title: intestinal crypts, WT_1mo_3

description:
ANG958A3_R1
BRGU 80.1c


title: JURKAT, 5uM DB2115, 12hr, RUNX1

status: Public on Jul 31 2024

type: SRA

city: Bronx

first: Samuel

middle: John

last: Taylor

state: NY

address: 1300 Morris Park Ave, Chanin building 601

country: USA

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
library strategy: CUT&Tag (ChIP Seq)
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Homo Sapiens transcriptome (hg38) using bowtie2 aligner using the options --end-to-end --very-sensitive --no-mixed --no-discordant --phred -I 10 -X 700.
Normalized bedgraphs were generated using genomecov with a normalization factor of 1,000,000/ number of total reads.
Assembly: hg38
Supplementary files format and content: Bedgraph of each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: hematopoietic

growth_protocol: MOLM13 & JURKAT cells were maintained in 10% FBS, 1% Pen Strep, RPMI media. Primary AML samples were maintained in StemSpan SFEMII media plus 1xCC100 growth cocktail plus 50ng/ml TPO

extract_protocol:
CUT&Tag was performed as follows, 5×10^5 cells per cell line were harvested and lightly fixed with 0.5% formaldehyde for 2 minutes. The cells were bound to Concavalin A-coated beads (Bangs laboratories) and incubated with the primary antibody at 4°C overnight. Samples were then incubated with a secondary antibody (guinea pig α-rabbit (Antibodies Online, ABIN101961)) followed by adding pre-loaded pA-Tn5 adapter complex (generated in house). Tagmentation buffer with magnesium was used to induce transposase fragmentation. And PCR based library preparation was conducted (see below).
DNA was extracted by phenol/chloroform/isoamyl alcohol and fragments were amplified with NEBNext HiFi 2x PCR Master mix and universal i5 and barcoded i7 primers for 13 cycles. AMPure XP beads (#A63880) were used for post-PCR clean-up of the libraries. Libraries were subject to 35 bp paired-end sequencing using Illumina NextSeq 500 platform with 35bp paired end reads on high output mode at the Einstein Epigenomics core. Fastq files were generated using Picard tools v2.17.1 with adapter trimming by TrimGalore v0.3.7 and QC assessment using FASTQC v0.11.4.

treatment_protocol: Cells were maintained at 1mill/ml before treatment with 5uM DB compound, or Vehicle (0.001% DMSO) for 12hrs

tag: tissue

value: hematopoietic

tag: cell line

value: JURKAT

tag: cell type

value: T cell lymphoblast

tag: antibody

value: RUNX1 antibody

tag: treatment


title: N2-RL5-18

city: Philadelphia

first: Huasheng

last: Yu

state: PENNSYLVANIA

address: 3610 Hamilton Walk

department: Neuroscience

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Raw sequencing data was demultiplexed with bcl2fastq2 v.2.20 (Illumina)
Demultiplexed data was trimmed with Cutadapt to remove Tn5 transposon adapter sequences.
The trimmed data were aligned to human genome using STAR v.2.7.9a49.
STAR quantMode GeneCounts was used to quantify unique mapped reads to gene counts.
Gene counts file was used for the downstream analysis
Assembly: human genome (GRCh38 GENCODE as the reference genome, and GRCh38.104. GTF as the annotation)
Supplementary files format and content: Comma-separated file includes raw counts for each Sample

molecule: total RNA

source_name: Dorsal root ganglia

extract_protocol:
Human DRG tissues were procured from National Disease Research Interchange (NDRI). The research application was approved by the NDRI Feasibility Committee (RLUW1 01). Six DRGs between T11 to L5 of three human donors aged from 23- 61 years were used in this study. The dissected DRG tissues from human donors were immediately imbedded in OCT, shipped to the Luo lab on dry ice and stored in -80 ℃ until use. The information of DRGs and dis-identified donors and screening criteria are summarized in the manuscript Supplementary Tables 1 & 2. The hDRGs imbedded in OCT were cryosectioned (Cryostat Leica Cm1950) into 20 μm sec-tions and mounted onto Arcturus PEN Membrane Frame Slides (Applied biosystems, LCM0521). One of every five consecutive sections was collected for laser capture microdissec-tion to avoid repeated dissection of the soma from the same neuron in different sections. The slides were stored in -80 ℃ until further use.On the day of laser capture microdissection, the slides were transferred to the SBDRC laser capture microdissection (LCM) core on dry ice. Before dissection, the section was briefly stained with RNase free Arcturus™ Histogene™ staining solution (Applied biosystems, 12241-05) for better visualization of neuronal soma: 70% cold EtOH for 30s; Histogene™ staining for 10s; 70% cold EtOH for 30s; 95% cold EtOH for 30s; 100% cold EtOH for 30s and air dry for 2min. Then, the slide was put onto laser capture microdissection microscope system (Leica LMD6) for the neuronal soma dissection. The laser was calibrated, and the laser intensity was adjusted to achieve best dissection efficiency. The dissected individual neuronal soma was col-lected in the cap of a 200 μl PCR tube containing 4 μl lysis buffer.
The sequencing library was generated following Smart-seq2 workflow. The libraries passing through all quality con-trols were selected for the final sequencing.

value: Dorsal root ganglia

tag: donor id

tag: age(years)

tag: race

value: Caucasian

tag: gender

value: Female

tag: region

value: lumbar 5

tag: sequencing batch

tag: dissected soma size

tag: cell identity


title: intestinal crypts, KO_1mo_5

city: London

first: Vivian

last: Li

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
ANG958A10_R1
VLDC 10.1e

data_processing:
Processed using NFCore RNASeq pipeline version 3.0, using STAR-RSEM
Generate fold-changes using DESeq2
Assembly: GRCm38/release-95
Supplementary files format and content: .genes.results' files are RSEM-STAR-quantified raw counts
Supplementary files format and content: differential' file is an excel spreadsheets of all inferential properties
Supplementary files format and content: vst' file is variance stabilised normalised counts from DESeq2

molecule: polyA RNA

organism: Mus musculus

source_name: intestinal crypts

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using polyA_KAPA_mRNA_Hyper_Prep kit following manufacturer's protocols.

treatment_protocol: WT and Arid3a conditional KO animals were injected with tamoxifen for 3 consecutive days and animals were culled by S1K at 1 month after the first tamoxifen injection. Intestinal crypts were collected as previously described (Baulies et al., 2020)

value: intestinal crypts

tag: genotype

value: KO

value: 1 month after tamoxifen


title: intestinal crypts, WT_1mo_2

description:
ANG958A2_R1
BRGU 80.1a

value: WT


title: stromal_t2_ko_AFGK76

city: Cambridge

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

institute: Univerity of Cambridge

data_processing:
The Illumina sequencing reads were pre-processed by removing adapters and trimming low-quality bases (phred score < 20) using cutadapt v3.4. To account for the Pico v2 SMART Adapter, we also trimmed the last 4 bp of read 1 (preceding the Illumina adapter, if it was detected in the read) and the first 4 bp of read 2. Read quality was assessed before and after trimming with FastQC v0.11.9. Further quality control metrics were obtained by aligning the reads to the GRCm38/mm10 mouse reference genome (Ensembl release 102) using STAR v2.7.9a, followed by rseqc v4.0.0 to estimate junction saturation and percentages of reads aligning to annotated features such as exons, introns or UTRs. These quality metrics were compiled using multiqc v1.10.1.  Transcript quantification was done using salmon v1.5.0 against the reference transcriptome annotation (GRCm38/mm10, Ensembl release 102). Differential expression analysis between WT/KO was performed using DESeq2 v1.32.0.
Assembly: GRCm38
Supplementary files format and content: Processed data provided are quant.sf files generated using Salmon. File includes gene name, gene legnth , effective Lenth, TPM, and Number of reads mapping to each transcript

source_name: Mammary Gland

extract_protocol: Libraries for RNA sequencing (RNA-seq) from sorted mammary cells were generated using SMARTer stranded total RNA-seq kit V2   Pico input mammalian (TaKaRa bio, 634414) according to the manufacturer's instructions. The quality and RNA integrity number were assessed using Bioanalyzer 2100 (Agilent), Qubit fluorometer (Thermo Fisher) and sequenced using the NovaSeq 6000 system (Illumina)

value: Mammary Gland

value: stromal

tag: timepoint

value: Gestation day 9.5


title: JURKAT, VEH, 12hr, RUNX1

value: VEH


title: N2-RL5-16


title: MOLM13, 5uM DB2115, 12hr, RUNX1, Rep2

value: Acute myeloid leukemia


title: basal_t2_ko_AFGK78

value: basal


title: intestinal crypts, WT_1mo_1

description:
ANG958A1_R1
BRGU 78.1a


title: N2-RL5-17


title: MOLM13, 5uM DB2115, 12hr, RUNX1 Rep1

value: hematopoietic


title: lumlo_t4_wt_M00467006

value: luminal differentiated  cells

value: wt

value: Lacation day 2


title: N2-RL5-15

value: Dorsal root ganglia

value: Caucasian


title: lumhi_t2_wt_M00433264

value: luminal progenitor cells


title: MOLM13, VEH, 12hr, RUNX1, Rep2

value: RUNX1 antibody


title: N2-RL5-14

value: Female

value: lumbar 5

value: hPropr


title: Forebrain, VEGF-C/D trap, replictae 2

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

description:
Sequenced cells were pooled from hemi-forebrains of 2 different mice
AbCD2

library_source: transcriptomic single cell

data_processing:
The single cell sequence preprocessing was performed using the standard10X Genomics Cell Ranger Single Cell Software Suite v.6.1.1
Raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering and differential expression analyses were performed using Seurat v.4.0.5.
Assembly: mm10
Supplementary files format and content: matix files

source_name: Forebrain

extract_protocol:
At week 5, animals were perfused with PBS containing 0.005% heparin, hemi-forebrains were collected and tissue was homogenized according to the Adult Brain Dissociation Kit (Miltenyi Biotec). Cells were further processed using 10x Genomics reagents and loaded into the 10x Genomics Chromium Controller.
Libraries were prepared for NGS Illumina Next Seq (NovaSeq S2 PE100) using the Chromium Next GEM Single Cell 3’ Kit v3.1 and following the manufacturer instructions.

treatment_protocol: Mice received 2 consecutive intraperitoneal injections (weeks 0 and 3) of 1010 viral particles of an AAV9 encoding mVEGFR34–7-Ig (control) or an AAV9 encoding mVEGFR31–3-Ig (VEGF-C/D trap).

tag: strain

tag: Sex

value: male

value: Forebrain

tag: age

value: 13 weeks


title: endo_t2_wt_M00424114

tag: tissue

value: Mammary Gland

value: endothelial

value: Gestation day 9.5


title: N2-RL5-13


title: Forebrain, VEGF-C/D trap, replicate 1

description:
Sequenced cells were pooled from hemi-forebrains of 2 different mice
AbCD1


title: Forebrain, control, replicate 2

description:
Sequenced cells were pooled from hemi-forebrains of 2 different mice
CCD2


title: basal_t2_wt_M00424115

tag: cell type

value: basal


title: N2-RL5-12


title: MOLM13, DB2115, 12hr, ChIP-seq

data_processing:
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Fastq files were mapped to the human or drosophila genome (hg38 or dm3) using bowtie2 (Version 2.2.3). Duplicates were then removed with Picard and normalization was performed by subsampling .bam files by a drosophila reads ratio of vehicle over DB2115.
The MACS2 package and callpeaks function was used to identify peaks in normalized files, and bigwig files were generated for IGV visualization
Assembly: hg38
Supplementary files format and content: bedgraph format

growth_protocol: Cells were maintained in 10% FBS, 1% Pen Strep, RPMI media

extract_protocol:
MOLM13 cells were treated with 5µM DB2115 for 12hr before cells were crosslinked in 0.5% formaldehyde for 7 minutes at room temperature. Samples were sonicated for 12 minutes to generate fragments below 1kb before being incubated with 5µg of PU.1 antibody (Santa-cruz, sc-352)
Library preparation was carried out using NEB Ultra II DNA Prep Kit (NEB) following the manufacturers recommendations.

treatment_protocol: Cells were maintained at 1mill/ml before treatment with 5uM DB2115, or Vehicle (0.001% DMSO) for 12hrs

value: hematopoietic

tag: cell line

value: Acute myeloid leukemia

tag: antibody

value: PU.1 antibody


title: Forebrain, control, replicate 1

description:
Sequenced cells were pooled from hemi-forebrains of 2 different mice
CCD1

tag: treatment


title: MOLM13, VEH, 12hr, ChIP-seq

value: VEH


title: stromal_t0_ko_M00398657

value: stromal

value: Nulliparous


title: N2-RL5-11

value: Dorsal root ganglia

tag: donor id

tag: age(years)

value: Caucasian


title: Untreated_Bisulfite_PCR_CLSY3_Promoter_MITEs

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The reads were aligned to PCR templates as genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density.
Assembly: Custome genome built from Oryza sativa japonica nipponbare genome – IRGSP1 with the PCR amplicon regions as template
Supplementary files format and content: bigwig files showing the methylation status across the genome.

organism: Oryza sativa

source_name: Leaf

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.

extract_protocol:
Total DNA was extracted from the tissues using CTAB method.
Bisulfite convertion by EZ DNA Methylation-Gold Kit (Catalog no-D5005) as per manufacturer’s protocol. Adapters used: Read1-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read2-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: WT tissues were handled in the same manner. Treated with Zymo bisulfite reagents

tag: subspecies

value: Indica

value: Leaf

tag: cultivar

value: Pusa Basmati1 (PB1)


title: MOLM13, 12hr DB2115, ATAC-seq Rep2

data_processing:
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Homo Sapiens transcriptome (hg38) using bowtie2 aligner using the options  --very-sensitive  -X 1000 -x
Normalized .bam files were generated using picard & samtools to remove mitochondrial reads/duplicates and subsample to equivalent read counts
MACS2 was used with -callpeak -f BAMPE -g hs options to generate peak files and bedgraphs
Assembly: hg38
Supplementary files format and content: narrowpeaks file of each sample

extract_protocol:
50,000 MOLM13 cells treated with either 5µM DB2115 or vehicle were subject to nuclei isolation with ATAC resuspension buffer (containing 0.1% NP-40, 0.1% Tween20 and 0.01% Digitonin) before transposition was performed using Tn5 transposase in TD buffer (Illumina Tagment DNA kit).
Transposed DNA was purified using a Minelute PCR purification kit (QIAGEN) before eluted DNA was amplified via PCR with custom PCR primers and cycle number was determined using a KAPA Library Quantification kit (KAPABiosystems).

treatment_protocol: Cells were maintained at 1mill/ml before treatment with 5uM DB2115, or Vehicle (0.001% DMSO) for 1-12hrs


title: lumlo_t0_ko_M00395206

value: luminal differentiated  cells


title: Mature_Panicle_Bisulfite_PCR_CLSY3_Promoter_MITEs

source_name: Mature Panicle

value: Mature Panicle


title: N2-RL5-10

tag: race

tag: gender

value: Female

tag: region

value: lumbar 5

tag: sequencing batch

value: hPropr


title: endo_t0_ko_M00373634

value: Mammary Gland

value: endothelial

tag: genotype

tag: timepoint


title: MOLM13, 12hr DB2115, ATAC-seq Rep1

value: hematopoietic

value: Acute myeloid leukemia


title: MOLM13, 4hr DB2115, ATAC-seq Rep2


title: N2-RL5-8

tag: dissected soma size

tag: cell identity


title: Endosperm_Bisulfite_PCR_CLSY3_Promoter_MITEs

source_name: Endosperm (20 days after anthesis)

tag: tissue

value: Endosperm (20 days after anthesis)


title: MOLM13, VEH, 12hr, RUNX1, Rep1

tag: cell type

value: RUNX1 antibody

value: VEH


title: N2-RL5-7

value: Dorsal root ganglia


title: basal_t0_wt_M00399832

value: basal

value: wt

value: Nulliparous


title: WT_CLSY3_Endosperm_RNAseq_Rep2

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic and rRNA sequences were removed using Sortmerna.
The processed reads were aligned to the rice genome using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Text delimited files including FPKM for each sample.

extract_protocol:
Total RNA was isolated from Embryo,Mature Endosperm, Young Endosperm. RNA was extracted using TRIzol method.
Libraries were prepared for sequencing using standard Illumina protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: WT and clsy3 knockdown lines were handled in the same manner.

value: Indica

value: Pusa Basmati1 (PB1)


title: stromal_t0_wt_M00394900

value: stromal


title: MOLM13, 1hr DB2115, ATAC-seq Rep2

tag: cell line


title: WT_CLSY3_Endosperm_RNAseq_Rep1


title: N2-RL5-5

value: Caucasian

value: Female


title: MOLM13, 1hr DB2115, ATAC-seq Rep1


title: lumlo_t0_wt_M00381049

value: luminal differentiated  cells


title: lumhi_t0_ko_M00384810

value: Mammary Gland

value: luminal progenitor cells


title: lumlo_t2_wt_M00439079

value: Gestation day 9.5


title: KD_CLSY3_Endosperm_RNAseq_Rep2


title: lumhi_t0_wt_M00373181


title: Leaf_Bisulfite_PCR_CLSY3_Promoter_MITEs

value: Leaf


title: N2-RL5-4

value: lumbar 5


title: endo_t4_ko_M00504337

value: endothelial

value: Lacation day 2


title: N2-RL5-9

value: Dorsal root ganglia


title: KD_CLSY3_Enosperm_RNAseq_Rep1

value: Endosperm (20 days after anthesis)


title: MOLM13, VEH, ATAC-seq Rep3

value: hematopoietic

value: Acute myeloid leukemia

value: VEH


title: MOLM13, VEH, ATAC-seq Rep2


title: N2-RL5-2


title: MOLM13, 4hr DB2115, ATAC-seq Rep1


title: N2-RL5-6


title: Young_Endosperm_RNAseq_Rep1

source_name: Young Endosperm(15 days after anthesis)

value: Indica

value: Pusa Basmati1 (PB1)

value: Young Endosperm(15 days after anthesis)


title: stromal_t4_ko_M00509904

value: stromal


title: MOLM13, VEH, ATAC-seq Rep1


title: CD14+ isolated monocytes, GEX, D60, S19

city: Rixensart

first: Viviane

middle: Jeanne

last: Bechtold

state: Brabant Wallon

address: rue de l'Institut 89

department: Molecular Biology

country: Belgium

institute: GSK

description:
10x genomic
19_D60
ANONYM_BulkRNAseqMono_19.csv

data_processing:
Reads were then aligned to the human genome (GRCh38), using the STAR program (Dobin et al, 2015).
Read counts per gene were quantified using the quantMode option of the aligner.
Normalization and differential expression were conducted using EdgeR methodology (Robineson et al, 2010).
Assembly: GRCh38
Supplementary files format and content: csv file represents Normalized counts

source_name: PBMCs

extract_protocol:
Isolated (CD14+) cells were directly harvested and lysed in RLT (+) buffer and RNA extracted using Rneasy plus micro kit.
The library preparation for polyA+ RNA sequencing was performed via TruSeq Stranded mRNA Library Prep Kit (Illumina) using enzymatic fragmented RNA.
After, first and second strand synthesis, the double stranded cDNA was purified (Agencourt AMPure XP, Beckman Coulter). The cDNA was end repaired and 3’ adenylated while Illumina sequencing adaptors were ligated onto the fragments ends. The polyA+ RNA stranded libraries were pre-amplified with PCR and purified (Agencourt AMPure XP). The libraries size distribution was validated, and quality inspected.

treatment_protocol: CD14+ monocytes were isolated using magnetic CD14+ beads from frozen PBMCs isolated at D0, D2, D30, D32 and D60 post- vaccination with AS01 adjuvaned HBS vaccine

tag: individual

value: CD14+ isolated monocytes

value: post HBS/AS01 vaccination

tag: time


title: Mature_Endosperm_RNAseq_Rep2

source_name: Mature Endosperm (25 days after anthesis)


title: N2-RL5-1

tag: donor id

value: Caucasian

value: Female


title: CD14+ isolated monocytes, GEX, D32, S19

description:
10x genomic
19_D32
ANONYM_BulkRNAseqMono_19.csv

tag: treatment


title: XXCN

city: Shijiazhuang

first: Ping'an

last: Ding

state: None Selected

address: Shijiazhuang 050011, China

country: China

institute: the Fourth Hospital of Hebei Medical University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo_sapiens.GRCh38 version101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Adjacent normal

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adjacent normal

tag: pair id

value: XXC


title: lumhi_t4_wt_M00483956

value: Mammary Gland

value: luminal progenitor cells

value: wt


title: Mature_Endosperm_RNAseq_Rep1

tag: subspecies

tag: cultivar

value: Mature Endosperm (25 days after anthesis)


title: WHDN

value: WHD


title: CD14+ isolated monocytes, GEX, D2, S19

description:
10x genomic
19_D2
ANONYM_BulkRNAseqMono_19.csv


title: N2-RL5-3

value: Dorsal root ganglia

tag: age(years)

tag: race

tag: gender

value: lumbar 5

value: hPropr


title: endo_t4_wt_M00460358

value: endothelial

tag: genotype

value: Lacation day 2


title: Embryo_RNAseq_Rep2

source_name: Embryo (25 days after anthesis)

value: Indica

value: Pusa Basmati1 (PB1)

value: Embryo (25 days after anthesis)


title: Young_Endosperm_RNAseq_Rep2

value: Young Endosperm(15 days after anthesis)


title: LFEN

value: LFE


title: basal_t4_wt_M00460359

value: basal

tag: timepoint


title: basal_t4_ko_M00490577


title: CD14+ isolated monocytes, GEX, D60, S14

description:
10x genomic
14_D60
ANONYM_BulkRNAseqMono_14.csv

value: CD14+ isolated monocytes

value: post HBS/AS01 vaccination


title: CD14+ isolated monocytes, GEX, D0, S19

description:
10x genomic
19_D0
ANONYM_BulkRNAseqMono_19.csv

value: pre HBS/AS01 vaccination


title: Embryo_RNAseq_Rep1


title: stromal_t4_wt_M00467006

value: Mammary Gland

value: stromal

value: wt


title: WT_Embryo_sRNA_Rep2

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using UEA sRNA workbench. The sRNAs of appropriate size class(16-35nt) was chosen further.
The processed reads were aligned to the rice genome using Bowtie with one allowed mismatch.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Text delimited files showing the sequence and raw abundance of the sRNAs.

source_name: Embryo

extract_protocol:
Total RNA from endosperm was extracted using Trizol (Invitrogen) reagent.
Size fractionation. adaptor_seq TGGAATTCTCGGGTGCCAAGG

tag: developmental stage

value: Embryo (20-25 days after anthesis)


title: XXCC

source_name: Gastric cancer

value: Gastric cancer

value: XXC


title: CD14+ isolated monocytes, GEX, D32, S14

description:
10x genomic
14_D32
ANONYM_BulkRNAseqMono_14.csv


title: WHDC

value: WHD


title: WT_Embryo_sRNA_Rep1


title: lumlo_t2_ko_M00438677

value: luminal differentiated  cells

value: Gestation day 9.5


title: lumhi_t2_ko_M00439062

value: luminal progenitor cells


title: lumlo_t4_ko_M00471543

value: Lacation day 2


title: WT_CLSY3_Endosperm_sRNA_Rep2

source_name: Endosperm

value: Indica

value: Pusa Basmati1 (PB1)

value: Endosperm (20 days after anthesis)


title: ZZJN

value: Adjacent normal

value: ZZJ


title: LFEC

value: LFE


title: CD14+ isolated monocytes, GEX, D30, S14

description:
10x genomic
14_D30
ANONYM_BulkRNAseqMono_14.csv

value: CD14+ isolated monocytes

value: post HBS/AS01 vaccination


title: CD14+ isolated monocytes, GEX, D30, S19

description:
10x genomic
19_D30
ANONYM_BulkRNAseqMono_19.csv


title: CD14+ isolated monocytes, GEX, D2, S14

description:
10x genomic
14_D2
ANONYM_BulkRNAseqMono_14.csv


title: WT_CLSY3_Endosperm_sRNA_Rep1


title: QHZN

value: QHZ


title: basal_t2_ko_AFGK76

value: Mammary Gland

value: basal


title: KD_CLSY3_Endosperm_sRNA_Rep2


title: CD14+ isolated monocytes, GEX, D0, S14

description:
10x genomic
14_D0
ANONYM_BulkRNAseqMono_14.csv

value: pre HBS/AS01 vaccination


title: KD_CLSY3_Endosperm_sRNA_Rep1


title: CD14+ isolated monocytes, GEX, D60, S12

description:
10x genomic
12_D60
ANONYM_BulkRNAseqMono_12.csv


title: stromal_t2_wt_M00439079

value: stromal

value: wt


title: ZZJC

value: Gastric cancer


title: Hindgut ZI418 Biological replicate 3

city: Planegg-Martinsried

first: Amanda

last: Glaser-Schmitt

address: Grosshaderner Str. 2

department: Biology

country: Germany

institute: LMU München

description:
HG_ZI418_3
HG_gcounts_allgenotypes_allreads.tsv

data_processing:
Reads were mapped to the reference transcriptomes using NextGenMap in paired-end mode. Read pairs matching more than one transcript of a gene were randomly assigned to one of the transcripts of that gene. For downstream analyses, we analyzed the sum of read counts across all of a gene’s transcripts (across all annotated exons), i.e. on the individual gene-level. To identify genes with poor mapping quality, for each parental transcriptome, we simulated RNA-seq data with 200 reads per transcript and 150 bp reads, then mapped the reads back to the corresponding transcriptome. Genes for which more than 5% of reads mapped incorrectly were removed from the analysis.
Assembly: FlyBase annotation version 6.29; Reference genomes for each parental strain were constructed using published genome sequence assemblies of SU26, SU58, ZI197, and ZI418 strains. If a nucleotide sequence difference on the major chromosome arms (X, 2R, 2L, 3R, 3L) occurred between a parental strain and the reference genome, the parental nucleotide variant was included in the new reference transcriptome. If the parental sequence contained an uncalled base (“N”), the reference sequence was used.
Supplementary files format and content: Tab separated file containing gene identifiers (FBgn and CG numbers), length, chromosome, and gene counts for all reads per sample (without subsampling) in the hindgut.
Supplementary files format and content: Tab separated file containing gene identifiers (FBgn and CG numbers), length, chromosome, and gene counts for all readsper sample (without subsampling) in the midgut.

organism: Drosophila melanogaster

source_name: hindgut

growth_protocol: Flies were reared on cornmeal-molasses medium under standard lab conditions (21°C, 14 hour light: 10 hour dark cycle). Reciprocal F1 hybrids were generated in both directions (i.e. parental genotypes were switched) by crossing 2–3 virgin females of one line with 4–5 males of the other line. Crosses were carried out in 8–13 replicate vials and parental strains were similarly reared (2–3 females and 3–5 males per vial with 8–12 replicate vials) in order to control for rearing density among genotypes.

extract_protocol:
Midguts (from below the cardia to the midgut/hindgut junction, 20 per biological replicate) and hindguts (from the midgut/hindgut junction to the anus, 60 per biological replicate) were dissected from 6-day-old females in cold 1X PBS and stored in RNA/DNA shield (Zymo Research Europe; Freiburg, Germany) at -80°C until RNA extraction. For F1 hybrids, half of the tissues were dissected from each of two reciprocal crosses in order to avoid potential parent-of-origin effects. RNA was extracted from three biological replicates per genotype and tissue type with the RNeasy Mini kit (Qiagen; Hilden, Germany) as directed by the manufacturer.
Poly-A selection, fragmentation, reverse transcription, library construction, and high- throughput sequencing was performed by Novogene (Hong Kong).

value: hindgut

tag: strain

tag: age

value: 6 days

tag: Sex

value: female


title: lumlo_t2_wt_M00433264

tag: tissue

tag: cell type

value: luminal differentiated  cells

value: Gestation day 9.5


title: CD14+ isolated monocytes, GEX, D30, S12

description:
10x genomic
12_D30
ANONYM_BulkRNAseqMono_12.csv

tag: individual

tag: time


title: CD14+ isolated monocytes, GEX, D32, S12

description:
10x genomic
12_D32
ANONYM_BulkRNAseqMono_12.csv

tag: treatment


title: Hindgut ZI418 Biological replicate 2

description:
HG_ZI418_2
HG_gcounts_allgenotypes_allreads.tsv


title: Hindgut ZI418 Biological replicate 1

description:
HG_ZI418_1
HG_gcounts_allgenotypes_allreads.tsv


title: lumhi_t2_wt_M00424114

value: luminal progenitor cells


title: endo_t2_wt_M00424115

value: endothelial


title: QHZC

tag: pair id


title: CD3+ depleted, epigenetic: GEX, D44, S19

description: 10x genomic

data_processing:
cell Ranger 6.0.2; bcl2Fastq2 V2.20.0
scRNA-Seq data were processed using the corresponding CellRanger pipelines after demultiplexing the sequencing data.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: .h5 as output by Cell Ranger

source_name: CD3+ depleted PBMCs

extract_protocol:
Cells were isolated from frozen PBMCs after depletion of CD3+ cells after magnetic cell separation using the CD3 microbeads (Miltenyi Biotec, cat#130-050-101) and the resuspension buffer (MACS BSA cat#: 130-091-376 and autoMACS Rinsing Solution cat#: 130-091-222). Cells were then processed for scRNA-seq using the 10X genomics technology.
The library preparations were based on the Chromium Next Gem Single Cell 3’ kit v3.1 (PN-1000121) User guide, CG000204 for the scRNA-seq.

value: CD3+ depleted PBMCs


title: endo_t2_ko_AFGK78


title: LSSC

value: LSS


title: CD3+ depleted, epigenetic: GEX, D32, S19

description: 10x genomic

value: post HBS/AS01 vaccination


title: CD14+ isolated monocytes, GEX, D2, S12

description:
10x genomic
12_D2
ANONYM_BulkRNAseqMono_12.csv

value: CD14+ isolated monocytes


title: CD14+ isolated monocytes, GEX, D0, S12

description:
10x genomic
12_D0
ANONYM_BulkRNAseqMono_12.csv


title: Hindgut ZI197 Biological replicate 2

description:
HG_ZI197_2
HG_gcounts_allgenotypes_allreads.tsv


title: Hindgut ZI197 Biological replicate 3

description:
HG_ZI197_3
HG_gcounts_allgenotypes_allreads.tsv


title: CD14+ isolated monocytes, GEX, D60, S10

description:
10x genomic
10_D60
ANONYM_BulkRNAseqMono_10.csv


title: Hindgut ZI197 Biological replicate 1

description:
HG_ZI197_1
HG_gcounts_allgenotypes_allreads.tsv


title: stromal_t0_ko_M00395206

value: Mammary Gland

value: Nulliparous


title: LSSN

value: Adjacent normal


title: CD3+ depleted, epigenetic: GEX, D180, S19

description: 10x genomic


title: lumlo_t0_ko_M00384810


title: CD14+ isolated monocytes, GEX, D32, S10

description:
10x genomic
10_D32
ANONYM_BulkRNAseqMono_10.csv


title: CD14+ isolated monocytes, GEX, D30, S10

description:
10x genomic
10_D30
ANONYM_BulkRNAseqMono_10.csv


title: CD3+ depleted, epigenetic: GEX, D60, S14

description: 10x genomic


title: Hindgut F1 hybrid SU58xZI418 Biological replicate 3

description:
HG_SU58xZI418_3
HG_gcounts_allgenotypes_allreads.tsv


title: CD14+ isolated monocytes, GEX, D2, S10

description:
10x genomic
10_D2
ANONYM_BulkRNAseqMono_10.csv


title: lumhi_t0_ko_M00373634


title: CD3+ depleted, epigenetic: GEX, D0, S19

description: 10x genomic

value: pre HBS/AS01 vaccination


title: Hindgut F1 hybrid SU58xZI418 Biological replicate 2

description:
HG_SU58xZI418_2
HG_gcounts_allgenotypes_allreads.tsv


title: basal_t0_ko_M00398657

value: basal


title: CD14+ isolated monocytes, GEX, D0, S10

description:
10x genomic
10_D0
ANONYM_BulkRNAseqMono_10.csv


title: CD14+ isolated monocytes, GEX, D60, S9

description:
10x genomic
9_D60
ANONYM_BulkRNAseqMono_9.csv


title: CD3+ depleted, epigenetic: GEX, D32, S14

description: 10x genomic


title: CD3+ depleted, epigenetic: GEX, D44, S14

description: 10x genomic


title: Hindgut F1 hybrid SU58xZI197 Biological replicate 3

description:
HG_SU58xZI197_3
HG_gcounts_allgenotypes_allreads.tsv


title: Hindgut F1 hybrid SU58xZI418 Biological replicate 1

description:
HG_SU58xZI418_1
HG_gcounts_allgenotypes_allreads.tsv


title: stromal_t0_wt_M00381049

value: stromal

value: wt


title: basal_t0_wt_M00394900


title: lumlo_t0_wt_M00373181


title: CD3+ depleted, epigenetic: GEX, D60, S12

description: 10x genomic


title: CD3+ depleted, epigenetic: GEX, D180, S14

description: 10x genomic


title: endo_t0_wt_M00399832


title: CD14+ isolated monocytes, GEX, D2, S9

description:
10x genomic
9_D2
ANONYM_BulkRNAseqMono_9.csv


title: Hindgut F1 hybrid SU58xZI197 Biological replicate 2

description:
HG_SU58xZI197_2
HG_gcounts_allgenotypes_allreads.tsv

value: hindgut

value: 6 days


title: CD14+ isolated monocytes, GEX, D0, S9

description:
10x genomic
9_D0
ANONYM_BulkRNAseqMono_9.csv


title: CD14+ isolated monocytes, GEX, D32, S9

description:
10x genomic
9_D32
ANONYM_BulkRNAseqMono_9.csv


title: Hindgut F1 hybrid SU58xZI197 Biological replicate 1

description:
HG_SU58xZI197_1
HG_gcounts_allgenotypes_allreads.tsv

value: female


title: Hindgut SU58 Biological replicate 1

description:
HG_SU58_1
HG_gcounts_allgenotypes_allreads.tsv


title: endo_t4_ko_M00490577

value: Lacation day 2


title: Hindgut SU58 Biological replicate 3

description:
HG_SU58_3
HG_gcounts_allgenotypes_allreads.tsv


title: basal_t4_ko_M00509904


title: lumlo_t4_wt_M00483956

value: luminal differentiated  cells


title: CD14+ isolated monocytes, GEX, D30, S9

description:
10x genomic
9_D30
ANONYM_BulkRNAseqMono_9.csv


title: lumhi_t4_ko_M00504337

value: luminal progenitor cells


title: Hindgut F1 hybrid SU26xZI418 Biological replicate 2

description:
HG_SU26xZI418_2
HG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: GEX, D44, S12

description: 10x genomic

value: CD3+ depleted PBMCs


title: Hindgut SU58 Biological replicate 2

description:
HG_SU58_2
HG_gcounts_allgenotypes_allreads.tsv


title: Hindgut F1 hybrid SU26xZI418 Biological replicate 1

description:
HG_SU26xZI418_1
HG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: GEX, D44, S9

description: 10x genomic


title: CD14+ isolated monocytes, GEX, D60, S8

description:
10x genomic
8_D60
ANONYM_BulkRNAseqMono_8.csv


title: CD3+ depleted, epigenetic: GEX, D32, S12

description: 10x genomic


title: stromal_t4_ko_M00471543


title: CD14+ isolated monocytes, GEX, D32, S8

description:
10x genomic
8_D32
ANONYM_BulkRNAseqMono_8.csv


title: CD3+ depleted, epigenetic: GEX, D0, S14

description: 10x genomic


title: CD3+ depleted, epigenetic: GEX, D180, S12

description: 10x genomic


title: Hindgut F1 hybrid SU26xZI418 Biological replicate 3

description:
HG_SU26xZI418_3
HG_gcounts_allgenotypes_allreads.tsv


title: CD14+ isolated monocytes, GEX, D30, S8

description:
10x genomic
8_D30
ANONYM_BulkRNAseqMono_8.csv


title: endo_t4_wt_M00460359

value: endothelial


title: CD3+ depleted, epigenetic: GEX, D32, S9

description: 10x genomic

value: post HBS/AS01 vaccination


title: lumhi_t4_wt_M00460358


title: CD14+ isolated monocytes, GEX, D0, S8

description:
10x genomic
8_D0
ANONYM_BulkRNAseqMono_8.csv

value: CD14+ isolated monocytes


title: CD3+ depleted, epigenetic: GEX, D180, S9

description: 10x genomic


title: basal_t4_wt_M00467006

value: Mammary Gland


title: CD14+ isolated monocytes, GEX, D2, S8

description:
10x genomic
8_D2
ANONYM_BulkRNAseqMono_8.csv


title: stromal_t2_ko_M00438677

value: Gestation day 9.5


title: CD14+ isolated monocytes, GEX, D60, S7

description:
10x genomic
7_D60
ANONYM_BulkRNAseqMono_7.csv


title: Hindgut F1 hybrid SU26xZI197 Biological replicate 3

description:
HG_SU26xZI197_3
HG_gcounts_allgenotypes_allreads.tsv


title: Hindgut F1 hybrid SU26xZI197 Biological replicate 2

description:
HG_SU26xZI197_2
HG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: GEX, D60, S8

description: 10x genomic


title: CD3+ depleted, epigenetic: GEX, D0, S12

description: 10x genomic


title: Hindgut F1 hybrid SU26xZI197 Biological replicate 1

description:
HG_SU26xZI197_1
HG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: GEX, D0, S9

description: 10x genomic


title: Hindgut SU26 Biological replicate 3

description:
HG_SU26_3
HG_gcounts_allgenotypes_allreads.tsv


title: lumlo_t2_ko_M00439062


title: CD3+ depleted, epigenetic: GEX, D44, S8

description: 10x genomic


title: CD14+ isolated monocytes, GEX, D30, S7

description:
10x genomic
7_D30
ANONYM_BulkRNAseqMono_7.csv


title: Hindgut SU26 Biological replicate 2

description:
HG_SU26_2
HG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: GEX, D32, S8

description: 10x genomic


title: endo_t2_ko_AFGK76


title: Hindgut SU26 Biological replicate 1

description:
HG_SU26_1
HG_gcounts_allgenotypes_allreads.tsv


title: CD14+ isolated monocytes, GEX, D2, S7

description:
10x genomic
7_D2
ANONYM_BulkRNAseqMono_7.csv


title: CD14+ isolated monocytes, GEX, D0, S7

description:
10x genomic
7_D0
ANONYM_BulkRNAseqMono_7.csv


title: basal_t2_wt_M00439079


title: CD3+ depleted, epigenetic: GEX, D44, S7

description: 10x genomic


title: CD14+ isolated monocytes, GEX, D60, S6

description:
10x genomic
6_D60
ANONYM_BulkRNAseqMono_6.csv


title: lumhi_t2_ko_AFGK78


title: lumlo_t2_wt_M00424114


title: CD3+ depleted, epigenetic: GEX, D32, S7

description: 10x genomic


title: CD14+ isolated monocytes, GEX, D32, S7

description:
10x genomic
7_D32
ANONYM_BulkRNAseqMono_7.csv


title: CD3+ depleted, epigenetic: GEX, D180, S7

description: 10x genomic


title: CD14+ isolated monocytes, GEX, D2, S6

description:
10x genomic
6_D2
ANONYM_BulkRNAseqMono_6.csv


title: Midgut ZI418 Biological replicate 3

description:
MG_ZI418_3
MG_gcounts_allgenotypes_allreads.tsv

source_name: midgut

value: midgut


title: CD14+ isolated monocytes, GEX, D30, S6

description:
10x genomic
6_D30
ANONYM_BulkRNAseqMono_6.csv


title: CD3+ depleted, epigenetic: GEX, D180, S8

description: 10x genomic


title: CD14+ isolated monocytes, GEX, D32, S6

description:
10x genomic
6_D32
ANONYM_BulkRNAseqMono_6.csv


title: Midgut ZI197 Biological replicate 2

description:
MG_ZI197_2
MG_gcounts_allgenotypes_allreads.tsv


title: endo_t0_ko_M00398657

value: Nulliparous


title: CD3+ depleted, epigenetic: GEX, D0, S8

description: 10x genomic

value: pre HBS/AS01 vaccination


title: CD14+ isolated monocytes, GEX, D60, S3

description:
10x genomic
3_D60
ANONYM_BulkRNAseqMono_3.csv


title: stromal_t2_wt_M00433264

value: stromal


title: basal_t0_ko_M00395206

value: basal


title: lumhi_t2_wt_M00424115

value: wt


title: Midgut ZI418 Biological replicate 2

description:
MG_ZI418_2
MG_gcounts_allgenotypes_allreads.tsv

value: 6 days


title: CD14+ isolated monocytes, GEX, D32, S3

description:
10x genomic
3_D32
ANONYM_BulkRNAseqMono_3.csv


title: Midgut F1 hybrid SU58xZI418 Biological replicate 3

description:
MG_SU58xZI418_3
MG_gcounts_allgenotypes_allreads.tsv

value: female


title: lumlo_t0_ko_M00373634


title: stromal_t0_ko_M00384810


title: CD14+ isolated monocytes, GEX, D0, S6

description:
10x genomic
6_D0
ANONYM_BulkRNAseqMono_6.csv


title: Midgut ZI418 Biological replicate 1

description:
MG_ZI418_1
MG_gcounts_allgenotypes_allreads.tsv


title: Midgut ZI197 Biological replicate 1

description:
MG_ZI197_1
MG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: GEX, D44, S3

description: 10x genomic


title: CD3+ depleted, epigenetic: GEX, D32, S3

description: 10x genomic


title: Midgut F1 hybrid SU58xZI418 Biological replicate 1

description:
MG_SU58xZI418_1
MG_gcounts_allgenotypes_allreads.tsv


title: CD14+ isolated monocytes, GEX, D30, S3

description:
10x genomic
3_D30
ANONYM_BulkRNAseqMono_3.csv


title: CD3+ depleted, epigenetic: GEX, D0, S7

description: 10x genomic


title: Midgut ZI197 Biological replicate 3

description:
MG_ZI197_3
MG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: GEX, D180, S3

description: 10x genomic


title: Midgut F1 hybrid SU58xZI418 Biological replicate 2

description:
MG_SU58xZI418_2
MG_gcounts_allgenotypes_allreads.tsv


title: CD14+ isolated monocytes, GEX, D2, S3

description:
10x genomic
3_D2
ANONYM_BulkRNAseqMono_3.csv


title: CD3+ depleted, epigenetic: GEX, D0, S3

description: 10x genomic


title: lumhi_t0_wt_M00399832


title: endo_t0_wt_M00394900


title: Midgut F1 hybrid SU58xZI197 Biological replicate 3

description:
MG_SU58xZI197_3
MG_gcounts_allgenotypes_allreads.tsv


title: basal_t0_wt_M00381049


title: CD3+ depleted, epigenetic: ATAC, D44, S19

description: 10x genomic

library_source: genomic single cell

data_processing:
bcl2Fastq2 V2.20.0 followed by cellranger- atac-2.0.0 (Satpathy, J. M. et al. Nat. Biotechnol. 37, 925-936 (2019) (v2.0.0))
scATAC-Seq data were processed using the corresponding Cell Ranger pipelines (G.X. Zheng, et al,  Nat. Commun (2017) after demultiplexing the sequencing data.
Assembly: refdata-gex-arc-GRCh38-2020-A 2.0.0
Supplementary files format and content: .h5 as output by Cell Ranger

extract_protocol:
Isolated cells were treated with DNAse prior to the extraction of their nuclei for which cells were centrifuged at 300 rcf during 5 min at 4°C and lysed with cold lysis buffer (20μl Tris-HCl (pH 7.4) 1M, 4μl NaCl 5M, 6μl MgCl2 1M, 20μl Tween 20 10%, 20μl Nonidet P40 Substitute 10%, 4μl Digitonin 5%, 200μl BSA 10%, 1726μl Nuclease-free water) after supernatant removal. This was followed by a 3mn incubation on ice and addition of cold washing buffer (20μl Tris-HCl (pH 7.4) 1M, 4μl NaCl 5M, 6μl MgCl2 1M, 200μl BSA 10%, 20μl Tween-20 10%, 1750μl Nuclease-free water). At last, the nuclei were harvested after centrifugation to 500 rcf at 4°C during 5 min in the nuclei buffer (Nuclei Stock Concentration Table in user guide Chromium Next Gem Single Cell ATAC library kit V1.1 (PN-1000175) CG000209. Cells were then processed for scATAC-seq using the 10X genomics technology.
The library preparations were based on the Chromium Next Gem Single Cell ATAC library kit V1.1 (PN-1000175) User Guide, CG000209.

treatment_protocol: Cells were isolated from frozen PBMCs after depletion of CD3+ cells after magnetic cell separation using the CD3 microbeads (Miltenyi Biotec, cat#130-050-101) and resuspension in buffer (MACS BSA cat#: 130-091-376 and autoMACS Rinsing Solution cat#: 130-091-222)


title: Midgut F1 hybrid SU58xZI197 Biological replicate 2

description:
MG_SU58xZI197_2
MG_gcounts_allgenotypes_allreads.tsv


title: stromal_t0_wt_M00373181


title: CD3+ depleted, epigenetic: ATAC, D32, S19

description: 10x genomic


title: CD3+ depleted, epigenetic: ATAC, D180, S19

description: 10x genomic


title: Midgut SU58 Biological replicate 3

description:
MG_SU58_3
MG_gcounts_allgenotypes_allreads.tsv


title: Midgut F1 hybrid SU58xZI197 Biological replicate 1

description:
MG_SU58xZI197_1
MG_gcounts_allgenotypes_allreads.tsv


title: R2: infected at MOI 0.0001 - Day 7

city: pittsburgh

first: Leonardo

last: D'aiuto

state: pa

address: 3811 O'Hare st

department: psychiatry

institute: UPMC

data_processing:
sequenced reads were processed and aligned using CLCbio v11
Sequences were trimmed based on quality score using the modified-Mott trimming algorithm as implemented in CLC bio software, using a trim cutoff error probability of 0.05.  Ambiguous bases were trimmed using a post trim maximal ambiguous base cutoff of 2.  The trimmed reads were then mapped to the human genome GRCh38/hg38, using sequence and annotation provided by Ensembl (release 82).
Assembly: GRCh38/hg38
Supplementary files format and content: csv format file with total counts, RPKM, TPM and CPM for each sample

source_name: iPSC line

growth_protocol: Neural progenitor cells (NPCs) were derived from hiPSC-neurons as previously described (D’Aiuto et al. Organogenesis. 2014;10(4):365-77).

extract_protocol:
Total RNA cellular RNA was extracted (RNeasy Mini Kits, Qiagen) and quantified using Agilent 4200 TapeStation (Agilent Technologies).
Total RNA libraries were generated using the Illumina TruSeq Stranded Total RNA Sample Preparation Guide, Revision E. The first step involved the removal of ribosomal and mitochondrial RNA using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, remaining RNA was fragmented using divalent cations under elevated temperature, which were then copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Subsequently, a single adenosine base was added to each of the cDNA fragments, followed by ligation of an adapter. The products were purified and enriched with PCR to create the final cDNA library. The cDNA libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorimeter. Quality was examined using an Agilent Bioanalyzer Tapestation 2200. The cDNA libraries were pooled at a final concentration 1.8pM. Cluster generation and 100 bp paired-read dual-indexed sequencing was performed on Illumina NextSeq 500 (Children’s Hospital of Pittsburgh, University of Pittsburgh).

treatment_protocol: NPCs were cultured in StemDiff Neural progenitor Medium, containing antivirals. All assays were conducted in quadruplicate.  Cells were harvested after 72 hours and the cellular RNA was extracted (RNeasy Mini Kits, Qiagen) and quantified using Agilent 4200 TapeStation (Agilent Technologies).

value: Neural progenitor cells (NPCs)

value: infected at MOI 0.0001 - Day 7


title: WT_Acetone_rep3

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

data_processing:
BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files
FASTQ files were mapped to the GRCm39.vm30 reference using STAR version 2.7.10a and the ENCODE standard options
calculate log counts per million, and normalization factors using the weighted trimmed mean of M-values (TMM) method of edgeR v3.36 and R v4.1.2
Limma v3.50.3, with the precision weights, ‘voom’ approach was used to perform linear models
Assembly: GRCm39.vm30
Supplementary files format and content: Tab-dilimeted text file with raw counts

source_name: whole ear tissue

extract_protocol:
RNA was isolated and purified using the Qiagen RNeasy mini kit (Qiagen #74104) and Qiagen RNase-Free DNase kit (Qiagen #79254) using the manufacturer's instructions
RNA ribo-depletion library was prepared using the NEBNext rRNA Depletion Kit (NEB #E7400X), xGen Broad-range RNA Library Prep (IDT #10010145), and xGen Normalase UDI Primers (IDT #10009811). An input of 484ng of total RNA was ribosomal depleted using the rRNA Depletion module. The rRNA-depleted RNA is then fragmented as determined by RIN (RNA Integrity Number) of input RNA as per protocol, then copied into first strand cDNA using reverse transcriptase and random primers. The 3 prime ends of the cDNA are then adenylated and adapters are ligated.  The products are purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by Qubit hsDNA (Thermofisher) and LabChip (Perkin Elmer)

treatment_protocol: Mice were treated with 20μl of 0.2mg/ml of TPA (Cell Signaling Technology #4174S), topically on the dorsal side of ear skin, with the other ear treated with acetone vehicle control

value: whole ear tissue

value: WT

value: 2 Acetone Tx


title: WT_Acetone_rep2


title: R3: infected at MOI 0.0001 - Day 7


title: Midgut SU58 Biological replicate 2

description:
MG_SU58_2
MG_gcounts_allgenotypes_allreads.tsv


title: WT_Acetone_rep1


title: CD3+ depleted, epigenetic: ATAC, D0, S19

description: 10x genomic

value: CD3+ depleted PBMCs


title: CD3+ depleted, epigenetic: ATAC, D60, S14

description: 10x genomic

value: post HBS/AS01 vaccination


title: R1: infected at MOI 0.0001 - Day 7


title: Q3: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 7


title: CD14+ isolated monocytes, GEX, D0, S3

description:
10x genomic
3_D0
ANONYM_BulkRNAseqMono_3.csv

value: CD14+ isolated monocytes


title: Midgut F1 hybrid SU26xZI418 Biological replicate 3

description:
MG_SU26xZI418_3
MG_gcounts_allgenotypes_allreads.tsv


title: Q2: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 7


title: CD3+ depleted, epigenetic: ATAC, D44, S14

description: 10x genomic


title: Midgut SU58 Biological replicate 1

description:
MG_SU58_1
MG_gcounts_allgenotypes_allreads.tsv


title: WT_TPA_rep3

value: 2 TPA Tx


title: CD3+ depleted, epigenetic: ATAC, D32, S14

description: 10x genomic


title: Midgut F1 hybrid SU26xZI418 Biological replicate 2

description:
MG_SU26xZI418_2
MG_gcounts_allgenotypes_allreads.tsv

value: midgut


title: WT_TPA_rep2


title: WT_TPA_rep1


title: P3: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 7


title: CD3+ depleted, epigenetic: ATAC, D180, S14

description: 10x genomic


title: Midgut F1 hybrid SU26xZI418 Biological replicate 1

description:
MG_SU26xZI418_1
MG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: ATAC, D0, S14

description: 10x genomic


title: K17null_Acetone_rep3


title: P2: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 7


title: Midgut F1 hybrid SU26xZI197 Biological replicate 3

description:
MG_SU26xZI197_3
MG_gcounts_allgenotypes_allreads.tsv


title: K17null_Acetone_rep2


title: CD3+ depleted, epigenetic: ATAC, D60, S12

description: 10x genomic


title: Midgut F1 hybrid SU26xZI197 Biological replicate 2

description:
MG_SU26xZI197_2
MG_gcounts_allgenotypes_allreads.tsv


title: K17null_Acetone_rep1


title: P1: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 7


title: O3: infected at MOI 0.001 - Day 7

value: infected at MOI 0.001 - Day 7


title: CD3+ depleted, epigenetic: ATAC, D44, S12

description: 10x genomic


title: K17null_TPA_rep3


title: Q1: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 7


title: CD3+ depleted, epigenetic: ATAC, D32, S12

description: 10x genomic


title: Midgut SU26 Biological replicate 3

description:
MG_SU26_3
MG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: ATAC, D180, S12

description: 10x genomic


title: K17null_TPA_rep2


title: Midgut SU26 Biological replicate 2

description:
MG_SU26_2
MG_gcounts_allgenotypes_allreads.tsv


title: CD3+ depleted, epigenetic: ATAC, D0, S12

description: 10x genomic

value: pre HBS/AS01 vaccination


title: Midgut SU26 Biological replicate 1

description:
MG_SU26_1
MG_gcounts_allgenotypes_allreads.tsv


title: N1: Uninfected + 5BVdU + IFN-alpha – Day 7

value: Uninfected + 5BVdU + IFN-alpha – Day 7


title: VillinCreERT2, 1month, replicate 1, scRNAseq

description: 10x Genomics

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Features were annotated using the cellranger count pipeline.
Assembly: GRCh38/hg19
Supplementary files format and content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

source_name: Intestine

extract_protocol:
Intestinal crypts were isolated according to standard protocol. Briefly, intestines were flushed with cold PBS, incubated in EDTA buffer and full intestinal crypts were dissociated in single cells with collagenase dispase solution. Subsequently, single cells were sorted for DAPI-negative to select for live cells, Epcam-positive to acquire epithelial cells, CD45-negative to exclude lymphocytes and CD31-negative to exclude endothelial cells. After sorting, cells were pelleted and re-suspended in 1000cells/ul final concentration and cell viability was assessed as a quality check parameter.
Only samples with viabilities higher tan 85% were processed for library preparation, which was done using 10X_3primer_mRNA as per manufacturer’s instructions.

treatment_protocol: Both Control and cKO animals were injected with tamoxifen at 8-10 weeks old and harvested at 1 month after the first injection.

value: Intestine

value: Epithelilal cells


title: O2: infected at MOI 0.001 - Day 7


title: O1: infected at MOI 0.001 - Day 7


title: K17null_TPA_rep1


title: MOLM13, DB2115, 20hr, RNA-seq rep3

description: Novogene seq. service

data_processing:
Cleaned and trimmed reads were analyzed by FastQC for base sequence quality, GC content, N content, and sequence duplication levels.
Sequencing reads passing quality control criteria were aligned to the Homo Sapiens transcriptome (hg38) using STAR aligner.
Raw counts were normalized and analyzed for differential expression in R using the Bioconductor package DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hematopoietic

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries by Novogene.
RNA libraries for RNA-seq were prepared by Novogene using company standard protocols.

treatment_protocol: Cells were maintained at 1mill/ml before treatment with 5uM DB2115, or Vehicle (0.001% DMSO) for 20hrs

value: hematopoietic

tag: cell line

value: Acute myeloid leukemia


title: VillinCreERT2_Arid3a fl/fl, 1month, replicate 2, scRNAseq

description: 10x Genomics

value: Arid3a cKO


title: M3: Uninfected - Day 7

value: Neural progenitor cells (NPCs)

value: Uninfected - Day 7


title: CD3+ depleted, epigenetic: ATAC, D32, S9

description: 10x genomic


title: MOLM13, DB2115, 20hr, RNA-seq rep2

description: Novogene seq. service


title: M2: Uninfected - Day 7


title: CD3+ depleted, epigenetic: ATAC, D180, S9

description: 10x genomic


title: VillinCreERT2_Arid3a fl/fl, 1month, replicate 1, scRNAseq

description: 10x Genomics


title: CD3+ depleted, epigenetic: ATAC, D0, S9

description: 10x genomic


title: 20233X20 Secretome 10

city: Salt Lake City

first: Micah

last: Drummond

state: UT

institute: University of Utah

description: Acute intramuscular injection with 50ul pluripotent stem cell secretome product

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 104 and reference database was created using STAR version 2.7.9a
Optical duplicates were removed using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.34.0
Assembly: mm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: Quadriceps

extract_protocol:
Total RNA was isolated by homogenizing myotubes in Qiazol Lysis Reagent (Qiagen, cat# 79306). The RNA was separated and precipitated using chloroform and isopropanol. Extracted RNA was washed with ethanol then suspended in nuclease-free water.
Libraries were prepared with Illumina Stranded Total RNA Library Prep NEB Ultra II directional and RNA was sequenced using Illumina NovaSeq S4 Reagent Kit v1.5 150x150 bp Sequencing

value: WT

value: Quadriceps

value: M


title: Midgut F1 hybrid SU26xZI197 Biological replicate 1

description:
MG_SU26xZI197_1
MG_gcounts_allgenotypes_allreads.tsv

value: 6 days

value: female


title: M1: Uninfected - Day 7


title: MOLM13, VEH, 20hr, RNA-seq rep3

description: Novogene seq. service

value: VEH


title: L3: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 5


title: 20233X19 Secretome 9


title: N2: Uninfected + 5BVdU + IFN-alpha – Day 7


title: CD3+ depleted, epigenetic: ATAC, D60, S8

description: 10x genomic

value: CD3+ depleted PBMCs

value: post HBS/AS01 vaccination


title: MOLM13, VEH, 20hr, RNA-seq rep2

description: Novogene seq. service


title: 20233X18 Secretome 8


title: CD3+ depleted, epigenetic: ATAC, D44, S9

description: 10x genomic


title: MOLM13, VEH, 20hr, RNA-seq rep1

description: Novogene seq. service


title: L1: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 5


title: L2: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 5


title: CD3+ depleted, epigenetic: ATAC, D44, S8

description: 10x genomic


title: 20233X16 Secretome 6


title: CD3+ depleted, epigenetic: ATAC, D180, S8

description: 10x genomic


title: 20233X17 Secretome 7


title: K3: infected at MOI 0.0001 - Day 5

value: infected at MOI 0.0001 - Day 5


title: CD3+ depleted, epigenetic: ATAC, D32, S8

description: 10x genomic


title: K2: infected at MOI 0.0001 - Day 5


title: 20233X15 Secretome 5


title: CD3+ depleted, epigenetic: ATAC, D0, S8

description: 10x genomic

value: pre HBS/AS01 vaccination


title: OCI-LY1 cells, DMSO

city: Chongqing

first: Sanxiu

last: He

state: -- None selected --

address: Department of Hematology Oncology

institute: Chongqing University Cancer Hospital

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by and the clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: txt, RSEM-generated expression levels of genes

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
The RNA library construction and subsequent RNA sequencing were performed by BGI-Shenzhen, China. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

value: DLBCL

value: control


title: MOLM13, DB2115, 20hr, RNA-seq rep1

description: Novogene seq. service

value: hematopoietic


title: 20233X14 Secretome 4


title: HCT116 cells, poly I:C, 7h, biol rep 3

city: Daejeon

first: Doyeong

last: Ku

address: Daehak-ro, 291

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Read counts were normalized by DESeq2 analysis.
Read counts of 3 replicates were compared against 3 replicates with the control group.
DEG gene list was ordered by the lowest adjusted p-values.
Supplementary files format and content: cvs
Supplementary files format and content: gene count, Differentially expressed gene analysis

growth_protocol: HCT116 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
TRIzol (Ambion) was added directly to the cell pellet obtained after centrifugation at 10,000 g for 30 sec. After precipitation of the extracted nucleic acids, DNase I (TaKaRa) was treated to remove DNA, and purified RNA was reverse transcribed using RevertAid reverse transcriptase
RNA libraries for RNA-seq were prepared using STruSeq Stranded Total RNA LT Sample Prep Kit (Gold) following TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

treatment_protocol: In HCT116 cells, 10 µg/ml of poly I:C was transfected for 7h. DEPC was used as control treatment.

value: human colon cancer cell

value: Poly I:C


title: CD3+ depleted, epigenetic: ATAC, D44, S7

description: 10x genomic


title: K1: infected at MOI 0.0001 - Day 5

value: Neural progenitor cells (NPCs)


title: HCT116 cells, poly I:C, 7h, biol rep 2


title: CD3+ depleted, epigenetic: ATAC, D32, S7

description: 10x genomic


title: HCT116 cells, poly I:C, 7h, biol rep 1


title: 20233X13 Secretome 3


title: 20233X12 Secretome 2


title: HCT116 cells, DEPC, 7h, biol rep 3

value: DEPC


title: J2: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 5


title: OCI-LY1 cells, CIN

value: WT

value: 40 nM Cinobufagin


title: J1: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 5


title: J3: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 5


title: 20233X10 Control 10

description: Acute intramuscular injection with 50ul saline (0.9%)

value: Quadriceps

value: M


title: HCT116 cells, DEPC, 7h, biol rep 2


title: HCT116 cells, DEPC, 7h, biol rep 1


title: I2: infected at MOI 0.001 - Day 5

value: infected at MOI 0.001 - Day 5


title: CD3+ depleted, epigenetic: ATAC, D32, S3

description: 10x genomic


title: CD3+ depleted, epigenetic: ATAC, D180, S7

description: 10x genomic


title: CD3+ depleted, epigenetic: ATAC, D44, S3

description: 10x genomic


title: I3: infected at MOI 0.001 - Day 5


title: MDA-MB-231-ASAH1 shRNA#2 replicate 3

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

description:
Cell stably expressing ASAH1 #2 shRNA
TrtC_3

data_processing:
Low quality sequences were removed using the software Trimmomatic (version 0.36) (Bolger et al 2014).
The trimmed fastq sequences were aligned to the human hg38 reference genome (GenBank assembly accession: GCA_000001405.28).
The alignments were carried out using STAR (version 2.7.1a) (Dobin et al 2013) with default parameters.
Gene expression was quantified as gene level using the htseq-count function (version 0.12.3) (Anders et al 2015). The UCSC gene annotations for the human genome were used. The htseq-count default parameters were used, except for the strand parameter which was set to reverse to consider the strandedness of library.
Differentially expressed genes were identified using DESeq2 (version 1.28) (Love et al 2014). DESeq2 was run with default parameters (Love et al 2014).
Assembly: GRCH38
Supplementary files format and content: CSV files - output from DESEQ2

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231cells were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: MDA-MB-231  cells expressing either control non-specific shRNA or ASAH1 shRNA (ASAH1#1 and ASAH1#2),  were harvested and were used for preparing the total RNA and to perfrom RNA Seq.

value: ASAH1 shRNA #2


title: 20233X9 Control 9


title: 20233X8 Control 8


title: 20233X11 Secretome 1


title: I1: infected at MOI 0.001 - Day 5


title: MDA-MB-231-ASAH1 shRNA#2 replicate 2

description:
Cell stably expressing ASAH1 #2 shRNA
TrtC_2


title: CD3+ depleted, epigenetic: ATAC, D0, S3

description: 10x genomic

value: CD3+ depleted PBMCs


title: MDA-MB-231-ASAH1 shRNA#2 replicate 1

description:
Cell stably expressing ASAH1 #2 shRNA
TrtC_1


title: 20233X6 Control 6


title: CD3+ depleted, epigenetic: ATAC, D0, S7

description: 10x genomic


title: H2: Uninfected + 5BVdU + IFN-alpha – Day 5

value: Uninfected + 5BVdU + IFN-alpha – Day 5


title: HEK293T_Chromseq_CBX1_rep3

city: Xi'an

first: Wei

last: Sun

state: Shaanxi

address: No. 229 Taibai North Road, Beilin District

department: College of Life Sciences and Medicine

institute: Northwest University

data_processing:
The raw sequencing reads were Quality Controled by FastQC(v0.11.8).
Then, raw reads were trimmed using fastp(v0.23.1) with the options: fastp -A -f 11 -F 0 -t 0 -T 11.
Clean reads were aligned using HISAT2(v.2.1.0) to the hg19 genome with the options: hisat2 -q -t --no-unal.
The aligned reads were quantified by featureCounts(v2.0.1) using the options: featureCounts -t gene -g gene_id --extraAttributes gene_name,gene_type -s 1 -p -C
Differential expression analysis using DESeq2 (v1.34.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file include three biological replicates raw counts for Control
Supplementary files format and content: tab-delimited text file include three biological replicates raw counts for CBX7
Library strategy: Chrom-seq

growth_protocol: Plate HEK293T cells co-expressing the corresponding GCN4 and APEX2 fusion constructs for 48 hours.

extract_protocol:
The total RNA was isolated by using the NEB Next Poly A+Isolation Kit (NEB, #E7490S/L).1-5 μg of total RNA was used for the construction of sequencing libraries.
Libraries were built using the Smart-seq protocol.

treatment_protocol: Cells were changed the medium to fresh medium containing 500 µM biotin-aniline and incubate at 37℃ under 5% CO2 for 30 min. Then, H2O2 was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 min.

value: Human embryonic kidney


title: MDA-MB-231-ASAH1 shRNA#1 replicate 3

description:
Cell stably expressing ASAH1 #1 shRNA
TrtB_3

value: ASAH1 shRNA #1


title: HEK293T_Chromseq_CBX1_rep2


title: MDA-MB-231-ASAH1 shRNA#1 replicate 2

description:
Cell stably expressing ASAH1 #1 shRNA
TrtB_2


title: G3: Uninfected - Day 5

value: Uninfected - Day 5


title: MDA-MB-231-ASAH1 shRNA#1 replicate 1

description:
Cell stably expressing ASAH1 #1 shRNA
TrtB_1


title: 20233X4 Control 4


title: HEK293T_Chromseq_CBX1_rep1


title: 20233X3 Control 3


title: G2: Uninfected - Day 5


title: HEK293T_Chromseq_Control_rep3


title: CD3+ depleted, epigenetic: ATAC, D180, S3

description: 10x genomic

value: post HBS/AS01 vaccination


title: MDA-MB-231-NS shRNA treated replicate 3

description:
Cell stably expressing control non-specific shRNA
CtrlA_3

value: non-specific (NS) shRNA


title: 20233X2 Control 2


title: 20233X1 Control 1


title: HEK293T_Chromseq_Control_rep2


title: MDA-MB-231-NS shRNA treated replicate 2

description:
Cell stably expressing control non-specific shRNA
CtrlA_2


title: G1: Uninfected - Day 5


title: HEK293T_Chromseq_Control_rep1


title: F3: Uninfected - Day 3

value: Uninfected - Day 3


title: MDA-MB-231-NS shRNA treated replicate 1

description:
Cell stably expressing control non-specific shRNA
CtrlA_1


title: 20233X7 Control 7


title: H3: Uninfected + 5BVdU + IFN-alpha – Day 5


title: 20233X5 Control 5


title: F2: Uninfected - Day 3


title: H1: Uninfected + 5BVdU + IFN-alpha – Day 5


title: U87MG-siH19

city: Cheongju-si

first: Wanyeon

last: Kim

state: Chungbuk

address: Taeseongtabyeonro 250, Gangnaemyeon, Heungdeokgu

department: Biology Education

institute: Korea National University of Education

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to hg19 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Trizol was added to the prepared mammalian cells, reacted for 5 minutes, and then chloroform was added and reacted for 3 minutes. After centrifugation at 4℃ and 1,3000 rpm for 15 minutes, the supernatant was transferred to a new tube. After adding isopropanol and reacting for 10 minutes, centrifugation was performed at 4℃ and 1,3000 rpm for 10 minutes. After discarding the supernatant, add 80% ethanol, centrifuge at 4℃ and 1,3000 rpm for 5 minutes, and discard the supernatant. After air drying for 5 minutes, add sterilized tertiary distilled water and store it.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: glioma

value: H19 knockdown

value: siH19 transfection


title: mouse CSF, treated with LPS for 24/48 hr; hashed together; 10X 3' scRNA-seq mRNA

city: Boston

first: Peter

last: Lotfy

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
FASTQs generated using CellRanger mkfastq; sample lanes combined
Alignment using CellRanger v6.0.1 to mm10-2020-A genome; include-introns = FALSE
Cells filtered by whitelisted hash barcodes and cell barcodes and by quality metrics discussed in manuscript
Hash demultiplexing using Seurat v4 HTODemux() function with threshold set to 0.99
Cell annotations conducted according to manuscript methods
Assembly: mm10
Supplementary files format and content: chp.h5 and csf.h5 are processed HDF5 files in 10X CellRanger format
Supplementary files format and content: associated metadata with cell annotations and associated hash assignments in chp_metadata.csv.gz and csf_metadata.csv.gz

source_name: cerebrospinal fluid

extract_protocol:
ChP and CSF collected after 24-72hr and processed for 10X 3' v3.1 scRNA-seq with sample hashing
10X 3' v3.1 scRNA-seq with Feature Barcoding protocol (10X genomics)

treatment_protocol: intracerebroventricular injection of LPS or PBS of mice

value: cerebrospinal fluid

value: LPS 24hr or LPS 48hr

tag: library type

value: Gene expression library


title: F1: Uninfected - Day 3

value: Neural progenitor cells (NPCs)


title: OE_2

city: Harbin

first: Shao

last: Lan

address: No.92, Xidazhi Street, Nangang District

institute: Harbin Institute of Technology

data_processing:
Hisat2 for sequence alignment
Stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
Samtools tools for related file processing
Assembly: hg18
Supplementary files format and content: Xls file include expression  values for each sample

source_name: liver

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using the RNeasy Mini Kit (Qiagen, Carlsbad, USA) according to the manufacturer’s instructions
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: liver

value: LINC01767 overexpression


title: E3: Uninfected + 5BVdU + IFN-alpha – Day 3

value: Uninfected + 5BVdU + IFN-alpha – Day 3


title: mouse choroid plexus, treated with PBS or LPS 24/72 hr; hashed together; 10X 3' scRNA-seq hashing

library_source: other

molecule: protein

source_name: choroid plexus

value: choroid plexus

value: PBS or LPS 24hr or LPS 72hr

value: Hashing library


title: OE_3


title: OE_1


title: E2: Uninfected + 5BVdU + IFN-alpha – Day 3


title: U87MG-cont

value: WT


title: NC_3

value: control


title: U87MG-H19oe

value: H19 overexpression

value: pcDNA3.1-H19 transfection


title: mouse choroid plexus, treated with PBS or LPS 24/72 hr; hashed together; 10X 3' scRNA-seq mRNA


title: A172-siH19

value: glioma


title: Colonic_muscle_DSS_female

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

description: 10x Genomics

data_processing:
Output data were processed using the 10X genomics Cell Ranger pipeline to generate barcode and feature count matrices for downstream analysis
To generate counts matrices of spliced and unspliced RNA the Velocyto read count pipeline was performed on the cellranger output of 10X Chromium samples with the standard cellranger gene annotation reference file (La Manno et al., 2018).
Assembly: mm10
Supplementary files format and content: CellRanger output data_barcodes_features_matrix.tsv
Supplementary files format and content: Velocyto output data_loom

source_name: Colonic muscularis propria

extract_protocol:
Colons from euthanized mice were pinned flat and cut along the mesenteric border in silicone-lined petri dishes with the mucosa and submucosa peeled under a dissection microscope. The muscularis propria was minced and digested in collagenase XI (1 mg mL−1; Sigma Aldrich, St. Louis, Missouri) and dispase (250 μg mL−1; STEMCELL Technologies, Vancouver, Canada) solution at 37˚C for 45 minutes and passed through a 35µm nylon mesh to generate single cell suspensions. For purification of leukocyte and glial cell populations, cell suspensions were incubated with anti-CD45 (clone 30-F11 conjugated to Alexa Fluor 488, Biolegend, CA, 1:100) and anti-CD49b (conjugated to Alexa fFuor 647, clone HMα2, Biolegend, 1:100) for 30 minutes at 37°C before washing, adding DAPI (1:100) and sorting live CD45+ and or CD49b+ cells by fluorescent activated cell sorting (FACS) using a BD FACSAria cell sorter (BD Biosciences, Franklin Lakes, New Jersey).  Cells were pooled at a ratio of 2/3 CD45+ cells and 1/3 CD49b+ cells prior to library preparation.
cDNA libraries were prepared using the Chromium Single Cell 3' Reagent Kit v3.0 (10X Genomics, CA) using the standard 10X Genomics workflow according to manufacturer’s instructions.

value: Colonic muscularis propria

value: female

value: DSS


title: D3: infected at MOI 0.001 - Day 3

value: infected at MOI 0.001 - Day 3


title: A172-cont


title: NC_1


title: Colonic_muscle_Naïve_female

description: 10x Genomics

value: naïve


title: mouse CSF, treated with LPS for 24/48 hr; hashed together; 10X 3' scRNA-seq hashing

value: cerebrospinal fluid

value: LPS 24hr or LPS 48hr


title: D2: infected at MOI 0.001 - Day 3

value: Neural progenitor cells (NPCs)


title: HepG2_BLM [RNA-seq]

city: Shanghai

first: Xiaoguang

address: 130 Dong-An Road

department: Department of Biochemistry and Molecular Biology

institute: Fudan University

data_processing:
For the completed sequencing data, using the Trim Galore software package for quality control of raw data to remove low-quality reads and sequencing adapters.
Using the TopHat software (v2.0.12) package on the data that has completed quality control to align the sequencing data to the human reference genome hg38, using default parameters.
After alignment, using the Cufflink software package v2.2.1 to calculate gene expression levels as FPKM values (Fragments Per Kilobase per Million mapped reads), using default parameters.
After obtaining the gene expression levels, using the Cuffdiff software package v2.2.1 to perform differential gene expression analysis between the experimental and control groups.
Using the topGO v2.42.0 package to perform GO enrichment analysis and plotting of differentially expressed genes.
Assembly: hg38
Supplementary files format and content: txt

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using TRIzol (Invitrogen) following the standard protocol. 2 μg of total RNA was used for the construction of sequencing libraries.
For RNA-seq, RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with 10 mg/ml (Sellect) of bleomycin for 24 hours.

value: Hepatoma cell

value: Bleomycin

value: Day 1


title: 72_SN__Rad_3

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

data_processing:
The sequencing quality of each sample was assessed using FastQC.
Read- and alignment-level quality were assessed using FastQ Screen, Preseq, Picard tools, RSeQC and QualiMap.
Reads were trimmed for adapter sequences and low-quality bases using Cutadapt prior to alignment against the human reference genome, hg38, using STAR in two-pass mode with GENCODE v19 annotation
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including raw counts for each samples

growth_protocol: All cells were cultured at 37°C, 5% CO2 in DMEM supplemented with 10% FBS, 1% L-Glutamine and 1% penicillin/streptomycin

extract_protocol:
mRNAs were extracted using the Qiagen Rneasy Plus kit according to the manufacturer’s instructions
Library was prepared with the Illumina® Stranded mRNA Ligation Kit according to the manufacturer’s instructions

treatment_protocol: Cells were transduced with lentiviral particles containing FLAG-Δ133p53α Wild-Type, FLAG-Δ133p53α R273H or control-RFP and selected with 1μg/ml Blasticidin. Cells were exposed to 50μM temozolomide (TMZ) for 5 days or were irradiated with 10 Grays X-rays and used for downstream experiments 5 days after treatment. Dimethyl-Sulfoxide (DMSO) was used as a control.

value: Glioblastoma

value: Radiations


title: 71_SN__Rad_2


title: D1: infected at MOI 0.001 - Day 3


title: Colonic_muscle_Naïve_male

description: 10x Genomics

value: male


title: HepG2_Ctrl [RNA-seq]

last: Ren

value: WT

value: Control


title: C3: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 3


title: aggregates_D7_6

city: Beijing

first: Yifei

last: Zhang

address: Haidian

institute: Peking University

description: mESCs_cocktail factor

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean data was generated by quality control and then mapped to the reference genome (Mus musculus, GRCm38_release95) using Hisat2.
Quantification of gene expression levels were measured by fragments per kilobase of transcript per million fragments mapped (FPKM) from Florea L,. F1000Res. 2013.
In the equation, cDNA Fragments represents the number of PE reads mapped to the specific transcript;  Mapped Fragments (Millions) is the number of all mapped reads, which is counted as 10^6;  Transcript Length(kb) is the length of transcript in unit of 10^3 b.
Assembly: Mus musculus, GRCm38_release95
Supplementary files format and content: tab-delimited list files include FPKM values for each Sample

source_name: mESC 129w2

growth_protocol: The mESC line (129w2, passages 13–16) used in our experiments was kindly provided by the Tang Fuchou Laboratory at Peking University. Cells were cultured in 6-well plates coated with 0.1% gelatin.

extract_protocol:
For RNA sequencing (RNA-seq), total RNA was extracted from aggregates using the RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: To initiate differentiation, colonies of mESCs were detached from the culture dish using Accutase, collected as a single-cell suspension in base differentiation medium SFEBq (serum-free floating culture of embryoid body like aggregates with quick reaggregation, GMEM medium (Gibco) supplemented with 1% glutamine, 1% penicillin/streptomycin, 0.1 mM NEAA, 1% sodium pyruvate, 2% KO serum replacement, and 0.1 mM β-mercaptoethanol). On day 0, cells were counted using a cell counter and distributed at a density of 3,000 cells in 150 μl per well into 96-well U-bottom ultra-low attachment plates (Corning). Cell aggregation was facilitated by centrifugation at 900 rpm for 5 min. These cell aggregates were then incubated at 37 °C incubator under 5% CO2 for 1 day. After this incubation period, half of the medium was changed by removing 75 μl of spent medium and adding 75 μl of fresh medium containing 4% growth factor reduced Matrigel (BD). On day 3 of differentiation, 37.5 μl of fresh differentiation medium containing 2% Matrigel and 2 ng/ml BMP4 was added, increasing the final volume to 187.5 μl. On day 4, 2% Matrigel, 25 ng/ml bFGF, and 1 μM RA were added in a volume of 25 μl per well, bringing the final volume to 212.5 μl per well. On day 5, the aggregates were transferred to individual wells of 24-well low-attachment plates (Corning) containing base differentiation medium with 1% Matrigel.

value: mESC 129w2


title: 70_SN__Rad_1


title: NC_2

value: liver

value: control


title: aggregates_D7_4

description: mESCs_cocktail factor


title: aggregates_D7_5

description: mESCs_cocktail factor


title: PARCLIP_FH_PKM2_Nuc_A

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

description:
5'adapter: GTTCAGAGTTCTACAGTCCGACGATCrNrNrNrN
3'adapter: NNAGTGTCTGGAATTCTCGGGTGCCAAGG

data_processing:
Library strategy: PAR-CLIP-Seq
bcl2fastq/2.20.0 was used to convert bcl to fastq
For RNA-Seq fastq files were aligned using star/2.7.2b.
differential expression was done using cuffdiff (cufflinks/2.2.1)
PARCLIP was analysed using Parpipes (https://github.com/ohlerlab/PARpipe)
Genome_build: hg38

source_name: Flp-In™ 293 T-REx

growth_protocol: HEK293 T-Rex Flp-In cells (Thermo Fisher Scientific, Cat# R78007) were cultured in DMEM medium (Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS), 100 μg/ml zeocin, and 10 μg/ml blasticidin (Gibco)

extract_protocol:
Trizol for RNA-Seq, For PARCLIP, the cytoplasm was extracted by resuspending cells in a modified hypotonic lysis buffer (10 mM Tris-HCl pH 7.5, 50 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 10% glycerol) for 2 min. The nuclear pellet was washed twice with the same buffer and lysed in NP-40 buffer(20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% (v/v) NP40, 0.5 mM DTT), followed by sonication.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

treatment_protocol: 2ug/ml Doxycycline

value: HEK293 T-Rex Flp-In

tag: molecule

value: FH-PKM2 cross-linked RNA footprints


title: C1: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 3

data_processing:
sequenced reads were processed and aligned using CLCbio v11
Sequences were trimmed based on quality score using the modified-Mott trimming algorithm as implemented in CLC bio software, using a trim cutoff error probability of 0.05.  Ambiguous bases were trimmed using a post trim maximal ambiguous base cutoff of 2.  The trimmed reads were then mapped to the human genome GRCh38/hg38, using sequence and annotation provided by Ensembl (release 82).
Assembly: GRCh38/hg38
Supplementary files format and content: csv format file with total counts, RPKM, TPM and CPM for each sample

extract_protocol:
Total RNA cellular RNA was extracted (RNeasy Mini Kits, Qiagen) and quantified using Agilent 4200 TapeStation (Agilent Technologies).
Total RNA libraries were generated using the Illumina TruSeq Stranded Total RNA Sample Preparation Guide, Revision E. The first step involved the removal of ribosomal and mitochondrial RNA using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, remaining RNA was fragmented using divalent cations under elevated temperature, which were then copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Subsequently, a single adenosine base was added to each of the cDNA fragments, followed by ligation of an adapter. The products were purified and enriched with PCR to create the final cDNA library. The cDNA libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorimeter. Quality was examined using an Agilent Bioanalyzer Tapestation 2200. The cDNA libraries were pooled at a final concentration 1.8pM. Cluster generation and 100 bp paired-read dual-indexed sequencing was performed on Illumina NextSeq 500 (Children’s Hospital of Pittsburgh, University of Pittsburgh).


title: A172-H19oe

value: glioma

value: H19 overexpression

value: pcDNA3.1-H19 transfection


title: 68_SNR_Rad_2


title: aggregates_cocktail factor_3

description: mESCs_cocktail factor

value: culture with cocktail factor


title: C2: infected at MOI 0.001 + 5BVdU + IFN-alpha - Day 3

value: Neural progenitor cells (NPCs)


title: Colonic_muscle_DSS_male

description: 10x Genomics

value: Colonic muscularis propria

value: DSS


title: E1: Uninfected + 5BVdU + IFN-alpha – Day 3

value: Uninfected + 5BVdU + IFN-alpha – Day 3


title: B3: infected at MOI 0.0001 - Day 3

value: infected at MOI 0.0001 - Day 3


title: 67_SNR_Rad_1

value: Glioblastoma

value: Radiations


title: PARCLIP_FH_PKM2_Cyt_A

description:
5'adapter: GTTCAGAGTTCTACAGTCCGACGATCrNrNrNrN
3'adapter: NNTAGTCGTGGAATTCTCGGGTGCCAAGG


title: B2: infected at MOI 0.0001 - Day 3


title: aggregates_cocktail factor_2

description: mESCs_cocktail factor


title: PARCLIP_FH_PKM2_Cyt_B


title: 66_SN__TMZ_3

value: Temozolomide


title: WT_Endosperm

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

institute: National Centre for Biological Sciences - TIFR

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The reads were aligned to PCR templates as genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density.
Assembly: Custome genome built from Oryza sativa japonica nipponbare genome – IRGSP1 with the PCR amplicon regions as template
Supplementary files format and content: bigwig files showing the methylation status across the genome.

source_name: Endosperm (20 days after anthesis)

extract_protocol:
Total DNA was extracted from the tissues using CTAB method.
Bisulfite convertion by EZ DNA Methylation-Gold Kit (Catalog no-D5005) as per manufacturer’s protocol. Adapters used: Read1-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read2-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: WT tissues were handled in the same manner. Treated with Zymo bisulfite reagents

tag: subspecies

value: Indica

value: Endosperm (20 days after anthesis)

tag: cultivar

value: Pusa Basmati1 (PB1)


title: aggregates_cocktail factor_1

description: mESCs_cocktail factor

value: mESC 129w2


title: B1: infected at MOI 0.0001 - Day 3


title: 65_SN__TMZ_2

tag: genotype


title: PARCLIP_FH_PKM2_Nuc_B

value: HEK293 T-Rex Flp-In

value: FH-PKM2 cross-linked RNA footprints


title: aggregates_D7_3


title: A3: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 3


title: CLSY3_KD_Endosperm


title: 69_SNR_Rad_3

value: control


title: 64_SN__TMZ_1


title: aggregates_D7_2


title: NKSW7-1 rep3

city: Urbana

first: Nurzhan

last: Kuanyshev

state: Illinois

address: 1206 W Gregory Dr

department: CABBI

institute: University of Illinois at Urbana Champaign

data_processing:
Adapters and low-quality reads were trimmed using Trimmomatic
Trimmed reads were mapped onto S. cerevisiae S288C reference genome (RefSeq assembly accession: GCF_000146045.2) using STAR version 2.6.1b
Read counts for each gene were calculated using featureCounts from the Subread package, version 1.5.2
Differential expression analysis was performed in R using edgeR and limma
Glimma and gplots were used for graphical representation of expression data
Assembly: S. cerevisiae S288C reference genome GCF_000146045.2
Supplementary files format and content: tab delitmeted txt file containing raw counts

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: cells were grown in YP 5 g/L glucose media and harvested in mid exponential phase

extract_protocol:
RNA was extracted using Quick-RNA™ Fungal/Bacterial Kits according to manufacturer protocol
The RNAseq libraries were prepared with Kapa Hyper Stranded mRNA library kit (Roche) . Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand

value: yeast cells

value: NKSW7-1 strain (PHO13::XYL1,XYL2,XYL3 ; ALD6::XYL1,XYL2,XYL3 ; HXT1-7 ::AtSWEET7, GAL2 ::AtSWEET7)


title: aggregates_D7_1


title: 63_SNR_TMZ_3


title: A1: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 3

first: Leonardo

last: D'aiuto

institute: UPMC

value: Neural progenitor cells (NPCs)


title: NKSW7-1 rep2


title: NKSW7-1 rep1


title: A2: infected at MOI 0.0001 + 5BVdU + IFN-alpha - Day 3


title: 62_SNR_TMZ_2


title: CT2-control rep3

value: CT2 strain (PHO13::XYL1,XYL2,XYL3 ALD6::XYL1,XYL2,XYL3)


title: CT2-control rep2


title: aggregates_co-culture_2

value: co-culture with mSMGs at D5-7


title: aggregates_co-culture_1


title: 60_SN__DMSO_3

value: DMSO


title: 61_SNR_TMZ_1


title: ATAC_H847

city: North Chicago

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

institute: AbbVie Inc.

data_processing:
Sequence quality for ATAC-seq and ChIP-seq samples was assessed by FastQC method. The sequences were aligned to human reference genome hg19 using BWA aligner, and alignment metrics were calculated using Picard and samtools.
Narrow peaks, e.g. the transcription factor binding peaks, were detected using macs2 with default cutoff parameters. Processed ChIP-seq datasets by MACS were further analyzed using the USeq platform for Intersecting Regions and Neighboring Gene identifications (http://useq.sourceforge.net/).
Further analysis of aligned bam files was done using NGSPlot (https://github.com/shenlab-sinai/ngsplot) to visualize heatmaps and generate average profile plots.
For ATAC-seq, in brief, 50K viable cells were flow sorted (FACS AriaII) on ice and transposase reactions were carried out using Tn5 transposase as previously described (Buenrostro et al, Curr Protoc Mol Biol, 2015).
Assembly: hg19
Supplementary files format and content: bedgraph

extract_protocol:
For ChIP-seq, cells were fixed for ten minutes with direct addition of 1% formaldehyde (ThermoFisher, Waltham, MA). The fixation was stopped with 0.125 mM glycine (Sigma-Aldrich, St. Louis, MO) for five minutes, followed by wash and collection in cold PBS and subsequent lysis (1% SDS, 10 uM EDTA, 50 uM TrisCl pH 8.0, 5 mM sodium butyrate, cOmpleteTM protease inhibitor cocktail tablets) (Sigma-Aldrich, St. Louis, MO). Chromatin was sheared to 300-500 kb using the Bioruptor (Diagenode, Denville, NJ). Lysates were mixed 1:4 with dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA, 16.7 uM Tris-Cl pH 8.0, 167 uM NaCl, 5mM sodium butyrate, protease inhibitor cocktail tablet). Immunoprecipitation was completed for four hours using antibodies directed against H3K27ac, MYC, MYCL1, and MYCN with M280 Sheep Anti-Rabbit IgG Dynabeads (ThermoFisher, 11203D). ChIPs were washed 1x with TE and 3x with Wash Buffer (100 mM Tris-Cl pH 8.0, 500 mM LiCl, 15 Igepal, 1% deoxycholic acid) supplemented with PMSF. Beads were resuspended in Elution Buffer (20 mM NaHCO3, 1% SDS, 150 mM NaCl) and cross-links were reversed overnight at 65C, followed by 1 hr RNase A and proteinase K digestion at 45 C. DNA was purified using ChIP DNA Clean & Concentrator (Zymo). For ATAC-seq samples, cells were harvested by centrifugation and 50,000 viable cells were flow sorted on ice (FACS AriaII). Cells were then washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Lysates were then incubated with Tn5 transposase at 37°C for 30 minutes. Following transposition, DNA was purified using the Qiagen MinElute PCR Purification Kit.
ChIP-seq and ATAC-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB).

value: small cell lung cancer

tag: chip antibody


title: ATAC_H889


title: 59_SN__DMSO_2

value: Glioblastoma


title: CT2-control rep1


title: ATAC_H69


title: LSK_PPM1BCKO_2

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong Province

address: No.6699, Qingdao Road, Huaiyin District

institute: Shandong First Medical University

data_processing:
Raw sequencing data were processed employing the TrimGalore toolkit(0.6.7) to cleanse low-quality reads and eliminate Illumina sequencing adapters.
Reads were mapped to mouse reference genome files using the Hisat2(2.2.0) alignment tool.
FeatureCounts(2.0.1 ) computed the number of reads attributed to genomic features (exons), generating the original count matrix for subsequent analyses.
Assembly: mm10
Supplementary files format and content: CountMatrix text file includes gene id,chromosome and counts value for each sample

source_name: Bone marrow

extract_protocol:
Total RNA from pre-sorted cells was extracted following TRIzol™ Reagent (ThermoFisher).
Library preparation was performed using the TruseqTM RNA sample prep Kit (Illumina) according to the manufacturer’s protocol.

value: Bone marrow

value: Lsk cells


title: 58_SN__DMSO_1


title: ATAC_H526


title: LSK_PPM1BCKO_1


title: LSK_PPM1Bfl/fl_2


title: ATAC_H524


title: PigCC

city: Hamburg

first: Sydney

last: Gies

state: Hamburg

address: Martinistraße 52

department: III. Medizinische Klinik und Poliklinik

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger  CellRanger software suite (version 6.1.1, 10x Genomics, Pleasanton, CA) including intronic counts
SoupX (v1.6.1) was applied with default parameters to remove ambient RNA contamination
Doublets were removed using Scrublet (default parameters, v0.2.2)
Assembly: Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: matrix files

organism: Sus scrofa

source_name: kidney

extract_protocol:
Lysis solution was prepared with Nuclei PURE lysis buffer, 1 mM dithiothreitol and 0.1 % Triton X-100 according to manufacturer protocol and an RNAse inhibitor mix was added. The single nuclei suspension was filtered through a 30 µm strainer  and centrifuged at 500g for 5 min at 4 °C. The pellet was resuspended and incubated for 2 min in 1ml red blood cell lysis buffer hybri-max™ , filtered through a 5 µm strainer and washed with 4 ml of ice -cold 0,01% BSA in DPBS with 0.04 U/µl SUPERaseIN RNAse Inhibitor and 0.04 U/µl RNAsin Plus RNAse Inhibitor at 500 g for 5 min at 4 °C. The pellet was resuspended in 1% BSA in DPBS with 0.04 U/µl SUPERaseIN RNAse Inhibitor and 0.04 U/µl RNAsin Plus RNAse Inhibitor.
Nuclei number was counted and samples were diluted prior to loading to the Chromium 10X device to capture ~ 6,000 nuclei of one snap frozen, one RNAlater and the CellCover stored sample and to capture ~ 10,000 nuclei of two snap frozen and one RNAlater stored sample The nuclei were separated into Gel Bead Emulsion droplets and libraries were prepared with the Chromium NEXT GEM Single Cell 3’ Reagent kits v3.1 according to manufacturer's protocol. The libraries were sequenced on an Illumina Novaseq6000 platform as symmetric paired end runs (150 bases) with 200 million raw sequencing reads per sample (pig)

value: kidney

value: CellCover


title: N6000

value: RNAlater


title: ATAC_SHP77


title: 56_SNR_DMSO_2


title: ATAC_H196


title: L2A

value: SnapFrozen


title: 55_SNR_DMSO_1