title: S3_1_6

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

institute: INRAE

data_processing:
Search of untagged reads in csfasta/qual files using Bowtie (version 1.2.2, options: -3 22 -n 0 -l 5 -C --integer-quals --col-keepends) on fasta reference containing both specific tags ("GCATAGGGGTAAA" and "GCGAGACTGAGAA") corresponding to another study.
Extraction from sam files of untagged (unmapped) reads names using Grep on the tag names.
Extract previous reads from the initial csfasta/qual using a custom Perl script.
Read mapping using Bowtie (version 1.2.2, options: -S -f -C -n 3 -l 18 -k 2 --best --chunkmbs 200 -e 3000 --nomaqround).
Structural reference annotation of Enterococcus faecalis V583 chromosome (AE016830.1) was enriched with sRNA annotation from Innocenti et al., 2015.
Read counts were obtained using HTSeq-count (version 0.9.1).
Differential expression analysis R library "DESeq2" and associated "median ratio method" normalization procedure.
DESeq2 p-values were converted into q-values using R library "fdrtool".
RPKM values processed using DESeq-2 with a prior-count of 33.
Genome_build: Enterococcus faecalis V583 chromosome (AE016830.1)
Supplementary_files_format_and_content: DCA_gene_expression.txt: Tab-delimited text file containing for each gene/sample raw data counts, log2rpkm with differential expression analysis results.

organism: Enterococcus faecalis

source_name: Cell culture

growth_protocol: E. faecalis strains were grown in standardized conditions as described in Fouquier D'hérouel, 2011. For all experiments, the strain frozen at -80°C was streaked on 1.5 % agar plate of Brain Heart Infusion (BHI), grown for 20 h at 37°C and incubated 2 h at room temperature. One single colony was used to inoculate 5 ml of liquid BHI and grown for 18 h at 37°C without agitation. The culture was then diluted 1/500-fold in a pre-warmed BHI liquid medium and grown to an OD600 ranging from 0.27 to 0.33 (OD600 ~ 0.3), as monitored manually on spectrophotometer at 600 nm weight length (Pharmacia Biotech, Novaspec II). At such a density, the bacterial population ranged from ~2 to 4 x 10^8 cfu/mL, as verified by viable cell counts on BHI plates.

extract_protocol:
Fouquier D'hérouel et al., 2011.
Innocenti et al., 2015 and Lacoux et al., 2020.

treatment_protocol: Fouquier D'hérouel et al., 2011; Lacoux et al., 2020.

tag: treatment

value: DCA

tag: time point (minutes)

tag: rpph

value: no

tag: biological replicate

tag: technical replicate


title: S3_1_3

status: Public on May 20 2022

type: SRA

country: France

library_source: transcriptomic

molecule: total RNA


title: BNT-5_II-D4

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

country: USA

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMCs

growth_protocol: Blood samples were collected from individuals both prior and after vaccinations.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: age

tag: gender

value: Female

tag: vaccine

value: 2nd dose, BNT162b2

tag: cell type

value: PBMCs


title: BNT-5_II-D7


title: RNA_wing_wildtype_rep3

city: New York

first: Ryan

last: Loker

state: NY

address: 3227 Broadway

institute: Columbia University

data_processing:
Reads taken from multiplexed Next-seq run were trimmed using the standard Basespace flowthrough (Bcl2Fastq) on pre-defined indices
RNA-seq raw count files generated by Rsubread FeatureCounts. GTF file; dm6.ensGene.gtf.gz, ignoreDup = FALSE, countMultiMappingReads = FALSE, GTF.featureType = "exon"
Bigwig files generated from BAM files using Deeptools (bamCoverage) and normalized to genome coverage - RPGC (ATAC-seq).
For ATAC Bowtie2 was used to map reads to Drosophila melanogaster genome (dm6) using default parameters with paired-end options (ATAC-seq).
For RNA-seq HISAT2 was used to map reads to the Drosophila melanogaster genome (dm6) with default parameters
Assembly: dm6
Supplementary files format and content: bigwig files generated from BAM files using Deeptools (bamCoverage) and normalized to genome coverage - RPGC (ATAC-seq) or RPKM (ChIP-seq)

organism: Drosophila melanogaster

source_name: L3 imaginal disc

growth_protocol: Drosophila larvae were raised on standard cornmeal food and kept at 25 degrees untill the wandering 3rd instar stage before harvesting of imaginal discs.

extract_protocol:
Imaginal discs of 3rd instar larvae were dissected in PBS on ice.
RNA-seq library constructed using NEBnext Ultra II directional RNA library prep kit for Illumina

tag: tissue

value: Wing imaginal disc

tag: genotype

value: yw


title: RNA_wing_wildtype_rep2


title: S3_1_15


title: E13.2_CD4CD8_rep1

city: Boston

first: Clara

middle: F

last: Alves-Pereira

state: MA

address: 450 Brookline Avenue, SM958b

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description:
E13.2_T_200HSCs_rep1
polyclonal sample derived from 200 HSCs

data_processing:
Reference preparation: imputed parental genomes were prepared (“pseudogenomes” (Crowley et al., 2015; Zou et al., 2014)) for each organism, using a custom script (all custom software tools mentioned are available on https://github.com/gimelbrantlab/ASEReadCounter_star); VCF file with one allele considered as a reference (maternal C57BL/6 or first phased allele) and the other as an alternative allele. Only heterozygous sites were used.
Alignment: RNA-seq reads were trimmed from nextera adapters with cutadapt v.1.14 using the wrapper trim_galore; reads were then aligned with STAR aligner v.2.5.4a (Dobin et al., 2013) on each of two pseudogenomes, with default threshold on quality of alignment. Only uniquely alligned reads were used.
Allele assigment. Given vcf file with heterozygous positions, coverage over each SNP was calculated using custom script based on samtools mpileup and parsed to obtain the table with allelic counts. Data processing steps from read alignment to allelic counts were based on a modification of the GATK pipeline (Castel et al., 2015), and described in: https://github.com/gimelbrantlab/ASEReadCounter_star
Allele counting per gene. All exons belonging to the same gene were merged into a single gene model based on GTF file (RefSeq GTF file, GRCm38.68, was downloaded from Ensemble ftp://ftp.ensembl.org/pub/release-68/gtf/ (Zerbino et al., 2018)), excluding overlapping regions that belong to multiple genes. This step was based on the GATK pipeline (Castel et al., 2015).
AI point estimate per gene obtained as a proportion of maternal gene counts to total allelic gene counts
RNA abundance: counts were obtained with featureCountstool from the subread v.2.0.0 package, using the same bam files processed during ASE analysis as described (previous to counts, alignments were performed on inputed parental genomes, then merged into one file, which was used as such to count reads with featureCounts); abundance was measured using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: allelic counts, allelic imbalance with confidence intervals, cpm (counts per million) values for RNA abundance

organism: Mus musculus

source_name: mouse thymus T-cells

extract_protocol:
RNA was isolated from sorted cells using Trizol reagent or Absolutely RNA Nanoprep Kit (Agilent #400753)  according to the manufacturer`s protocol.
10 nanogram RNA samples were used to prepare sequencing libraries with SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc., California, USA) according to the manufacturer`s protocol.

tag: strain

value: C57BL/6 x CAST/EiJ F1

tag: cells

tag: rna extraction

value: Trizol

tag: number of cells sorted for rna isolation

tag: library replicate

tag: Sex

value: female

tag: donor animal

value: donor animal #13

tag: recipient animal

value: recipient animal #13.2


title: E13.1_CD4CD8_rep4

description:
E13.1_T_200HSCs_rep4
polyclonal sample derived from 200 HSCs

value: recipient animal #13.1


title: mgR-mRNA-10week [mgR613]

type: RNA

city: Montreal

first: Rongmo

last: Zhang

state: QC

address: 3640 Rue university

department: Anatomy and Cell Biology

country: Canada

institute: McGill University

description: RNA from Fbn1mgR/mgR aorta

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data processing and statistical analyses were performed by the Transcriptome Analysis Console software (Affymetrix). Normalized intensities between the aortae from wild-type and Fbn1mgR/mgR mice were compared using one-way ANOVA, followed by multi-testing correction using the Benjamini-Hochberg false discovery rate (FDR)-controlling procedure for all expressed genes. All p-values indicated refer to FDR-adjusted p-values.

label: biotin

source_name: snap frozen fresh aorta

label_protocol: standard Affymetrix protocol

growth_protocol: Heterozygous mutant Fbn1mgR/+ mice on a C57BL/6J genetic background were bred to generate wild-type and Fbn1mgR/mgR mice for experiments.

extract_protocol: Extraction of total RNA was performed using the miRNeasy Mini Kit (Qiagen, cat# 217004), according to the manufacturer’s instructions.

treatment_protocol: All mouse experiments strictly followed the guidelines of the Canadian Council on Animal Care and were approved by the McGill University Animal Care Committee (protocol 2017–7979).

value: male

value: aorta


title: WT-mRNA-10week [WT676]

description: RNA from wild-type aorta

value: wild-type


title: mgR-mRNA-10week [mgR614]

description: RNA from Fbn1mgR/mgR aorta


title: S3_1_10

tag: treatment

tag: time point (minutes)

tag: rpph


title: mgR-mRNA-10week [mgR611]

description: RNA from Fbn1mgR/mgR aorta

tag: age


title: ATAC_wing_nub1_rep2

library_source: genomic

molecule: genomic DNA

extract_protocol:
Imaginal discs of 3rd instar larvae were dissected in PBS on ice.
ATAC libraries made according to Buenrostro et al. 2015


title: S3_1_25

tag: biological replicate

tag: technical replicate


title: mgR-mRNA-10week [mgR612]

description: RNA from Fbn1mgR/mgR aorta


title: BNT-4_II-D4

tag: gender

tag: vaccine

tag: cell type


title: WT-mRNA-10week [WT742]

description: RNA from wild-type aorta

tag: genotype

tag: tissue


title: BNT-5_II-D0


title: BNT-4_II-D7


title: WT-mRNA-10week [WT744]

description: RNA from wild-type aorta


title: WT-mRNA-10week [WT675]

description: RNA from wild-type aorta


title: E13.1_CD4CD8_rep3

description:
E13.1_T_200HSCs_rep3
polyclonal sample derived from 200 HSCs

tag: strain

tag: cells

tag: rna extraction


title: E13.1_CD4CD8_rep2

description:
E13.1_T_200HSCs_rep2
polyclonal sample derived from 200 HSCs, not processed (QC no pass)

tag: number of cells sorted for rna isolation

tag: library replicate

tag: Sex


title: E13.2_CD4CD8_rep2

description:
E13.2_T_200HSCs_rep2
polyclonal sample derived from 200 HSCs

tag: donor animal

tag: recipient animal


title: ATAC_wing_wildtype_rep2


title: S3_1_0

tag: treatment

tag: time point (minutes)

tag: rpph


title: S3_1_0ssRPPH

value: yes

tag: biological replicate

tag: technical replicate


title: E13.1_CD4CD8_rep1

description:
E13.1_T_200HSCs_rep1
polyclonal sample derived from 200 HSCs, not processed (QC no pass)


title: S2_1_6

value: DCA


title: ATAC_wing_nub1_rep1


title: RNA_wing_wildtype_rep1


title: HULEC-5a shScramble(N2)

city: Shanghai

first: Yi

last: Chen

address: No.160 Pujian Road

department: Department of Anesthesiology

country: China

institute: Renji Hospital, Jiaotong University School of Medicine

data_processing:
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
Assembly: hg19
Supplementary files format and content: Number of raw count and normalized count

growth_protocol: The HLVEC line (HULEC-5a) was purchased from the ATCC and cultured in MCDB131 medium supplemented with 10% fetal bovine serum, 10 ng/ml EGF, 1 µg/ml hydrocortisone, 10 mM L-Glutamine, 100 U/ml of penicillin, and 100 µg/ml streptomycin

extract_protocol:
RNA extraction protocol
library construction protocol

treatment_protocol: Cells were stimulated with LPS (1 μg/mL) for 12h.

value: Human lung microvascular endothelial cells

tag: passages

tag: cell line

value: shScramble


title: BNT-4_II-D0

tag: age

tag: gender

value: Female

tag: vaccine

value: 2nd dose, BNT162b2

tag: cell type


title: HULEC-5a shScramble(N1)


title: ATAC_wing_wildtype_rep1

tag: tissue

value: Wing imaginal disc

tag: genotype


title: control_CD4CD8_rep4

description:
non-clonal_T_rep4
polyclonal sample isolated directly from donor mouse without transplantation

tag: strain

tag: cells

tag: rna extraction

tag: number of cells sorted for rna isolation

tag: library replicate

value: donor animal #17


title: HULEC-5a shMETTL3-2

tag: treatment


title: S2_1_3

tag: time point (minutes)

tag: rpph

value: no


title: HULEC-5a shMETTL3-1


title: control_CD4CD8_rep1

description:
non-clonal_T_rep1
polyclonal sample isolated directly from donor mouse without transplantation, not processed (QC no pass)

value: C57BL/6 x CAST/EiJ F1

value: Trizol

tag: Sex

tag: donor animal


title: control_CD4CD8_rep3

description:
non-clonal_T_rep3
polyclonal sample isolated directly from donor mouse without transplantation

value: female


title: PRP22-OE_S2

city: Richmond

first: Alaattin

last: Kaya

state: VA

address: 1000 West Carry St, Room 126

department: Biology

institute: Virginia Commonwealth University

data_processing:
QC: NGSQCTools
Mapping : STAR
count : RSEM
Normalization : FPKM
Differential expression analysis : edgeR+limma+voom.
Supplementary files format and content: The raw and normalized counts(fpkm) tables (.csv) contains expression of 5,824 genes.

organism: Saccharomyces cerevisiae

source_name: Liquid yeast cell culture

growth_protocol: Two independent culture for each strain grown in -URA liquid medium with 2% glucose. OD600= 0.4 cells were collected with centrifugation and pellets were flash frozen with liquid nitrogen. Two biological replicates for each strain.

extract_protocol:
Total RNA from each sample was isolated using Quick-RNA 96 Kit from Zymo Research (Cat. number: R1053)
After the QC procedures, Illumina TruSeq RNA library preparation kits were used according to the user manual.

treatment_protocol: No treatment

value: Liquid yeast cell culture


title: control_CD4CD8_rep2

description:
non-clonal_T_rep2
polyclonal sample isolated directly from donor mouse without transplantation, not processed (QC no pass)


title: S2_1_15

tag: biological replicate

tag: technical replicate


title: PRP22-OE_S1


title: S2_1_25


title: HULEC-5a shScramble.N-2.Input

data_processing:
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of all libraries were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps.
Assembly: hg19
Supplementary files format and content: Result of m6A peaks calling

extract_protocol:
Total RNA was extractedcells using TRIzol Reagent (15596026; Invitrogen, Carlsbad, CA, USA).
The MeRIP-seq library was constructed according to Kit Protocol,fragmented RNAs were incubated with anti-m6A polyclonal antibodies (Synaptic Systems, 202003). The mixture was incubated with Pierce protein A/G agarose (ThermoFisher, 20421) at 4 °C for an additional 2 h. Beads with captured RNA fragments were then immediately washed 3 times with ice-cold IP buffer. Then, the bound mRNAs were eluted from the beads with N6-methyladenosine (Berry & Associates, 1867-73-8) in IP buffer, and were extracted with Trizol reagent. Both of the input samples and the m6A-IP samples were prepared for RNA-seq library construction using the NEBNext® Ultra II Directional RNA Library Prep Kit (NEB, E7760).

tag: passages

tag: cell line

tag: merip antibody


title: S2_1_10


title: HULEC-5a shScramble.N-1.Input

tag: cell type

value: anti-m6A polyclonal antibodies (Synaptic Systems, 202003)


title: UTP6-OE_S1

tag: tissue

tag: genotype


title: TIF35-OE_S2

tag: strain


title: ScACS-6-2B_S11 [AAK_SMG]

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

institute: University of Alberta

data_processing:
Partek Flow: Trim bases Trim based on quality score (Phred score minimum of 20, Trim from 3-prime end, min read length of 25)
Partek Flow: Alignment (STAR 2.7.3a) Default settings from Partek Flow
Partek Flow: Quantify to annotation model (Partek E/M) Transcript model: hg38-RefSeq Transcripts 94 - 2020-05-01
Partek Flow: Filter features Exclude features where maximum ≤ 50.0. Processed data file included with filtered raw gene counts
Partek Flow: Normalize counts Normalization methods: Add 1.0, TMM, Log 2.0. Processed data file included with normalized gene counts for differential expression analysis
Genome_build: Partek Flow: ANOVA for DEGs Factors: Treatment + Sex + Treatment*Sex. Shrinkage of error term variance: Limma-trend
Supplementary_files_format_and_content: Normalize counts

source_name: human engineered meniscus

growth_protocol: Meniscus cells (meniscus fibrochondrocytes) were isolated from partial meniscectomy tissue samples. They were expanded in normoxia (standard 5% CO2, 95% air incubator) to passage 2 (~3 population doublings) with supplementation of TGF-beta1 and FGF-2. They were then seeded onto cylindrical type I collagen scaffolds (6/10 mm diameter, 3.5 mm height) at a density of 5x10^6 million/cm^3 and cultured for 2 weeks in normoxia in a standard chondrogenic medium containing TGF-beta3 to form engineered meniscus tissues before treatment.

extract_protocol:
RNA was extracted using LunaNano PureSPIN columns with a DNAse digestion step. RNA concentrations were measured using a NanoDrop One. Equal masses of RNA from 4 replicate tissues from each donor in each condition were then pooled together to reduce inter-replicate variability (12 pools in total). These samples were then shipped to the UBC Biomedical Research Center for RNA sequencing.
Illumina NextSeq 500: PolyA selection, 20million paired reads

treatment_protocol: After preculture period, tissues were randomly allocated into treatments in static or SMG for 3 weeks. On the last day, tissues were put into TRIzol reagent and frozen to preserve RNA level changes.

value: M

tag: mechanical condition

value: SMG


title: HULEC-5a shScramble.N-1.IP


title: S2_1_0ssRPPH


title: HULEC-5a shScramble.N-2.IP


title: ScACS-5-2B_S8 [AAK_SMG]


title: HULEC-5a METTL3-2.Input


title: TIF35-OE_S1


title: S2_1_0


title: S1_2_6


title: LSM5-OE_S2


title: UTP6-OE_S2


title: ScACS-5-1B_S7 [AAK_SMG]

value: Static


title: S1_2_3


title: LSM5-OE_S1


title: ScACS-4-1B_S4 [AAK_SMG]

value: F


title: ScACS-4-2B_S5 [AAK_SMG]


title: S1_2_25

value: DCA


title: HULEC-5a METTL3-2.IP

value: Human lung microvascular endothelial cells


title: HULEC-5a METTL3-1.IP


title: Wt_S1

value: WT


title: WT_S2


title: S1_2_15


title: S1_2_10


title: HULEC-5a METTL3-1.Input


title: ptsI 90 min

city: Newark

first: Yuzhi

last: Hong

state: NJ

address: 225 Warren St

department: PHRI, New Jersey Medical School

institute: Rutgers, the University of New Jersey

description: Sample of an independent experiment

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3 (Langmead, B. and S. L. Salzberg, 2012).  HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected.
Genome_build: NZ_CP009273.1

organism: Escherichia coli K-12

source_name: Bacterial cultures

growth_protocol: Overnight cultures of the wildtype and ΔptsI strains were diluted 100-fold into fresh LB medium, and were grown to mid-log phase (OD600 = 0.3) at 37 °C with shaking.

extract_protocol:
Total RNAs were prepared using an RNA extraction kit following the manufacturer protocol (Tiangen, China).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Briefly, rRNAs were removed by the Ribo-zero kit to enrich mRNAs, which were then digested into short fragments. The fragmented mRNAs were used as template to generate one-strand DNA using a six-base random primer and the corresponding double-stranded cDNA. After purification, the cDNA was firstly end-repaired, A-tailed and ligated to a sequencing linker. The size of fragments was selected using AMPure XP beads. PCR amplification was performed, and the amplified products were then purified using AMPure XP beads to obtain the final library.
The cDNA library was sequenced (RNA-seq) on an Illumina novaseq platform, and paired-end reads were generated.

treatment_protocol: These log-phase cultures were treated with 0.1 μg/ml (5 MIC) ciprofloxacin. After treatment for 90 min, cells were collected by centrifugation,  frozen using liquid nitrogen, and then stored at -80 °C for subsequent total RNA extraction. The cultures immediately before ciprofloxacin treatment were used as a control (time 0).

value: Strain 686

value: 0.1 μg/ml ciprofloxacin for 90 min


title: ScACS-3-2B_S2 [AAK_SMG]


title: SF3B1-K700E&DDX46-3

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

data_processing:
The raw data was processed by Trim Galore (Version 0.6.5) to get the clean data.
The clean reads were aligned to the hg38/GRCh38 by Tophat2 (Version 2.1.1)
The output bam files were sorted using SAMtools (Version 1.10).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from transfected HEK-293T cells using RNAiso Plus (Takara).
RNA-seq libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®

treatment_protocol: Transient transfection of SF3B1 and DDX42 was performed by using lipofectamine 2000 (Invitrogen).

value: SF3B1 K700E mutation & DDX46 wildtype


title: SF3B1-K700E&DDX46-5


title: S1_1_3


title: S1_1_6


title: SF3B1-K700E&DDX46-4


title: ptsI 0 min

description: Sample of an independent experiment

value: No treatment


title: WT 90 min

description: Sample of an independent experiment

value: Strain 685


title: ScACS-2-1B_S21 [AAK_SMG]


title: ScACS-1-2B_S19 [AAK_SMG]


title: SF3B1-K700E&DDX46-2


title: ScACS-2-2B_S22 [AAK_SMG]


title: S1_1_25

value: no


title: ScACS-6-1B_S10 [AAK_SMG]


title: WT 0 min

description: Sample of an independent experiment


title: SF3B1-K700E&DDX46-1


title: SF3B1-K700E&DDX42-4

value: SF3B1 K700E mutation & DDX42 wildtype


title: ScACS-3-1B_S24 [AAK_SMG]


title: S1_1_0


title: SF3B1-K700E&DDX42-5


title: S1_1_15


title: ScAAK101_S6 [AAK_SMG]


title: SF3B1-K700E&DDX42-3


title: ScACS-1-1B_S18 [AAK_SMG]


title: WT-miRNA-10week [WT520]

description: RNA from wild-type aorta

extract_protocol: Extraction of total RNA including both miRNAs and mRNAs was performed using the miRNeasy Mini Kit (Qiagen, cat# 217004), according to the manufacturer’s instructions.

value: male

value: wild-type

tag: age

value: aorta

tag: molecule type

value: total RNA including microRNA


title: ScAAK81_S5 [AAK_SMG]

value: M

value: SMG


title: WT-miRNA-10week [WT504]

description: RNA from wild-type aorta


title: SF3B1-K700E&DDX42-1


title: WT-miRNA-10week [WT510]

description: RNA from wild-type aorta


title: SF3B1-K700E&DDX42-2


title: 22h_t2_1

city: Beijing

first: Meng-Ru

last: Wu

address: Beichen West Road

department: State Key Laboratory of Microbial Resources

institute: Institute of Microbiology, Chinese Academy of Sciences

description: 22 h after the amendment of ammonium sulfate, biological replicate 2

data_processing:
Alta-Cyclic software used for basecalling
Raw data was trimmed using Sickle and SeqPrep software
Clean reads were mapped into the complete genome of Alcaligenes sp. HO-1 using Bowtie 2
Gene transcription levels were quantified by RSEM and reported as TPM values
Normalization and differential expression analysis was performed by DESeq2
Genome_build: Reference sequences of Alcaligenes sp. HO-1 is under the accession number CP049362
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with gene TPM values for every gene and every sample and fold changes for samples of every time points compared with samples of 0 h

organism: Alcaligenes ammonioxydans

source_name: bacteria cells

growth_protocol: Alcaligenes sp. HO-1 was cultured in HNM medium containing 83 mM succinate and 14 mM ammonium sulfate, aerobically at 30°C.

extract_protocol:
Cells from samples were immediately collected by centrifuging and rapidly frozen with liquid nitrogen. Total RNA was extracted using the E.Z.N.A.TM Bacterial RNA Kit (Omega, USA). Genomic DNA was removed with RNase-free DNase I (TaKaRa, Japan). Purified RNA was quantified by Nanodrop 2000. RNA quality was detected by agarose gel electrophoresis and an Agilent 2100 Bioanalyzer system (Agilent Technologies, USA).
Paired-end RNA-Seq sequencing libraries were constructed by TruSeqTM RNA sample preparation Kit (Illumina, USA)

treatment_protocol: After incubation for about 58 h when ammonium was depleted, the culture was amended again with  ammonium sulfate (final concentration, 14 mM) and cultivation was continued.

tag: isolation source

value: wastewater treatment system

tag: treatment

value: HO-1 + 14 mM ammonium sulfate 22h


title: esophagus organoids, X7_5__12_NS

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the human genome hg38AnalysisSet assembly with STAR (version 2.7.0c) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax =10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”). The featureCounts function from the Bioconductor rsubread package was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (gene annotation: Ensembl release 96).
All subsequent RNA-seq data analysis was performed using the R software (version 4.0.3) and Bioconductor 3.12 packages.
Genome_build: hg38
Supplementary_files_format_and_content: gene_counts.tsv.gz: gzipped text file with tab-separated RNA-seq read counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Ensembl ID, 2.-11. read counts per gene and sample.

source_name: esophagus organoids

growth_protocol: Esophageal organoids were grown for 11days in Cultrex BME Type 2 PathClear (Cat No. 3532-010-02) and KSFM culture medium (Cat No. 17005042) supplemented with 50ug/ml BPE, 1ng/ml EGF and 0.51mM Ca2+

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit (Cat No.74104) and was quantified and quality-controlled on a Bioanalyzer instrument.
RNA-seq library preparation (Illumina Truseq stranded kit) was performed at the Genomics Facility Basel of the ETH Zurich, Basel, starting from 50 ng of total RNA. Sequencing was performed on the Illumina NextSeq 500 platform to produce paired-end 38nt reads.

treatment_protocol: Stimulation of esophageal organoids by addition of IL-19 (Cat No. 1035-IL-025) ,IL-20 (Cat No. 1102-IL-025) and IL-24 (Cat No. 1965-IL-025) to the culture medium for 24h

tag: condition

value: Non-stimulated

tag: donorid

value: Male


title: WT-miRNA-10week [WT464]

description: RNA from wild-type aorta

tag: Sex


title: 22h_t1_1

description: 22 h after the amendment of ammonium sulfate, biological replicate 1


title: ScAAK92_S7 [AAK_SMG]

value: F

value: Static


title: mgR-miRNA-10week [mgR514]

description: RNA from Fbn1mgR/mgR aorta


title: 10h_t3_1

description: 10 h after the amendment of ammonium sulfate, biological replicate 3

value: HO-1 + 14 mM ammonium sulfate 10h


title: SF3B1-K700E-5

value: SF3B1 K700E mutation


title: 10h_t2_1

description: 10 h after the amendment of ammonium sulfate, biological replicate 2


title: SF3B1-K700E-4


title: mgR-miRNA-10week [mgR513]

description: RNA from Fbn1mgR/mgR aorta


title: esophagus organoids, X7_4__12_IL20

value: Stimulated


title: esophagus organoids, X7_3__18_NS


title: SF3B1-K700E-3


title: 10h_t1_1

description: 10 h after the amendment of ammonium sulfate, biological replicate 1


title: 22h_t3_1

description: 22 h after the amendment of ammonium sulfate, biological replicate 3


title: 3_5h_t3_1

description: 3.5 h after the amendment of ammonium sulfate, biological replicate 3

value: HO-1 + 14 mM ammonium sulfate 3.5h


title: SF3B1-K700E-2


title: esophagus organoids, X7_2__18_IL20


title: esophagus organoids, X6_8__17_IL20


title: SF3B1-WT-5

value: SF3B1 wild type


title: 3_5h_t1_1

description: 3.5 h after the amendment of ammonium sulfate, biological replicate 1


title: esophagus organoids, X6_7__15_NS


title: ScAAK72_S4 [AAK_SMG]


title: 0h_t3_1

description: 0 h after the amendment of ammonium sulfate, biological replicate 3

value: HO-1 + 14 mM ammonium sulfate 0h


title: esophagus organoids, X6_6__15_IL20


title: mgR-miRNA-10week [mgR512]

description: RNA from Fbn1mgR/mgR aorta

value: male


title: WT-miRNA-4week [WT459]

description: RNA from wild-type aorta

value: wild-type

value: aorta


title: SF3B1-K700E-1


title: 3_5h_t2_1

description: 3.5 h after the amendment of ammonium sulfate, biological replicate 2


title: WT-miRNA-4week [WT409]

description: RNA from wild-type aorta

value: total RNA including microRNA


title: esophagus organoids, X6_5__14_NS

value: Female


title: SF3B1-WT-3


title: mgR-miRNA-4week [mgR456]

description: RNA from Fbn1mgR/mgR aorta


title: WT-miRNA-4week [WT407]

description: RNA from wild-type aorta


title: esophagus organoids, X7_1__17_NS


title: SF3B1-WT-4


title: mgR-miRNA-4week [mgR439]

description: RNA from Fbn1mgR/mgR aorta


title: S1_1_10

value: DCA

tag: time point (minutes)

tag: rpph

value: no

tag: biological replicate


title: 0h_t2_1

description: 0 h after the amendment of ammonium sulfate, biological replicate 2

value: wastewater treatment system


title: SF3B1-WT-2


title: esophagus organoids, X6_4__14_IL20


title: SF3B1-WT-1


title: mgR-miRNA-10week [mgR529]

description: RNA from Fbn1mgR/mgR aorta


title: WT-miRNA-4week [WT408]

description: RNA from wild-type aorta


title: DU145 B9 clone-TLR3 overexpression 3

status: Public on May 19 2022

city: Brno

first: Jirina

last: Prochazkova

address: Kralovopolska 135

department: Cytokinetics

country: Czech Republic

institute: Institute of Biophysics CAS

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
6-nt long UMIs were extracted and subseqeuntly used for deduplication of aligned reads by UMI-tools v. 1.1.1.
6-nt long barcode sequence related to Lexogen QuantSeq Library Prep Kit were trimmed using seqtk 1.3-r106, the adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed RNA-Seq reads were mapped against the human genome (hg38) and Ensembl GRCh38 v.91 annotation using STAR v. 2.7.3a with default parameters default parameters except -outFilterMismatchNoverLmax 0.1 and -twopassMode Basic
Gene counts were produced using featureCounts tool v1.6.3 with settings -s 2 -T 10 -F GTF -Q 0 -d 1 -D 25000
The differential gene expression analysis was performed using Bioconductor package DESeq2 v1.20.0. Samples from experiment were compared as joined conditions in a form EV-A6+EV-D7 over OE-B9+OE-C12. Genes were considered as differentially expressed based on a cut-off of adjusted p-value<0.05 and log2(fold-change) ≥1 or ≤-1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includeraw counts values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample gathered by featureCounts tool
Supplementary_files_format_and_content: Resulting table based on the analysis of differential gene expression performed by DESeq2 tool containing foldchanges and related statistics supplied with matrix with normalized counts for every gene and every sample

growth_protocol: DU145 AG cells in suspension were electroporated with hTLR3-pcDNA3 construct (#32712, Addgene) using Neon Electroporation System (TFS) and immediately seeded to antibiotic-free media. After at least 24 hours, the medium was replaced by fresh complete medium, containing G418 (TSF) for selection. Stable clones for empty vector controls A6 and D7 and for TLR3 overexpression B9 and C12 were established.

extract_protocol:
RNA was isolated from DU145 A6, D7, B9 and C12 clones (1x10^6 cells) by the use of High Pure RNA isolation kit (cat.n. 11828665001, Roche), which consists of cell lysis, RNA binding to filter, incubation with DNase, washing steps and elution. RNA concentration was evaluated immediately upon isolation by Eppendorf BioSpectrometer. RNA was diluted for each sample at the final concentration 100 ng/ul: 10 ul were transferred to 1.5 ml tube for RNAseq analysis;
500 nanograms of total RNA per sample was used as an input for library preparation using QuantSeq FWD 3’mRNA Library Prep Kit (Lexogen). Briefly, RNA was transcribed into cDNA using oligodT primer (FS1) at half volume compared to the manufacturer's instructions to minimize the off-target products. Following the first strand synthesis, RNA removal and second strand synthesis were performed using the UMI Second Strand Synthesis Mix (USS) containing Unique Molecular Identifiers (UMIs) that allow detection and removal of PCR duplicates. Finally, sequencing libraries were created by PCR with i5 Unique Dual Indexing Add-on Kit for Illumina (Lexogen). The quality and quantity of libraries was determined using Fragment Analyzer by DNF-474 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies) and QuantiFluor dsDNA System (Promega). Final library pool was sequenced on Illumina NextSeq 500 with 75 bp single-ends

tag: genotype/variation

value: TLR3 overexpression


title: DU145 B9 clone-TLR3 overexpression 2


title: mgR-miRNA-4week [mgR411]

description: RNA from Fbn1mgR/mgR aorta


title: DU145 B9 clone-TLR3 overexpression 1


title: DU145 D7 clone-empty vector control 3

value: empty vector


title: HCT116 transfected by Control siRNA vs HCT116 transfected by NOX5 siRNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: HCT116 colorectal cancer cell line

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HCT116 cells were cultured in Dulbecco’s modified Eagle’s medium. This culture media was supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted from the cells using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol at 48 h after transfection.  Total RNA of cells transfected with control siRNA and NOX5 siRNA were labeled with Cy5 and Cy3.

treatment_protocol: HCT116 cells were transfected with control siRNA (n = 1) and NOX5 siRNA (n = 1). HCT116 cells were transfected with 10 nmol/L NOX5 siRNA (Stealth siRNA #HSS128403, Invitrogen, Waltham, MA, USA) using Lipofectamine RNAi MAX Transfection Reagent (Invitrogen) according to the manufacturer’s protocol. The medium containing siRNA was replaced with fresh medium 24 h after transfection. We used the Stealth RNAiTM siRNA Negative Control Med GC Duplex #2 (12935112, Invitrogen) as a negative control siRNA.

tag: cell line

value: control siRNA

value: NOX5 siRNA


title: APOE3MG, CM, A

city: Cambridge

first: Hiruy

last: Meharena

address: 43 Vassar St

department: The Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

data_processing:
FASTQ reads were aligned using STAR (v.2.6.1a)
Transcripts were quantified using HTSeq
data was normalized utilizing RUV-seq
Assembly: GRCh37 reference genome (GENCODE 19)
Supplementary files format and content: counts file

source_name: iPSC derived from a 75 year old female (AGO9173) with APOE3/3 genotype

growth_protocol: All human iPSCs were maintained in feeder-free conditions in mTeSR1 medium (STEMCELL Technologies) on Matrigel-coated plates (Corning; hESC-Qualified Matrix) iPSCs were passaged at 60–80% confluence using ReLeSR (STEMCELL Technologies) and reseeded 1:6 onto Matrigel-coated plates.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1-3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Ultra II RNAseq Kit following manufacturer's protocols.

treatment_protocol: After 4 weeks in culture, APOE3 or APOE4 iMGLs pre-conditioned in unspent neuronal media for 24hrs were further incubated with spheroid conditioned neuronal media for 2 hours.

tag: cell type

value: iPS-derived Microglia

value: Neuronal Conditioned Media

tag: time

value: 2 Hours


title: APOE4MG, B

source_name: APOE isogenic iPSCs derived from a 75 year old female (AGO9173) with APOE3/3 genotype edited to harbor APOE4/4

tag: genotype

value: Baseline

value: 0 Hours


title: APOE4MG, A

value: APOE isogenic iPSCs derived from a 75 year old female (AGO9173) with APOE3/3 genotype edited to harbor APOE4/4


title: APOE3MG, CM, B

value: iPSC derived from a 75 year old female (AGO9173) with APOE3/3 genotype


title: APOE4MG, CM, C


title: APOE4MG, CM, B


title: APOE4MG, CM, A


title: APOE3MG, CM, C


title: APOE4MG, C


title: DU145 C12 clone-TLR3 overexpression 1


title: 0h_t1_1

description: 0 h after the amendment of ammonium sulfate, biological replicate 1

tag: strain

value: HO-1 + 14 mM ammonium sulfate 0h


title: APOE3MG, C


title: DU145 C12 clone-TLR3 overexpression 2


title: DU145 D7 clone-empty vector control 1


title: APOE3MG, B


title: DU145 D7 clone-empty vector control 2


title: DU145 A6 clone-empty vector control 3


title: DU145 C12 clone-TLR3 overexpression 3


title: DU145 A6 clone-empty vector control 2


title: mgR-miRNA-4week [mgR436]

description: RNA from Fbn1mgR/mgR aorta

value: male

tag: tissue

value: aorta

value: total RNA including microRNA


title: APOE3MG, A


title: DU145 A6 clone-empty vector control 1


title: silicosis patient 3

city: Changsha

first: Zhouyangfan

last: Peng

address: No.138 Tongzipo Road

institute: Third Xiangya Hospital, Central South University

data_processing:
Raw sequencing data was processed via the Cell Ranger pipeline (10xGenomics, version 4.01 ) to generate a count matrix from the bcl files.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell. Raw counts are also provided on each sample record for that particular sample.

source_name: bronchoalveolar lavage fluid cells

extract_protocol:
bronchoalveolar lavage fluid cells was obtained immediately after lung washing therapy
Cells were processed the manufacturer’s protocol and sequenced on Illumina NextSeq sequencer.

value: bronchoalveolar lavage fluid cells

tag: source

value: silicosis patient 3


title: silicosis patient 2

value: silicosis patient 2


title: silicosis patient 1

value: silicosis patient 1


title: exposure patient 1

value: exposure patient 1


title: exposure patient 2

value: exposure patient 2


title: 8h_Vneg_LCMV_M3 [38]

city: Epalinges

first: Nicolas

last: Fasel

address: Chemin des Boveresses 155

department: Department of Biochemistry

institute: University of Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013)
Reads were aligned against the Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012). Reads were also aligned to the Mus musculus.GRCm38.92 transcriptome using STAR (v. 2.5.3a, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Statistical analysis was performed for genes independently in R (R version 3.4.4). Genes with low counts were filtered out according to the rule of 1 count(s) per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization. Subsequently, the normalized counts were transformed to cpm values, and a log2 transformation was applied, by means of the function cpm with the parameter setting prior.counts = 1 (EdgeR v 3.20.9; Robinson et al. 2010).
Assembly: Mus musculus GRCm38.92 genome
Supplementary files format and content: tab-delimited text files (normalized logcpm)

source_name: Bone marrow derived macrophages

growth_protocol: Macrophages were isolated from bone marrow of C57BL/6 mice (wild-type). Hind leg bones were collected and the bone marrow was flushed out with complete DMEM medium, containing DMEM (Dulbecco’s modified Eagle’s medium, Gibco), supplemented with 10% heat-inactivated FBS (Gibco), 1% Penicillin-Streptomycin Solution (BioConcept) (i.e. 100 IU/ml and 100 µg/ml respectively), 1% HEPES (BioConcept) (i.e. 10mM). The cells were differentiated into macrophages for 6 days in complete DMEM medium containing 50 ng/ml recombinant mouse Macrophage Colony Stimulating Factor (rmM-CSF, ImmunoTools), at 37°C and 5% CO2, in Sterilin Petri Dish (Thermo Scientific). Then, the bone marrow-derived macrophages (BMDMs) were detached with 1X DPBS (Gibco) containing 5 mM EDTA, washed and resuspended with complete DMEM medium. The cells were plated in 12-well plates (TPP) with 1.95 million cells per well. They were finally put back in culture at 37°C and 5% CO2.

extract_protocol:
BMDMs were cleared out of supernatants and lysed with 350 µl RLT buffer (Qiagen) supplemented with 40 mM DTT (Dithiotreitol) for RNA extraction. Plates were then frozen at -80°C until the RNA purification. The RNA samples were purified with the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. Purified RNA was eluted with 30 µl RNase-free water (Qiagen).
Library preparation and sequencing were performed at the Lausanne Genomic Technologies Facility (GTF), University of Lausanne (UNIL), Switzerland

treatment_protocol: One day after their plating, murine BMDMs were infected with stationary-phase Leishmania promastigotes with a multiplicity of infection (MOI) of 3. Co-treatment with LCMV was done with MOI of 1. Cells were also alternatively treated with IFNa or IFNb. The cells were incubated at 35°C and 5% CO2.

value: Bone marrow derived macrophages

value: Wild type

tag: time point

value: LgyLRV1- and LCMV


title: 8h_Vneg_M5 [46]


title: 8h_Vneg_LCMV_M5 [48]


title: 8h_Vneg_IFNa_M5 [49]

value: LgyLRV1- and IFNa


title: 8h_Vneg_IFNb_M3 [40]

value: LgyLRV1- and IFNb


title: 8h_Vpos_M3 [37]


title: 8h_Vneg_IFNb_M2 [35]


title: 8h_Vneg_M3 [36]


title: 8h_Vneg_IFNa_M2 [34]


title: 8h_Vneg_M2 [31]


title: 8h_Vneg_LCMV_M2 [33]


title: 24h_Vneg_IFNa_M5 [24]


title: 8h_Vneg_IFNb_M5 [50]


title: 24h_Vneg_M5 [21]


title: 24h_Vneg_IFNa_M3 [14]


title: 8h_Vneg_IFNa_M3 [39]


title: 24h_Vneg_IFNb_M3 [15]


title: 24h_Vneg_LCMV_M3 [13]


title: 8h_Vpos_M2 [32]


title: 24h_Vneg_LCMV_M5 [23]


title: 24h_Vpos_M3 [12]


title: 24h_Vneg_M3 [11]


title: 24h_Vpos_M5 [22]


title: 24h_Vpos_M2 [07]


title: 24h_Vneg_M2 [06]


title: 24h_Vneg_LCMV_M2 [08]


title: 24h_Vneg_IFNb_M5 [25]


title: 24h_Vneg_IFNb_M2 [10]


title: 24h_Vneg_IFNa_M2 [09]


title: 8h_Vpos_M5 [47]


title: Jurkat NI-PSS, replicate 3

city: New York City

last: Vabret

address: 1470 Madison Avenue, Hess 5th floor

department: Hematology/Oncology

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

description:
5'P tagged RNA
counts_run4.txt
run4_NI-3-PSS

data_processing:
mapping reads to the genome with STAR
assigning reads to the annotated genes/repeat elements using featureCounts
mapping the unassigned reads to consensus sequence of repeat elements/assigning them
adding counts from step 2 and step 3
Assembly: hg38
Supplementary files format and content: text file, read counts
Library strategy: 5'-PPP RNA-seq

source_name: Immortalized cell line

growth_protocol: A549 (DMEM) ; Jurkat (RPMI) + 10% heat-inactivated fetal calf serum (FCS, ThermoFisher Scientific) and Penicillin-Streptomycin (PS, Life Technologies).

extract_protocol:
Trizol follow by column purification with (zymogen)
After RNA purification, ribosomal RNA molecules were depleted using the riboPOOL Kit for human (siTOOLs Biotech). To control for enrichment bias during library preparation, an aliquot of ERCC RNA Spike-In Mix 1 (ThermoFisher) was treated with 5' RNA polyphosphatase (Epicentre) and mixed with untreated spike-in mix in approximately equal amounts, to form a 5’-PPP/5’-P 1:1 ratio. 1 μl of a 1:10 dilution was added to each total RNA preparation. RNA samples were first poly(A)-tailed using poly(A) polymerase. Then, the 5' Illumina TruSeq sequencing adapters, which carry sequence tags ATTACTCG and TCCGGAGA were ligated to the 5' mono-phosphate groups (5'-P) of sampled transcripts. Remaining fragments with unligated 5’-P ends are removed with 5’-phosphate-dependent XRN-1 (NEB). The samples were then treated with 5' RNA polyphosphatase (Epicentre) in order to convert 5' triphosphate structures into 5' monophosphate ends. To the newly formed 5'-P groups the 5' Illumina TruSeq sequencing adapters were ligated, which carry sequence tag CGCTCATT and GAGATTCC. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. After sequencing, reads corresponding to RNA molecules initially harboring 5’-PPP and 5’-P moieties were inferred from sequence tags. Library preparations and sequencing were performed at Vertis Biotechnology.

treatment_protocol: For infection conditions - Jurkat were FACS-sorted 48h after infection with HIV-GFP WT or HIV-GFP ΔVPR bsed on GFP positivity

value: Immortalized cell line

value: Jurkat

value: T cell

value: CTL

value: NI


title: A549 CTL-TSS, replicate 3

description:
5'PPP tagged RNA
counts_run4.txt
run4_CTL-3-TSS

value: Lung cancer


title: Jurkat HIVwt-TSS, replicate 2

description:
5'PPP tagged RNA
counts_run4.txt
run4_HIV-dVPR-2-TSS

value: HIV WT


title: Jurkat HIVwt-PSS, replicate 2

description:
5'P tagged RNA
counts_run4.txt
run4_HIV-dVPR-2-PSS


title: Jurkat NI-TSS, replicate 3

description:
5'PPP tagged RNA
counts_run4.txt
run4_NI-3-TSS


title: Jurkat HIVdVPR-PSS, replicate 1

description:
5'P tagged RNA
counts_run4.txt
run4_HIV-WT-1-PSS

value: HIV dVPR


title: Jurkat HIVdVPR-TSS, replicate 3

description:
5'PPP tagged RNA
counts_run4.txt
run4_HIV-WT-3-TSS


title: A549 CTL-PSS, replicate 3

description:
5'P tagged RNA
counts_run4.txt
run4_CTL-3-PSS


title: Jurkat HIVwt-TSS, replicate 3

description:
5'PPP tagged RNA
counts_run4.txt
run4_HIV-dVPR-3-TSS


title: Jurkat HIVdVPR-TSS, replicate 2

description:
5'PPP tagged RNA
counts_run4.txt
run4_HIV-WT-2-TSS


title: A549 CTL-TSS, replicate 2

description:
5'PPP tagged RNA
counts_run4.txt
run4_CTL-2-TSS


title: A549 D11-PSS, replicate 3

description:
5'P tagged RNA
counts_run4.txt
run4_Dusp11-3-PSS

value: DUSP11 KO


title: Jurkat HIVwt-PSS, replicate 3

description:
5'P tagged RNA
counts_run4.txt
run4_HIV-dVPR-3-PSS


title: A549 D11-TSS, replicate 3

description:
5'PPP tagged RNA
counts_run4.txt
run4_Dusp11-3-TSS


title: Jurkat HIVwt-PSS, replicate 1

description:
5'P tagged RNA
counts_run4.txt
run4_HIV-dVPR-1-PSS


title: Jurkat HIVdVPR-PSS, replicate 2

description:
5'P tagged RNA
counts_run4.txt
run4_HIV-WT-2-PSS


title: A549 D11-TSS, replicate 2

description:
5'PPP tagged RNA
counts_run4.txt
run4_Dusp11-2-TSS


title: Jurkat HIVdVPR-TSS, replicate 1

description:
5'PPP tagged RNA
counts_run4.txt
run4_HIV-WT-1-TSS


title: Jurkat HIVwt-TSS, replicate 1

description:
5'PPP tagged RNA
counts_run4.txt
run4_HIV-dVPR-1-TSS


title: A549 D11-TSS, replicate 1

description:
5'PPP tagged RNA
counts_run4.txt
run4_Dusp11-1-TSS


title: Jurkat HIVdVPR-PSS, replicate 3

description:
5'P tagged RNA
counts_run4.txt
run4_HIV-WT-3-PSS


title: Jurkat NI-TSS, replicate 2

description:
5'PPP tagged RNA
counts_run4.txt
run4_NI-2-TSS


title: Jurkat NI-PSS, replicate 1

description:
5'P tagged RNA
counts_run4.txt
run4_NI-1-PSS


title: A549 CTL-TSS, replicate 1

description:
5'PPP tagged RNA
counts_run4.txt
run4_CTL-1-TSS


title: A549 CTL-PSS, replicate 2

description:
5'P tagged RNA
counts_run4.txt
run4_CTL-2-PSS


title: A549 CTL-PSS, replicate 1

description:
5'P tagged RNA
counts_run4.txt
run4_CTL-1-PSS


title: Jurkat NI-PSS, replicate 2

description:
5'P tagged RNA
counts_run4.txt
run4_NI-2-PSS


title: Jurkat NI-TSS, replicate 1

description:
5'PPP tagged RNA
counts_run4.txt
run4_NI-1-TSS


title: A549 D11-PSS, replicate 2

description:
5'P tagged RNA
counts_run4.txt
run4_Dusp11-2-PSS


title: A549 D11-PSS, replicate 1

description:
5'P tagged RNA
counts_run4.txt
run4_Dusp11-1-PSS


title: Jurkat D11-TSS, replicate 2

description:
5'PPP tagged RNA
counts_run3.txt
run3_D11-2-TSS


title: Jurkat CTL-PSS, replicate 3

description:
5'P tagged RNA
counts_run3.txt
run3_CTL-3-PSS


title: Jurkat CTL-PSS, replicate 1

description:
5'P tagged RNA
counts_run3.txt
run3_CTL-1-PSS


title: Jurkat D11-TSS, replicate 1

description:
5'PPP tagged RNA
counts_run3.txt
run3_D11-1-TSS


title: Jurkat D11-TSS, replicate 3

description:
5'PPP tagged RNA
counts_run3.txt
run3_D11-3-TSS


title: Jurkat CTL-TSS, replicate 2

description:
5'PPP tagged RNA
counts_run3.txt
run3_CTL-2-TSS


title: Jurkat CTL-PSS, replicate 2

description:
5'P tagged RNA
counts_run3.txt
run3_CTL-2-PSS


title: Jurkat CTL-TSS, replicate 1

description:
5'PPP tagged RNA
counts_run3.txt
run3_CTL-1-TSS


title: Jurkat D11-PSS, replicate 1

description:
5'P tagged RNA
counts_run3.txt
run3_D11-1-PSS


title: Jurkat CTL-TSS, replicate 3

description:
5'PPP tagged RNA
counts_run3.txt
run3_CTL-3-TSS


title: Experiment2, 19 hours no Dox, scRNAseq

city: St. Louis

first: Barak

last: Cohen

state: Missouri

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
NIH3T3-CG cells were released from 6-well plates using Trypsin and we followed manufacturer's instructions to generate single-cell suspension (single cell 3’ v3.1 protocol, 10x Genomics).
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Embryonic fibroblasts

tag: sag treatment

value: 19 hours no Dox


title: WT-1 rep1

city: Wuhan

first: ju

middle: qiong

last: wang

address: Ba yi Road

department: College of Life Sciences

institute: Wuhan University

data_processing:
Illumina Bcl2fastq (v2.17.1.14) used for base calling.
Removed the technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data. then mapped to hg19 whole genome and followed by Hisat2(v2.0.1) with default parameters.
Fragments Per Kilo bases per Million reads (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Dulbecco's Modified Eagle Medium (DMEM) supplemented with 100 units ml-1 penicillin, 100 μg ml-1 streptomycin sulfate, and 10% fetal bovine serum (FBS).

extract_protocol:
Removed the medium, washed with prechilled phosphate buffered saline (PBS) and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On day 0, Huh7 cells were set up at a density of 6×105, then on day 1, cells were  transfected with siRNA targeting sramble (WT) and  targeting ASGR1 (AS2) for 72 hours, then cells were harvested for RNA extraction.

tag: treatment

value: Transfected with siControl for 72 hours


title: AS2-3 rep3

value: Transfected with siASGR1 for 72 hours


title: Experiment2, 0 hours Dox, scRNAseq

description: 10x Genomics

value: 0 hours Dox


title: AS2-1 rep1


title: hair follicles of baseline groups (after isolated HFs, collect samples immediately)

city: Guangzhou

first: Damao

last: Dai

state: Guangdong

address: 1838 North Guangzhou AV

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

data_processing:
Hisat2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
TPM(Transcripts Per Kilobase of Exon Model Per Million mapped reads) is the most commonly used method for estimating gene expression levels, considering the effect of sequencing depth and gene length on reads count. Bam files obtained by sequencing were mapped to GTF annotation files of reference species to obtain gene expression levels, and regional statistics of gene expression levels of genomes were carried out according to statistical methods to reflect the overall expression levels of samples. TPM density profile was used to investigate the gene expression pattern of samples.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and raw gene counts for every gene and every sample

source_name: hair follicles from follicular unit excision(FUE) patients

extract_protocol:
After collecting hair follicle tissues in different treatments, total RNA was isolated from the tissues using the Trizol (invitrogen) as soon as possible. RNA purity was assessed and each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RIN above 7.0. rRNAs were removed from Total RNA using EpicentreRibo-Zero rRNA Removal Kit (illumina, USA). Subsequently, the purified RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low- cycle. The purified l library products were diluted to 10 pM for cluster generation in situ on the pair-end flow cell followed by sequencing (2×150 bp) HiSeq3000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: baseline group(after isolated hair follicles---HFs,collect samples immediately), 0G group(sham irradiation, collect organ-cultured HFs for 3 days),and 5G group(5G dose irradiation, collect organ-cultured HFs for 3 days) in ex vivo organ-cultured HFs

value: hair follicles


title: AS2-2 rep2


title: Experiment2, 30 hours no Dox, scRNAseq

description: 10x Genomics

value: 30 hours no Dox


title: WT-2 rep2


title: hair follicles of 0G groups (sham irradiation, collect organ-cultured HFs for 3 days)


title: hair follicles of 5G groups (5G dose irradiation, collect organ-cultured HFs for 3 days)


title: Experiment2, 0 hours no Dox, scRNAseq

description: 10x Genomics

value: 0 hours no Dox


title: Experiment1, 17 hours, scRNAseq

description: 10x Genomics

value: 17 hours


title: Experiment1, 0 hours, scRNAseq

description: 10x Genomics

value: 0 hours


title: WT-3 rep3


title: Experiment1, 30 hours, scRNAseq

description: 10x Genomics

value: 30 hours


title: Jurkat D11-PSS, replicate 3

description:
5'P tagged RNA
counts_run3.txt
run3_D11-3-PSS

value: Immortalized cell line

value: Jurkat

value: T cell


title: Jurkat D11-PSS, replicate 2

description:
5'P tagged RNA
counts_run3.txt
run3_D11-2-PSS


title: Experiment2, 19 hours Dox, scRNAseq

description: 10x Genomics

value: 19 hours Dox


title: Experiment2, 30 hours Dox, scRNAseq

description: 10x Genomics

value: 30 hours Dox


title: chip wt es H3K4me2 2

city: jerusalem

first: Muhammad

last: Awawdy

address: The Hebrew University, The Edmond J. Safra Campus - Givat Ram

country: Israel

institute: Hebrew university of jerusalem

data_processing:
Illumina output was analyzed using an in-house Perl script that produced a reads matrix that was aligned using RSEM with Bowtie. The resulting matrix was analyzed in R
For bulk data analysis the transcript per million (TPM) values were used to compare between libraries
scRNA-seq data was analyzed using the Seurat v2.4 pipeline
cells with more than 10,000 unique molecular identifiers were retained for further analysis. A global-scaling normalization was performed on the filtered dataset using “LogNormalize” with a scale factor of 10,000. Identification of highly variable genes was performed with the following parameters: x.low.cutoff = 0.2, x.high.cutoff = 5, y.cutoff = 0.5, and y.high.cutoff = 10. Cell-to-cell variation in gene expression driven by batch, cell alignment rate, and the number of detected molecules were regressed out and a linear transformation was applied. A principal component analysis was performed on the scaled data with 12 principal components. Clustering was done with resolution of 0.6, and tSNE or UMAP was using for visualization.
CHIP-seq Sequencing data were aligned using Bismark and Bowtie (https://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf) using paired-ended approach. TDF genomic browser files were produced using IGV count. We applied HOMER to find peaks using ChIP-seq criteria and used BEDTools to intersect bins with genomic intervals such as promoters, genes, and predicted enhancers.
Genome_build: mm9, GRC38

source_name: R1 mESC cell line

growth_protocol: ESCs were seeded on 0.1% gelatin-coated plates (Sigma-Aldrich, G1393) and grown in ES medium (Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D5671), 10% fetal bovine serum (FBS, Biological Industries, 04-007-1A), 1 mM sodium pyruvate (Biological Industries, 03-042-1B), 0.1 mM nonessential amino acids (Biological Industries, 01-340-1B), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, M3148), 1000 U/ml LIF (Mercury, ESG1107)). The cells were maintained at an incubator at 37 °C with 5% CO2 humidified air. For pluripotent conditions, 3 µM CHIR99021 (PeproTech, SM-2520691-B) and 0.2 µM PD0325901 (PeproTech, SM-3911091-B) were added to the ES medium.

extract_protocol:
ChIP Antibodies (H3K4me1 abcam ab8895, H3K27Ac abcam ab4729, H3K36me abcam ab9050, 2 µg antibody per 2x107 cells) were incubated with 25 µL protein A Dynabeads (Thermo Scientific) previously washed twice with blocking buffer (0.5% BSA, 0.5% Tween-20 in PBS) for 2 h at 4 °C in blocking buffer. The conjugated beads were washed twice with blocking buffer before adding the lysate. Lysates were prepared as follows: Cells were trypsinized, washed with PBS, and resuspended with 500 μL PBS per 2x107 cells. The same volume of lysis buffer with 100 U/mL MNase was added, and the cells were incubated for 10 min on ice and then for 15 min at 37 °C. Reactions were stopped by adding 20 mM EGTA followed by centrifugation (20,000 g, 2 min). Supernatants were added to the conjugated beads, and samples were incubated overnight with rotation. Supernatants were removed, and the beads were washed twice with RIPA buffer (10 mM Tris-HCl [pH 8], 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM EDTA), twice with RIPA buffer high salt (10 mM Tris-HCl [pH 8], 360 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM EDTA), twice with LiCl wash buffer (10 mM Tris-HCl [pH 8], 250 mM LiCl, 0.5% sodium deoxycholate, 1 mM EDTA, 0.5% IGEPAL CA-630 [Sigma]), and twice with 10 mM Tris-HCl [pH 8]. The beads were resuspended in 45 μL 10 mM Tris-HCl [pH 8] and 20 µg RNase A. The beads were incubated for 30 min at 37 °C, and 60 µg proteinase K was added. The beads were further incubated for 2 h at 37 °C. Proteinase K was inactivated by heating to 65 °C for 15 min, and 50 μL elution buffer (10 mM Tris-HCl [pH 8], 300 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM EDTA) was added, and the samples were incubated in 65 °C for 15 min. DNA was purified from supernatants using Ampure XP beads (Beckman Coulter). DNA was eluted with 22 μL 10 mM Tris-HCl [pH 8].
 DNA samples were converted to blunt-ended, phosphorylated DNA using the End-It DNA End-Repair Kit (Lucigen). DNA was purified using ratio of 1:1.8 sample to AMPure XP beads. Adenosine was added to the 3’ end of the DNA fragments using Klenow (3’-5’ exo-) (New England Biolabs). DNA was purified using ratio of 1:1.8 sample to AMPure XP beads. Ilumina adapters were added by ligation using DNA ligase (New England Biolabs). DNA was purified using ratio of 1:1.2 sample to AMPure XP beads. DNA samples were amplified using KAPA HiFi HotStart (Roche) with 25 μM PE1 and PE2 full-length primers containing Illumina library indices for multiplexing (Table 1). Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads and eluted in 22 μL 10 mM Tris-HCl [pH 8]. Aliquots of 15 μL of resulting libraries were run in a 2% agarose gel, and the desired 200-600 bp DNA library fragments were selected and isolated using the PureLink DNA gel extraction kit (Invitrogen). Library quality was confirmed using the Agilent 2200 TapeStation nucleic acids system and the Agilent High Sensitivity D1000 DS DNA kit. The resulting libraries had an average size of 350-550 bp. Size-selected libraries were diluted to 4 nM concentration and combined for paired-end, single index sequencing on the Illumina NextSeq 550 instrument using an illumina 550 High Output v2 (75 cycles) kit. Cycle distribution was 45 cycles for Read 1, 35 cycles for Read 2, and 8 cycles for the library index read.

treatment_protocol: RA (Sigma-Aldrich, R2625) dissolved in dimethyl sulfoxide (ENCO, 0219605580) at 1 μM in LIF-free media with 10% FBS, on 0.1% gelatin-coated plates.

value: R1 mESC cell line

tag: developmental stage

value: Embrionic stem cells in early differentiation

tag: state

value: ES state

tag: differentiated days


title: chip wt es H3K4me1 2


title: chip ko es H3K4me1 2


title: chip ko es H3K4me1 1


title: chip ko es H3K4me2 2


title: chip ko es H3K4me2 1


title: T. pseudonana culture, synchrony hour 9, replicate 1

city: La Jolla

first: Raffaela

last: Abbriano

state: CA

address: 9500 Gilman Dr

department: Scripps Institution of Oceanography

institute: University of California San Diego

data_processing:
Demultiplexing: Custom perl script
Alignment: Tophat2 : tophat2   --b2-sensitive --solexa1.3-quals  --read-realign-edit-dist 0  --no-coverage-search  --library-type fr-firststrand  --min-intron-length 40 --max-intron-length 2000
Raw counts: HTSeq 0.6.1p1: htseq-count --stranded
Normalized counts : DESeq2_1.6.3: padj was calculated using the likelihood ratio test with deviance between biological replicates as the reduced model (dds <- DESeq(dds, test = "LRT", reduced = ~replicate))
Assembly: Thaps3_chromosomes_assembly_chromosomes_repeatmasked.fasta,  Thaps3_bd_unmapped_assembly_scaffolds_repeatmasked.fasta
Supplementary files format and content: csv file containing deseq2 normalized count data for each sample

organism: Thalassiosira pseudonana CCMP1335

source_name: Cell culture

growth_protocol: Axenic cultures of Thalassiosira pseudonana (CCMP1335) were synchronized as previously described (Hildebrand et al. 2007; Shrestha et al. 2012). Exponentially-grown cells were harvested by centrifugation, rinsed once and placed in silicon-free medium. After 24 hours of Si starvation, rhodamine 123 (R123) and 200 μM sodium silicate were added to the culture. Samples were collected prior to and then every hour after silicate addition. Aliquots of R123-labeled cells were visualized under a fluorescent microscope to monitor synchronous cell cycle progression. Experiments were conducted in biological duplicate.

extract_protocol:
Total RNA was extracted from cell pellets using TriReagent as described in Hildebrand & Dahlin, 2000.
cDNA libraries were prepared from 4 µg of total RNA for each sample using the Illumina TruSeq Stranded mRNA Sample Prep kit (Illumina, San Diego, CA) according to manufacturer's protocols (Rev. D), which includes a poly-A purification step. The resulting libraries were evaluated for size on an Agilent DNA High Sensitivity chip following the manufacturer's instructions, and quantified by quantitative PCR according to Illumina's protocols. Each library was diluted to 2 nM with 10 mM Tris-Cl, 0.1% Tween 20. Bar-coded libraries were then pooled (10 or 11 per pool), and sequenced on an Illumina HiSeq 2000 with 100 nt paired end reads.

treatment_protocol: Cells were harvested by filtration, pelleted and stored at -80° C until extraction.

value: Cell culture

value: CCMP 1335

value: unicellular

value: Wild type

value: 9 hour silicon readdition


title: PseudoTime RA 2d SC g2 1

extract_protocol:
mRNA extraction was performed using Invitrogen Dynabeads mRNA DIRECT Purification Kit (61011) according to the protocol included with the kit.
The library for differential gene expression analysis was prepared using 100-1000 ng of mRNA. First, RNA was fragmented using an RNA fragmentation kit (Ambion, AM8740) following the manufacturer’s protocols. Fragmented RNA was purified with 1.4x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 10 μl TE buffer (10 mM Tris–HCl, pH 8.0, 0.1 mM EDTA). The resulting fragmented RNA was reverse transcribed using an oligo dT primer: First, 10 μl of RNA were mixed with 2 μl of 50 μM oligo dT primer (Bio-Rad, 1725038) and 1 μl of 25 mM dNTP mix (NEB, N0447S), and samples were incubated for 3 minutes at 65 °C and transferred to ice. The following components were added to the reaction, for a total volume of 20 μl: 4 μl of 5x First-Strand SuperScript III buffer (Invitrogen, 18080044), 2 μl of 0.1 M DTT (Invitrogen, 18080044), 1 μl murine RNase inhibitor (NEB, M0314L), and 1 μl of 200 U/μL SuperScript III RT enzyme (Invitrogen, 18080044). The reaction product (in the form of a cDNA:RNA hybrid) was purified with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 16 μl TE buffer as described above. For second-strand synthesis, 16 μl of the digestion reaction product were combined with 2 μl second-strand synthesis (SSS) buffer and 1 μl of SSS enzyme mix of mRNA Second Strand Synthesis Module kit (NEBNext, E6111S) and incubated at 16 °C for 2.5 hours, followed by 20 minutes at 65 °C. The resulting product was purified with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted with 20.4 μl TE buffer. cDNA edges were repaired using End-It DNA End-Repair Kit (Danyel Biotech, ER81050) by combining the 20.4 μl sample with 3 μl 10X End-repair Buffer, 3 μl 2.5 mM dNTPs, 3 μl 10 mM ATP, and 0.6 μl END-IT enzyme mix at room temperature for 45 minutes, followed by purification with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and elution with 32 μl TE buffer. Klenow-mediated addition of an adenine to the 3’ end of the DNA fragments was performed using the Klenow fragment (3'→5' exo-) kit (NEB, M0212L) by combining the 32 μl sample with 5 μl 10X Klenow Buffer NEB 2, 10 μl 1 mM dATP, and 0.6 μl 5 U/μl Klenow (3’-5’ exo-) at 37 °C for 30 minutes, followed by purification with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and elution with 8 μl TE buffer. Illumina library adaptors were added to the resulting cDNA fragment using DNA ligase (NEB, M2200S) by incubation with 5 μl 2x Ligase Buffer, 0.5 μl adapter Oligo mix (1:10 in H2O), and 0.5 μl 1 U/ml DNA Ligase at room temperature for 15 minutes. The ligated product was purified with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 11.5 μl TE buffer. The resulting libraries were PCR amplified using standard PE1/PE2 full-length primer mix containing Illumina library indices for multiplexing (sequences are given in Supplementary Table X). Each PCR reaction contained 11.5 μl post-RT cDNA library, 12.5 μl 2x KAPA HiFi HotStart PCR mix (Zotal, KK-KK2601), and 1 μl of 25 μM 2p Fixed (+barcode) and 2p Fixed primer mix (Supplementary Table 3). Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 32 μl TE buffer. A 15-μl aliquot of each resulting library was run in a 2% agarose gel, and size selection for the desired 200-800 bp DNA library fragments was performed using PureLink DNA gel extraction kit (Invitrogen, K210012). Library quality was confirmed by Agilent 2200 TapeStation Nucleic Acids System.  The in vitro transcription sequencing (IVT) library was prepared using 75-100 ng of mRNA, extracted as described above. First-strand synthesis was performed using SuperScript III Reverse Transcriptase (Invitrogen, 18080044) and the T7RTPolyT primer (Supplementary Table X) at 50 °C for 2 hours followed by 15 minutes at 70 °C and 1 minute at 4 °C. To remove unused primers and primer dimers, the reaction product was combined with 20 μl digestion mix containing 5 μl ExoI (NEB, M0293S), 5 μl HinFI (NEB, R0155S), 5 μl ExoI buffer (NEB, B0293S), 5 μl CutSmart buffer (NEB, B7204S), and 30 μl nuclease-free water and incubated for 1 hour at 37 °C and 10 minutes at 80 °C. The reaction product (in the form of a cDNA:RNA hybrid) was purified with 1.5x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 13.5 μl TE buffer. For second-strand synthesis, the 13.5 μl digestion reaction product was combined with 1.5 μl SSS buffer and 1 μl of SSS enzyme mix from the mRNA Second Strand Synthesis Module kit (NEBNext, E6111S) and incubated at 16 °C for 2.5 hours, followed by 20 minutes at 65 °C. For linear amplification by in vitro transcription, 16 μl of SSS reaction products were combined with 24 μl HiScribe T7 High Yield RNA Synthesis Kit (NEB, E2040S) reagent mix containing 4 μl T7 Buffer, 4 μl ATP, 4 μl CTP, 4 μl GTP, 4 μl UTP, and 4 μl T7 enzyme mix. The reaction was incubated at 37 °C for 13 hours, and the resulting RNA was purified with 1.3x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted with 20 μl TE buffer. Aliquots of 9 μl of each sample were frozen for backup at -80 °C, 2 μl of each sample was directly analyzed, and the remaining 9 μl were used in subsequent library preparation steps. RNA was fragmented using the RNA fragmentation kit (Ambion, AM8740) by combining 9 μl sample with 1 μl of RNA fragmentation reagent and incubating at 70 °C for 2 minutes. After transfer to ice, 40 μl fragmentation stop mix containing 5 μl fragmentation stop solution and 35 μl TE buffer was added. Fragmented RNA was purified with 1.4x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 10 μl TE buffer. The resulting amplified and fragmented RNA was reverse transcribed using a random hexamer primer (IDT) as follows: First, 10 μl of RNA were mixed with 2 μl of 100 μM PvG748-SBS12-RT random hexamer primer (Supplementary Table X) and 1 μl of 10 mM dNTP mix (NEB, N0447S), incubated for 3 minutes at 65 °C and transferred to ice. The following components were then added to the reaction for a total volume of 20 μl: 4 μl of 5x First-Strand SuperScript III buffer (Invitrogen, 18080044), 1 μl 0.1 M DTT (Invitrogen, 18080044), 1 μl murine RNase inhibitor (NEB, M0314L), and 1 μl of 200 U/µL SuperScript III RT enzyme (Invitrogen, 18080044). Following reverse transcription, the reaction volume was raised to 50 μl by adding 30 μl nuclease-free water, and the resulting cDNA was purified with 1.2x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 11.5 μl TE buffer. Library amplification was performed using 12.5 µl 2x KAPA HiFi HotStart ReadyMix PCR kit (Zotal, KK-KK2601) and 1 μl of 25 μM 2p fixed primers (Supplementary Table X). Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads (Beckman Coulter, A63881) and eluted in 30 μl nuclease-free water. Aliquots of 15 μl of each library were run in 2% agarose gels, and size selection for the desired 200-600 bp DNA library fragments was performed using PureLink DNA gel extraction kit (Invitrogen, K210012). Library quality was confirmed using the Agilent 2200 TapeStation Nucleic Acids System (Agilent).  For scRNA-seq, encapsulation of cells with Reverse Transcription mix (IGEPAL CA-630- Sigma-Aldrich I8896-50ML , SuperScript III Reverse Transcriptase Invitrogen 18080044, Deoxynucleotide (dNTP) Solution Set Ornat N0446S, D,L-DITHIOTHREITOL Bio-Lab 000448235200, TRIS-HCL  1 M STOCK SOLUTIONS  PH 7.5  B 1L Sigma-Aldrich T2319-1L, RNase Inhibitor, Murine NEB M0314L) and gels with unique molecular identifiers was performed using the FLUIGENT Smart Microfluidics Pump Syste

value: RA differentiation


title: T. pseudonana culture, synchrony hour 9, replicate 2


title: T. pseudonana culture, synchrony hour 7, replicate 2

value: 7 hour silicon readdition


title: T. pseudonana culture, synchrony hour 8, replicate 2

value: 8 hour silicon readdition


title: PseudoTime RA 2d SC g1 2


title: PseudoTime RA 0d SC g1 2


title: PseudoTime RA 0d SC g2 2


title: T. pseudonana culture, synchrony hour 7, replicate 1


title: T. pseudonana culture, synchrony hour 6, replicate 1

value: 6 hour silicon readdition


title: chip wt es H3K4me2 1


title: PseudoTime RA 2d SC g1 1


title: T. pseudonana culture, synchrony hour 8, replicate 1


title: T. pseudonana culture, synchrony hour 6, replicate 2


title: PseudoTime RA 0d SC g1 1


title: RA G2_1 4D SC Chemical Med


title: T. pseudonana culture, synchrony hour 5, replicate 2

value: 5 hour silicon readdition


title: chip wt es H3K4me1 1


title: T. pseudonana culture, synchrony hour 5, replicate 1


title: RA G2_2 4D SC Chemical Med


title: RA G1_3 4D SC Chemical Med


title: RA G1_1 4D SC Chemical Med


title: T. pseudonana culture, synchrony hour 4, replicate 2

value: 4 hour silicon readdition


title: PseudoTime RA 2d SC g2 2


title: Ebs diff bulk ko2

source_name: ZHBTC4 mESC cell line

value: ZHBTC4 mESC cell line

value: EB differentiation


title: PseudoTime RA 0d SC g2 1


title: T. pseudonana culture, synchrony hour 4, replicate 1


title: Ebs diff bulk ko3


title: T. pseudonana culture, synchrony hour 3, replicate 2

value: 3 hour silicon readdition


title: T. pseudonana culture, synchrony hour 3, replicate 1


title: T. pseudonana culture, synchrony hour 2, replicate 2

value: 2 hour silicon readdition


title: Ebs diff bulk wt  3

value: Embrionic stem cells in early differentiation


title: Ebs diff bulk wt 2


title: T. pseudonana culture, synchrony hour 2, replicate 1


title: T. pseudonana culture, synchrony hour 1, replicate 2

value: 1 hour silicon readdition


title: T. pseudonana culture, synchrony hour 0, replicate 2

value: Cell culture

value: 0 hour silicon readdition


title: T. pseudonana culture, synchrony hour 1, replicate 1

value: CCMP 1335

value: unicellular


title: XEN diff bulk ko 2

value: xen differentiation


title: T. pseudonana culture, synchrony hour 0, replicate 1

value: Wild type


title: XEN diff bulk wt 3


title: XEN diff bulk ko 3


title: Ebs diff bulk wt 1


title: XEN diff bulk ko 1


title: OST-3

city: CHANGSHA

first: Hequn

last: Chen

state: HUNAN

address: 87 Xiangya Road, Kaifu DIstrict

department: Department of Urology

institute: Xiangya Hospital, Central South University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM/counts for each Sample

source_name: renal medulla

growth_protocol: Human renal interstitial fibroblasts (hRIFs) were isolated through mixed enzyme digestion combined with differential adhesion. Briefly, normal renal tissues without tumor invasion were obtained as previously described. Renal medulla tissue (10 g) was appropriately selected, finely minced with scissors, digested with 20 ml of enzyme mix (0.2 mg/ml Collagenase Ⅰ (Sigma-Aldrich, USA), 0.2 mg/ml Collagenase Ⅳ (Sigma-Aldrich, USA) and 0.25 mg/ml trypsin (Sigma-Aldrich, USA)) and incubated at 37 ℃ for 1 h with gentle agitation. The entire suspension was passed through a 100 μm cell strainer and centrifuged for 5 min at 800×g. Cells were incubated in Dulbecco's modified Eagle's medium (BI, Israel) containing 10% fetal bovine serum (BI, Israel), 100 U/mL penicillin (BI, Israel), and 100 μg/mL streptomycin (BI, Israel) for 1 hour at 37°C in the presence of 5% CO2, and the medium was then replaced with new medium to obtain adherent fibroblasts. For renal fibroblast identification, immunofluorescence staining was used to detect the expression of vimentin and E-cadherin. Passages 4 were selected for further experiments.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Takara, Japan)
the purified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit (Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

treatment_protocol: Osteogenic differentiation of hRIFs was induced at approximately 70% confluence using osteogenic medium with 10 mM β-glycerophosphate (Sigma-Aldrich, USA), 200 μM ascorbic acid (Sigma-Aldrich, USA) and 100 nM dexamethasone (Sigma-Aldrich, USA) for 7 days.  Normal control group of hRIFs was cultured in Dulbecco's modified Eagle's medium (BI, Israel) containing 10% fetal bovine serum (BI, Israel), 100 U/mL penicillin (BI, Israel), 100 μg/mL streptomycin (BI, Israel) for 7 days.  Osteogenic differentiation of hRIFs was induced at approximately 70% confluence using osteogenic medium (Dulbecco's modified Eagle's medium (BI, Israel) containing 10% fetal bovine serum (BI, Israel), 100 U/mL penicillin (BI, Israel), 100 μg/mL streptomycin (BI, Israel), 10 mM β-glycerophosphate (Sigma-Aldrich, USA), 200 μM ascorbic acid (Sigma-Aldrich, USA) and 100 nM dexamethasone (Sigma-Aldrich, USA) for 7 days.

value: renal medulla

value: Fibroblasts

value: primary human renal interstitial fibroblasts (hRIFs)

value: Osteogenic differentiation

value: Day 7


title: OST-2


title: Ebs diff bulk ko1

value: ZHBTC4 mESC cell line


title: XEN diff bulk  wt 2


title: OST-1


title: Ctrl-2

value: Normal Control


title: XEN diff bulk  wt 1


title: 4D diff G2 1 in bulk

value: R1 mESC cell line

value: RA differentiation


title: 4D diff G2 2 in bulk

value: Embrionic stem cells in early differentiation


title: Ctrl-3


title: Ctrl-1


title: ESC 4D RA SC G1


title: ESC 2D RA SC G2


title: 4D diff G1 2 in bulk


title: 4D diff G1 1 in bulk


title: ESC 2D RA SC G1


title: 2D diff G2 2 in bulk


title: T47D, siGRHL2, Veh, Rep 3 [TGV5]

city: Madison

first: Elaine

last: Alarid

state: WI

address: 1111 Highland Avenue

department: McArdle Laboratory for Cancer Research, Department of Oncology and Carbone Comprehensive Cancer Center

institute: University of Wisconsin - Madison

data_processing:
Quality control assessment of fastq files was performed using FASTQC. Adaptor trimming to remove Illumina adaptors was performed using Cutadapt through Trim Galore.
Reads were aligned to the hg38 genome with STAR. Reads were assigned to genes using featureCounts from the Subread package and the hg38 NCBI RefSeq GTF (available at http://ftp.ensembl.org/pub/current_gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz)
Assembly: hg38
Supplementary files format and content: Raw counts (*.txt) are from featureCounts

growth_protocol: MCF7 cells were maintained in 10% CO2 at 37ᵒC with high-glucose (4.5 g/L) Dulbecco’s modified Eagles Medium (DMEM; Thermo Fisher, #11965092) supplemented with 10% HyClone fetal bovine serum (FBS; Cytiva, #SH30910.03), 100U/mL penicillin 100ug/mL streptomycin (1% Pen/Strep; Gibco, #15140-122), and 1mM sodium pyruvate (Gibco, #11360-070). T47D cells were maintained in Roswell Park Memorial Institute 1640 (RPMI; Thermo Fisher, #11875-093) supplemented with 10% FBS and Pen/Strep.

extract_protocol:
RNA isolation was performed using the Qiagen RNeasy Mini Kit (#74106) including the optional treatment with DNase (Qiagen, #79254).
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep kit (Illumina, # 20020595) and sequenced for 150bp paired-end reads on the NovaSeq6000 by the Next Generation Sequencing department at the UW-Madison Biotechnology Center.

treatment_protocol: Cells were stripped of estrogens by culturing them for three days in phenol-red free DMEM or RPMI supplemented with 10% charcoal stripped FBS (ssDMEM/ssRPMI; Cytiva, #SH30910.03, stripped in-house), 100U/mL penicillin 100ug/mL streptomycin, 2mM L-glutamine (Thermo Fisher, #25030-081), and 1mM sodium pyruvate (DMEM only). Cells were treated with vehicle (0.1% EtOH) or 10nM 17β-estradiol (E2; Millipore Sigma #E2257) for 24 hours.

value: breast

tag: transfection

value: Veh


title: T47D, siGRHL2, Veh, Rep 1 [TGV1]


title: 2D diff G1 2 in bulk


title: T47D, siGRHL2, E2, Rep 3 [TGE5]


title: 2D diff G1 1 in bulk


title: T47D, siGRHL2, E2, Rep 1 [TGE1]


title: T47D, siGRHL2, E2, Rep 2 [TGE3]


title: ZHBTC4 KO rep 2


title: T47D, siCtrl, Veh, Rep 2 [TCV3]

value: siCtrl


title: ZHBTC4 WT rep1


title: ESC 4D RA SC G2


title: ZHBTC4 KO rep 1


title: ZHBTC4 WT rep2


title: T47D, siCtrl, Veh, Rep 1 [TCV1]


title: Bulk RNA ESC G2/M 2

value: ES state


title: T47D, siCtrl, Veh, Rep 3 [TCV5]


title: T47D, siCtrl, E2, Rep 2 [TCE3]


title: T47D, siCtrl, E2, Rep 1 [TCE1]


title: Bulk RNA ESC G2/M 1


title: T47D, siCtrl, E2, Rep 3 [TCE5]


title: Bulk RNA ESC lateG1 3


title: MCF7, siGRHL2, Veh, Rep 3 [MGV4]


title: Bulk RNA ESC G2/M 3


title: Bulk RNA ESC lateG1 2


title: 2D diff G2 1 in bulk


title: T47D, siGRHL2, Veh, Rep 2 [TGV3]


title: MCF7, siGRHL2, Veh, Rep 1 [MGV1]


title: R1C1 4D RA late G1 rep1


title: MCF7, siGRHL2, E2, Rep 3 [MGE4]


title: Bulk RNA ESC lateG1 1


title: R1C1 4D RA late G1 rep2


title: MCF7, siGRHL2, E2, Rep 1 [MGE1]


title: R1C1 4D RA G2 rep 1


title: MCF7, siCtrl, Veh, Rep 3 [MCV4]


title: R1C1 4D RA early G1 rep2


title: R1C1 4D RA early G1 rep1


title: MCF7, siGRHL2, Veh, Rep 2 [MGV3]


title: MCF7, siCtrl, Veh, Rep 2 [MCV3]


title: MCF7, siGRHL2, E2, Rep 2 [MGE3]


title: R1C1 4D RA G2 rep 2


title: MCF7, siCtrl, Veh, Rep 1 [MCV1]


title: RKO_shZNF280C_rep2

city: Shenzhen

first: Xing-sheng

last: Shu

address: No 3688, Nanhai Avenue

department: Medical School

institute: Shenzhen University

description: Expression_RKO_cell_line_matrix-FPKM-combat.txt

data_processing:
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on BGISEQ-500 platform. Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the pair-end 150bp sequence tags from MGISEQ-2000 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
The bowtie2 was used to generate the bam file of each sample from fastq with following parameters: -3 5 --local -x hg19 -U SE_clean.fq
htseq-count was used to get the count of each gene from bam using -r name -f bam bamfile gencode.v19.annotation.gtf
edgeR was used to identify the differentially expressed genes between groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM for each sample.

source_name: colon cancer cells

growth_protocol: RKO cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from  cells using Trizol reagent from Thermofisher according to manufacturer's instructions
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: RKO colon cancer cells stably expressing a ZNF280C-targeting shRNA controlled by a tetracycline-inducible promoter were treated with or without 1 ug/ml doxycycline for 72 hours, and the cells were harvested for analysis as described below. For transgenic mice experiments, Zfp280c knock-out or wild-type C57BL/6J mice were sacrificed at 12 weeks of age and colon tissues were havested for transriptomic analysis as described below.

tag: shRNA

value: RKO


title: RKO_shZNF280C_rep3


title: RKO_shZNF280C-DOX_ATAC-seq

data_processing:
Raw reads were aligned to hg19 using bwa. The sam files were converted to bam with samtools.
MACS2 was used to call peaks on the bam files with signals from input DNA as reference.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage from Deeptools.

source_name: RKO colon cancer cells

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature (RT) with gentle swirling, and crosslinking was stopped by adding glycine to a final concentration of 0.125 M and incubating at RT for 5 min. Cells were harvested and an aliquot of 1 × 107 cells were used per ChIP reaction. Each cell aliquot was resuspended in 0.5 mL of RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS in PBS, pH 7.4), and chromatin was fragmented on ice to 200 to 500 bp in size with 5 pulses of 30 sec at 50% power with a Sonics VibraCell sonicator. 5-10 μg primary antibodies or control IgG were pre-conjugated with Protein G magnetic beads (Pierce) at 4°C overnight. 1% of sheared chromatin was saved as input, and the rest was incubated with pre-conjugated antibody on a rotator at 4°C overnight. The beads were washed 5 times with LiCl wash buffer (0.1 M Tris, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate, pH 7.5) followed by a single wash with TE buffer (10 mM Tris-HCl, 0.1 mM Na2EDTA, pH 7.5). The beads were then resuspended in 200 μL IP elution buffer (1% SDS, 0.1 M NaHCO3) and incubated at 65°C for 1 hour in a heat block with vortexing. The supernant was collected and together with input was incubated at 65°C for 16 hours to reverse cross-links. DNA was purified with QIAquick PCR Purification Kit (Qiagen) and eluted in 50 μL EB.
ChIP’s DNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated fragments. Fragments were amplified by PCR and PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit.

treatment_protocol: RKO colon cancer cells stably expressing a ZNF280C-targeting shRNA controlled by a tetracycline-inducible promoter were treated with or without 1 ug/ml doxycycline for 72 hours, and the cells were harvested for analysis as described below.

value: RKO colon cancer cells

tag: agent

value: doxycycline


title: RKO_shZNF280C_rep1


title: MCF7, siCtrl, E2, Rep 2 [MCE3]


title: MCF7, siCtrl, E2, Rep 3 [MCE4]


title: Immature fin ECs_plate1

city: Rehovot

first: Yaara

last: Tevet

state: Israel

address: Hertzel 234

department: Department of Biological Regulation

institute: Weizmann Institute of Science

data_processing:
GRCz10 genome mapping was done using Bowtie2 with default parameters
Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell-barcodes in Read2, and performed as described in Jaitin et al. 2014
Genome_build: GRCz10
Supplementary_files_format_and_content: AB006.txt, AB007.txt, AB008.txt: expression dataset- txt files containing UMI counts table per plate. Single_cell_metadata_p1.xslx: xslx file, sheet1- pool barcode of plate1, sheet2- cell barcodes and coordinates  required for MARS seq pipeline (Jaitin et al., 2014), sheet3- plate1 analyzed cell names. Single_cell_metadata_p2.xslx: xslx file, sheet1- pool barcode of plate2, sheet2- cell barcodes and coordinates required for MARS seq pipeline (Jaitin et al., 2014), sheet3- plate2 analyzed cell names. Single_cell_metadata_p3.xslx: xslx file, sheet1- pool barcode of plate3, sheet2- cell barcodes and coordinates required for MARS seq pipeline (Jaitin et al., 2014), sheet3- plate3 analyzed cell names

organism: Danio rerio

source_name: fli1a:dsRed positive cells

extract_protocol:
80 anal fins were dissected, manually chopped with a sterile razor and enzymatically digested using Liberase I, Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution (UPW, 8nM poly-dT barcodes, 0.1%triton and RNAse inhibitor)
MARS seq libraries were prepared as described (Jaitin et al Science 2014)

value: Anal fin

value: endothelial cells

tag: Stage

value: II-III


title: Immature fin ECs_plate2


title: RKO_shZNF280C-Dox_rep3

tag: cell line

tag: tag


title: RKO_shZNF280C-DOX_H2AK119Ub

tag: cell type

tag: antibody


title: RKO_shZNF280C_H2AK119Ub


title: RKO_shZNF280C_ATAC-seq


title: RKO_shZNF280C-Dox_rep2


title: MCF7, siCtrl, E2, Rep 1 [MCE1]

tag: time


title: RKO_SMCHD1


title: RKO_shZNF280C_ZNF280C


title: RKO_shZNF280C_Rad21


title: RKO_shZNF280C-Dox_rep1


title: Wild Type, Veh, GRHL2, Rep 3 [WT_VG-3]

data_processing:
Quality control assessment of fastq files was performed using FASTQC. Adaptor trimming to remove Illumina adaptors was performed using Cutadapt through Trim Galore.
Reads were aligned to the hg38 genome with Bowtie2 using --local, and peaks were called with MACS2 using an FDR of 0.01 using the narrowPeak setting.
Bigwig files were generated using Deeptools bamCoverage.
Assembly: hg38
Supplementary files format and content: *.bed files are peaks called for each replicate
Supplementary files format and content: *bw files are for visualizing data for individual replicates in a genome browser

growth_protocol: MCF7 wild type and S118A knock-in cells were maintained in 10% CO2 at 37ᵒC with high-glucose (4.5 g/L) Dulbecco’s modified Eagles Medium (DMEM; Thermo Fisher, #11965092) supplemented with 10% HyClone fetal bovine serum (FBS; Cytiva, #SH30910.03), 100U/mL penicillin 100ug/mL streptomycin (1% Pen/Strep; Gibco, #15140-122), and 1mM sodium pyruvate (Gibco, #11360-070).

extract_protocol:
Cells were fixed for 10 minutes with 1.5% formaldehyde and quenched with 0.125M glycine. Nuclei were extracted from cell pellets and sonicated to shear DNA. DNA was immunoprecipitated using an anitbody against GRHL2 (Millipore Sigma, #HPA004820). DNA was purified after reverse-crosslinking using the Qiagen PCR purification kit (Qiagen, #28104).
Libraries were constructed using the NEBNext Ultra II DNA Library Prep kit (#E7103) and NEBNext Multiplex Oligos for Illumina (#E6440) according to vendor instructions. Samples were sequenced by paired-end 150bp sequencing on an Illumina NovaSeq 6000 by the Next Generation Sequencing department at the UW-Madison Biotechnology Center.

treatment_protocol: Cells were plated at a density of six million cells per 10cm plate with two plates per condition and were stripped of estrogens by culturing them for three days in phenol-red free DMEM supplemented with 10% charcoal stripped FBS (ssDMEM; Cytiva, #SH30910.03, stripped in-house), 100U/mL penicillin 100ug/mL streptomycin, 2mM L-glutamine (Thermo Fisher, #25030-081), and 1mM sodium pyruvate. Cells were treated with vehicle (0.1% EtOH) or 10nM 17β-estradiol (E2; Millipore Sigma #E2257) for 30 minutes.

tag: chip antibody

value: 30 min


title: liver, iKO-3

city: Nanjing

first: Zhenzhen

last: Sun

address: Guangzhou Road#72

institute: Children’s Hospital of Nanjing Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to 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: mm9
Supplementary files format and content: txt file includes TPM, FPKM, Readcount values for each Sample

source_name: liver

extract_protocol:
Liver tissues were harvested and rapidly frozen in liquid nitrogen. Total RNA was extracted from the tissues using Trizol (Invitrogen) according to the instruction manual.
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 100 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).

tag: tissue

value: liver

value: Ten days after tamoxifen injection

tag: genotype

value: NEK7 whole body knockout


title: Immature fin ECs_plate3


title: Wild Type, Veh, GRHL2, Rep 2 [WT_VG-2]


title: Wild Type, Veh, GRHL2, Rep 1 [WT_VG-1]


title: liver, iKO-2


title: RKO_shZNF280C_H3K4me3


title: liver, iKO-1


title: Wild Type, E2, GRHL2, Rep 3 [WT_EG-3]


title: RKO_shZNF280C-DOX_ZNF280C