title: eCLIP,GFP_IP,bio_rep2

city: New Haven

first: Lian-Huan

last: Wei

state: CT

address: 295 Congress Ave BCMM141

department: Department of Neuroscience

institute: Yale University

description: paired-end sequencing was performed but only read1 was used

data_processing:
demultiplex
Adapters were trimmed using Cutadapt 3.2
For CRISPR screen, reads were map to GeCKOv2 library reference with STAR 2.7; For eCLIP, reads to sequentially mapped to rRNA, tRNA and mRNA with STAR 2.7
eCLIP reads were deduplicated with UMI tools
Assembly: hg38 for eCLIP
Supplementary files format and content: tab-delimited text files include reads count for each CRISPR screen sample
Supplementary files format and content: comma-delimited csv files include reads count for each eCLIP sample

source_name: Human embryonic kidney

extract_protocol:
For CRISPR screen, genomic DNA was extracted using the Zymo Research Quick-gDNA Midiprep Plus kit (D4075); For eCLIP, RNAs were extracted using the RBP-eCLIP kit (ECLIPSEbio) according to the manufacturer's instructions.
For CRISPR screen, sgRNA sequences were amplified by PCR following the previously described procedure (Joung et al, 2017, Nat Protoc); For eCLIP, libraries were constructed using the RBP-eCLIP kit (ECLIPSEbio) according to the manufacturer's instructions.

value: Human embryonic kidney

value: GFP IP


title: OV.P20190304_T

status: Public on Jul 11 2024

type: SRA

city: Beijing

first: Yu

last: Yang

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: Academy for Advanced Interdisciplinary Studies

country: China

institute: Peking University

description:
10X
counts.mtx.gz
features.tsv
barcodes.tsv
meta.tsv.gz

library_source: transcriptomic single cell

data_processing:
For 10X data, Cell Ranger 3.0.0 was used to quantify gene expression level.
Assembly: GRCh38 for RNA expression
Supplementary files format and content: text files for expression matrices, cell metadata

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
10x Chromium Single cell 5’ Library
Single cell suspensions were stained with antibodies against CD45 and 7AAD for FACS sorting, performed on a BD Aria SORP instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.

tag: tissue

value: Tumor

tag: patientid

tag: cancer type

value: OV


title: PACA.P20181121_T

value: PACA


title: eCLIP,GFP_IP,bio_rep1

country: USA

library_source: transcriptomic

molecule: total RNA

tag: cell line

tag: treatment


title: SR004261_H3K4me1_wt_PBS.4

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 South Euclid Ave

institute: Washington University In St Louis

description: H3K4me1 Chipmentation in mouse HSC/MPP

library_source: genomic

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by BWA with the ENCODE DCC TF/Histone ChIP-Seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2, v1.1.6)
Signal strength relative to the control samples were generated using MACS2.
Broad peaks were called using MACS2, and overlapping peaks across pseudo-replicates were genereated using the same approach as that used by the ENCODE pipeline for overlap optimal peaks.
genome build/assembly: GRCm38/mm10
processed data files format and content: bigwig, broadPeak

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

treatment_protocol: PBS or G-CSF 5 mcg daily x2 days

value: bone marrow

tag: cell type

value: HSC/MPP

tag: genotype

value: wildtype

value: PBS vehicle control


title: mRNA_HeLa_NSUN6_knockdown_Label_rep1

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Zhejiang University

data_processing:
For batch paired-end reads of m5C-seq libraries, a sample-barcoded-sequence (Pos 1-6) and random-4-base (pos7-10) in Read1 and a 10nt unique molecular identifier (UMI) was included in the adaptor that ligates to the 3’end of cDNA so it locates in Read2 (Pos1-10). Firstly, m5C-seq batch libraries were demultiplexed into individual samples, using fastq-multx（with -m 1 parameters）that distributes reads into a sample FASTQ file(Read1.fq file and Read2.fq file) according to the sample-barcoded-sequence in Read1 (Pos 1-6). For every individual sample, only Read2 data with UMI was used for subsequent analyses. Illumina sequencing reads were first treated with trim_galore(version 0.6.4) for adapter removal and quality trimming. Work commands are as follows: trim_galore --fastqc --phred33 --length 30. We then used Seqkit (version 0.10.0) to deduplicate based on 10 bp UMI at the 5′ end of reads R2, key process parameters are as follows: seqkit rmdup -s. Finally, Fastp (version 0.23.2) was used to remove the 10 bp UMI in the deduplication read. 10 bases at the 3′ end of inserted sequences were also removed, using the key parameters: fastp -f 10 -t 10 -l 20.
Processed reads were mapped to reference genome (human GRCh19 reference / mouse mm10 reference) using HISAT2-3N (version 2.2.1-3n-0.0.3). The key parameters are as follows: hisat3n --base-change C,T --directional-mapping --repeat -p 20 -k 1. Considering a creditable m5C signal, the alignments are further filtering using python house-scripts, the alignments hosts >=3 C-to-T mismatches or >= 3 other type mismatches or the length of alignments < 20nt are filtered. Next, we parse BAM file using pysamstats (version 1.1.2), with commands as follow: pysamstats -D 100000 -S "nofilter" -t variation.
To identify the methyltransferase-dependent m5C sites, we calculated the C-to-T ratios for the m5C-TACseq-identified m5C sites in WT and all knockout/knockdown samples. Then, the fold change and difference of C-to-T ratio between KO/KD samples and WT/Control samples were calculated. For the identification of enzyme-dependent sites by comparing the KO and WT samples, the fold change in C-to-T ratio (KO sample/WT sample) was required to be less than 60% in two replicates, and the difference in C-to-T ratio (WT sample - KO sample) was required to be > 1.5%. Considering the presence of residual enzymes upon knockdown, to identify enzyme-dependent sites by comparing the KD and Control samples, the fold change in C-to-T ratio (KD sample/Control sample) was required to be less than 60% in at least one replicate.
The analysis of CLIP-seq data was performed using CLIP Tool Kit (CTK, v1.1.3). The processed reads were mapped to the mouse genome (Ensembl annotation of mm10) using hisat2 v2.2.1 with default settings.
Assembly: hg19(UCSC)/mm10(UCSC)/tRNA-referenece(tRNAdb)
Supplementary files format and content: tab-delimited text file includes every C base coverage and C-to-T signal
Supplementary files format and content: excel file,in xls file format
Library strategy: m5C-seq

source_name: cell line

growth_protocol: The mESC cell line was cultured in a complete ESC culture medium, comprising Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% heat-inactivated fetal bovine serum (FBS), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1000 U/mL recombinant leukemia inhibitory factor (LIF), and 100 U/mL penicillin/streptomycin. For differentiation assays, mESC cells were cultured without LIF for six days. HeLa and HEK 293T cell lines were cultured in DMEM supplemented with 10% FBS and 100 U/mL penicillin/streptomycin.

extract_protocol:
Total RNA extraction from the cell lines was accomplished using the RNA isolater total RNA extraction reagent (Vazyme, R401-01). Prior to size selection, RNA underwent DNase I treatment at 37 ℃ for 15 min and subsequently was purified using RNA isolater extraction and ethanol precipitation (Vazyme, EN401-01). The small RNA fraction, characterized by a size of less than 200nt, was enriched from the total RNA utilizing the RNA Clean & Concentrator-25 Kit (Zymo, R1018). For mRNA purification, two successive rounds of poly(A)+ selection were performed employing oligo(dT)25 dynabeads (Life Technologies, 61005). Additionally, chromatin-associated RNA was isolated following subcellular fractionation assay, DNase I treatment, and rRNA depletion (Vazyme, N406-01). Modification-free control RNAs were prepared from HeLa or mESC mRNA, adhering to a previously published protocol (PMID: 34594034, 36593412).
The RNA samples were initially dephosphorylated using T4 polynucleotide kinase (Vazyme, N102-01) at 37℃ for 1 hour, followed by ethanol precipitation. Subsequently, they were ligated to the 3' RNA linker using T4 RNA ligase 2, truncated at 25°C for 2 hours, followed by an overnight incubation at 16°C (Beyotime, R0635L). To remove excess adaptors, the samples underwent treatment with 5´ Deadenylase (NEB, M0331S), RecJf (NEB, M0264S), and Proteinase K (NEB, P8102). RNA samples intended for group comparisons were pooled and then purified through Tris-phenol extraction followed by ethanol precipitation. The barcoded and pooled samples were labeled by 5-(2-azidoethyl)-1,3-indandione (AI) and subsequently subjected to a click reaction. The m5C-modified RNA was subjected to RNA pull-down to be enriched, followed by reverse transcription using the HiScript III RT SuperMix (Vazyme, R323-01). The excess reverse transcription primer was digested with exonuclease I (NEB, M0293S). The cDNA was purified by silane beads and then performed to 5′ adapter ligation on beads with T4 RNA ligase 1, high concentration (NEB, M0437M). cDNA was purified using silane beads (Invitrogen, 37002D), and subsequently, the purified cDNA was amplified using the KAPA HiFi HotStart ReadyMix (Roche, KK2602). Finally, PCR products were purified using 1.8X VAHTS DNA Clean Beads (Vazyme, N411-02) and 7% TBE gel.

value: cell line

value: HeLa

value: cervical cancer cells

value: NSUN6 knockdown

value: TET2 oxidation and AI Labeling


title: eCLIP,GFP_input,bio_rep2

value: GFP input


title: SR004261_H3K4me1_wt_PBS.3

description: H3K4me1 Chipmentation in mouse HSC/MPP


title: mRNA_HeLa_NSUN2_knockdown_Label_rep2

value: NSUN2 knockdown


title: SR004261_H3K4me1_wt_PBS.2

description: H3K4me1 Chipmentation in mouse HSC/MPP


title: OV.P20181225_T

value: FTC


title: mRNA_HeLa_NSUN2_knockdown_Label_rep1


title: SR004261_H3K4me1_wt_PBS.1

description: H3K4me1 Chipmentation in mouse HSC/MPP


title: mRNA_HeLa_NSUN6_knockdown_Label_rep2


title: ESCA.P20191129_N

source_name: Adjacent normal tissue

value: Adjacent normal tissue

value: ESCA


title: ESCA.P20191129_T

value: Tumor


title: SR004261_H3K4me1_wt_GCSF.4

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: G-CSF x2 days


title: mRNA_HeLa_shControl_Label_rep2

value: Control


title: SR004261_H3K4me1_wt_GCSF.3

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: bone marrow


title: eCLIP,eIF2A_IP,bio_rep1

value: Human embryonic kidney

value: eIF2A-GFP IP


title: mRNA_HeLa_shControl_Label_rep1


title: eCLIP,eIF2A_input,bio_rep2

value: eIF2A-GFP input


title: ESCA.P20191125_T


title: SR004261_H3K4me1_wt_GCSF.2

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: HSC/MPP

value: wildtype


title: OV.P20190304_N

value: OV


title: ESCA.P20191125_N


title: eCLIP,eIF2A_input,bio_rep1


title: eCLIP,GFP_input,bio_rep1


title: HeLa_IVT_Label_Rep1

description: in vitro transcribed (IVT) RNA, polyA_RNA template

data_processing:
For batch paired-end reads of m5C-seq libraries, a sample-barcoded-sequence (Pos 1-6) and random-4-base (pos7-10) in Read1 and a 10nt unique molecular identifier (UMI) was included in the adaptor that ligates to the 3’end of cDNA so it locates in Read2 (Pos1-10). Firstly, m5C-seq batch libraries were demultiplexed into individual samples, using fastq-multx（with -m 1 parameters）that distributes reads into a sample FASTQ file(Read1.fq file and Read2.fq file) according to the sample-barcoded-sequence in Read1 (Pos 1-6). For every individual sample, only Read2 data with UMI was used for subsequent analyses. Illumina sequencing reads were first treated with trim_galore(version 0.6.4) for adapter removal and quality trimming. Work commands are as follows: trim_galore --fastqc --phred33 --length 30. We then used Seqkit (version 0.10.0) to deduplicate based on 10 bp UMI at the 5′ end of reads R2, key process parameters are as follows: seqkit rmdup -s. Finally, Fastp (version 0.23.2) was used to remove the 10 bp UMI in the deduplication read. 10 bases at the 3′ end of inserted sequences were also removed, using the key parameters: fastp -f 10 -t 10 -l 20.
Processed reads were mapped to reference genome (human GRCh19 reference / mouse mm10 reference) using HISAT2-3N (version 2.2.1-3n-0.0.3). The key parameters are as follows: hisat3n --base-change C,T --directional-mapping --repeat -p 20 -k 1. Considering a creditable m5C signal, the alignments are further filtering using python house-scripts, the alignments hosts >=3 C-to-T mismatches or >= 3 other type mismatches or the length of alignments < 20nt are filtered. Next, we parse BAM file using pysamstats (version 1.1.2), with commands as follow: pysamstats -D 100000 -S "nofilter" -t variation.
To call m5C signal, C-to-T rate of each C nucleotide in the reference sequences was calculated for both treat (TET2 +) and control (TET2 –) samples. Two parameters were deﬁned to evaluate the dynamic change of C-to-T rate in the treat and control samples: difference of C-to-T rate (Diff) and fold change of C-to-T rate (FC). Diff was calculated by subtracting the mismatch rate in the treat sample from that in the corresponding control sample, while FC was calculated by dividing the C-to-T rate in the control sample that in the treat sample. C position was identiﬁed as an m5C site when the following criteria were met: (1) label sample coverage >= 20; (2) ctrl sample coverage >= 5; (3) C2T reads number >= 5 in both treat sample replications and C2T_reads_num >= 10 at least in one treat sample; (4) diff (treat sample -ctrl sample) >= 5% in both replications; (5) FC (treat sample/ctrl sample) >= 3 in both replications; (6) both control sample mismatch ratio <= 5%; (7) region around C position（+-50nt）mismatches number <= 6 in treat sample. To give our final m5C signal list, we overlapped two lists from two samples, only counted overlapped signals into our final m5C list.
To call m5C signal in KO samples, we took our final m5C list as a reference to find the C-to-T rate in KO samples. Then, we calculated the C-to-T rate fold change and difference between KO samples and WT samples. For enzyme-dependent sites, the C-to-T rate of KO sample is decrease to less than 60% of the WT-sample, the C-to-T rate difference (treat sample – control sample) is required to be >1.5%. To give our final KO-dependent sites list, we overlapped two lists from two KO repeats, and only counted overlapped signals into our final KO-dependent list.
Assembly: hg19(UCSC)/mm10(UCSC)/tRNA-reference(tRNAdb)
Supplementary files format and content: tab-delimited text file includes every C base coverage and C-to-T signal
Supplementary files format and content: excel file,in xls file format
Library strategy: m5C-seq

source_name: HeLa

value: HeLa

value: cervical cancer cells

value: WT

tag: fraction

value: in vitro transcribed (IVT) RNA


title: mRNA_HEK293T_NSUN6_knockdown_Label_rep1

value: cell line

value: human embryonic kidney cells

value: NSUN6 knockdown

value: TET2 oxidation and AI Labeling


title: ESCA.P20190916_T

value: Tumor

value: ESCA


title: HeLa_IVT_Ctrl_Rep2

value: control


title: HeLa_IVT_Label_Rep2


title: SR004261_H3K4me1_ko_PBS.4

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: bone marrow

value: Kmt2c deleted

value: PBS vehicle control


title: Day14, libraryB, GFP_to_mCherry_low, bio_rep1

value: Human embryonic kidney

value: FACS sorted cell


title: SR004261_H3K4me1_wt_GCSF.1

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: HSC/MPP

value: wildtype

value: G-CSF x2 days


title: HeLa_IVT_Ctrl_Rep1

value: HeLa

value: cervical cancer cells

value: WT


title: Day14, libraryB, GFP_to_mCherry_low, bio_rep2


title: eCLIP,eIF2A_IP,bio_rep2

value: eIF2A-GFP IP


title: ESCA.P20190613_T


title: Day14, libraryB, GFP_to_mCherry_high, bio_rep2


title: ESCA.P20190613_N

value: Adjacent normal tissue


title: SR004261_H3K4me1_ko_PBS.3

description: H3K4me1 Chipmentation in mouse HSC/MPP


title: mRNA_HeLa_Label_Rep2

value: TET2 oxidation and AI Labeling

value: polyA RNA


title: Day14, libraryB, GFP_to_mCherry_high, bio_rep1


title: ESCA.P20190411_T

value: Tumor

value: ESCA


title: SR004261_H3K4me1_ko_PBS.2

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: bone marrow


title: mRNA_HeLa_Label_Rep1


title: Day14, libraryA, GFP_to_mCherry_low, bio_rep2


title: Day14, libraryA, GFP_to_mCherry_low, bio_rep1


title: ESCA.P20190410_T


title: Day14, libraryA, GFP_to_mCherry_high, bio_rep2


title: SR004261_H3K4me1_ko_GCSF.4

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: Kmt2c deleted


title: mRNA_HeLa_Ctrl_Rep1

value: control


title: mRNA_293T_Label_Rep2

value: human embryonic kidney cells


title: SR004261_H3K4me1_ko_GCSF.3

description: H3K4me1 Chipmentation in mouse HSC/MPP


title: Day14, libraryA, GFP_to_mCherry_high, bio_rep1

value: Human embryonic kidney

value: FACS sorted cell


title: SR004261_H3K4me1_ko_GCSF.2

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: HSC/MPP


title: ESCA.P20190404_T


title: Day7, libraryB, GFP_to_mCherry_low, bio_rep2


title: ESCA.P20190404_N


title: SR004261_H3K4me1_ko_GCSF.1

description: H3K4me1 Chipmentation in mouse HSC/MPP

value: G-CSF x2 days


title: mRNA_293T_Label_Rep1


title: Day7, libraryB, GFP_to_mCherry_low, bio_rep1


title: mRNA_293T_Ctrl_Rep2


title: ESCA.P20181123_T


title: mRNA_HeLa_Ctrl_Rep2

value: HeLa


title: mRNA_293T_Ctrl_Rep1


title: Day7, libraryB, GFP_to_mCherry_high, bio_rep2


title: TGA1-GFP_GFP

city: Nagoya

first: Yuri

last: Ohkubo

address: Chikusa

department: Department of Biological Science

country: Japan

institute: Nagoya University

data_processing:
The reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
ChIP-enriched peaks were called uing MACS2.
Assembly: TAIR10
Supplementary files format and content: bed file

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
The roots of TGA1-GFP plants were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with GFP antibodies.
DNA (100 ng) was used to prepare ChIP-seq libraries, using a NEBNext Ultra II RNA Library Prep Kit for illumina (NEB) according to the manufacturer's instructions.

value: Root


title: ESCA.P20190411_N


title: Kyp   Rep3

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

country: France

institute: Universite Paris Saclay

description: readcount.txt.gz

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using Hisat2 v 2.2.1 with the following setting "-x hisat2_index -p 8 --rna-strandness RF -a -1  -2 " against the genome of SollycM82_v1.0.
Quality filtering: mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 " to remove reads of quality under 30
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the commands "samtools fixmate -m"  and "samtools markdup -r "
Raw read counts were extracted using featureCounts based on the gene annotations in SollycM82_v1.0.gtf
Differentially expressed genes were identified using R 3.5.1(www.R-project.org) and the package DESeq2 (adj. p value < 0.05)
Assembly: SollycM82_v1.0
Supplementary files format and content: Count matrix of all samples obtained with featureCounts

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Plants were grown in pots in growth chambers at 24 °C under long-day (16 h of light) conditions.

extract_protocol:
Total RNA were extracted from 1g of 4-week-old tomato fourth leaves with Nucleospin RNA kit (Macherey-Nagel), according to the manufacturer’s instructions.
RNA-seq libraries were prepared from 2μg of total RNA using NEBNext Ultra II Directional RNA library Preparation Kit (NEB) according to the manufacturer’s instructions. RNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and subjected to 2 × 150 bp high-throughput sequencing by NovaSeq 6000 (Illumina).

tag: cultivar

value: Kyp mutant

value: Leaf

value: Normal condition

tag: bio rep

value: Bio rep 3


title: Day7, libraryB, GFP_to_mCherry_high, bio_rep1


title: ESCA.P20181123_N

value: Adjacent normal tissue


title: ESCA.P20190410_N


title: Kyp   Rep2

description: readcount.txt.gz

value: Bio rep 2


title: GFP-GrxS5_2

data_processing:
RNA-seq data was mapped to Arabidopsis TAIR10 genome release using the bioinformatic pipeline of illumina Base Space Sequence Hub. Assembly: TAIR10 Supplementary files format and content: tab-delimited text files include TPM values for each Sample
RNA-seq data was mapped to Arabidopsis TAIR10 genome release using the bioinformatic pipeline of illumina Base Space Sequence Hub.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was prepared from roots and shoots of the plants using an RNeasy kit (Qiagen).
Total RNA (1 µg) was used to prepare RNA-seq libraries, using a TruSeq RNA Sample Prep Kit v2 (MiniSeq) and NEBNext Ultra II RNA Library Prep Kit (NextSeq550) (illumina) according to the manufacturer's instructions.


title: BC.P20190403_T

value: Tumor

value: BC


title: Day7, libraryA, GFP_to_mCherry_low, bio_rep1


title: GFP-GrxS5_1


title: Col_3


title: BC.P20190123_T


title: M82  Rep3

description: readcount.txt.gz

value: WT


title: Col_2


title: BC.P20190123_N


title: M82  Rep2

description: readcount.txt.gz


title: Day7, libraryA, GFP_to_mCherry_high, bio_rep2


title: TGA1-GFP_IgG


title: Day7, libraryA, GFP_to_mCherry_high, bio_rep1


title: M82  Rep1

description: readcount.txt.gz

value: Bio rep 1


title: Col_1


title: CRSIPRcap_rep1

status: Public on Jul 10 2024

city: Dallas

first: Donghong

last: Cai

state: TX

address: Dallas

institute: UTSW

data_processing:
The reads were aligned to the hg38 reference genome by STAR(20). Only reads that covered the targeted sites of CRISPR sgRNA and allowed for genotyping were retained for downstream analysis. The distributions of 5’ end positions of transcripts with UMIs between WT reads and MUT promoter sequences were compared.
Assembly: hg38
Supplementary files format and content: tsv. crispr_cap.tsv contains CRISPR-cap reads information after filtering to relevant reads, including the TSS position and the mutation information (if the read carries a deletion)

extract_protocol:
TRIzol was used to extract total RNA
We designed one single guide RNAs (sgRNAs) targeting each TSS motif containing the NGG PAM sequence (Table S7). Synthesized sgRNA oligos were mixed with purified CRISPR-Cas9 protein at 2:1 ratio to form RNP complexes in OptiMEM for 10 min. The RNP complexes were transfected into HEK293T cells by lipofectamine 3000. HEK293T was cultured in DMEM supplemented with 10% FBS at 37℃ with 5% CO2. To maximize the efficiency of Cas9 editing, the second transfection was performed after 2 days. After two rounds of RNP transfection, cells were isolated total RNA by TRIzol. Then each 1ug of total RNA was treated with 2U DNase I for 15min at 37℃. DNase I was removed by TRIzol extraction, and the RNA was diluted by nuclease-free water. Then each 1ug of RNA was dephosphorylated by 0.5ul of calf intestinal alkaline phosphatase (CIP; NEB cat. no. M0525S). The reaction was cleaned up by TRIzol. Then the 5’ cap of RNA was removed using Cap-Clip Acid Pyrophosphatase (cat. no. C-CC15011H from CELLSCRIPT, CCAP) for each 1ug RNA with 0.05ul CCAP. The reaction was clean up. Ligated TAPCCAP-treated RNA with 5’end RNA oligo (GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNN) with 1 ug RNA for 100uM oligo at 16°C for 16 h using 0.2 µl T4 RNA Ligase 1 (ssRNA Ligase, NEB, cat. no. M0204L), followed by TRIzol clean up. 8nt of random nucleotide in the 3` end of RNA oligo can be considered as UMI.  First strand cDNA synthesis was performed using 1µl of Superscript IV (50°C for 60 min, 70 °C for 15 min; Invitrogen, cat. no. 18091050) using a 20bp gene-specific RT primer (Table S7) for 2.5–5 µg of RNA in 20 µl. Then 1 µl of 10 mg/ml RNaseA was added to remove the RNA at 37 °C for 15 min. Finally, cDNA was amplified for pair-end sequencing using Illumina NextSeq 2000 by the sequencing primer AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA and gene-specific PCR primers (Table S7) with the Illumina adapter sequence (TTCAGACGTGTGCTCTTCCGATCTN20). All samples were pooled and amplified by Illumine sequencing adapters. The read 1 primer was replaced by Illumina small RNA TrueSeq primer for 5’ end RNA ligator (TCTACACGTTCAGAGTTCTACAGTCCGACGATC). The sequencing was performed using NextSeq 2000 by 80 (read1), 0 (index1), 8 (index2), and 150 (read2) with 200-cycle P3 kit.


title: CRSIPRcap_rep2


title: ESCA.P20181114_T

value: ESCA


title: STAP-seq

data_processing:
The reads were aligned to the hg38 reference genome by STAR(20). Only reads that covered the targeted sites of CRISPR sgRNA and allowed for genotyping were retained for downstream analysis. The distributions of 5’ end positions of transcripts with UMIs between WT reads and MUT promoter sequences were compared.
Assembly: hg38
Supplementary files format and content: tsv contains STAP-seq information, one file per oligmer, each containing TSS count at each position relative to the oligomer start position


title: GS014

city: New York

first: Richard

middle: A

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

data_processing:
RTA (Illumina) was used for base calling. bcl2fastq2 (version 2.19) to convert
from BCL to fastq format, coupled with adaptor trimming.
Peudoalignment was performed with Kallisto (Version 0.44.0 with ENSEMBL 96 annotation
Assembly: GRCh38.p12
Supplementary files format and content: txt file with number of reads for each gene

source_name: Human cardiomyocyte/fibroblast tissue model

extract_protocol:
Tissues were snap frozen in liquid nitrogen and stored at -80*C until use.
To isolate RNA, snap-frozen tissues were added to 300 mL of RNA lysis buffer
(Qiagen) with a stainless-steel bead (BioSpec, 11079123) and homogenized with
a Mini-Beadbeater (Biospec, C321001) for 5-10 seconds or until tissue samples
were not visible. RNA was then isolated using a Qiagen RNeasy Micro Kit
(Qiagen, 74004), according to manufacturer’s instructions.
RNA for each sample was then analyzed for quality/quantity using an
Agilent bioanalyzer, Qubit 2.0 at Columbia’s Molecular Pathology core.
cDNA amplification for Sequencing was performed the SMART-Seq® v4 Ultra® Low
Input RNA Kit (TaKaRa) for according to manufacturer's instructions. A library
was  prepared using the Nextera XT DNA Library Preparation kit (Illumina) with
100-150pg starting material, ccording to manufacturer's instructions. Libraries
were sequenced to a targeted depth of ~40M 100bp paired-end reads on a NovaSeq
6000

treatment_protocol:
The IgG antibody fraction was isolated from patient sera using the NAb Protein
A/G Spin Kit, (Thermo Fisher Scientific, cat. no. 89950), according to the
manufacturer’s protocol. Autoantibody purification from the patients’ sera
was performed.  0.5 mg/mL of the purified IgG was added to the culture medium on
day 14, with tissues stimulated at 2 Hz and maintained for an additional 14 days.
During this time, the frequency of electrical stimulation was stepwise increased
to 6 Hz by day 21 and decreased to 2 Hz thereafter and maintained until day 28.

tag: patient

value: antibody


title: Day7, libraryA, GFP_to_mCherry_low, bio_rep2

value: Human embryonic kidney

value: FACS sorted cell


title: Kyp   Rep1

description: readcount.txt.gz


title: A375 untreated control sample

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

data_processing:
Custom amplicon-seq on the PCR product comprised of sgRNA expression cassette integrated into A375 cells.
The raw sequencing data were transformed into a table of the absolute amount of sgRNA read detected from each sample using MAGeCK package
Differential gene expression was called from the normalized and log-transformed sgRNA counts from each sample using LIMMA package.
Assembly: custom sgRNA library: Heidelberg CRISPR library sub-library A
Supplementary files format and content: .fastq.gz: sequence reads of sgRNA expression cassette integrated into A375 genome
Library strategy: Amplicon-seq

source_name: melanoma

growth_protocol: A375 melanoma cells were cultured in RPMI 1640 supplemented with 10 % FCS, 2 mM L-glutamine, and 1 % Penicillin/Streptomycin. Primary NK cells were cultured in SCGM media or in NK MACS media both supplemented with 10% human AB serum, 1% Penicillin/Streptavidin, 2nm L-Glutamine and 400U/ml of IL-2.

extract_protocol:
gDNA from 50 million melanoma from each sample was isolated using QIAGEN Blood & Cell Culture DNA Maxi Kit. PCR was performed on the purified gDNA to amplify the sgRNA expression cassette.
As previously described in Henkel, L., Rauscher, B., Schmitt, B., Winter, J., & Boutros, M. (2020). Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library. BMC biology, 18, 1-21.

treatment_protocol: After sgRNA library transduction and puromycin selection, the A375 cells were co-cultured with or without NK cells in an effector-to-target ratio between 1:1 - 1:1.5 which represent medium killing and high killing treatments. Another part of A375 remained untreated and serve as control sample. The co-culture proceeded for 24h followed by NK cell removal. The remaining A375 cell were allowed to expand for 2 days before harvest.

value: melanoma

value: adherent

value: Cas9 overexpression

tag: library treatment

value: Heidelberg CRISPR library sub-library A

value: untreated


title: Differentiated (day 41) - short reads -  rep 1

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: Quebec

address: 740 Dr. Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Short RNA-seq reads were processed using RSEM 13 (version 1.3.3, following alignment with bowtie2 version 2.4.2),
salmon  (version 1.3.0, with the --validateMappings and --gcBias flags ),
kallisto  (version 0.48.0) and MPAQT.
Assembly: GRCh38.p13
Supplementary files format and content: count matrices, csv files

source_name: neurons

growth_protocol: The hESC line was maintained in feeder-free conditions with the E8 medium. Neural differentiation was initiated when the cells reached 90-100% confluency. From days 0-11, the cells were maintained in neural induction medium (10 µM SB431542 and 100 nM LDN193189 in E6 medium) with medium change every two days. From day 12, the cells were fed the cortical neuron medium (10 ng/mL GDNF, 100 µM ascorbic acid, 1x Glutagro, 1x N2 supplement, 1x B27 without vitamin A in neurobasal medium) with medium change every other day until rosette structures became visible. Then, neurons were detached using Accutase and replated on poly-L-ornithin/fibronection/laminin-coated plates. Neurons were maintained in cortical neuron medium with medium change every other day. On days 22-24, neurons were checked for the presence of axonal projections and 10 µM DAPT was included in the cortical neuron medium until the projections appeared. From day 30, neurons were considered mature with the medium feeding frequency reduced to 1-2 times per week

extract_protocol:
RNA extraction using Zymo Quick-RNA Microprep kit according to the manufacturer’s protocol. SIRV set 4 (Lexogen) was spiked at 1% in the hESC and differentiated neuron-derived RNA samples.
libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3. Libraries were sequenced on a NextSeq 550 sequencer (2x75 bp paired-end).

value: neurons


title: Differentiated (day 61) - short reads -  rep 1


title: hESC (day 0) – short reads - rep 1

source_name: human embryonic stem cells

value: human embryonic stem cells


title: Differentiated (day 41) - short reads -  rep 2


title: Differentiated (day 61) - short reads -  rep 2


title: A375 co-cultured with medium ratio of NK cells

value: medium amount of human NK cells for 24 hours


title: A375 co-cultured with high ratio of NK cells

value: high amount of human NK cells for 24 hours


title: Bladder cancer cell xenograft, TS268RA

type: RNA

city: Bangor

first: Tim

last: Smith

address: Dean Street

department: School of Computer Science and Engineering

country: United Kingdom

institute: University of Bangor

hyb_protocol: Sample hybridization on Clariom S arrays was carried out by Yourgene Health (Manchester, UK). Batches of CEL files were GC SST (Signal Space Transformation with probe Guanine Cytosine Count Correction) RNA normalised using Affymetrix Array Power Tools. (https://www.thermofisher.com/uk/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-developers-network.html)

data_processing: The log2-summarised gene level expression values generated were batch-corrected using the ComBat function from the Bioconductor package sva.

label: biotin

source_name: xenograft tissue pimo low

label_protocol: RNA extracted from both sample cohorts were subject to Clariom S analysis. RNA (8 ng/µl in a 9 µl volume) was prepared for gene expression arrays with the Clariom S pico HT human assay (Thermo Fisher Scientific).

growth_protocol: HT1376 cells were inplanted into the flank of a nude mouse. A xenograft allowed to grow to 0.7cm in diamter.

extract_protocol: Sections (10µm) were taken and Haemotoxylin and Eosin statining and pimonidazole immunohistochemistry carried out on sections above and below  sections used for microdissection to guide high and, low hypoxic regions excluding necrotic regions. RNA was extracted from the sections using the Roche High Pure FFPET RNA isolation kit. RNA yield was determined on Qubit fluorometer (Invitrogen, Paisley, UK).

treatment_protocol: The mouse was administered with pimonidaole and euthanised after 1h.

value: xenograft tissue

tag: tissue region

value: pimo low


title: PKS44iPS4PGCLC_rep1 (bulkRNAseq)

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description: Processed data in raw_counts_bulkRNAseq.csv.gz. Samples designated by column using sample name

data_processing:
(SINGLE CELL) Raw data were demultiplexed with the mkfastq command in Cell Ranger (v7.1.0) to generate Fastq files. Trimmed sequence files were mapped to the reference genome for humans (GRCh38) provided by 10X Genomics using Cell Ranger mkfastq. Read counts were obtained by using cellranger count.
(SINGLE CELL) Secondary data analyses were performed in Python with Scanpy 1.8.1 or in R (v.4.1.0) with the Seurat (v.4.3.0), SeuratObject (v4.1.3), SeuratWrappers (v0.3.2), tidyverse (v.1.3.2), destiny (v3.10.0), pheatmap (v1.0.12), plot3D (v1.4) and Matrix (v.1.5-1) packages and Excel (Microsoft).
(BULK) Raw fastq files were demultiplexed with bcl2fastq2 (v.2.20.0.422). Barcodes and adapters were removed with Trimmomatic (v.0.32). Fastq files were mapped to UCSC human reference genome (GRH38) using STAR (2.7.10a). The raw gene count table was generated with featurecounts, and weakly expressed genes were filtered with edgeR with the filterByExpr function with default parameters. Briefly, the raw counts were normalized to library size, and then genes with counts per million above 10 were included in downstream analysis. DEGs were analyzed with edgeR (v.3.36.0) with log2fold change >1, p-value <0.05, and FDR <0.05. Reads per kilobase per million (RPKM) values were calculated in edgeR, and the gene length was obtained from the UCSC table browser. Downstream data analyses and visualization were performed with R (v.4.1.0). Hierarchical clustering was performed with hclust in R (v.4.1.0).
Assembly: GRCh38-3.0.0
Supplementary files format and content: raw counts in .csv.gz format

source_name: PGCLCs

extract_protocol:
For seminoma tissues and testicular tissues beyond 15 wpf, ttissues were minced by scissors and dissociated into single cells by Multi Tissue Dissociation Kit 1 (Miltenyi Biotec) according to the manufacturer’s protocol. For testicular or other fetal tissues below 12 wpf, isolated tissue fragments were washed twice with PBS followed by being minced with scissors in 500 μl of 0.1% trypsin/EDTA solution, then incubated for 9 min at 37°C with gentle pipetting every 3 min. After quenching of the reaction by addition of 500 μl of dissection medium (10% fetal bovine serum in Dulbecco's Modified Eagle Medium), cell suspensions were strained through a 70 µm nylon cell strainer to remove cell clumps then centrifuged at 220 g for 5 min. Cell pellets were resuspended in 0.1% BSA in PBS and counted. All samples were stained with trypan blue and confirmed to be over 80% viable.
Total RNA of iPSCs and ITGA+EPCAM+ hPGCLCs are extracted with RNeasy Plus Micro Kit (#74034, QIAGEN). RNA-seq libraries were made using SMRT-Seq HT plus kit (#R400748, Takara) according to the manufacturer’s protocol.
(SINGLE CELL) Chromium Single Cell 3ʼ Reagent (v3.1 chemistry) and Chromium Single Cell Multiome ATAC + Gene Expression Kits were used for library preparation

value: PGCLCs

tag: pathology

value: marker chromosome


title: Bladder cancer cell xenograft, TS267RA

source_name: xenograft tissue pimo high

value: pimo high


title: Bladder cancer cell xenograft, TS270RA


title: Bladder cancer cell xenograft, TS269RA


title: Bladder cancer cell xenograft, TS266RA


title: Bladder cancer cell xenograft, TS265RA


title: PKS44iPS4_rep1 (bulkRNAseq)

source_name: iPSC

value: iPSC


title: PKS44iPS4_rep2 (bulkRNAseq)


title: PKS44iPS4PGCLC_rep2 (bulkRNAseq)


title: RC.P20181224_T

value: Tumor

value: RC


title: PKS19iPS3-PGCLC_rep2 (bulkRNAseq)

value: without marker chromosome


title: PKS19iPS3_rep2 (bulkRNAseq)


title: PKS19iPS1-PGCLC_rep2 (bulkRNAseq)


title: PKS19iPS1-PGCLC_rep1 (bulkRNAseq)


title: PKS19iPS1_rep2 (bulkRNAseq)


title: PKS19iPS1_rep1 (bulkRNAseq)


title: PKS19iPS3_rep1 (bulkRNAseq)


title: PKS12iPS7-PGCLC_rep2 (bulkRNAseq)


title: hESC (day 0) - short reads -  rep 2


title: PKS12iPS7-PGCLC_rep1 (bulkRNAseq)


title: PKS19iPS3-PGCLC_rep1 (bulkRNAseq)


title: PKS12iPS6-PGCLC-9-9 (bulkRNAseq)


title: PKS12iPS1-PGCLC-9-15 (bulkRNAseq)


title: PKS12iPS6_rep2 (bulkRNAseq)


title: PKS12iPS1_rep1 (bulkRNAseq)


title: Ht16_human_testis_5yo (scRNAseq)

description: Sample Ht16 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column

molecule: cytoplasmic RNA

source_name: Testis

value: Testis

tag: Stage

value: Normal


title: Ht9_human_testis_GW23_6_ATAC (scMultiome)

description: Sample Ht9 (ATAC) in paper.

library_source: genomic single cell


title: PKS12iPS7_rep1 (bulkRNAseq)


title: PKS12iPS6_rep1 (bulkRNAseq)


title: Se3_seminoma_GEX (scMultiome)

description: Sample Se3 (GEX) in paper.

molecule: nuclear RNA

value: Seminoma


title: 9A13iPS_rep2 (bulkRNAseq)


title: PKS12iPS7_rep2 (bulkRNAseq)


title: Se2_seminoma (scRNAseq)

description: Sample Se2 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Se3_seminoma_ATAC (scMultiome)

description: Sample Se3 (ATAC) in paper.


title: Ht18_human_testis_12yo (scRNAseq)

description: Sample Ht18 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: 9A13iPS-PGCLC_rep1 (bulkRNAseq)


title: Ht9_human_testis_GW23_6_GEX (scMultiome)

description: Sample Ht9 (GEX) in paper.


title: Ht14_human_testis_GW37 (scRNAseq)

description: Sample Ht14 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht13_human_testis_GW30_rep1 (scRNAseq)

description: Sample Ht13 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht7_human_testis_GW10 (scRNAseq)

description: Sample Ht7 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht10_human_testis_GW17_2 (scRNAseq)

description: Sample Ht10 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht15_human_testis_GW37_4M (scRNAseq)

description: Sample Ht15 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht3_human_testis_GW7 (scRNAseq)

description: Sample Ht3 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: PKS12iPS1_rep2 (bulkRNAseq)


title: 9A13iPS-PGCLC_rep2 (bulkRNAseq)


title: 9A13iPS_rep1 (bulkRNAseq)


title: Ht12_human_testis_GW18_5 (scRNAseq)

description: Sample Ht12 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column

value: GW18 5d


title: Ht11_human_testis_GW18 (scRNAseq)

description: Sample Ht11 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht1_human_testis_GW6 (scRNAseq)

description: Sample Ht1 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht5_human_testis_GW8_4 (scRNAseq)

description: Sample Ht5 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht4_human_testis_GW8 (scRNAseq)

description: Sample Ht4 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht8_human_testis_GW14_2 (scRNAseq)

description: Sample Ht8 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Se1_seminoma (scRNAseq)

description: Sample Se1 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: Ht13_human_testis_GW30_rep2 (scRNAseq)


title: Ht2_human_testis_GW7 (scRNAseq)

description: Sample Ht2 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: C_albicans_200μM_HSL-1.

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of C. auris B8441 and C. albicans SC5314.
The DESeq algorithm (StrandNGS software) was used to obtain normalized gene transcription values.
Gene transcription differences between treated and control groups were compared by a moderated t test; the Benjamini-Hochberg false discovery rate was used for multiple-testing correction, and a corrected P value of <0.05 was considered significant.
Assembly: genome: https://fungi.ensembl.org/_candida_auris_gca_002759435/Info/Index; features: http://www.candidagenome.org/download/gff/C_auris_B8441/archive/C_auris_B8441_version_s01-m01-r11_features_with_chromosome_sequences.gff.gz
Supplementary files format and content: excell file includes p , corrected p. fold change, log fold change values and raw data for each Samples

organism: Candida albicans

source_name: fungal cells

growth_protocol: The C. albicans SC5314 reference strain and C. auris isolate 12 (NCPF 8973), derived from the South Asian/Indian lineage, were used in this study. Both strains were maintained on YPD agar plates [YPD broth (VWR, 1% yeast extract, 2% peptone, 2% glucose) and 2% agar (VWR), pH 5.8)] at 37 °C.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Strains were pre-cultured in YPD broth overnight at 37 °C, diluted to an OD640 of 0.1 in YPD broth (20 mL aliquots in 100 mL Erlenmeyer flasks). Cultures were incubated at 37 °C and 140 rpm for 6 h. HSL (100 or 200 μM final concentration) was added after 4 h of incubation to the exponentially growing phase cultures. Samples were collected after 2 h HSL exposure then were washed three times with physiological saline. Total RNA was isolated from lyophilized fungal cells in three biological replicates.

value: fungal cells

value: 200 μM HSL treated


title: C_albicans_Control-2

value: untreated


title: C_albicans_Control-6


title: Ht17_human_testis_8yo (scRNAseq)

description: Sample Ht17 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: C_albicans_100μM_HSL-3.

value: 100 μM HSL treated


title: C_albicans_200μM_HSL-3.


title: C_albicans_Control-5


title: Ht6_human_testis_GW10_5 (scRNAseq)

description: Sample Ht6 in paper. Processed data in raw_counts.csv, sample name appended to the cell ID in each column


title: C_albicans_Control-1


title: C_albicans_Control-3


title: C_albicans_100μM_HSL-1.


title: C_albicans_100μM_HSL-2.


title: C_albicans_200μM_HSL-2.


title: C_albicans_Control-4


title: ND2

city: Shenyang

first: Shengjun

last: Dong

address: No.120 Dongling Road, Shenhe District, Shenyang, Liaoning Province, P.R.China.

institute: Shenyang Agricultural University

data_processing:
The sequencing-obtained raw image data were converted to sequence reads using CASAVA.
The raw data was filtered by R language, and finally the clean reads for subsequent analysis were obtained.
Trinity v2.4.0 program was used to stitch and assemble clean reads of all samples. Redundancy was removed by clustering with Corset hierarchy, The longest transcript of each gene was selected as Unigene for subsequent analysis.
The transcript sequence obtained by splicing with Trinity was used as a reference sequence. RSEM software (version v1.2.15) (bowtie2, mismatch=0) (bowtie2 default parameters, mismatch = 0)was used to compare clean reads of each repeated sample with reference sequences, and the readcount of each gene was counted and compared. FPKM (fragments per kilobase of exon per million mapped fragments) was used to standardize the readcount of genes.
The DEGseq R package (1.12.0) was used for differential expression analyses. The P-value was calculated based on a negative binomial distribution model. P-values was adjusted using the Benjamini-Hochberg mothed (Benjamini and Hochberg, 1995). Genes with an adjusted P-value < 0.05 and log2(Fold change) > 1 were assigned as differentially expressed.
Genome_build: Ziziphus jujuba Mill.
Supplementary_files_format_and_content: fpkm file includes gene ID and expression for each sample.

organism: Ziziphus jujuba var. spinosa

extract_protocol:
Leaves of Zizyphus jujuba var. Spinosa families under drought stress for 15 days were selected, RNA was extracted by CTAB method, and sequencing library was constructed by using Illumina sequencing platform to extract RNA
The six RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stress

value: control

value: Leaf

tag: development stage

value: Two-year-old seedling


title: ND1

tag: tissue


title: ND3


title: DR3

value: drought stress


title: DR2


title: DR1


title: Sperm, Western Diet, Rep3

city: Barcelona

first: Arnaud

last: Obri

address: C/ del Rosselló, 149

country: Spain

institute: IDIBAPS

data_processing:
TrimGalore v0.6.10 was used to apply adapter and quality trimming to FastQ files
The resulting paired-end reads were aligned to the mouse mm10 reference genome using Bowtie2 v2.4.5 with arguments -N 1 -L 25 -X 2000 -k 20 --no-mixed --no-discordant.
PICARD v2.24.0 was used to mark duplicate reads for posterior removal. Unmapped reads, reads with a low quality alignment score (<Q5), and duplicate reads were filtered out using Samtools. In addition, reads mapping to mitochondrial DNA, chromosome Y, and alternative chromosomes were also removed.
Aligned reads were shifted +4/-5 bp for forward/reverse strands respectively, accounting for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase and achieve base-pair resolution of TF motif-related analyses. Reads were subsequently splitted in two groups of fragments between 50-115 bp (THSS), and 180-247 bp (mono-nucleosomal).
We performed peakcalling on the THSS reads using MACS2 v2.2.7.1 [3] with parameters -q 0.05 -f BED --nomodel --shift -100 --extsize 200 --keep-dup all --call-summits; using BED files (converted from the THSS BAM) as input. The resulting narrowPeak files were used in subsequent analyses.
Assembly: mm10 (Mus musculus GRCm38 DNA primary assembly from Ensembl)
Supplementary files format and content: narrowPeak processed files are BED6+4 format files which contain the peak locations together with peak summit, pvalue and qvalue

source_name: Mature sperm cells from cauda epididymis

growth_protocol: Three-week-old C57BL/6JRccHsd virgin male and female mice were acquired from Envigo

extract_protocol:
Mouse mature sperm extraction was carried out in accordance with the protocol used for murine in vitro fertilization. For each dissection, a Petri dish was prepared containing 1mL of 1x PBS at its center, subsequently overlaid with paraffin oil. Following euthanasia of the male mouse by cervical dislocation, both caudae epididymides were excised and positioned on the paraffin oil in the Petri dish. Each cauda was incised midway using scissors, releasing the sperm clusters, which were then coaxed towards the 1x PBS at the dish's center. After a 10-minute incubation at room temperature, the PBS containing the sperm was collected and centrifuged at 600g at 4ºC for 5 minutes. The sperm was then washed twice with 1x PBS and subjected to counting.
After mature sperm isolation ATAC-seq was performed following the Omni-ATAC protocol. Briefly, the purified sperm pellet was resuspended in the transposase reaction mix containing 1% of digitonin and incubated for 30min at 37ºC. Following incubation, sperm were treated with proteinase K at 55ºC for 2h and genomic DNA (gDNA) was isolated by Phenol:Chlorophorm:Isoamyl alcohol (PCI) and subsequent EtOH precipitation. Library amplification was performed using 2X KAPA HiFi mic and 25uM indexed primers, with PCR conditions as it follows: 72ºC for 5min; 98ºC for 30s; and 8-11 cycles at 98ºC for 10s; 63ºC for 30s; and 72ºC for 1min. Each ATAC-sew experiment was conducted with 4 and 6 biological replicates on Chow diet (F0 CD) and Western diet (F0 WD) groups respectively, and each one contained at least 60 million reads after all the quality control steps.

treatment_protocol: The males were randomly divided into two dietary groups: one group was fed with a standard chow diet (maintenance diet with 14% protein; Envigo), while the other group was given a Western diet (#D12079B, 40% kcal from fat and 43% kcal from carbohydrates; Research Diets) for six months.

value: Wild type

value: Western diet

tag: strain

tag: Sex

value: male

tag: time

value: 6 months


title: Sperm, Western Diet, Rep1

value: Mature sperm cells from cauda epididymis

tag: treatment


title: Sperm, Chow Diet, Rep6

tag: cell type

value: Chow diet


title: Sperm, Chow Diet, Rep4

tag: genotype


title: Sperm, Chow Diet, Rep5


title: Sperm, Chow Diet, Rep3


title: inflamed_CCR1_rep2

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

institute: University of Glasgow

data_processing:
Data was aligned to the mouse genome (GRCm38.91) using STAR (2.7.10a). The index was built for an overhang of 74 bp (read length -1).
Read counts were produced via STAR, under default settings.
Counts were combined into a single read count table using R.
Assembly: GRCm38.91
Supplementary files format and content: Raw read counts produced by alignment of each library to GRCm38 v91.

source_name: Bone

growth_protocol: Wild type and REP(13) mice were housed in a specific pathogen free animal facility at the University of Glasgow. All animal experimentation was carried out under the auspices of a UK Home Office licence and all procedures were approved by the local University of Glasgow ethics committee. All mice used were female between the ages of 8-12 weeks.

extract_protocol:
Cell suspensions were stained for 20 minutes at 4°C with 100 μL of fixable viability stain (eBioscience) and washed in FACS buffer (PBS containing 2mM EDTA and 2% FBS). Next, cells were stained for 20min at 4°C with 50 μL of subset-specific antibody cocktails (Supplementary Table 1) and washed in FACS buffer. For flow cytometry analysis, stained cells were fixed for 20min at 4°C in 100 μL of Fixation Buffer (BioLegend) and analysed on a BD LSRFortessa flow cytometer (BD Biosciences). For monocyte isolation and transcriptomic analysis, stained cells (Supplementary Table 2) were analysed on a FACS Aria sorter (BD Biosciences) without previous fixation. Monocytes expressing either CCR1/2 or CCR2 only were sorted in RLT buffer (Qiagen) containing 10 μL/mL of b-mercaptoethanol and stored at -80oC for RNA extraction.
RNA from sorted monocytes was isolated using the RNeasy® Micro Kit (Qiagen) as per manufacturer’s instructions. Next, mRNA libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs).
Paired-end sequencing was performed in a NextSeq2000 sequencing platform (Illumina) aiming for 40 million reads sequencing depth.

value: Bone

value: female

value: monocytes

value: inflamed


title: inflamed_CCR1_2_rep4


title: Sperm, Chow Diet, Rep1


title: inflamed_CCR1_2_rep3


title: inflamed_CCR1_rep3


title: inflamed_CCR2_rep1


title: resting_CCR2_rep4

value: resting


title: inflamed_CCR2_rep2


title: bone marrow, CCR1/2+ monocytes, resting transcriptome

data_processing:
Reads were aligned using the count function in 10x Genomics Cell Ranger and outputs were imported into R (version 4.2.2) for downstream analysis using Seurat(15, 16). Cells were removed from the analysis if they failed quality control thresholds for the number of features and counts; the range of features included in downstream analysis was 200-3200 and the range of counts was 100-20,000.  In addition, cells were removed if they did not meet the threshold for mitochondrial percentage (<2.5%).
Data were normalized and principal component analysis (PCA) performed using the function RunPCA.  Eleven principal components (PC) were included in downstream analysis.  The FindClusters function was run at a range of resolutions (0.5 – 0.1) in order to select a resolution that could discriminate unique sub-populations based on Top20 gene expression; a resolution of 0.1 was selected. Fifty-nine contaminating B-cells were subsetted out of the data for downstream analysis. Data was re-scaled and cell cycle analysis was performed using the function CellCycleScoring.  The effect of cell cycle was then regressed out of the data.  UMAP dimensionality reduction was applied for visualization.
Assembly: GRCm38.91
Supplementary files format and content: Cell barcodes file, in standard cell ranger format.
Supplementary files format and content: Gene features file, in standard cell ranger format.
Supplementary files format and content: Expression matrix, in standard cell ranger format.

source_name: bone marrow

extract_protocol:
CCR1/2+ monocytes (CD45+, CD11b+, Ly6Chi, Ly6G-, SiglecF-, CCR2+, CCR1+) were sorted from the bone marrow of REP mice using BD FACS Aria and collected into 1% BSA in PBS.
Single cell libraries were generated using 10X Genomics Chromium NextGEM Single Cell 3’ kit (v 3.1) and following the manufacturer’s instructions.  Cells were added to the 10X Genomics NextGEM Chip G at a concentration between 700 and 1200 cells/µl, with a targeted cell recovery of 7000 cells. Cells were combined with Gel Beads-in-Emulsion (GEMs) on the Chromium Controller prior to lysis and reverse transcription. GEMs were then broken and cDNA amplification and fragmentation performed.  Post-fragmentation, the i7 sample index was ligated, and Illumina P5 and P7 adapters added.
Sequencing was performed by Glasgow Polyomics on the Illumina NextSeq-2000 sequencer using a custom paired end sequencing run (28x90bp) to yield 250M reads.

value: bone marrow

value: CCR1/2+ monocytes

value: GGIREPC


title: resting_CCR2_rep1


title: inflamed_CCR1_2_rep2


title: resting_CCR2_rep3


title: inflamed_CCR1_rep1


title: inflamed_CCR1_rep4


title: resting_CCR2_rep2


title: SR004261_H3K4me1_ko_PBS.1

description: H3K4me1 Chipmentation in mouse HSC/MPP

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by BWA with the ENCODE DCC TF/Histone ChIP-Seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2, v1.1.6)
Signal strength relative to the control samples were generated using MACS2.
Broad peaks were called using MACS2, and overlapping peaks across pseudo-replicates were genereated using the same approach as that used by the ENCODE pipeline for overlap optimal peaks.
genome build/assembly: GRCm38/mm10
processed data files format and content: bigwig, broadPeak

value: HSC/MPP

value: Kmt2c deleted

value: PBS vehicle control


title: resting_CCR1_2_rep2


title: resting_CCR1_2_rep3


title: resting_CCR1_2_rep4


title: Sperm, Western Diet, Rep2

value: Wild type


title: Sperm, Western Diet, Rep4

value: Western diet


title: resting_CCR1_2_rep1


title: Sperm, Chow Diet, Rep2

value: male


title: ScRNA-seq, hashtag library, Thymus

city: Marseille

first: Magali

last: IRLA

address: 163, avenue de Luminy - Case 906

institute: Center of Immunology Marseille Luminy (CIML)

data_processing:
mRNA and Cell Hashing FASTQ raw files were processed using Cell Ranger v6.0.1 (10X genomics Inc.) software with default parameters to performs alignment, filtering, barcode counting and unique molecular identifier (UMI) counting. Reads were aligned to the mouse mm10 genome.
A total number of 4,798 cells were identified with a mean of 44,015 reads per cell and a median of 1,992 genes per cell.
Assembly: GRCm38
Supplementary files format and content: Gzipped tab separated value and matrix files containing the cellular bacrodes (barcodes.tsv.gz), the liste of features (features.tsv.gz) and the matrix count of UMI (matrix.mtx.gz).

source_name: Thymus

extract_protocol:
Single cell suspensions of thymus were obtained by scratching organs through a 70-μm nylon mesh cell strainer with a plastic plunge in PBS 5%BSA 1mM EDTA. Thymic cell suspensions were then incubated with red blood cell lysis buffer for 3 minutes at room temperature and enriched for CD4+ thymocytes by depletion of CD8+ and CD11c+ cells using the AutoMACS® Pro Separator with the Deplete program (Miltenyi). We used cell hashing with hashtag oligonucleotides (HTO) to multiplex the two samples from 2 individual mice. Cell surface staining used for gating cells from the Treg lineage and staining for distinct barcoded anti-mouse CD45 antibody (Biolegend; A0304 and A0305 for Foxp3eGFP and Foxp3eGFPxLta-/- Treg cells, respectively) were performed in PBS 5%BSA 1mM EDTA for 30 min on ice. For each sample, cells from the Treg lineage Live Dead-CD4+CD8-CCR6-CD3e+ expressing either CD25, Foxp3eGFP or both were bulk-sorted with BD FACS Aria II. Sorted cell samples (20,000 Foxp3eGFP Treg cells and 20,000 Foxp3eGFPxLta-/- Treg cells) were pooled with a target of 10,000 captured cells and loaded in a single capture well for subsequent 10x Genomics Single Cell 3’ v3.1 workflow.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent. The pellet and supernatant fractions were separated for subsequent HTO and gene expression library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. The HTO library was constructed using Truseq D701 and D702 sequences containing i7 indexes. The resulting libraries were pooled and sequenced on an Illumina NextSeq2000 platform with a P2 flow cell (100 cycles).

value: Thymus

value: Treg cells

value: C57BL/6 Foxp3eGFP or Foxp3eGFPxLta-/-


title: ScRNA-seq, mRNA library, Thymus


title: Pol-I-IAA-Rep1

city: Vancouver

first: Sheila

last: Teves

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

institute: Life Science Institute

data_processing:
Quality Assurance was done using FastQC to check metrics
CUT&Tag reads were aligned to the mouse mm10 genome using bowtie2 with parameters: --no-unal –local –very-sensitive-local –no-discordant –no-mixed –contain –overlap –dovetail –phred33 -I 10 -X 9999 with PCR duplicates being kept
bigwig generation was done using the spike-in normalization factor or RPKM
Heatmaps, IGV tracks, and other downstream analysis were generated from bigwig files using Deeptools/ComputeMatrix
RPKM read counts were generated with DeepTools for Pol I, TBP and TRF2 using using bigwig files and the –outFileNameMatrix command with 10bp bins
ChrRNA-seq and NET-seq read counts were generated with bedtools multicov and each replicate was scaled to the spike-in scaling factor, summed and then log2 transformed
Replicates were merged using BigWigMerge
Assembly: mm10
Supplementary files format and content: bigWig, xlsx files with read counts
Library strategy: CUT&Tag

source_name: C64, IAA-treated, rep1

growth_protocol: Cells were cultured on gelatin-coated plates in ESC media (Knockout DMEM, 15% FBS, 0.1mM MEM non essential amino acids, 2mM GlutaMAX, 0.1mM 2-mercaptoethanol and 1000 units/ml of ESGRO. ES cells are fed daily, cultured at 37C in a 5% CO2 incubator and passaged every two days via trypsinization.)

extract_protocol:
Extract protocol was done following the CUT&Tag published protocol where cells and DNA were sheared using 10uL 0.5M EDTA, 3uL 10% SDS, 2.5uL 20mg/mL Proteinase followed by phenol chloroform isoamyl extracted
Librarires were prepared following the CUT&Tag protocol. Briefly 21uL(out of 30uL) was used with 2uL Universal i5 primer (10uM) +2uL uniquely barcoded i7 primers (10uM) using a different unique barcode for each sample. 25UL of NEBNext HiFi 2x PCR Master mix (NEB M0541L) was used for the PCR reaction following the PCR protocol for CUT&Tag using 12 cycles. Library was cleaned up using Ampure XP beads using 1.1x volume and samples were pooled by volume and bead cleaned again before sequencing

treatment_protocol: mESCs were treated with 500nM auxin at 37 °C in a 5% CO2 incubator for 6 hours.

tag: cell line

value: embryonic stem cell

tag: antibody

value: Pol I, SCB

value: 500nM auxin for 6h


title: inflamed_CCR2_rep4

value: Bone

value: female

value: monocytes

value: inflamed


title: inflamed_CCR2_rep3


title: Pol-I-IAA-Rep2

source_name: C64, IAA-treated, rep2


title: Pol-I-Control-Rep2

source_name: C64, Control, rep2


title: RNA_pellet_2

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

institute: RIKEN

description: RNA-seq_and_rRNA_depletion_with_ribopools

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38,mm10,SacCer-3,dm6,TAIR10,NC_000913.2
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Supplementary files format and content: csv files contain mapped reads and depleted reads information as indicated in the colunms

extract_protocol:
HEK cells  were cultured in a 10 cm dish in preparation for the RocA treatment, and in a 6-well plate for the heat shock treatment. The cells were then lysed in 500 µl and 100 µl of lysis buffer. Human skin cells cultured in a well of 6-well plates were lysed in 100 μl of lysis buffer. The mouse forebrain was dissected on ice and disrupted using a loose fitting Dounce homogenizer in 3 mL ice-cold homogenizing buffer.The homogenate was treated with an equal volume of 2× lysis buffer and incubated for 10 min on ice. S2 cells, cultured for 3 days, were seeded in 10 cm dishes. To these cells, 10 μl of 100 mg/ml cycloheximide was added, followed by immediate centrifugation at 1,000 × g to collect the cell pellet. The pellet was then washed with PBS and treated with 400 μl of lysis buffer. E. coli MG1655 cells grown overnight at 37°C in LB media were diluted 1:100 in fresh LB media and grown at 37°C until the OD600 was 0.4-0.5. Cells were then collected by filtration and snap frozen in liquid nitrogen. The frozen cell pellet and lysis buffer were disrupted using a multi-beads shocker. For yeast, cells collected in ribosome profiling lysis buffer were pulverised using a Multi-Beads Shocker with a pre-cooled chamber and ball using liquid nitrogen.  0.2 g of frozen Arabidopsis wild-type (Col-0) seedlings were combined with 400 μl of Arabidopsis lysis buffer.This mixture was then subjected to grinding using a multi-bead shocker
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification..For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) or SMARTerseq (Illumina). For Escherichia coli, MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)


title: RNA_sup_2


title: RNA_sup_1


title: Pol-I-Control-Rep1

source_name: C64, Control, rep1


title: RNA_pellet_1


title: BC70, Etest

city: Graz

first: Paul Jakob

last: Schmid

address: Neue Stiftingtalstraße 6

department: Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine

country: Austria

institute: Medical University of Graz

description:
Flow cell FLO-MIN106
BC70etest_ATCC14579etest_DGE.csv
BC70etest_BC70mh_DGE.csv
BC70etest_BC70swarming_DGE.csv

data_processing:
Sequencing data was basecalled using Guppy 6.4.6 in super-accurate mode.
Passed reads from technical replicates were analyzed for differential expression analysis using EPI2ME Desktop (v5.0.2) with the nextflow transcriptomics workflow (v0.2.0).
Reference-guided workflow was used with default parameters (gffcompare: -r -R minimap index opts: -k14 minimap2 opts: -uf minimum mapping quality: 40 stringtie opts: --conservative).
Differential expression analysis by edgeR in Epi2Me was performed with default parameters (min gene expr: 10 min feature expr: 3 min samps gene expr: 3 min samps feature expr: 1).
Assembly: The NCBI RefSeq assembly reference genome and the RefSeq annotation of Bacillus cereus (genome assembly ASM222028v1, RefSeq GCF_002220285.1, strain FORC47) were used for reference-based transcriptome assembly and reference annotation, respectively.
Supplementary files format and content: Comma-separated values (CSV) files include output data from differential expression analysis for the follwing samples/conditions: barcode01 (BC70, Etest) - barcode04 (ATCC14579, Etest), barcode01 (BC70, Etest) - barcode08(BC70, MH), barcode01 (BC70, Etest) - barcode11 (BC70, swarming). The CSV files include gene ID, log2 fold change between experimental conditions, the log-scaled counts per million measure of abundance, the p-value and the false discovery corrected p-value (FDR) for all transcripts.

organism: Bacillus cereus

growth_protocol: The BC70 isolate and ATCC 14579 were initially cultured on columbia agar with 5% sheep blood at 37°C over night. Further experiments were carried out on MH agar at 37°C.

extract_protocol:
Total RNA was extracted using the RNeasy Protect Bacteria Mini Kit.  Approximately 1.8 OD600 of cells were used and all the RNA harvested was used to build the library.
Total RNA was further purified using the DNA-free Kit (ThermoFisher). Bacterial ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit Bacteria (NEB) followed by polyadenylating with E. coli poly(A) polymerase. The direct cDNA Kit (Oxford Nanopore) was used for reverse transcription and library construction. The Native Barcoding Expansion 1-12 (Oxford Nanopore) was used for multiplexing the cDNA samples. All steps were carried out according to the manufacturers protocol. Quantification and quality control of RNA and cDNA were reduced to a minimum to obtain sufficiently high amounts of RNA or cDNA.

treatment_protocol: For vancomycin susceptibility testing, BC70 and ATCC 14579 were collected to obtain bacterial suspensions equal to McFarland 0.5. The suspensions were then evenly streaked on MH agar and Etest gradient strips with vancomycin were applied. For swarming condition, 5 µl of a bacterial suspension were spotted on MH agar with 0.7% agar. BC70 was also streaked on MH agar as additional control. All conditions were incubated at 37°C for exactly 13 h.

tag: isolate

value: Bacillus cereus sensu lato

tag: group

value: isolate

tag: origin

value: food packaging material

value: MH agar with Etest Vancomycin

tag: pooled biological_replicates

value: 4 agar plates


title: ATCC14579, Etest

description:
Flow cell FLO-MIN106
BC70etest_ATCC14579etest_DGE.csv

value: reference strain

value: Leibniz Insitute - DSMZ


title: BC70, swarming

description:
Flow cell FLO-MIN106
BC70etest_BC70swarming_DGE.csv

value: MH swarming agar

value: 2 agar plates


title: BC70, MH

description:
Flow cell FLO-MIN106
BC70etest_BC70mh_DGE.csv

value: MH agar

value: 12 colonies from 2 agar plates


title: P2875.FFPE

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Samples were hybridized for 16 hours at 65C

scan_protocol: Detection and scanning were performed by the nCounter SPRINT Profiler analysis system.

data_processing: Raw count data from nCounter was normalized

label: fluorescence barcode

source_name: tumor

label_protocol: Sample RNA is hybridized with target-specific capture and reporter probes. This creates a library of unique target-probe complexes. Each target is labelled with a specific barcode, which can be detected and counted using an automated fluorescence microscope.

extract_protocol: RNA was extracted from FF tissue using RNA-Bee (Tel-Test inc., USA) and Trizol (ABP Biosciences, Rockville, USA) according to manufacturer’s protocol. Samples with a tumor percentage <30% were excluded. For FFPE tissue, three 10 µm-slides with flanking H&Es were prepared and tissue deparaffinisation was performed with Xylene. Subsequently, tumor tissue was macro-dissected to enrich for tumor tissue. RNA was extracted using the RNeasy FFPE kit (QIAGEN GmbH, Hilden, Germany) according to manufacturer’s instructions. RNA quantity and quality were measured using Tapestation (Agilent).

value: FFPE

value: III

tag: age

tag: gender

value: Male

value: right

tag: ptstage

tag: pnstage

tag: death

tag: recurrence


title: P2419.FFPE

tag: tissue

tag: Stage


title: P2248.FFPE


title: P1595.FFPE


title: P2400.FFPE

value: Female


title: P1588.FFPE


title: P1597.FFPE

value: left


title: P2792.FFPE


title: P1584.FFPE


title: P2469.FFPE


title: P2617.FFPE


title: P2632.FFPE


title: P1409.FFPE


title: P2808.FFPE


title: P1566.FFPE


title: P1378.FFPE


title: P1236.FFPE


title: P1083.FFPE


title: P991.FFPE


title: P2231.FFPE


title: P687.FFPE


title: P969.FFPE


title: P2117.FFPE


title: P1902.FFPE


title: P2153.FFPE


title: P1945.FFPE


title: P2319.FFPE


title: P2297.FFPE


title: P1631.FFPE


title: P272.FFPE


title: P1823.FFPE


title: P617.FFPE


title: P192.FFPE


title: P1871.FFPE


title: P2057.FFPE


title: P1794.FFPE


title: P242.FFPE


title: P46.FFPE


title: P1865.FFPE


title: P1713.FFPE


title: P926.FFPE


title: P238.FFPE


title: P903.FFPE


title: P37.FFPE


title: P61.FFPE


title: P1805.FFPE


title: P360.FFPE


title: P459.FFPE


title: P593.FFPE


title: P604.FFPE


title: P441.FFPE


title: P517.FFPE


title: P340.FFPE


title: P306.FFPE


title: P229.FFPE


title: P1979.FFPE


title: P566.FFPE


title: P387.FFPE


title: P280.FFPE


title: P628.FFPE


title: P888.FFPE


title: R68.FFPE


title: R67.FFPE


title: R84.FFPE


title: P181.FFPE


title: R64.FFPE


title: R83.FFPE


title: R81.FFPE


title: R65.FFPE


title: P333.FFPE


title: R85.FFPE


title: R82.FFPE


title: P329.FFPE


title: R66.FFPE


title: P322.FFPE


title: P166.FFPE


title: R62.FFPE


title: R59.FFPE


title: R61.FFPE


title: R80.FFPE


title: R58.FFPE


title: R63.FFPE


title: R60.FFPE


title: R57.FFPE


title: R79.FFPE


title: R78.FFPE


title: R77.FFPE


title: R76.FFPE


title: R75.FFPE


title: R73.FFPE


title: R74.FFPE


title: R71.FFPE


title: R70.FFPE


title: R44.FFPE


title: R42.FFPE


title: R39.FFPE


title: R38.FFPE


title: R36.FFPE


title: R41.FFPE


title: R43.FFPE


title: R35.FFPE


title: R54.FFPE


title: R56.FFPE


title: R37.FFPE


title: R34.FFPE


title: R52.FFPE


title: R51.FFPE


title: R50.FFPE


title: R53.FFPE


title: R33.FFPE


title: R47.FFPE


title: R49.FFPE


title: R48.FFPE


title: R45.FFPE


title: R40.FFPE


title: R46.FFPE


title: R72.FFPE


title: R55.FFPE


title: R18.FFPE


title: R16.FFPE


title: R17.FFPE


title: R15.FFPE


title: R14.FFPE


title: R13.FFPE


title: Cryptosporidium parvum, stomach, adult, rep3

city: NOUZILLY

first: Julie

last: TOTTEY

address: INRAE  Val de Loire UMR ISP 1282

institute: INRAE

data_processing:
Raw sequence data were assessed for quality using the FastQC v0.11.3 tool
Sequenced reads were aligned to the C. parvum IOWA-ATCC reference genome (assembly ASM1524537v1) using the STAR software
Gene counts were determined using the STAR software
R-based packages DESeq2 and edgeR were used to normalise data
Assembly: NCBI Genome assembly ASM1524537v1
Supplementary files format and content: Tab-delimited text file including raw counts for all samples

organism: Cryptosporidium parvum

source_name: C. parvum parasites

extract_protocol:
RNA extracted using Direct-zol RNA Microprep kit (Zymo Research), Dnase I-treated using Dnase I Set kit (Zymo Research) and further purified using RNA Clean & Concentrator-5 kit (Zymo Research)
RNA libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep kit FWD for Illumina (Lexogen)

treatment_protocol: Child or adult digestion in the dynamic TIM-1 in vitro gastrointestinal model

value: C. parvum parasites

value: C. parvum INRAE Nluc

tag: digestive compartment

value: Gastric effluents

tag: time

tag: age condition

value: Adult


title: R9.FFPE


title: R12.FFPE


title: Cryptosporidium parvum, ileum, child, rep1

tag: cell type

tag: genotype

value: Ileal effluents

value: Child


title: R11.FFPE


title: Cryptosporidium parvum, ileum, child, rep2


title: Cryptosporidium parvum, stomach, adult, rep2


title: Cryptosporidium parvum, ileum, adult, rep3


title: Cryptosporidium parvum, ileum, adult, rep2


title: R8.FFPE


title: R32.FFPE


title: R29.FFPE


title: Cryptosporidium parvum, stomach, adult, rep1


title: Cryptosporidium parvum, stomach, child, rep3


title: R7.FFPE


title: Cryptosporidium parvum, stomach, child, rep2


title: R28.FFPE


title: R69.FFPE


title: R27.FFPE


title: R26.FFPE


title: Cryptosporidium parvum, ileum, adult, rep1


title: R25.FFPE


title: Cryptosporidium parvum, ileum, child, rep3


title: R10.FFPE


title: Cryptosporidium parvum, stomach, child, rep1


title: Cryptosporidium parvum, inoculum, rep3

value: Inoculum

value: 0 min


title: Cryptosporidium parvum, inoculum, rep2


title: R24.FFPE


title: LXR dko refed 24h 3

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Binary Base Call (BCL) output files from a Nextseq 500 machine were converted to FASTQ format, using BCL to FASTQ (bcl2fastq v2.20.0.422 Copyright (c) 2007-2017 Illumina, Inc.).
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10
Supplementary files format and content: BAM files contain aligned reads

source_name: Liver

extract_protocol:
Total RNA was isolated from liver pieces (30 mg) using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol.
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421).

value: Liver

tag: Sex

tag: strain

value: 8 weeks-old

value: lxr dko

tag: treatment

value: refeeding 24h


title: floxed refed 24h 3

value: floxed


title: LXR dko refed 24h 1

value: Male


title: LXR dko refed 24h 2


title: floxed refed 24h 2


title: R23.FFPE

value: FFPE

value: III

value: right


title: R22.FFPE

value: Female

value: left


title: R21.FFPE


title: floxed refed 24h 1


title: floxed mice fasted for 24h followed by refeeding of 24h_3

extract_protocol:
Liver pieces (150 mg) were cross-linked with phosphate-buffered saline (PBS) containing 2mM disuccinimidyl glutarate (DSG, Santa Cruz biotechnologies cat# sc-285455). Livers were homogenized with a Dounce homogenizer and rotated for 30 min at room temperature. Samples were spun down and pellet was crosslinked again with PBS containing 1% formaldehyde (Electron Microscopy Sciences, cat# 15714). After 10 min, samples were quenched with 0.125 M glycine. Samples were then washed with PBS, resuspended in ChIP lysis buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH8) and sonicated (Bioruptor Plus, Diagenode) to release 100–1000 bp fragments. Samples were diluted 1:5 with ChIP dilution buffer (170 mM NaCl, 17 mM Tris-HCl pH8, 1.2 mM EDTA, 1.1% Triton x-100, 0.01% SDS). Antibody against LXRα (R&D Systems cat# PP-PPZ0412-00, 4 µg per sample), was conjugated to magnetic beads (Sera-Mag, Merck, cat# GE17152104010150) for 2 h at 4°C. Chromatin was immunoprecipitated with antibody-bead conjugates for 16 h at 4°C. Immunocomplexes were washed sequentially with the following buffers: low salt buffer (0.01% SDS, 1%Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl), high salt buffer (0.01% SDS, 1%Triton x-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 500 mM NaCl), LiCl buffer (0.25M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid, 1mM EDTA, 10mM Tris pH8.1) and twice with TE buffer (10 mM Tris-HCl, 1 mM EDTA pH8). Chromatin was eluted, de-crosslinked for 4 h at 65°C and deproteinized with proteinase K (Hy Labs, cat# EPR9016) for 1 h at 50°C. DNA was subsequently isolated using MinElute DNA purification kit (Qiagen cat# 20-28006).
ChIP DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).

tag: antibody

value: LXRalpha


title: R6.FFPE

tag: age


title: R5.FFPE

tag: gender


title: R19.FFPE

tag: ptstage


title: R20.FFPE

tag: pnstage


title: R3.FFPE

tag: death


title: floxed mice fasted for 24h followed by refeeding of 24h_2


title: R2.FFPE

tag: recurrence


title: Cryptosporidium parvum, inoculum, rep1

value: C. parvum parasites

value: C. parvum INRAE Nluc


title: R1.FFPE

tag: tissue


title: P3064.FFPE

tag: Stage


title: floxed mice fasted for 24h followed by refeeding of 24h_1


title: ATAC_LXR dko mice fasted for 24h followed by refeeding of 24h_2

extract_protocol: To isolate nuclei, liver samples (50 mg) were homogenized in hypotonic sucrose buffer (250 mM sucrose, 10 mM Tris-Hcl pH 7.8, 0.1% Igepal, 3mM MgCl2, 10mM KCl, 0.2 mM Dithiothreitol, 0.5 mM spermidine, protease inhibitor cocktail) in a dounce homogenizer. Homogenate was filtered through a 20 µM filter, spun and washed (10 mM Tris-Hcl pH 7.5, 3 mM MgCl2, 10 mM NaCl, 0.1% tween-20). 50,000 nuclei were included for next steps as described (Korenfeld et al., 2023). Each sample was sequenced at a depth of at least 50X10^6 reads (paired-end).


title: LXR dko mice fasted for 24h followed by refeeding of 24h


title: P2786.FFPE


title: R4.FFPE


title: ATAC_LXR dko mice fasted for 24h followed by refeeding of 24h_3


title: ATAC_LXR dko mice fasted for 24h followed by refeeding of 24h_1


title: P2779.FFPE


title: ATAC_floxed mice fasted for 24h followed by refeeding of 24h_3


title: ATAC_floxed mice fasted for 24h followed by refeeding of 24h_2


title: ATAC_floxed mice fasted for 24h followed by refeeding of 24h_1


title: RNA_fasting for 24h followed by 24h of refeeding, 3

source_name: liver

growth_protocol: Males, 8 weeks-old mice (C57BL/6J) were randomly assigned to either group (6 mice per group). The experiment started after 1 week of acclimation. The Adlib group had ad libitum access to food (Teklad TD2018) and water throughout the experiment. For the rest of the groups, food was removed at the beginning of the inactive phase (shortly after lights on, zeitgeber time 1). For the Refed groups, food was put back in the cage 24 h later while the fasted group was anesthetized and euthanized. The Refed groups were euthanized 3 h, 10 h and 24 h after food reintroduction. At each group endpoint, mice were anesthetized and euthanized (ketamine:xylazine 30:6 mg/ml) and the liver was excised.

value: liver

value: wt


title: P2003.FFPE


title: RNA_fasting for 24h followed by 24h of refeeding, 2

treatment_protocol: Males, 8 weeks-old mice (C57BL/6J) were randomly assigned to either group (6 mice per group). The experiment started after 1 week of acclimation. The Adlib group had ad libitum access to food (Teklad TD2018) and water throughout the experiment. For the rest of the groups, food was removed at the beginning of the inactive phase (shortly after lights on, zeitgeber time 1). For the Refed groups, food was put back in the cage 24 h later while the fasted group was anesthetized and euthanized. The Refed groups were euthanized 3 h, 10 h and 24 h after food reintroduction. At each group endpoint, mice were anesthetized and euthanized (ketamine:xylazine 30:6 mg/ml) and the liver was excised.


title: P1938.FFPE


title: P1900.FFPE


title: RNA_fasting for 24h followed by 24h of refeeding, 1


title: RNA_fasting for 24h followed by 10h of refeeding, 3


title: RNA_fasting for 24h followed by 10h of refeeding, 2


title: RNA_fasting for 24h followed by 10h of refeeding, 1


title: P1608.FFPE


title: P1615.FFPE


title: RNA_fasting for 24h followed by 3h of refeeding, 3


title: P1624.FFPE


title: P1625.FFPE


title: RNA_fasting for 24h followed by 3h of refeeding, 2


title: P1375.FFPE


title: RNA_fasting for 24h followed by 3h of refeeding, 1


title: P1360.FFPE


title: P1540.FFPE


title: RNA_fasting for 24h, 2

value: fasting for 24h


title: RNA_fasting for 24h, 3


title: P1263.FFPE


title: P1133.FFPE


title: RNA_fasting for 24h, 1


title: P1892.FFPE


title: RNA_ad-libitum feeding, 3

value: ad-libitum feeding


title: P738.FFPE


title: P1742.FFPE


title: RNA_ad-libitum feeding, 2

value: 8 weeks-old


title: fasting for 24h followed by 24h of refeeding, 2


title: P563.FFPE


title: P2140.FFPE


title: P500.FFPE


title: P488.FFPE


title: P381.FFPE


title: P458.FFPE


title: fasting for 24h followed by 10h of refeeding, 2


title: P370.FFPE


title: fasting for 24h followed by 10h of refeeding, 1


title: fasting for 24h followed by 3h of refeeding, 3


title: P347.FFPE


title: P277.FFPE


title: fasting for 24h followed by 3h of refeeding, 1


title: P247.FFPE


title: P1081.FFPE


title: RNA_ad-libitum feeding, 1


title: fasting for 24h, 3


title: P979.FFPE


title: fasting for 24h followed by 24h of refeeding, 3


title: fasting for 24h, 1


title: fasting for 24h followed by 24h of refeeding, 1


title: P976.FFPE


title: fasting for 24h followed by 10h of refeeding, 3


title: P966.FFPE


title: ad-libitum feeding, 3


title: P887.FFPE


title: P349.FFPE


title: ad-libitum feeding, 2


title: P878.FFPE


title: P583.FFPE


title: P850.FFPE


title: P882.FFPE


title: fasting for 24h followed by 3h of refeeding, 2


title: fasting for 24h, 2


title: P743.FFPE


title: nti-hg-1

city: Lille

first: Souhila

last: amanzougarene

address: 1 place de Verdun

department: Nord

institute: CNRS

description: nt-hg-VS-nti-hg.tsv

data_processing:
Raw data from Illumina Novaseq have been demultiplexed using bcl2fastq v2.20.0.422 (Illumina). An adapters trimming step has been executed using trimmomatic version 0.39 (MINLEN:35 AVGQUAL:20). Mapping has been done using STAR version 2.7.3a with hg38 genome. Raw and normalized counting steps were done using RSEM v1.3.1 using a GTF from encode version 39 (hg38), and Ensembl version 105 for genes names annotations.   The differential analysis was performed in R version 3.6.3 with DESeq2 v1.24.0.
Assembly: the human genome GRCh38
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes Differential expression for nt-hg-VS-nti-hg

source_name: pancreatic beta cell

extract_protocol:
RNA was extracted from EndoCβH5 cells using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany), following manufacturer’s recommendations
NextFlex Poly(A) Bead 2.0 (v21.01; PerkinElmer Waltham, USA)

value: pancreatic beta cell

tag: cell line

value: primary

value: wild type

value: naltrindole


title: nt-hg-5

description: nt-hg-VS-nti-hg.tsv


title: P739.FFPE

value: FFPE


title: P1395.FFPE

value: III


title: ad-libitum feeding, 1

value: Male


title: P1813.FFPE

value: right


title: P768.FFPE

value: Female


title: P1006.FFPE

value: left


title: nti-hg-4

description: nt-hg-VS-nti-hg.tsv


title: nt-hg-2

description: nt-hg-VS-nti-hg.tsv


title: P704.FFPE


title: nt-hg-3

description: nt-hg-VS-nti-hg.tsv


title: P410.FFPE


title: P5, Baseline, scRNA-seq

city: Beijing

first: Sen

last: Qin

address: 38, Xueyuan Road

institute: Peking University

description: 10x Genomics

data_processing:
For single-cell RNA-seq analysis, we used CellRanger (10x Genomics, v.6.1.2) to pre-process the single-cell RNA-seq data after obtaining the paired-end raw reads. Cell barcodes and unique molecular identifiers (UMIs) of the library were extracted from read 1. Then, the reads were split according to their cell (barcode) IDs, and the UMI sequences from read 2 were simultaneously recorded for each cell. Quality control on these raw readings was subsequently performed to eliminate adapter contamination, duplicates, and low-quality bases. After filtering barcodes and low-quality readings that were not related to cells, we mapped the cleaned readings to the human genome (GRCh38) and retained the uniquely mapped readings for UMIs counts. Next, we estimated the accurate molecular counts and generated a UMI count matrix for each cell by counting UMIs for each sample. Finally, we generated a gene-barcode matrix that showed the barcoded cells and gene expression counts.
Assembly: hg38
Supplementary files format and content: The naming convention of the files was following the sampling time points of the MM patients receiving BCMA CAR-T therapy. Specifically, the 14 BM specimens that performed scRNA-seq were collected from 7 relapsed or refractory MM patients (i.e. 'P1, P2, P3, P4, P5, P6, and P7') before and after BCMA CAR-T therapy. For these specimens, the baseline (i.e. 'B') specimens (P1_B, P2_B, P3_B, P4_B, P5_B, P6_B, and P7_B) were collected from P1-P7 on day -4 before BCMA CAR-T therapy, and the remission stage (i.e. 'R') specimens (P1_R, P2_R, P3_R, P4_R, P5_R, P6_R, and P7_R) were collected from P1-P7 on day 28 after BCMA CAR-T cell infusion. The files contained gene-barcode matrix that showed the barcoded cells and gene expression counts. In these matrices, each row represents a barcoded cell name, and each column represents a gene name. Thus, the analysis of the expression level of each gene in each cell was available.

source_name: Bone Marrow

extract_protocol:
The BM aspirate samples were collected during the diagnostic procedure. Bone marrow mononuclear cells (BMMCs) were isolated using Ficoll Paque Plus (Cytiva) and washed three times with Hanks Balanced Salt Solution (HBSS, Solarbio). Following centrifugation at 1,000 rpm for 5 min, the supernatant was discarded, and the sediment was resuspended in 1 ml phosphate-buffered saline (PBS, Solarbio). To eliminate red blood cells, 1-2 ml red blood cell lysis buffer (BD) was added at 4°C for 10 min. After centrifugation at 500 g for 5 min, the cells were suspended in PBS. The cell viability was assessed using trypan blue (Sigma) and examined under a microscope.
Utilizing the 10x Genomics Chromium Single Cell 3′ v3 Library Kit and Chromium instrument, approximately 17,500 cells were partitioned into nanoliter droplets to achieve single-cell resolution for a maximum of 10,000 individual cells per sample. The resulting cDNA was tagged with a common 16 nt cell barcode and 10 nt Unique Molecular Identifier during the RT reaction. Full-length cDNA from poly-A mRNA transcripts was enzymatically fragmented and size selected to optimize the cDNA amplicon size (approximately 400 bp) for library construction (10x Genomics). The concentration of the 10x single-cell library was accurately determined through qPCR (Kapa Biosystems) to produce cluster counts appropriate for the HiSeq4000 or NovaSeq6000 platform (Illumina). In all, 26 × 98 bp (3′ v3 libraries) sequence data were generated targeting between 25 and 50K read pairs/cell, which provided digital gene expression profiles for each individual cell.

value: Bone Marrow

tag: subject id

value: Bone marrow mononuclear cells

tag: time point

value: Baseline


title: nt-hg-4

description: nt-hg-VS-nti-hg.tsv

tag: cell type


title: P6, Baseline, scRNA-seq

description: 10x Genomics


title: P401.FFPE


title: P365.FFPE


title: P402.FFPE


title: P4, Remission, scRNA-seq

description: 10x Genomics

value: Remission


title: P3, Remission, scRNA-seq

description: 10x Genomics


title: P112.FFPE


title: P4, Baseline, scRNA-seq

description: 10x Genomics


title: P256.FFPE


title: P3, Baseline, scRNA-seq

description: 10x Genomics


title: P2, Baseline, scRNA-seq

description: 10x Genomics


title: P5, Remission, scRNA-seq

description: 10x Genomics


title: P807.FFPE


title: P140.FFPE


title: P125.FFPE


title: P2, Remission, scRNA-seq

description: 10x Genomics


title: P120.FFPE


title: P1, Remission, scRNA-seq

description: 10x Genomics


title: nti-hg-5

description: nt-hg-VS-nti-hg.tsv

tag: genotype


title: P92.FFPE


title: P7, Baseline, scRNA-seq

description: 10x Genomics


title: LB2 pA-DamID,HeLa, replicate 2, dam-LB2

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 20 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig files of log2-normalized LaminB2  pA-DamID scores for 20 kb genomic bins.
Library strategy: pA-DamID

source_name: HeLa

growth_protocol: HCT116 (Top2A-AID, from Vassilis Roukos, Goethe Mol cell 2019) cell line were grown in McCoy's Modified Medium (Gibco, 16600082) FBS0 10%, 1% penicillin-streptomycin (Gibco, 15070063). HeLa cell line were grown in DMEM (Gibco, 16600082) FBS0 10%, 1% penicillin-streptomycin (Gibco, 11965092)  Cells were passaged every 2 days. Mycoplasma contamination was ruled out by regular testings (#LT07-318; Lonza).

extract_protocol:
LMNB2 pA-DamID maps were generated as previously described (van Shaik, 2022, 36050765). Briefly, one million of HAP1 were collected by centrifugation (500 g, 3 min) and washed sequentially in ice-cold PBS and digitonin wash buffer (D-Wash) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, cOmplete Protease Inhibitor Cocktail). Cells were rotated for 2 hours at 4 °C in 200 μL D-Wash with 1:200 LMNB2 (Abcam, ab8983) followed by a wash step with D-Wash. Following this step, cells were incubated with a solution of D-Wash buffer and Rabbit-anti-mouse IgG (1:200, Abcam, ab6709), followed by a wash step. This incubation was repeated with a 1:200 pA-Dam solution (equivalent to nearly 60 Dam units from NEB), followed by two wash steps. Dam activity was induced by incubation for 30 min at 37 °C in 100 μL D-Wash supplemented with the methyl donor SAM (30 µM) while gently shaking (500 rpm). Genomic DNA was isolated and processed similarly to DamID, except that the DpnII digestion was omitted, and 65-bp reads were sequenced. For every condition, another 1 million cells were processed in only D-Wash and, during Dam activation, incubated with 4 units of Dam enzyme (NEB, M0222L). We use Dam control samples to account for DNA accessibility and amplification biases.
Genomic DNA was isolated (Bioline, bio-52067) and ~ 500 ng were digested with DpnI (10 U, NEB, R0176L) in CutSmart Buffer 1X (8h 37°C, 20 min 80°C) in a total volume of 10 µL. A-tailing was performed by addition of 5 µL of the A-tailing mix (0.5 µL of Cutsmart buffer 10X, 0.25 µL Klenow 50 U/µL (NEB, M0212M), 0.05 µL dATP 100 mM, 4.2 µL H2O) and incubation 30 min at 37°C followed by 20 min at 75°C. Adapters were ligated by adding 15 µL of the ligation mix (3 µL T4 Ligase Buffer 10X, 0.5 µL T4 ligase (5 U/µL , Roche, 10799009001), 0.25 µl of x-Gene Stubby Adapter 50 mM (IDT), 11.25 µl H2O) and incubating samples 16h at 16°C and 10 min at 65°C. Finally, the Methyl Indexed PCR was performed by mixing 4 µL of ligated DNA with x-Gen Dual combinatorial Indexes (IDT) (125 nM final concentration) and MyTaq RedMix (Bioline, BIO-25048) in a final volume of 40 µL. The following PCR program was used: 1 X (1 min 94°C), 14 X (30 sec 94°C, 30 sec 58°C, 30 sec 72°C), 1X (2 min 72°C). Libraries were sequenced on Illumina platform Hiseq2500 with single end 65 bp reads.

treatment_protocol: No treatment

value: HeLa

value: control


title: P1, Baseline, scRNA-seq

description: 10x Genomics


title: LB2 pA-DamID,HeLa, replicate 2, dam only


title: LB2 pA-DamID,HeLa, replicate 1, dam-LB2


title: P179.FFPE


title: P200.FFPE


title: X24

city: New York

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

data_processing:
FastQC v0.11.8 for Sequencing QC
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Counts for sample sequenced with multiple lanes were added to produce a single column of value
Assembly: GRCh37
Supplementary files format and content: target.mod.tsv: Tab delimited raw gene counts of each sample

source_name: Keratinoocyte cell

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit and the On-column DNase digestion (Qiagen, Hilden, Germany).
RNA samples were analyzed by quantitative real-time polymerase chain reaction (PCR) using TaqMan Fast Virus 1-Step Master Mix with the QuantStudio 7 Flex Real-Time PCR System (All from Thermo Fisher Scientific).

value: Keratinoocyte cell


title: P48.FFPE


title: P7.FFPE


title: P54.FFPE


title: X23


title: LB2 pA-DamID,HeLa, replicate 1, dam only


title: P6.FFPE


title: P24.FFPE


title: X22


title: X21


title: X20


title: P73.FFPE


title: P3010.FFPE


title: P76.FFPE


title: P6, Remission, scRNA-seq

description: 10x Genomics


title: X18


title: P2870.FFPE


title: nti-hg-2

description: nt-hg-VS-nti-hg.tsv

value: pancreatic beta cell


title: P2572.FFPE


title: X16


title: P7, Remission, scRNA-seq

description: 10x Genomics


title: P2726.FFPE


title: P2659.FFPE


title: X15


title: X14


title: P1815.FFPE


title: P2268.FFPE


title: P2567.FFPE


title: P2156.FFPE


title: P2090.FFPE


title: X11


title: X13


title: X10


title: P1047.FFPE


title: X17


title: P769.FFPE


title: X8


title: P832.FFPE


title: X9


title: P816.FFPE


title: X19


title: X6


title: P594.FFPE


title: X5


title: X4


title: X3


title: P573.FFPE


title: X2


title: X1


title: P1054.FF

value: FF