyzer software.

data_processing:
Microarray data analysis was performed with free software genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM. GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes.
Using a sliding window algorithm to calculate the mean and standard deviation within a window surrounding each data point and define a z-score where z measures the number of standard deviations a data point is from the mean. Where zi is the z-score for each element, Ri is the log-ratio for each element, and sd(R) is the standard deviation of the log-ratio. With this criterion, the elements with a z-score > 2 standard deviations would be the significantly differentially expressed genes.

label: Alexa 555

source_name: Total RNA from infected macrophages with Brucella melitensis BM16M 4 h p.i.

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen)

growth_protocol: THP-1 monocytes diferenciated to macrophage with PMA for 72 h were cultured in RPMI supplemented 10% FBS, 37°C, 5% CO2. Bacteria was cultured in Brucella broth.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Macrophages were infected with strains of brucella melitensis for 2 or 4 h.

tag: sample type

value: Macrophages from THP1 cell line, diferenciated with PMA for 72 h.

label: Alexa 647

source_name: Total RNA from infected macrophages with Brucella melitensis BMLVM31 4 h p.i.


title: arterial blood, CRAO, CRAO_A1


title: HCC70_24h_J_b

value: triple negative breast cancer line

value: WT


title: Chlamydomonas, Mannitol, 60 minutes, rep3

value: 60 minutes


title: GD-BC_12

city: Verona

first: Barbara

last: Mariotti

state: Verona

address: strada le grazie 8

department: Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
Adapters and base quality trimming were performed using Trim Galore script with parameters -length 50 and -three_prime_clip_R1 3
Reads were mapped onto the Ensembl human transcriptome (version 94) with Hisat2 and quantified at the gene-level using HTSeq-count (-m intersection-nonempty -t exon -i gene_id)
Gene abundance was indicated as FPKM calculated according to the DESeq2 instruction.
Differential gene expression analysis and gene counts normalization among various samples was performed using DESeq2. Differentially expressed genes were identified by using as selection parameter an adjusted p-values (padj) lower than 0.05.
Genome_build: GrCh38 (Ensembl annotated transcriptome version 94)
Supplementary_files_format_and_content: Matrix of FPKM values for each sample

growth_protocol: Mononuclear cells and granulocytes were separated by density gradient centrifugation of the PB from GD, NSCLC/HNC  patients or HDs onto either Ficoll-Paque or Biocoll under endotoxin-free conditions. LDNs/PMN-MDSCs were isolated from the mononuclear cell fraction, while NDNs were isolated from the granulocyte fraction, by either flow cytometry sorting  or magnetic bead selection. Neutrophils precursors were purified from the mononuclear cell fraction from the PB of GDs by  flow cytometry sorting.

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
Libraries for transcriptome analysis were prepared using Smart-seq2 protocol (PMID: 24056875)

treatment_protocol: freshly isolated cells

tag: cell purification

value: CD66b+CD10-CD11b+CD16+  cells isolated by flow cytometry sorting

value: Band cells purified from GCSF-treated donor

value: Freshly purified


title: GD-BC_8


title: HCC70_24h_B6_b

value: BTZ

value: 6 nM

value: 24 hr


title: Infected macrophages with BM133 vs infected macrophages with BMLVM31 4 h p.i.

description: Human macrophages diferenciated with PMA for 72 h, from THP1 human cell line, infected with Brucella melitensis 133 for 4 h and BM LVM31for 4 h.

source_name: Total RNA from infected macrophages with Brucella melitensis BM133 4 h p.i.


title: Chlamydomonas, Mannitol, 30 minutes, rep3

value: Mannitol

value: 30 minutes


title: Chlamydomonas, NaCl, 30 minutes, rep3

value: Vegetative, haploid, Cells

value: NaCl


title: HCC70_24h_B6_a


title: HCC70_24h_DMSO_b


title: Chlamydomonas, Mannitol, 15 minutes, rep3

value: Wild-type

value: 15 minutes


title: Infected macrophages with BM133 vs infected macrophages with BM16M 4 h p.i.

description: Human macrophages diferenciated with PMA for 72 h, from THP1 human cell line, infected with Brucella melitensis 133 for 4 h and BM 16M for 4 h.


title: GD-BC_7

source_name: peripheral blood


title: PREC_125_1

value: Cell line


title: LNCAP_500_1

description: transformed prostate cancer cell line

source_name: LNCaP cells


title: Chlamydomonas, NaCl, 15 minutes, rep3


title: GD-BC_6


title: Chlamydomonas, Control, 0 hours, rep5

value: Control

value: 0 hours


title: Infected macrophages with BM16M vs infected macrophages with BMLVM31 2 h p.i.

description: Human macrophages diferenciated with PMA for 72 h, from THP1 human cell line, infected with Brucella melitensis 16M for 2 h and BM LVM31 for 2 h.

source_name: Total RNA from infected macrophages with Brucella melitensis BM16M 2 h p.i.

value: Macrophages from THP1 cell line, diferenciated with PMA for 72 h.

source_name: Total RNA from infected macrophages with Brucella melitensis BMLVM31 2 h p.i.


title: HCC70_24h_B3_a

value: triple negative breast cancer line

value: WT

value: 3 nM


title: HCC70_24h_B2_b

value: 2 nM


title: HCC70_24h_B2_a

value: BTZ


title: Chlamydomonas, Control  24 hours, rep4

value: Control  24 hours


title: GD-MM_7

value: CD66b+CD10-CD11b+CD16+/dim cells isolated by flow cytometry sorting

value: Metamyelocytes purified from GCSF-treated donor

value: Freshly purified


title: Infected macrophages with BM133 vs infected macrophages with BM16M 2 h p.i.

description: Human macrophages diferenciated with PMA for 72 h, from THP1 human cell line, infected with Brucella melitensis 133 for 2 h and BM 16M for 2 h.

source_name: Total RNA from infected macrophages with Brucella melitensis BM133 2 h p.i.


title: HCC38_Erastin_b

description: count matrix for ferroptosis inducers - HCC38.csv

value: Erastin

value: 1 μM

value: 9 hr


title: Chlamydomonas, Mannitol, 24 hours, rep2

value: Vegetative, haploid, Cells

value: Wild-type

value: Mannitol

value: 24 hours


title: LNCAP_125_1

description: transformed prostate cancer cell line

value: Cell line


title: GD-MM_6


title: rtt105 rep8

city: Boston

first: Xin

last: Wang

address: 300 Longwood Ave,

institute: Boston children's hospital

description: The library has the forward index: ttg and reverse index:ctg A total of  57520 colony number was in this library.

data_processing:
Large insertion detection: https://github.com/gucascau/iDSBins.git
Large insertion feature: https://github.com/gucascau/LargeInsertionFeature.git
Reference: RPA and Rad27 limit templated and inverted insertions at DNA breaks
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown overnight in YPD (1% yeast extract, 2% peptone, 2% dextrose), washed twice with YP-raffinose (1% yeast extract, 2% peptone, 2% raffinose) media, inoculated into 10 mL YP-raffinose media, and incubated at 30 °C overnight.

extract_protocol:
All colonies from YEP-Galactose plates were collected, pooled together and mixed vigorously. ~80 μl cells were spun down and the genomic DNA was extracted using standard glass beads and phenol chloroform. The genomic DNA was treated with RNase A overnight. The genomic DNA was dissolved with water and adjusted to a concentration of 10 ng/μl.
The construction of the amplicon sequencing library was adapted from Illumina’s protocol #15044223 Rev. B. Briefly, the sequencing libraries were constructed with two rounds of PCR using KAPA HiFi HotStart ReadyMix polymerase (Roche, 7958927001). For the first round of PCR, 3.2 μL genomic DNA and 0.5 μL 10 μM primers were used for a total volume of 25 μL. The forward and reverse primers targeting the MATa locus are located 11 bp upstream or 18 bp downstream of the HO cleavage site respectively, containing Illumina adapter sequence and 3 bases unique home index as described (7). The thermocycling conditions were: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. After the first round of PCR, 18μL PCR product was purified with an equal volume of AMPure XP beads (Beckman Coulter, A63880). The DNA was eluted with 52.5 μL of 10 mM Tris (pH 8.5) and used as the templates for the second round of PCR. For the second round of PCR, 5 μl template DNA, 5 μL index primer N7xx and 5 μL index primer S5xx from Nextera XT V2 Index kit (Illumina, FC-131-2001) were used for the total volume of 50 μL. The following conditions were used for the second round of PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. Then, the PCR product was purified with 1.2x volume of AMPure XP beads and eluted with 10 mM Tris pH 8.5. The average size of each sample was measured with TapeStation and the DNA concentration was measured with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850). Then, the DNA was diluted to a concentration of 4 nM. An equal volume of DNA from ~20 samples was pooled into the library. The 0.2 M NaOH was used to denature the pooled library and PhiX library (Illumina, FC‐110‐3001). After diluting the libraries with pre-chilled HT1 to 12 pM, pooled library and PhiX library were mixed with the ratio 9:1, further denatured by incubating at 96 °C for 2 min and immediately put in an ice-water bath for 5 min.
The denatured combined library was loaded into the MiSeq Reagent Kit v3 (600 cycle) (Illumina, MS-102-3003) for amplicon sequencing.

treatment_protocol: When the cell density was about 2x107/mL, 500 µL cells were spread onto YP-galactose (1% yeast extract, 2% peptone, 2% galactose, 2.5% agar) plates to induce HO expression and the DSB at MATa locus, and incubated at 30 °C for 5 days.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139

value: rtt105::hphMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30C


title: HCC38_Erastin_a

value: triple negative breast cancer line

value: WT


title: rtt105 rep7

description: The library has the forward index: tgg and reverse index:cct A total of  64960 colony number was in this library.


title: rtt105 rep6

description: The library has the forward index: tcg and reverse index:gat A total of  59120 colony number was in this library.


title: HCC70_24h_B3_b

value: BTZ

value: 3 nM

value: 24 hr


title: Chlamydomonas, NaCl, 6 hours, rep2

value: NaCl

value: 6 hours


title: HCC70_DMSO_b

value: DMSO


title: Chlamydomonas, Control  24 hours, rep3

value: Control  24 hours


title: GD-PM-MY_12

value: CD66b+CD10-CD11bdim/-CD16- cells isolated by flow cytometry sorting

value: Promyelocytes/myelocytes purified from GCSF-treated donor

value: Freshly purified


title: GD-MM_12

value: CD66b+CD10-CD11b+CD16+/dim cells isolated by flow cytometry sorting

value: Metamyelocytes purified from GCSF-treated donor


title: Infected macrophages with BM133 vs infected macrophages with BMLVM31 2 h p.i.

description: Human macrophages diferenciated with PMA for 72 h, from THP1 human cell line, infected with Brucella melitensis 133 for 2 h and BM LVM31 for 2 h.

value: Macrophages from THP1 cell line, diferenciated with PMA for 72 h.


title: Chlamydomonas, NaCl, 15 minutes, rep2

value: Vegetative, haploid, Cells

value: Wild-type

value: 15 minutes


title: GD-MM_8


title: HCC38_DMSO_b

value: triple negative breast cancer line

value: WT

value: 9 hr


title: GD-PM-MY_8


title: HCC38_DMSO_a


title: rtt105 rep5

description: The library has the forward index: tag and reverse index:gta A total of  44240 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139

value: rtt105::hphMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30C


title: Chlamydomonas, NaCl, 60 min, rep2

value: NaCl

value: 60 min


title: rtt105 rep4

description: The library has the forward index: ttc and reverse index:gtc A total of  55200 colony number was in this library.


title: GD-PM-MY_7

value: CD66b+CD10-CD11bdim/-CD16- cells isolated by flow cytometry sorting


title: GD-PM-MY_6

value: Promyelocytes/myelocytes purified from GCSF-treated donor


title: rtt105 rep3

description: The library has the forward index: tgc and reverse index:gca A total of  46080 colony number was in this library.


title: Chlamydomonas, Mannitol, 24 hours, rep1

value: Mannitol

value: 24 hours


title: E11

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to human genome using cellranger version 5.0.1
UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object (V4)
Assembly: GRCh38 (hg38)
Supplementary files format and content: .h5 files, RNA count matrix

source_name: tumor tissue

growth_protocol: N/A primary human cells

extract_protocol:
Minced tumor cells were put into single-cell suspension and loaded into 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions.
Library construction was performed per 10x instructions v3 chemistry
Each prepared library was sequenced on the NovaSeq using dual index sequencing

treatment_protocol: N/A no treatment

tag: cancer type

value: High-grade serous ovarian cancer

tag: location

value: Omentum


title: E12

value: Primary


title: rtt105 rep2

description: The library has the forward index: atg and reverse index:gct A total of  19824 colony number was in this library.


title: Chlamydomonas, NaCl , 24 hours, rep2

value: Vegetative, haploid, Cells

value: Wild-type


title: HNC-PMN-MDSC_5

value: CD66b+CD10+CD11b+CD16+ cells isolated by flow cytometry sorting

value: mPMN-MDSC purified from head and neck cancer patient

value: Freshly purified


title: rtt105 rep1

description: The library has the forward index: agg and reverse index:gga A total of  27360 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139


title: Chlamydomonas, Control, 0 hours, rep4

value: Control

value: 0 hours


title: E9


title: E10

value: Abdominal wall


title: Chlamydomonas, NaCl , 24 hours, rep1

value: NaCl


title: rad27 rep14

description: The library has the forward index: ttc and reverse index:gtc A total of  63648 colony number was in this library.

value: rad27::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 37C


title: HNC-PMN-MDSC_4


title: HCC70_24h_JB6_b

description: count matrix for combinations - HCC70 24h.csv

value: triple negative breast cancer line

value: WT

value: JQ1 + BTZ

value: 24 hr


title: E7

value: High-grade serous ovarian cancer

value: Omentum


title: Chlamydomonas, Mannitol, 60 minutes, rep2

value: Vegetative, haploid, Cells

value: Wild-type

value: Mannitol

value: 60 minutes


title: rad27 rep13

description: The library has the forward index: tgc and reverse index:gca A total of  45888 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139


title: E4

value: Low-grade serous ovarian cancer

value: Right ovary


title: Chlamydomonas, Mannitol, 30 minutes, rep2

value: 30 minutes


title: HNC-PMN-MDSC_2

value: CD66b+CD10+CD11b+CD16+ cells isolated by flow cytometry sorting

value: mPMN-MDSC purified from head and neck cancer patient

value: Freshly purified


title: Chlamydomonas, Control  24 hours, rep2

value: Control  24 hours


title: HNC-PMN-MDSC_3


title: E3

value: Left ovary


title: Chlamydomonas, Mannitol, 4 hours, rep2

value: 4 hours


title: HNC-mNDN_5

value: mNDN purified from head and neck cancer patient


title: E2


title: E1


title: HNC-mNDN_4


title: Chlamydomonas, Mannitol, 30 minutes, rep1


title: Chlamydomonas, Mannitol, 4 hours, rep3


title: rad27 rep10

description: The library has the forward index: ctg and reverse index:cca A total of  32352 colony number was in this library.

value: rad27::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30C


title: HNC-mNDN_3


title: HNC-mNDN_2


title: HNC-mNDN_1


title: Chlamydomonas, NaCl, 6 hours, rep1

value: Vegetative, haploid, Cells

value: NaCl

value: 6 hours


title: rad27 rep9

description: The library has the forward index: cag and reverse index:gag A total of  62208 colony number was in this library.


title: rad27 rep12

description: The library has the forward index: tcc and reverse index:ctt A total of  109824 colony number was in this library.

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 37C


title: HNC-PMN-MDSC_1


title: Donor_EB037 - CD74KO [KO3]

city: Paris

first: Eliane

last: Piaggio

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
Bulk RNAseq
D646T006

data_processing:
Raw-sequencing quality was assessed usingFastQC (v0.11.8)
Raw-sequencing data were aligned using STAR aligner (v2.5.3a)
Counting after alignement were performed
Differentially expressed genes were identified using DESeq2 R package in Bulk RNAseq (R version 4.0.3)
Assembly: hg38
Supplementary files format and content: Raw counts matrix of genes

source_name: Regulatory T cells

growth_protocol: CD127negCD25hi sorted Tregs are expanded during 21 days with 3 rounds of activation with aCD3aCD28 coated beads and IL-2

extract_protocol:
Expanded Tregs were washed with PBS (1X) and RNA was harvested using single-cell RNA purification kit (Norgen, Cat#51800) with 10 ng of cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (NovaSeq 6000)

value: Healthy donor blood

value: Regulatory T cells

tag: conditions

value: CRISPRCas9 RNPs targeting two exons of CD74


title: Chlamydomonas, Mannitol, 6 hours, rep2

tag: cell line

value: Wild-type

value: Mannitol


title: Donor_EB036 - CD74KO [KO2]

description:
Bulk RNAseq
D646T004

tag: cell type


title: rad27 rep11

description: The library has the forward index: tac and reverse index:cga A total of  39456 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139

tag: genotype


title: Donor_EB037 - WT [WT3]

description:
Bulk RNAseq
D646T005

value: CRISPRCas9 control RNP


title: Donor_EB036 - WT [WT2]

description:
Bulk RNAseq
D646T003


title: rad27 rep7

description: The library has the forward index: tgg and reverse index:cct A total of  36240 colony number was in this library.

tag: treatment

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 23C


title: rad27 rep8

description: The library has the forward index: ttg and reverse index:ctg A total of  25536 colony number was in this library.


title: rad27 rep6

description: The library has the forward index: tcg and reverse index:gat A total of  61440 colony number was in this library.


title: HD-mNDN_4_B

value: CD66b+CD10+CD11b+CD16+ cells isolated by flow cytometry sorting

value: mNDN purified from healthy donor

value: Freshly purified


title: Chlamydomonas, Control, 0 hours, rep3

value: Control

value: 0 hours


title: Chlamydomonas, Mannitol, 60 minutes, rep1

value: Vegetative, haploid, Cells

value: 60 minutes


title: rad27 rep5

description: The library has the forward index: tag and reverse index:gta A total of  17472 colony number was in this library.

value: rad27::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30C


title: HD-mNDN_3_B


title: Donor_EB035 - CD74KO [KO1]

description:
Bulk RNAseq
D646T002

value: Healthy donor blood


title: rad27 rep4

description: The library has the forward index: ttc and reverse index:gtc A total of  15072 colony number was in this library.


title: HD-mNDN_2_B


title: Donor_EB035 - WT [WT1]

description:
Bulk RNAseq
D646T001

value: Regulatory T cells


title: Chlamydomonas, NaCl, 15 minutes, rep1

value: NaCl

value: 15 minutes


title: rad27 rep3

description: The library has the forward index: tgc and reverse index:gca A total of  40896 colony number was in this library.


title: Chlamydomonas, NaCl, 30 minutes, rep2

value: Wild-type

value: 30 minutes


title: rad27 rep2

description: The library has the forward index: ctc and reverse index:ggt A total of  130000 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139


title: Chlamydomonas, Mannitol, 15 minutes, rep2

value: Mannitol


title: OI_22_05

first: Jiahao

last: Shi

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District,

department: Department of Ophthalmology

institute: Shanghai 9th Peoples Hospital Affiliated to Shanghai Jiaotong University School of Medicine

description: IOI

data_processing:
Illumina bcl2fastq software used for basecalling and original sequenced reads conversion, called Raw Data. And fastQC software were used for base quality control.
Sequenced reads were trimmed off primer/adaptor contaminated reads,and masked for  Low quality reads and N overtop reads,called clean reads
The clean reads were mapped onto the reference gene set by using Bowtie1 software
Use Stringtie software to calculate the reads count and convert it to the FPKM of the transcript.And then the low-abundance transcripts,  were removed
The differential expressed genes were identified by using limma R package after normalization. A |log2FC|>=1 and p-Value<=0.05 were set as the threshold for DEGs
Assembly: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: idiopathic orbital inflammation

extract_protocol:
Total RNA were isolated from tissues by using the Trizol Reagent according to the manufacture’s protocol
The poly-A containing mRNA molecules were purified from the 3 μg of total RNA by using poly-T oligo-attached magnetic beads. The cleaved RNA fragments were reversely transcribed into first strand cDNA using random hexamers, following by second strand cDNA synthesis using DNA Polymerase I and RNase H. The cDNA fragments were purified, end blunted, 'A' tailed, and adaptor ligated. PCR was used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. The number of PCR cycles was minimized to avoid skewing the representation of the library. The library were qualified by Agilent 2100 bioanalyzer and quantified by Qubit and qPCR.

value: lyphoma specimen


title: OI_22_04

description: IOI


title: NSCLC-PMN-MDSC_3

value: CD66b+CD10+CD11b+CD16+ cells isolated by immunomagnetic selection

value: mPMN-MDSC purified from non-small cell lung cancer patient


title: HD-mNDN_1_B

value: CD66b+CD10+CD11b+CD16+ cells isolated by flow cytometry sorting

value: mNDN purified from healthy donor

value: Freshly purified


title: OI_22_02

description: IOI


title: NSCLC-PMN-MDSC_1


title: NSCLC-mNDN_9

value: mNDN purified from non-small cell lung cancer patient


title: OI_22_03

description: IOI


title: LP_22_09

description: RLH

source_name: reactive lymphoid hyperplasia


title: rad27 RFA1-t33 rep2

description: The library has the forward index: ctg and reverse index:cca A total of  672 colony number was in this library.

value: rfa1-t33 rad27::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: Chlamydomonas, Mannitol, 6 hours, rep1

value: Vegetative, haploid, Cells

value: 6 hours


title: rtt105 rad27 rep3

description: The library has the forward index: tgc and reverse index:gca A total of  30912 colony number was in this library.

value: rtt105::hphMX rad27::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30C


title: Chlamydomonas, NaCl, 4 hours, rep2

value: NaCl

value: 4 hours


title: rtt105 rad27 rep2

description: The library has the forward index: tcc and reverse index:ctt A total of  60960 colony number was in this library.


title: NSCLC-mNDN_3


title: Chlamydomonas, NaCl, 30 minutes, rep1

value: Wild-type

value: 30 minutes


title: Chlamydomonas, Control, 0 hours, rep1

value: Control

value: 0 hours


title: rtt105 rad27 rep1

description: The library has the forward index: tac and reverse index:cga A total of  19968 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139


title: NSCLC-PMN-MDSC_9

value: CD66b+CD10+CD11b+CD16+ cells isolated by immunomagnetic selection

value: mPMN-MDSC purified from non-small cell lung cancer patient


title: HD-mNDN_9_A

value: mNDN purified from healthy donor


title: Chlamydomonas, Mannitol, 4 hours, rep1

value: Mannitol


title: LP_22_05

description: RLH

value: lyphoma specimen


title: Chlamydomonas, NaCl, 60 min, rep1

value: 60 min


title: HD-mNDN_3_A

value: Freshly purified


title: LP_22_07

description: RLH


title: Chlamydomonas, Control, 0 hours, rep2

value: Vegetative, haploid, Cells


title: LP_22_04

description: RLH


title: HD-mNDN_1_A


title: EM_22_21

description: EMZL

source_name: ocular adnexal lymphoma; extranodal marginal zone lymphoma


title: Endo CD8-replicate-2

city: Beijing

first: Gang

last: Jin

address: Zhongguancun North street

department: Institute for Immunology

institute: Tsinghua University

data_processing:
Quality control of raw sequencing reads was determined by FASTQC.
After getting clean reads, HISAT was used to align the clean reads to the reference genome.
Bowtie2 was used to get the alignment results.
Differential analysis, DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene read counts for every gene and every sample

extract_protocol:
At indicated time points after transfer, Thy1.1+CD8+ CAR19TIF cells or endogenous CD8+ T cells were sorted by  flow cytometry with purity > 95% from spleen of recipient mice. RNA samples were isolated and purified using  TIANGEN RNAprep Pure Cell/Bacteria Kit.
RNA samples were shipped to BGI and libraries were prepared by BGI company according to DNBSEQ's instructions

tag: strain


title: RFA1-t33 rep1

description: The library has the forward index: agg and reverse index:gga A total of  23424 colony number was in this library.

value: rfa1-t33 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: LP_22_08

description: RLH


title: rad27 RFA1-t33 rep1

description: The library has the forward index: cag and reverse index:gag A total of  14304 colony number was in this library.

value: rfa1-t33 rad27::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30C


title: RFA1-t33 rep2

description: The library has the forward index: atg and reverse index:gct A total of  9552 colony number was in this library.


title: Chlamydomonas, NaCl, 4 hours, rep1

value: NaCl

value: 4 hours


title: GD-mLDN_12

value: CD66b+CD10+CD11b+CD16+ cells isolated by flow cytometry sorting

value: mLDN purified from GCSF-treated donor


title: EM_22_20

description: EMZL


title: rad27 rep1

description: The library has the forward index: cac and reverse index:cat A total of  140000 colony number was in this library.

value: rad27::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: pol32 rep2

description: The library has the forward index: agc and reverse index:cta A total of  21648 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139

value: pol32::natMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: GD-mLDN_11


title: NSCLC-mNDN_1

value: CD66b+CD10+CD11b+CD16+ cells isolated by immunomagnetic selection

value: mNDN purified from non-small cell lung cancer patient


title: LP_22_06

description: RLH


title: GD-mLDN_10


title: Chlamydomonas, Mannitol, 15 minutes, rep1

value: Wild-type

value: Mannitol

value: 15 minutes


title: EM_22_19

description: EMZL

value: lyphoma specimen


title: pol32 rep1

description: The library has the forward index: acc and reverse index:gaa A total of  22512 colony number was in this library.


title: RFA1-t33 rep3

description: The library has the forward index: cac and reverse index:cat A total of  20208 colony number was in this library.


title: Endo CD8-replicate-1


title: CAR19TIF-3mon-replicate-2

source_name: Thy1.1+ CAR19TIF

value: Thy1.1+ CAR19TIF


title: GD-mLDN_8

value: Freshly purified


title: rad30 rep1

description: The library has the forward index: aag and reverse index:cgt A total of  17472 colony number was in this library.

value: rad30::kanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: CAR19TIF-3mon-replicate-1


title: GD-mLDN_7


title: EM_22_18

description: EMZL


title: EM_22_17

description: EMZL


title: CAR19TIF-Day10-replicate-2


title: EM_22_15

description: EMZL


title: GD-mLDN_6


title: EM_22_16

description: EMZL


title: GD-mLDN_5


title: CAR19TIF-Day10-replicate-1


title: mre11 rep2

description: The library has the forward index: acc and reverse index:gaa A total of  25152 colony number was in this library.

value: mre11::hphMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30C


title: mre11 rep1

description: The library has the forward index: ttg and reverse index:ctg A total of  27024 colony number was in this library.


title: exo1 rep2

description: The library has the forward index: ctg and reverse index:cca A total of  23616 colony number was in this library.

value: exo1::TRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: EM_22_14

description: EMZL


title: exo1 rep1

description: The library has the forward index: cag and reverse index:gag A total of  30624 colony number was in this library.


title: sgZc3h12a-Day10-replicate-1

source_name: sgZc3h12a CAR19T

value: sgZc3h12a CAR19T


title: sgZc3h12a-Day10-replicate-2


title: GD-mNDN_12

value: CD66b+CD10+CD11b+CD16+ cells isolated by flow cytometry sorting

value: mNDN purified from GCSF-treated donor


title: rad30 rep2

description: The library has the forward index: acg and reverse index:gtg A total of  19824 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139


title: EM_22_13

description: EMZL


title: lig4 rep2

description: The library has the forward index: atc and reverse index:cag A total of  47840 colony number was in this library.

value: lig4::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: GD-mNDN_11


title: EM_22_12

description: EMZL


title: iWAT, Cebpa-E2, rep3

city: Chengdu

first: Xiaokai

last: Li

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
We used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Sequence reads were aligned to the mouse reference genome (GRCm38/mm10) by HISAT2 (v2.2.1).
Sequence reads were quantified by featureCounts from Rsubread package (v2.8.1).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

source_name: Inguinal white adipose tissue

growth_protocol: Six-week-old male and female C57BL/6J mice were housed in the animal facility were fed a high-fat diet (HFD) (TD.08811, 4.7 Kcal/g, ENVIGO) with water ad libitum for one week. Seven-week-old female mice were anaesthetized with 1% pentobarbital sodium. After injection, mice were fed ad libitum HFD until sacrifice.

extract_protocol:
Total RNA was isolated from tissue with TRIzol reagent (Invitrogen).  1 μg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, E7530L) following manufacturer's protocols.

treatment_protocol: Seven-week-old female mice were anaesthetized with 1% pentobarbital sodium. C57BL/6J mice were divided into two groups (iWAT_Cebpa-En2 group versus dCas9-KRAB-GFP group). dCas9-KRAB-En2 and dCas9-KRAB-GFP lentiviruses were generated using pLV-hU6-sgRNA-hUbC-dCas9-KRAB-T2a-Puro (Addgene, #71236) and pLV-hU6-sgRNA-hUbC-dCas9-KRAB-T2a-GFP (Addgene, #71237) plasmids, respectively. Lentivirus was injected directly into the inguinal white adipose tissue (iWAT) of mice by multi-point subcutaneous injection on each side. Then, the mice were injected with lentivirus once every three days for 4 times injections. Each mouse was injected with a total of 800 μL lentivirus. iWAT_Cebpa-En2 group mice were injected dCas9-KRAB-En2 lentiviruses, and the control group mice were injected dCas9-KRAB-GFP lentiviruses. After injection, mice were fed ad libitum HFD until sacrifice.

value: Inguinal white adipose tissue

value: Injection of lentiviruses into inguinal adipose tissue in vivo

tag: developmental stage


title: iWAT, Cebpa-E2, rep2

tag: tissue


title: lig4 rep1

description: The library has the forward index: agc and reverse index:cta A total of  17440 colony number was in this library.


title: GD-mNDN_10


title: EM_22_11

description: EMZL


title: yku70 rep2

description: The library has the forward index: acc and reverse index:gaa A total of  29440 colony number was in this library.

value: yku70::TRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: EM_22_09

description: EMZL


title: iWAT, Cebpa-E2, rep1


title: GD-mNDN_9


title: iWAT, dCas9-KRAB-GFP, rep3


title: yku70 rep1

description: The library has the forward index: aac and reverse index:gtt A total of  17520 colony number was in this library.


title: rev3 rep2

description: The library has the forward index: ttc and reverse index:gtc A total of  35600 colony number was in this library.

value: rev3::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: GD-mNDN_8


title: GD-mLDN_3

value: mLDN purified from GCSF-treated donor


title: EM_22_07

description: EMZL

value: lyphoma specimen


title: EM_22_05

description: EMZL


title: iWAT, dCas9-KRAB-GFP, rep1


title: iWAT, dCas9-KRAB-GFP, rep2


title: EM_22_04

description: EMZL


title: GD-mNDN_6


title: mre11-H125N rep2

description: The library has the forward index: tcc and reverse index:ctt A total of  80000 colony number was in this library.

value: mre11-H125N::URA3 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: rev3 rep1

description: The library has the forward index: tgc and reverse index:gca A total of  28560 colony number was in this library.


title: 4C-Seq 3T3-L1-AD, dCas9-KRAB, rep3

source_name: Mouse embryo

growth_protocol: 3T3-L1 cells were grown in DMEM supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Invitrogen) at 37℃ in 5% CO2. Adipocyte differentiation of 3T3-L1 cells was performed according to a standard adipogenic MDI cocktail (MDI: IBMX, dexamethasone, and insulin).After reaching confluence, the medium was changed, and the cells were incubated for 48 h. To induce differentiation, the cells were incubated for 48 h in DMEM supplemented with MDI cocktail (2 μg/mL of dexamethasone, 0.5 mM IBMX, and 10 μg/mL of insulin) and 10% FBS. Then, the medium was changed with DMEM containing 10 µg/mL insulin and 10% FBS every two days until the cells exhibited an adipocyte phenotype at day 7 post induction.

extract_protocol:
Total RNA was isolated from cells with TRIzol reagent (Invitrogen).  1 μg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, E7530L) following manufacturer's protocols.

treatment_protocol: 3T3-L1 cells were plated in 12-well plates overnight. When confluence reaches about 50-60%, cells were infected with 1 mL lentiviruses medium containing dCas9-KRAB-En2-sgRNAs (Experimental group) or dCas9-KRAB (Control group) at the multiplicity of infection (MOI) of 100 for 12 h. The medium was then replaced after 24 h post-infection. At 48 h post-infection, cells were selected with 2 μg/mL puromycin (Sigma). Untreated 3T3-L1 and 3T3-L1 stably expressing dCas9-KRAB-sgRNA or dCas9-KRAB were induced to adipogenic differentiation using a standard MDI cocktail.

value: Mouse embryo

value: Adipocyte

value: Lentiviral transduction of the dCas9-KRAB system

tag: time

value: Adipogenic induced differentiation day 7


title: GD-mNDN_7

value: Freshly purified


title: GD-mNDN_4


title: EM_22_02

description: EMZL


title: mre11-H125N rep1

description: The library has the forward index: tac and reverse index:cga A total of  64320 colony number was in this library.

value: Cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus at 30C


title: GD-mNDN_2

value: CD66b+CD10+CD11b+CD16+ cells isolated by flow cytometry sorting


title: sgs1 rep2

description: The library has the forward index: acc and reverse index:gaa A total of  22800 colony number was in this library.

value: sgs1::KanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: EM_22_03

description: EMZL


title: DB_22_04

description: DLBCL

source_name: ocular adnexal lymphoma; diffuse large b-cell lymphoma


title: 4C-Seq 3T3-L1-AD, dCas9-KRAB, rep2


title: sgs1 rep1

description: The library has the forward index: aac and reverse index:gtt A total of  83280 colony number was in this library.

value: S. cerevisiae haploid strain, mutant isogenic to JKM139


title: DB_22_03

description: DLBCL


title: sgs1 exo1 rep4

description: The library has the forward index: GCT and reverse index:CTA A total of  15000 colony number was in this library.

value: sgs1::KanMX exo1::TRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: GD-mNDN_1

value: mNDN purified from GCSF-treated donor


title: DB_22_02

description: DLBCL


title: HD-mNDN_15

value: mNDN purified from healthy donor


title: sgs1 exo1 rep3

description: The library has the forward index: GCT and reverse index:CTA A total of  10000 colony number was in this library.


title: ABCP_2d

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: Differentiating cells cultured in ABCP condition for 48h

data_processing:
Quality checks, UMI identification, alignment to the mouse reference genome and cell calling were performed using the cellranger software (v6.1.1) with default parameters. Violin plots of the distribution of counts, features, mitochondrial and ribosomal RNA were created and upper and lower bounds were introduced to avoid data heterogeneity and exclude potentially problematic cells.
The data was normalised using the Seurat R package (v4.0.5). Dimensionality reductions (PCA and UMAP), as well as clustering were also performed using the Seurat R package, with the number of clusters being the optimal selected by the software. For the subsequent analysis, we focused on the 3000 most variable genes. Markers for each cluster were identified by testing for differential gene expression, using the Seurat R package.
Clustering stability was evaluated using the ClustAssess R package (https://cran.r-project.org/package=ClustAssess). Enrichment analysis on the markers identified per cluster was performed using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.2.1). RNA velocity trajectory analysis was performed with the velocyto software (v0.17.17) and the scvelo python package (https://doi.org/10.1038/s41587-020-0591-3). Further analysis was performed with the above tools, focused on sub-clusters of biological interest.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)  Mouse reference, mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: Sparse matrix of raw abundances for each gene, per cell

source_name: induced pluripotent stem cells

growth_protocol: Human iPSCs (FS13B line) were cultured on plates coated with 10 µg/ml vitronectin in 37°C and 5% CO2. For maintenance, cells were daily supplied with E6 media supplemented with 2 ng/mL TGFb and 25 ng/mL FGF2, and were passaged every 5-7 days using 0.5 mM EDTA in PBS.

extract_protocol:
Cells were washed once with PBS and treated with accutase for 5 minutes at 37°C for single cell dissociation.
RNA libraries were prepared for sequencing using standard Illumina protocols for 10X Single Cell GEX v3.

treatment_protocol: For directed differentiation, the human iPSCs were plated as single cells at 4.0-5.0x10^4 cells/cm2 using Accutase and 10 µM Y27632. Two days in the maintenance media after the splitting, cells were supplied every 24 hours with the ABCP media (CDM-PVA media supplemented with 100 ng/ml Activin A, 10 ng/ml BMP4, 3 μM CHIR99021 and 1 µM PD0325901).

value: induced pluripotent stem cells

value: 2 days

tag: condition

value: ABCP


title: ABCP_3d

description: Differentiating cells cultured in ABCP condition for 72h

value: 3 days


title: sgs1 exo1 rep2


title: HD-mNDN_12


title: GD-mNDN_3


title: 4C-Seq 3T3-L1-AD, dCas9-KRAB, rep1


title: ABCP_1d

description: Differentiating cells cultured in ABCP condition for 24h

value: 1 days


title: sgs1 exo1 rep1


title: PLU_0d

description: Pluripotent cells before differentiation

value: 0 days

value: PLU


title: HD-mNDN_11


title: HD-mNDN_7


title: WT_GFP, rep2

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

data_processing:
Raw reads were trimmed using cutadapt v4.4 with parameters -q 15,10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -m 20
Clean reads were aligned to the TAIR10 genome using bowtie2 v2.5.1 with default parameters
Duplicates were marked with sambamba v1.0. Alignments were filtered using samtools (v1.17) view with options -q 5 -F 4 -F 1024
BigWig files were obtained using bedtools (v2.31.0) genomecov and UCSC bedGraphToBigWig. Bigwigs were scaled to their normalization factors using wiggletools (v1.2.11) scale
For FLAG-ELF7, GFP-VIP3 and Pol II ChIPs, samples were scaled by sequencing depth (CPM). H2Bub samples were normalized by the amount of Drosophila reads in the IP and the input as in Nassrallah et al. 2018
Peaks were called using macs2 v2.2.7.1 with options --keep-duplicates all --nomodel --extsize 200 --broad --broad-cutoff 0.05 -gs 119144248
Assembly: TAIR10
Supplementary files format and content: Raw bigwigs
Supplementary files format and content: broadPeaks

organism: Arabidopsis thaliana

source_name: whole seedlings

extract_protocol:
H2B and H2Bub ChIP-Rx were conducted in parallel using the same two biological replicates of 7-day-old WT and elf7-3 seedlings grown under standard conditions. For each biological replicate, two immunoprecipitations (IP) were performed using an anti-H2Bub antibody (MM-0029-P, Medimabs) and one using an anti-H2B (ab1790, abcam). 100 µg of Arabidopsis chromatin mixed with 3 µg of Drosophila chromatin was used for each IP. DNA eluted from the two technical replicates of H2Bub IP was pooled before library preparation. Library preparation and sequencing were carried out by the CRG Genomics Core Facility (Barcelona, Spain). Flag-ELF7 and GFP-VIP3 ChIP-seq was performed using 7-day-old seedlings and an anti-Flag M2 antibody (F1804, Sigma). We used double in vitro crosslinking using 1.5 mM ethylene glycol bis (succinimidyl succinate) for 20 min and then with 1% formaldehyde for 10 min at room temperature. Library preparation and sequencing were carried out by the CRG Genomics Core Facility (Barcelona, Spain). ChIP-seq for RNAPII was done using the anti-NRPB1 antibody (active motif, Clone: 4H8) using similar growth conditions and protocol than for H2Bub profiling without Drosophila cells spike-in. Library preparation and sequencing were carried out by the Epigenomics platform at IPS2 (Paris, France).
Libraries were prepared using commercial kits as follows: GFP-VIP3, H2B and H2Bub with NEBNext® Ultra DNA Library Prep for Illumina® kit, PolII with NEBNext® Ultra II DNA Library Prep for Illumina® kit, and Flag-ELF7 with Ovation Ultralow System V2.

value: whole seedlings

value: 7-day-old seedlings

value: wild type

tag: chip antibody

value: anti-GFP (ab290, abcam)


title: 4C-Seq 3T3-L1-AD, Cebpa-L1-AD-En2, rep2

value: Mouse embryo

value: Adipocyte

value: Lentiviral transduction of the dCas9-KRAB-En2 system

value: Adipogenic induced differentiation day 7


title: 4C-Seq 3T3-L1-AD, Cebpa-L1-AD-En2, rep1


title: HD-mNDN_14

source_name: peripheral blood

value: CD66b+CD10+CD11b+CD16+ cells isolated by flow cytometry sorting

value: Freshly purified


title: HD-mNDN_6

value: mNDN purified from healthy donor


title: WT_GFP, rep1


title: HD-mNDN_13


title: HD-mNDN_5


title: 4C-Seq 3T3-L1-AD, Cebpa-L1-AD-En2, rep3


title: hCMEC/D3, mock-2

city: Palma

first: Cristofol

last: Vives-Bauza

address: Crta Valldemossa km.7.5

institute: University of Balearic Islands

description:
CTL2
Scramble control

hyb_protocol: Samples were hybridized with GeneChip Human Clariom S Arrays (Affymetrix, Thermo Fisher Scientific) and scanned at the IdISBa Genomic Core Facility.

scan_protocol: Array scanning was performed by using the GeneChip Scanner 3000 7G according to the manufacturer's instruction (Affymetrix, Thermo Fisher Scientific).

data_processing: Preprocessing was performed in R/Bioconductor using the oligo package. Raw CEL files were summarized and normalized through RMA (Robust Multichip Average) and quantile normalization (oligo::rma). Quality control analyses were performed with arrayQualityMetrics package. Probes were annotated with packages pd.clariom.s.human, clariomshumantranscriptcluster.db and annotation file from Affymetrix (Clariom S Array, human Transcript Cluster Annotations, CSV, Release 36).

label: biotin

source_name: cell line + treatment

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the GeneChip WT Plus Reagent Kit (Affymetrix, Thermo Fisher Scientific) and then fragmented and biotin-labeled with the WT Terminal Labeling Kit (Affymetrix, Thermo Fisher Scientific).

growth_protocol: Cells were grown in flasks coated with rat tail collagen type I high concentration and cultured in EGM-2 Endothelial Cell Growth Medium-2 BulletKit (CC-3162).

extract_protocol: Total RNA was extracted using QIAzol Lysis Reagent from miRNeasy Mini Kit following the manufacturer's protocol.

treatment_protocol: Lentiviral particles carrying PATJ shRNA were generated with the Trans-Lentiviral shRNA Packaging Kit using Calcium Phosphate Transfection Reagent, following the manufacturer's instructions.

value: human brain microvascular endothelial cell line (RRID:CVCL_U985)

value: Mock


title: hCMEC/D3, mock-3

description:
CTL3
Scramble control


title: VIP3-GFP, rep1


title: hCMEC/D3, PATJ knockdown-4

description:
PATJ KD4
Endothelial cells with PATJ stably depleted using lentiviral particles

value: PATJ KD


title: HD-mNDN_1


title: VIP3-GFP, rep2


title: ELCs-3

status: Public on Mar 06 2024

city: Suita

first: Tatsuya

last: Inui

state: Osaka

country: Japan

institute: Osaka university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic.
Trimmed sequence reads were mapped to GRCh38 using HISAT2.
Read count extraction and nomalization were performed using samtools and featureCounts.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

source_name: human iPS cell-derived enterocyte-like cells

growth_protocol: ELCs and ELC-org-mono were maintained in intestinal final differentiation medium, DMEM high-glucose medium containing 10% KSR, 1% NEAA, P/S, , 0.5 × B27 supplement minus vitamin A and 1 × GlutaMAX supplemented with 2 μM SB431542 (SB; FUJIFILM Wako Pure Chemical Industries), 3 nM LY2090314 (LY; MedChem Express),　100nM 1α,25-dihydroxyvitamin D3 (VD3; Cayman Chemical), 3 μM PD0325901 (PD; FUJIFILM Wako Pure Chemical Industries),and 50 ng/mL epidermal growth factor (EGF; R&D Systems). ELC-org-mono were maintained in the previous report[Fujii., et al,  Cell Stem Cell, 2018]

extract_protocol:
RNA was isolated using ISOGENE.
According to the manufacturer's instructions, library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA). Libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

value: cultured cell


title: ELCs-2

value: human iPS cell-derived enterocyte-like cells


title: hCMEC/D3, PATJ knockdown-3

description:
PATJ KD3
Endothelial cells with PATJ stably depleted using lentiviral particles


title: ELCs-1


title: ELC-org-mono-3

source_name: monolayers derived from human intestinal organoid


title: hCMEC/D3, PATJ knockdown-1

description:
PATJ KD1
Endothelial cells with PATJ stably depleted using lentiviral particles


title: CON1_ASTN2-/-.2

city: Nagoya

first: Yu

last: Hayashi

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: psychiatry

institute: Nagoya University

hyb_protocol: Cyanine 3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851B) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Scans were performed on a SureScan Agilent DNA Microarray Scanner (G2600D) in a one-color scan setting on 8x60k array slides.

data_processing: All data analyses were performed using the GeneSpring GX Software Program (version 13; Agilent Technology). Absolute expression values were normalized by using the 75th percentile signal intensity. The statistical criteria for differential expression were as follows: moderated t-test, Bonferroni correction for multiple testing correction.

label: Cyanine 3

source_name: ASTN2 -/-, replicate 2

label_protocol: The Low Input Quick Amp Labeling Kit, One-Color generates fluorescent cRNA (complimentary RNA) with a sample input RNA range between 10 ng and 200 ng of total RNA or a minimum of 5 ng of poly A+ RNA for one-color processing. The method uses T7 RNA Polymerase Blend (red cap), which simultaneously amplifies target material and incorporates Cyanine 3-CTP.

growth_protocol: After the passage of iPS cells onto feeder cells (Day 0), the iPS cells were cultured in an iPS cell medium comprising Dulbecco’s Modified Eagle Medium (DMEM/F12) supplemented with 20% knockout serum replacement (KSR), 2 -mM l-glutamine, 0.1-mM nonessential amino acids, 0.1-mM 2-mercaptoethanol, 100-units/mL penicillin, 100-μg/mL streptomycin, and 4-ng/mL basic fibroblast growth factor (bFGF). On day 1, SB431542 (3 μM), CHIR99021 (3 μM), and dorsomorphin (3 μM) were added to the iPS cell medium, and the iPS cells were incubated for 6 days (days 1–7). On day 7, they were dissociated into single cells with 0.5× TrypLE select and cultured in NS medium consisting of DMEM/F12 supplemented with 1× N-2 supplement, 0.6% glucose, 100-units/mL penicillin, 100-μg/mL streptomycin, 5-mM HEPES, 1× B-27 supplement, 20-ng/mL bFGF, 10-ng/mL hLIF, 10-μM Y-27632, 3-μM CHIR99021, and 2-μM SB431542 for 2 weeks (days 7–21). The cells were dissociated into single cells once on day 14 for passage. Then, the cells were cultured in a 5% CO2/18%–22% O2 atmosphere during all experiments.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Netherland).

value: neurosphere

tag: disease state

value: psychiatric patient

value: ASTN2 -/-


title: CON1_ASTN2-/-.3

source_name: ASTN2 -/-, replicate 3


title: ELC-org-mono-2

value: monolayers derived from human intestinal organoid


title: ELC-org-2

source_name: human intestinal organoid

value: human intestinal organoid


title: hCMEC/D3, PATJ knockdown-2

description:
PATJ KD2
Endothelial cells with PATJ stably depleted using lentiviral particles


title: ELC-org-mono-1


title: ELC-org-3


title: hCMEC/D3, mock-1

description:
CTL1
Scramble control


title: CON1.2

source_name: ASTN2 +/+, replicate 2

value: healthy control

value: ASTN2 +/+


title: CON1.3

source_name: ASTN2 +/+, replicate 3


title: CON1_ASTN2-/-.1

source_name: ASTN2 -/-, replicate 1


title: HD-mNDN_4


title: RYGB 22

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

description: Sample 22

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V4.1.2, Rstudio V1.4.1717 and biomaRt V2.50.1
DESeq2  V1.34 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: Mouse
Supplementary files format and content: tab-delimited text containing DESeq2 normalized counts and raw counts

source_name: liver

extract_protocol:
Liver were removed, fresh frozen on liquid nitrogen and RNA was harvested using Trizol and Rneasy Mini Kit (Cat#ID-74104).
Quant-Seq  3' mRNA-Seq Library Prep Kit
indexed and pooled samples, 50bp forward read

treatment_protocol: RYGB surgery or caloric restriction was used as a treatment compared to a sham surgery.

value: liver

tag: group

value: RYGB


title: RYGB 28

description: Sample 23


title: RYGB 15

description: Sample 19


title: RYGB 29

description: Sample 24


title: RYGB 10

description: Sample 17


title: WM 30

description: Sample 16

value: WM


title: RYGB 19

description: Sample 21


title: WM 25

description: Sample 14


title: WM 27

description: Sample 15


title: WM 20

description: Sample 13


title: RYGB 11

description: Sample 18


title: WM 9

description: Sample 11


title: WM 13

description: Sample 12


title: WM 7

description: Sample 10


title: ELC-org-1


title: Sham 17

description: Sample 7

value: Sham


title: Sham 23

description: Sample 8


title: Sham 16

description: Sample 6


title: CON1.1

source_name: ASTN2 +/+, replicate 1


title: hCMEC/D3, mock-4

description:
CTL4
Scramble control


title: WM 1

description: Sample 9


title: Sham 14

description: Sample 5


title: Sham 6

description: Sample 4


title: Seedlings, short day, ZT0, rep3, ChIP

city: Austin

first: Wenli

state: Texas

department: Molecular Biosciences

institute: university of Texas at Austin

data_processing:
Quality check using FastQC
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30
Reads were aligned on the TAIR10 genome using Bowtie2
SAM files generated from mapping were then converted into BAM files and sorted using Samtools.
Bigwig files for IGV visualization were created using deeptools
Assembly: TAIR10
Supplementary files format and content: bigWig, Peak

source_name: whole seedling

growth_protocol: Seedlings were germinated and grown on MS medium in short day condition for a week

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor (30 s on/2 min 30 s off cycles) with high-power output to obtain 200- to 500-bp DNA fragments.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Short day conditions (8-h light, 16-h dark)  at 22°C for a week, samples collected at ZT0

value: whole seedling

value: plant cell

value: H3K27me3 (Active Motif #39155)


title: Sham 5

description: Sample 3


title: Sham 3

description: Sample 2


title: Seedlings, short day, ZT0, rep1

data_processing:
Quality check using FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to TAIR10 genome using STAR
Read count extraction and normalization were performed using edgeR
Assembly: TAIR10
Supplementary files format and content: Gene counts for each Sample

extract_protocol:
RNA was harvested using Rneasy Plant mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) following manufacturer's protocols.

treatment_protocol:
Short day conditions (8-h light, 16-h dark) at 22°C for a week, samples collected at ZT0
Short day conditions (8-h light, 16-h dark)  at 22°C for a week, samples collected at ZT0

value: short day


title: Seedlings, short day, ZT0, rep3


title: cop1_6_3

source_name: Seedlings, short day, ZT6, rep3

treatment_protocol:
Short day conditions (8-h light, 16-h dark) at 22°C for a week, samples collected at ZT0 and ZT6
Short day conditions (8-h light, 16-h dark)  at 22°C for a week, samples collected at ZT0 and ZT6


title: Seedlings, short day, ZT0, rep1, ChIP


title: Seedlings, short day, ZT0, rep2, ChIP


title: Seedlings, short day, ZT0, rep2


title: v1c1_6_3


title: v1c1_6_1

source_name: Seedlings, short day, ZT6, rep1


title: Seedlings, short day, ZT0, rep1_input


title: cop1_6_1


title: col_6_3

value: WT


title: v1c1_6_2

source_name: Seedlings, short day, ZT6, rep2


title: cop1_6_2


title: vil1_6_3


title: vil1_6_2


title: v1c1_0_3

source_name: Seedlings, short day, ZT0, rep3


title: col_6_2


title: vil1_6_1


title: cop1_0_2

source_name: Seedlings, short day, ZT0, rep2


title: col_6_1


title: vil1_0_3


title: RYGB 18

description: Sample 20


title: vil1_0_2


title: v1c1_0_2


title: v1c1_0_1

source_name: Seedlings, short day, ZT0, rep1


title: col_0_3


title: cop1_0_1


title: cop1_0_3


title: col_0_2


title: v1c1_3


title: col_0_1


title: v1c1_1


title: cop1_2


title: cop1_1


title: cop1_input


title: v1c1_2


title: v1c1_input


title: vil1_3


title: vil1_input


title: col_3


title: vil1_2


title: col_2


title: col_1


title: col_input


title: CLIP_AGO_GBM4

city: New York

first: Yuhki

last: Saito

state: NY

address: 1230 York Ave

institute: Rockefeller University

library_source: other

data_processing:
CLIP: We followed standard/BruU-CLIP data analysis pipeline using CTK (https://zhanglab.c2b2.columbia.edu/index.php/Standard/BrdU-CLIP_data_analysis_using_CTK). The deposited fastq files are raw data before collapsing PCR duplicates.
CLIP: removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG), collapsing of exact sequences and stripping of random barcodes
CLIP: alignment with BWA (hg19). RNAseq: alignment with STAR (hg19)
CLIP: collapsing of PCR duplicates (unique CLIP tags)
CLIP: Peak calling by using unique CLIP tags
Assembly: hg19
Supplementary files format and content: Bedgraph files generated from NOVA1 or AGO unique CLIP tags and RNAseq reads for genome browser
Library strategy: CLIP-Seq

molecule: other

source_name: GBM cells derived from a patient

growth_protocol: DMEM/N2/EGF/FGF medium. Detailed desription in accompanying paper.

extract_protocol:
GBM cells derived from a patinet were UV-irradiated and subjected to CLIP with  anti-NOVA1 antibody (ab183024 from Abcam) and anti-AGO antibody (2A8: from Dr. Zissimos Mourelatos) and RNAseq (shControl vs shNOVA1KD1 & 2).
CLIP: Partial RNase A digestion, linker ligation, reverse transcription, criculation and PCR amplificiation. RNAseq: Illumina High-throughput TruSeq RNA Sample preparation: ribozero or poly(A) selection.

value: GBM cells derived from a patient

value: GBM


title: CLIP_AGO_GBM3


title: CLIP_AGO_GBM1


title: CLIP_AGO_GBM2


title: CLIP_NOVA1_GBM4_2


title: CLIP_NOVA1_GBM4_1


title: CLIP_NOVA1_GBM2_2


title: cop1_3


title: CLIP_NOVA1_GBM1_2


title: CLIP_NOVA1_GBM3_1


title: CLIP_NOVA1_GBM2_1


title: vil1_1


title: CLIP_NOVA1_GBM3_2


title: SLIM1OX.25_DAS44_rep1

first: Sarah

middle: J

last: Whitcomb

address: 502 Walnut St

department: Cereal Crops Research Unit

institute: USDA-ARS

data_processing:
Clean reads were generated from raw reads by removing adaptor sequences, contamination, and low-quality reads. Specifically, SOAPnuke software was used with the following parameters, " -n 0.01 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --polyX 50 -- minReadLen 150 (Chen et al., 2018)
The clean reads were aligned to the Arabidopsis genome (NCBI assembly TAIR10) using CLC genomics (Keohavong and Grant, 2004) v23.0.4 with default settings. The genome annotations are based on Araport11.
Assembly: TAIR10 with Araport11
Supplementary files format and content: tab delimted file which includes raw read counts per gene in each sample
Supplementary files format and content: tab delimted file which includes median of ratios normalized read counts (DESeq2 v1.40.2) per gene in each sample

source_name: rosette

growth_protocol: Sterilized seeds were were sown on MS agar medium supplemented with 1 % sucrose (w/v) and were stratified at 4 degrees C for 48 h before the plates were moved to a controlled environment chambers. OxSLIM1 seeds were sown on plates additionally supplemented with 30 mg/L hygromycin, since the experiment was performed with T2 generation plants. The seeds germinated under a 16 h photoperiod with 100 µmol photons m–2 s−1 irradiance. The temperature inside the chambers was maintained at 21 degrees C during the day and 19 degrees C at night. 12 days after sowing (DAS), the seedlings were transplanted into soil-filled round pots with a diameter of 6 cm. These pots were placed in a phytotron with controlled conditions:  photoperiod of 16 hours with an irradiance of 120 µmol photons m–2 s−1, temperature of 20 degrees C during the day and 16 degrees C at night, and a humidity level of 60-75%. To minimize the potential effects of uneven lighting, the positions of the pots were regularly rearranged within the phytotron.

extract_protocol:
Total RNA was extracted from approximately 100 mg of rosette tissue using the SIGMA Spectrum Plant total RNA KIT (1003037777) according to the manufacturer’s instructions with on-column DNase treatment. RNA concentration, quality, and purity was determined using a Bioanalyzer Agilent 2100. All the samples had RIN value between 6.50 and 8.50.
BGI prepared the libraries and performed the sequencing. The ribosomal RNA (rRNA) pool was depleted by polyA enrichment. Finally, the strand specific libraries were sequenced with DNBseq platform (paired-end 150 bp reads with a coverage of 40 M reads per library)
DNBSEQ Eukaryotic Strand-specific mRNA library

treatment_protocol: The stalk and the reproductive tissue was excluded from the tissue sampled which was the rosette. The time between the stalk removal and the rosette harvesting was approximately 4 min. The rosette samples were collected at 3 timepoints (30 DAS, 37 DAS, and 44 DAS) and immediately frozen in liquid nitrogen. For all timepoints, only rosette tissue was harvested. The samples were homogenized while frozen using a Retschmill MM400.

value: rosette


title: SLIM1OX.17_DAS44_rep3


title: SLIM1OX.17_DAS44_rep1


title: slim1KO_DAS44_rep3


title: SLIM1OX.17_DAS44_rep2


title: SLIM1OX.25_DAS44_rep2


title: slim1KO_DAS44_rep2


title: SLIM1OX.25_DAS44_rep3


title: slim1KO_DAS44_rep1


title: Col0_DAS44_rep2


title: SLIM1OX.25_DAS37_rep3


title: Col0_DAS44_rep3


title: Sham 2

description: Sample 1


title: SLIM1OX.25_DAS37_rep2


title: Col0_DAS44_rep1


title: SLIM1OX.25_DAS37_rep1


title: SLIM1OX.17_DAS37_rep3


title: SLIM1OX.17_DAS37_rep1


title: SLIM1OX.17_DAS37_rep2


title: slim1KO_DAS37_rep2


title: slim1KO_DAS37_rep3


title: slim1KO_DAS37_rep1


title: Col0_DAS37_rep2


title: SLIM1OX.25_DAS30_rep1


title: Col0_DAS37_rep3


title: SLIM1OX.25_DAS30_rep3


title: slim1KO_DAS30_rep1


title: Col0_DAS37_rep1


title: SLIM1OX.17_DAS30_rep1


title: SLIM1OX.25_DAS30_rep2


title: SLIM1OX.17_DAS30_rep3


title: slim1KO_DAS30_rep2


title: SLIM1OX.17_DAS30_rep2


title: slim1KO_DAS30_rep3


title: Col0_DAS30_rep3


title: EV_DAS30_rep1


title: Col0_DAS30_rep1


title: Col0_DAS30_rep2


title: vil1_0_1


title: KN99alpha Old 1

city: Stony Brook

first: Bettina

middle: C

last: Fries

address: HSC T 15 Room 080, 101 Nicholls Rd

institute: Stony Brook University

data_processing:
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 GCcontent the clean data were calculated.
Assembly: Clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: Raw data were processed by removing reads containing adapters, reads containing unknown nucleotides, and low-quality reads. Differential expression analysis was performed employing the DESeq2 R package. Genes with an adjusted p-value ≤ 0.05 and |log2FoldChange| ≥ 1 were assigned as differentially expressed.
Supplementary files format and content: count, fpkm

organism: Cryptococcus neoformans

growth_protocol: Cells were grown in synthetic media 1.7 g yeast nitrogen base without amino acids ,1 g Drop-Out mix , 0.4% ethanol, 5 g (NH4)2SO4, 3.3 g NaCl, with 2% glucose per 1L

extract_protocol:
RNA was extracted using the RNAeasy Plus kit
RNASeq was performed by Novogene Co. Libraries were clustered and sequenced on an Illumina NovaSeq 6000 platform, which utilizes a paired-end 150bp sequencing strategy according to the manufacturer's instructions.

treatment_protocol: Young and old cells were isolated using streptavidin magnetic beads. Briefly, yeast cells (5x107) from an exponential culture were washed with phosphate-buffered saline (PBS) and labeled with 8 mg/mL sulfosuccinimidyl-6-(biotin-amido) hexanoate (Sulfo-NHS-LC-LC-Biotin) for 30 min at room temperature (RT). Next, cells were washed with PBS and grown for five doubling times in SM media at 37°C. Cells were washed with PBS and incubated in 200μL streptavidin microbeads for 30 mins at 4°C. Biotin-streptavidin-labeled cells were isolated using LS Columns following the manufacturer’s guidelines. The positive cell fractions were combined, washed in PBS, and grown again in SM media for an additional five doubling times at 37°C. Subsequently, the cells were washed, incubated in streptavidin microbeads and separated again.

tag: age

value: Old


title: RNAseq golden hamster 4

city: Shanghai

first: Wei

last: Liu

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

data_processing:
We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs, tsRNA (tRNA-derived small non-coding RNA), rsRNA (rRNA-derived small non-coding RNA), small snoRNAs, lncRNA, and mRNA, successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo-siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others.
We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM (transcripts per kilobase of exon model per million mapped reads) by StringTie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM values or raw counts for each Sample

organism: Mesocricetus auratus

source_name: oocyte

extract_protocol:
Total RNA from oocytes of different species were extracted with TRIzol Reagent (Ambion, USA), respectively.
Small RNA library construction. Briefly, the single oocytes were incubated at 72 °C for 3 min then cooled in ice. After 3′ adapter ligation, the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de-adenylates. Small RNAs were reverse-transcribed after 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel.
mRNA library construction. In brief, single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte, 1 μl of a 1/500,000-1/50,000 dilution of the ERCC RNA Spike-In Mix (Invitrogen, 4456740) was added. After reverse transcription and PCR pre-amplification, cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.

value: oocyte

tag: Sex

value: female

tag: Stage

value: MII

value: wild type


title: KN99alpha Old 2


title: KN99alpha Young 1

value: Young


title: EV_DAS30_rep2


title: KN99alpha Young 2


title: RNAseq golden hamster 3


title: CLIP_NOVA1_GBM1_1


title: EV_DAS30_rep3


title: RNAseq golden hamster 1


title: golden hamster control

value: control


title: small RNA golden hamster 2

tag: molecule subtype

value: small RNA


title: small RNA golden hamster 4


title: small RNA golden hamster 3