title: Early2Cell_KO_H7G_8

city: Bethesda

first: Guanghui

last: Yang

state: Maryland

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using TrimGalore ver. 0.6.7 by indicating “--nextera” as the adapter, then mapped to the reference genome using hisat-3n version 2.2.1-3n compiled following its online tutorial. The reference genome contains sequences of GRCm38 and cl857 Sam7 Lambda DNA.
picard ver. 2.26.9 was used to remove duplicates in the aligned sam files.
Deduplicated sam files were processed by hisat-3n-table to get cytosines as well as their genomic coordinates and methylation states into .tsv files for each sample.
Cytosines in the tsv files were annotated with GRCm38 sequence to get their genomic contexts. Cytosines in GCs of from mouse chromosomes 1-19,X,Y were extracted to profile chromatin accessibility and cytosines in CGs from mouse chromosomes 1-19,X,Y were extracted to profile DNA methylation following the scNMT-seq protocol.
Assembly: GRCm38
Supplementary files format and content: Zipped tab-delimited text files including cytosines identified as well as their genomic coordinates and methylation states representing chromatin accessibility and DNA methylation profiles for each sample.

source_name: single embryo

extract_protocol:
Zygotes were collected from 6-8-week-old female mice after hormone simulation and mating. The zygotes were cultured in vitro to collect embryos at different developmental stages.The embryos were washed in PBS and transferred into acidic Tyrode’s solution to remove zonae pellucidae. Single zona-free embryos were finally lysed and processed following the scNMT-seq protocol.
Genomic DNA in the supernatant after capturing of poly-A RNA of each sample was processed following scNMT-Seq protocol to construct the single embryo bisulfite sequencing library.

tag: strain

tag: developmental stage


title: Rax-GFP ESCs, day 4, three biological replicate pool, scRNAseq

status: Public on Jun 07 2023

type: SRA

city: Chicago

first: NOZOMU

last: TAKATA

state: Illinois

address: 303 East Superior Street, 10-220

department: Center for Vascular and Developmental Biology

country: USA

institute: Northwestern University Feinberg School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Single cell data was further processed with Seurat, version 2.3.4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: ESC-derived eye organoids (Rax-GFP ESCs)

growth_protocol: The method was descrived previously Nature Protocols volume 7, pages69–79 (2012).

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).  Chromium Single Cell v2 Reagent Kit and Controller (10X Genomics, Pleasanton, CA, USA)

tag: tissue

value: eye organoid

tag: cell type

value: retina progenitors

tag: genotype

value: Rax-GFP knockin Het

tag: treatment

value: culture day 4


title: Early2Cell_KO_H7G_6

library_source: genomic

molecule: genomic DNA


title: Early2Cell_KO_H7G_5


title: Early2Cell_KO_H7G_7


title: Early2Cell_KO_H7G_4


title: Rax-GFP ESCs, H3K27ac antagonist Rep 2

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using Bowtie2 version 2.4.5
Peak calling and bigWig generation was performed using HOMER v4.10.4
Assembly: mm10
Supplementary files format and content: bigWig files

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: antibody

value: Acetyl-Histone H3 (Lys27) (Cell Signaling technology, #8173S)


title: Early2Cell_KO_H7G_2


title: Early2Cell_KO_H7G_3


title: Early2Cell_KO_H6G_2


title: Early2Cell_KO_H6G_7


title: Early2Cell_KO_H6G_1


title: Early2Cell_KO_H6G_5


title: Early2Cell_KO_H6G_8


title: Early2Cell_KO_H6G_4


title: Early2Cell_KO_H4G_8


title: Early2Cell_KO_H4G_7


title: Early2Cell_KO_H4G_6


title: Early2Cell_KO_H4G_5


title: Early2Cell_KO_H6G_3


title: Early2Cell_KO_H6G_6


title: Early2Cell_KO_H4G_3


title: Early2Cell_KO_H4G_4


title: Early2Cell_KO_H4G_2


title: Early2Cell_KO_H3G_8


title: Early2Cell_KO_H3G_7


title: Early2Cell_KO_H3G_3


title: Early2Cell_KO_H3G_6


title: Early2Cell_KO_H3G_4


title: Early2Cell_KO_H3G_5


title: Early2Cell_KO_H7G_1


title: Early2Cell_KO_H3G_2


title: Early2Cell_KO_H3G_1


title: Early2Cell_KO_H2G_7


title: Early2Cell_KO_H2G_6


title: Early2Cell_KO_H2G_5


title: Early2Cell_KO_H2G_4


title: Early2Cell_KO_H2G_1


title: Early2Cell_KO_H4G_1


title: Early2Cell_KO_H2G_3


title: Early2Cell_KO_H2G_2


title: Early2Cell_KO_H1G_2


title: Early2Cell_Het_G9G_6


title: Early2Cell_KO_H1G_8


title: Early2Cell_KO_H1G_3


title: Early2Cell_Het_G9G_7


title: Early2Cell_KO_H1G_6


title: Early2Cell_KO_H1G_5


title: Early2Cell_KO_H1G_7


title: Early2Cell_KO_H1G_1


title: Early2Cell_Het_G9G_5


title: Early2Cell_KO_H1G_4


title: Early2Cell_KO_H2G_8


title: Early2Cell_Het_G9G_2


title: Early2Cell_Het_G9G_1


title: Early2Cell_Het_G9G_3


title: Early2Cell_Het_G7G_8


title: Early2Cell_Het_G7G_7


title: Early2Cell_Het_G9G_4


title: Early2Cell_Het_G7G_6


title: Early2Cell_Het_G7G_4


title: Early2Cell_Het_G7G_3


title: Early2Cell_Het_G7G_2


title: Early2Cell_Het_G9G_8


title: Early2Cell_Het_G6G_6


title: Early2Cell_Het_G7G_5


title: Early2Cell_Het_G6G_7


title: Early2Cell_Het_G6G_5


title: Early2Cell_Het_G5G_5


title: Early2Cell_Het_G5G_6


title: Early2Cell_Het_G4G_8


title: Early2Cell_Het_G6G_3


title: Early2Cell_Het_G4G_5


title: Early2Cell_Het_G4G_7


title: Early2Cell_Het_G5G_7


title: Early2Cell_Het_G6G_2


title: Early2Cell_Het_G5G_3


title: Early2Cell_Het_G6G_1


title: Early2Cell_Het_G6G_4


title: Early2Cell_Het_G4G_6


title: Early2Cell_Het_G5G_8


title: Early2Cell_Het_G5G_4


title: Early2Cell_Het_G4G_2


title: Early2Cell_Het_G4G_1


title: Early2Cell_Het_G5G_1


title: Early2Cell_Het_G1G_7


title: Early2Cell_Het_G4G_4


title: Early2Cell_Het_G4G_3


title: Early2Cell_Het_G1G_6


title: Early2Cell_Het_G1G_8


title: Early2Cell_Het_G1G_3


title: Early2Cell_Het_G1G_4


title: Early2Cell_Het_G1G_5


title: Early2Cell_Het_G1G_2


title: Early2Cell_Het_G7G_1


title: Early2Cell_Het_G6G_8


title: Early2Cell_Het_G5G_2


title: PN5_KO_F8G_6


title: PN5_KO_F8G_5


title: PN5_KO_F8G_4


title: PN5_KO_F8G_7


title: Early2Cell_Het_G1G_1


title: PN5_KO_F8G_8


title: PN5_KO_F8G_1


title: PN5_KO_F8G_2


title: PN5_KO_F7G_5


title: PN5_KO_F7G_6


title: PN5_KO_F7G_8


title: PN5_KO_F7G_7


title: PN5_KO_F7G_2


title: PN5_KO_F6G_6


title: PN5_KO_F7G_3


title: PN5_KO_F6G_5


title: PN5_KO_F7G_1


title: PN5_KO_F6G_8


title: PN5_KO_F6G_7


title: PN5_KO_F6G_1


title: PN5_KO_F6G_3


title: PN5_KO_F6G_4


title: PN5_KO_F6G_2


title: PN5_KO_F5G_8


title: PN5_KO_F5G_7


title: PN5_KO_F5G_6


title: PN5_KO_F5G_5


title: PN5_KO_F8G_3


title: PN5_KO_F7G_4


title: PN5_KO_F5G_4


title: ATRA 100nM+6AF 10µM_72h

status: Public on Jun 08 2023

type: RNA

city: Sendai-shi

first: Susumu

last: Suzuki

country: Japan

institute: Tohoku Medical and Pharmaceutical University

hyb_protocol: standard Affymetrix Protocol

scan_protocol: standard Affymetrix Protocol

data_processing: The data were analyzed using Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific).

label: biotin

organism: Homo sapiens

source_name: NB4 cell

label_protocol: standard Affymetrix Protocol

growth_protocol: RPMI containing 10% heat-inactivated fetal bovine serum (FBS) under 5% CO2 at 37°C in a humidified atmosphere.

extract_protocol: RNA extraction was performed using Sepasol®-RNA I Super G (nacali tesque) according to the manufacturer's instructions.

treatment_protocol: Cells were seeded at a density of 2-3×10^5 cells/ml and treated with DMSO, 100 nM ATRA, 10 µM 6AF and 100 nM ATRA+10 µM 6AF for 72h.

tag: disease state

value: acute promyelocytic leukemia

value: ATRA 100nM+6AF 10µM_72h


title: PN5_KO_F5G_3


title: PN5_KO_F5G_1


title: PN5_KO_F5G_2


title: PN5_KO_F4G_8


title: PN5_KO_F4G_6


title: PN5_KO_F4G_7


title: PN5_KO_F4G_2


title: PN5_KO_F4G_4


title: PN5_KO_F4G_3


title: PN5_KO_F4G_1


title: PN5_KO_F3G_5


title: PN5_KO_F3G_4


title: PN5_KO_F3G_3


title: PN5_Het_E6G_7


title: PN5_KO_F3G_8


title: PN5_Het_E6G_5


title: PN5_Het_E6G_6


title: PN5_KO_F3G_1


title: PN5_Het_E6G_4


title: PN5_KO_F3G_7


title: PN5_Het_E6G_8


title: PN5_KO_F3G_2


title: PN5_KO_F3G_6


title: PN5_Het_E6G_2


title: PN5_Het_E6G_3


title: PN5_Het_E5G_6


title: PN5_Het_E5G_4


title: PN5_Het_E6G_1


title: PN5_Het_E5G_3


title: PN5_Het_E5G_2


title: PN5_KO_F4G_5


title: PN5_Het_E5G_5


title: PN5_Het_E5G_8


title: PN5_Het_E5G_7


title: PN5_Het_E5G_1


title: PN5_Het_E4G_8


title: PN5_Het_E4G_7


title: PN5_Het_E4G_5


title: PN5_Het_E4G_4


title: PN5_Het_E3G_8


title: PN5_Het_E3G_7


title: PN5_Het_E3G_5


title: PN5_Het_E4G_2


title: PN5_Het_E3G_6


title: PN5_Het_E4G_1


title: PN5_Het_E4G_3


title: PN5_Het_E3G_2


title: PN5_Het_E2G_8


title: PN5_Het_E2G_7


title: PN5_Het_E2G_6


title: PN5_Het_E2G_5


title: PN5_Het_E3G_3


title: PN5_Het_E3G_1


title: PN5_Het_E3G_4


title: PN5_Het_E2G_2


title: PN5_Het_E2G_4


title: PN5_Het_E2G_3


title: PN5_Het_E1G_8


title: PN5_Het_E1G_5


title: PN5_Het_E1G_6


title: PN5_Het_E2G_1


title: PN5_Het_E4G_6


title: PN5_Het_E1G_7


title: PN5_Het_E1G_4


title: PN5_Het_E1G_3


title: PN5_Het_E1G_2


title: HNF4a2Tg_rep3

first: Valentin

last: David

address: 320 E Superior Street

department: Medicine

institute: Northwestern University

library_source: transcriptomic

data_processing:
StrandNGS 4.0 was used for alignment and differential expression
Sequenced reads were trimmed for adaptor sequence,  masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Strand NGS 4.0
Genome_build: mm10
Annotation: UCSC Transcripts (2018.02.25)
Reads were filtered using the Filter by Read Metrics filter with the following parameters: Quality threshold >= 20; N's allowed in read <= 0; Number of multiple matches allowed <= 1; Removed non-primary multiply mapped reads; Removed reads that are failing vendor's QC.
Reads were further filtered on read quality metrics using the Filter by Genic Region and we retained only reads mapping the Exonic, Intronic and Exon Intron Junction.
Strand specific reads: false
Max EM Iterations: 1000
Convergence criterion for EM: 0.001
Normalization Type = Deseq
Threshold for normalization = 1
Baseline type =  median of all samples
Supplementary_files_format_and_content: Matrix table with raw and normalized gene counts for every gene and every sample and differential group expression

source_name: Calvaria

growth_protocol: Cells were cultured for 21 days in αMEM medium supplemented with 10% FBS (Corning, New York, USA), 10 U/ml penicillin, 100 μg/ml streptomycin (Thermo Fisher Scientific, Whaltman, USA), 10 mM β-glycerophosphate, and 50 μg/ml ascorbic acid (Sigma-Aldrich, St. Louis, USA) to induce differentiation.

extract_protocol:
We isolated total RNA from cell cultures using TRI reagent (Waltham, MA, USA) and purified RNA using RNeasy kit (Qiagen, Germantown, MD, USA) and submitted 1 µg of total RNA for sequencing.
Libraries were prepared according to Illumina's instructions, i.e, total RNA library for each individual sample was prepared using the TruSeq Total RNA-Seq Library Preparation Kit (Illumina, San Diego, CA), and the bar-coded cDNA libraries were sequenced for 50 bp single reads using Illumina HiSeq 4000.

value: osteoblast-like

tag: age

value: 21 days of culture

tag: cell line

value: MC3T3-E1 subclone 4 (ATCC CRL-2593)

tag: expression vector

value: HNF4a2 cDNA


title: HNF4a2Tg_rep2


title: HNF4a2Tg_rep1


title: HNF4a1Tg_rep1

value: HNF4a1 cDNA


title: HNF4a1Tg_rep2


title: HNF4a1Tg_rep3


title: Ctr_rep1

value: Ctr

value: empty vector


title: PN5_Het_E1G_1


title: 8.Hnf4a2TgM49.halo.rep2

data_processing:
The Encode Chipseq pipeline2 v 7.0 (https://github.com/ENCODE-DCC/chip-seq-pipeline2) was used to process the samples from fastqs to overlapping naïve peaks.
Alignment:bwa
Genome_build: mm10
Peak caller:spp with fdr 0.01
Supplementary_files_format_and_content: *peak.regionPeak.gz: encode region peak files for each individual experiement
bed file for overlapping peaks from separate experiments
HNF4a1_Peaks.bed:  Peaks found in 2 or more experiments for which in at least one experiment cells overexpress Hnf4a1. The other(s) peaks should derive from  either Ctr cells and/or cells overexpressing Hnf4a1.
HNF4a2_Peaks.bed: Peaks found in 2 or more experiments for which in at least one experiment cells overexpress Hnf4a2. The other(s) peaks should derive from  either Ctr cells and/or cells overexpressing Hnf4a2.
HNF4a1-2_Peaks.bed: Peaks found in 2 or more experiments for which in at least one experiment cells overexpress Hnf4a1 and at least one Hnf4a2.  The other(s) peaks should derive from  either Ctr cells and/or cells overexpressing Hnf4a1 or Hnf4a2.

extract_protocol:
Cell cultures  were subjected to ChIP assay following the protocol provided by manufacturer (SimpleChIP Plus Enzymatic Chromatin IP Kit with magnetic beads, Cell Signaling Technology, Danvers MA, USA). Briefly, protein-chromatin crosslinking was carried out in cell medium containing 1% formaldehyde (Sigma-Aldrich, St. Louis, MO, USA) at room temperature for 10 minutes. After stopping the crosslinking reaction using 10X glycine for 5 min, cells were washed 3 times in PBS and scraped into cold PBS containing protease inhibitor cocktail. Collected cells were centrifuged at 2000xg for 5 min at 4C. After nuclei extraction, chromatin was digested with micrococcal nuclease, and nuclear membranes were disrupted by sonication. Lysates were clarified by centrifugation at 9400xg for 10 min at 4C. Per IP reaction, 10 µg of digested, cross-linked chromatin were incubated with anti-HNF4α antibodies for immunoprecipitation: 5 µg of OASG03561 (Aviva Systems Biology, San Diego, CA, USA), 10 µg of ab41898 (Abcam, Cambridge, UK), or 10 µg of anti-Halotag antibody (G9281, Promega, Madison, WI, USA) for 4h at 4C. Then, 30 μl of Dynabeads Protein G Magnetic Beads was added to the IP chromatin solution and incubated for 2h at 4C. After several washing steps using buffers with ascending NaCl concentrations, chromatin was eluted, and the supernatant was incubated with proteinase K overnight at 65C to reverse crosslinking. Finally, DNA fragments were purified using silica columns.
The total DNA library for each individual sample was prepared using the TruSeq ChIP-Seq Library Prep Kit (Illumina, San Diego, CA), and the bar-coded cDNA libraries were sequenced for 100 bp single reads using  the Illumina Hiseq 4000. The ENCODE pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) v 1.7.1 was used to identify naive overlapping peaks in each experiment. Enriched regions were consolidated based on their representation in two or more experiments as follow: HNF4α1/2 peaks if detected in samples expressing Hnf4α1 and Hnf4α2; HNF4α1 peaks if detected in two or more samples overexpressing Hnf4α1 or Ctr cells; HNF4α2 peaks if detected in two or more samples overexpressing Hnf4α2 or Ctr cells.

value: HNF4a2 cDNA N terminus Halo Tag

tag: chip antibody

value: G9281 (Promega, Madison, WI, USA)


title: 8.Hnf4a2TgM49.halo.rep1


title: 7.Hnf4a2TgM50.halo.rep1

value: HNF4a2 cDNA C terminus Halo Tag


title: 7.Hnf4a2TgM50.halo.rep2


title: 7.Hnf4a2TgM50.halo.rep3


title: 6.Hnf4a1Tg.ab.rep2

value: ab41898 (Abcam, Cambridge, UK)


title: 6.Hnf4a1Tg.ab.rep3


title: 5.Hnf4a2Tg.ab.rep1


title: 5.Hnf4a2Tg.ab.rep3


title: 6.Hnf4a1Tg.ab.ctl

value: input sample, no antibody


title: 5.Hnf4a2Tg.ab.ctl


title: 4.MC3T3.ab.rep3


title: Ctr_rep3


title: 4.MC3T3.ab.rep1


title: 4.MC3T3.ab.ctl


title: 3.Hnf4a1Tg.av.rep3

value: OASG03561 (Aviva Systems Biology, San Diego, CA, USA)


title: 7.Hnf4a2TgM50.halo.ctl


title: 8.Hnf4a2TgM49.halo.rep3


title: twi, pooled CD45+ cells

city: Farmington

first: Stephen

last: Crocker

state: Connecticut

address: 263 Farmington Ave.

department: Neuroscience

institute: University of Connecticut School of Medicine

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
brain tissues were collected inot RPMI media and enzymatically dissociated using collagenase/dispase and DNAase (1h/37C). Following this, the cellular suspension was filtered (70uM) and then separated on a 70/30 Percoll gradient where leukocytes were collected at tht interphase. CD45+ cells were collected by flowcyotmetry (FACSARIA II, Becton-Dickinson).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). CD4+ cells were resuspended in a master mix that was loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

value: brain

value: Postnatal Day 21

value: galc-/-


title: wt littermate, pooled CD45+ cells

description: 10X Genomics

value: galc+/+


title: 6.Hnf4a1Tg.ab.rep1

value: osteoblast-like


title: 5.Hnf4a2Tg.ab.rep2

value: 21 days of culture


title: 2.Hnf4a2Tg.av.rep3

value: MC3T3-E1 subclone 4 (ATCC CRL-2593)


title: 2.Hnf4a2Tg.av.rep2

value: HNF4a2 cDNA


title: 3.Hnf4a1Tg.av.rep1

value: HNF4a1 cDNA


title: 3.Hnf4a1Tg.av.ctl


title: 2.Hnf4a2Tg.av.rep1


title: 4.MC3T3.ab.rep2

value: Ctr


title: 2.Hnf4a2Tg.av.ctl


title: 1.MC3T3.av.rep3

value: empty vector


title: 1.MC3T3.av.rep2


title: 3.Hnf4a1Tg.av.rep2


title: 1.MC3T3.av.rep1


title: 1.MC3T3.av.ctl


title: HNF4acKO-rep4

source_name: Tibia-Bone

extract_protocol:
We isolated total RNA from  bone using TRI reagent (Waltham, MA, USA) and purified RNA using RNeasy kit (Qiagen, Germantown, MD, USA) and submitted 1 µg of total RNA for sequencing.
Libraries were prepared according to Illumina's instructions, i.e, total RNA library for each individual sample was prepared using the TruSeq Total RNA-Seq Library Preparation Kit (Illumina, San Diego, CA), and the bar-coded cDNA libraries were sequenced for 50 bp single reads using Illumina HiSeq 4000.

value: Bone

value: 6 week-old mice


title: HNF4acKO-rep2


title: WT-rep4

value: WT


title: HNF4acKO-rep1


title: HNF4acKO-rep3


title: WT-rep3


title: WT-rep2


title: Ctr_rep2


title: 8.Hnf4a2TgM49.halo.ctl

value: HNF4a2 cDNA N terminus Halo Tag


title: miR-205 inducible skin cells

first: Rui

last: Yi

address: 765 N FAIRBANKS CT

department: Pathology, Feinberg School of Medicine

data_processing:
The Cell Ranger Single-Cell Software Suite was used to perform barcode processing and single-cell 3’ gene counting (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Genome_build: mm10
Supplementary_files_format_and_content: tsv and matrix file

source_name: P53 skin cells

extract_protocol:
Gender matched mice (Ctrl and miR-205Ind) harboring a K14-H2BGFPallele were fed doxycycline for 4 days and euthanized to collect back skin samples. Hair coats were shaved and removed. Subcutaneous fat was removed, and back skin samples were minced into small pieces and incubated with 0.25% collagenase (Worthington, LS004188) in 10 mL 1x HBSS buffer at 37°C for 2 hours with rotation. After collagenase treatment, 10 mL cold PBS was added, and sample suspension was centrifugated at 400 g for 10 minutes at 4°C to get the pellet. The pellet was resuspended with 5 ml pre-warmed 0.25% trypsin/EDTA (Gibco) for 7 minutes at 37°C and the digestion was blocked by adding 10 mL cold 1x PBS with 3% chelated FBS. The suspension was extensively triturated with a 25 ml pipette and filtered through a 40 m cell strainer, followed by centrifugation at 400 g for 5 minutes at 4°C. The pelleted cells were resuspended in cold 1x PBS with 3% chelated FBS. Suspended cells were incubated with appropriated antibodies for 1 hour on ice. After washing away unbounded antibodies, DAPI was used to exclude dead cells. Cells from both control and miR-205 inducible animals  were collected from FACS sorting machine with cell surface proteins and H2BGFP signals such that the epidermal cells, hair follicle cells and dermal cells are 3: 5: 2 ratio.
Single-cell RNA-seq was performed according to manufacturer’s instruction (10X Genomics). Each sample was targeted to obtain ∼5,000 cells.
single cell RNA-seq

treatment_protocol: miR-205 inducible mouse was feed Doxcyclin chow for 4 days from P49-P53.

tag: cells

value: epithelial and dermal cells

value: treated with doxcyclin for 4 days


title: control skin cells

value: untreated


title: Early_2cell_KI_Input_S24

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file, then mapped to GRCm38 reference genome using STAR ver. 2.7.6a.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference (release 101) downloaded from ENSEMBL.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM, TPM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Early 2-cell embryos

extract_protocol:
200-250 M2 eggs or early 2-cell embryos were collected from Eif4e1b with C terminal FLAGHA knock-in female or WT female mice as one sample. After removing the zona pellucida, washed with PBS, embryos for a same sample were transferred into a 1 ml nuclease free centrifuge tube with a minimal volume of PBS.
EZ-Manga RIP kit and anti-HA beads were used to perform RIP experiment. RNA in supernatant after IP was purified with RNAclean XP beads and used as input. Smart-Seq2 protocol was used to process RNA bound by anti-HA bead or RNAclean XP beads and finally finish the RNA-Seq libraries.

value: Early 2-cell

tag: female mouse donor genotype

value: Eif4e1b FLAGHA knock-in


title: WT-rep1


title: H1_KO_3

city: Berkeley

first: Michael

last: Rapé

state: CA

address: 330F Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California Berkeley

data_processing:
Mapping to reference was performed with hisat2 (Version 2.0.5) using default parameters
Quantification was performed with featureCounts (Version 1.5.0-p3)
Differential analysis was performed using DESeq2 (Version 1.20.0) and edgeR (Version 0.22.0)
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample

source_name: H1 hESC

growth_protocol: HEK 293T cells were maintained in DMEM/GlutaMAX + 10% FBS in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using the Macherey-Nagel NucleoSpin Mini Kit
RNA libraries for RNA-seq were prepared by Novogene

value: H1 hESC

value: UBR5 siRNA


title: H1_KO_2


title: M2_KI_Input_S23

source_name: M2 eggs


title: M2_KI_Input_S22


title: M2_KI_Input_S21


title: H1_WT_3

value: Non-targeting control siRNA


title: H1_WT_2


title: Early_2cell_KI_Input_S20


title: H1_KO_1


title: H1_WT_1


title: M2_WT_Input_S19


title: KO_3_Rep2

source_name: HEK 293T

value: HEK 293T


title: KO_1_Rep2


title: M2_WT_Input_S17


title: Early_2cell_KI_IP_S16


title: KO_2_Rep2


title: Early_2cell_KI_IP_S15


title: Early_2cell_KI_Input_S13


title: WT_1_Rep2


title: WT_3_Rep2


title: CD4_SLE_P14_M

type: genomic

city: Pittsburgh

first: Amr

middle: H

last: Sawalha

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

description: Patient 14 (Male)

hyb_protocol: Standard protocol

scan_protocol: Standard protocol

data_processing:
DNA methylation data analysis was performed in the R statistical computing environment (v.3.6.3). Raw .idat files were generated for each sample and underwent quality control and downstream analysis in the R package minfi (v.1.32.0). The following probes were removed based on best practices as used in DNAmArraypackage (v.0.1.1): probes with less than three beads and zero intensity values across all samples. Thereafter, correction for background signal and dye bias and normalization of signal intensities using functional normalization in the preprocessFunnorm.DNAmArray function was done. The first three principal component values, calculated from signal intensities of control probes present on all array spots to correct for technical variation, were utilized. More probes were removed, which included the following: probes with detection P-values < 0.01 and probes that returned signal intensities in fewer than 98% of samples. Remaining probes’ signal intensities were converted to M-values with limits of ±16. To reduce the number of probes with potential technical issues, we followed the criteria described by Zhou, Laird & Shen (2017) to mask any probes: a unique probe sequence of less than 30bp, mapping to multiple sites in the genome, polymorphisms that cause a color channel switching in type I probes, inconsistencies in specified reporter color channel and extension base, mapping to the Y chromosome, and/or having a polymorphism within 5bp of the 3’ end of the probe with a minor allele frequency (MAF) > 1% with exception of CpG-SNPs with C>T polymorphisms which we retained for analysis.  ComBatfunction in the sva (v.3.34.0) package was used to perform batch correction.
Average Beta

label: Cy5 and Cy3

source_name: CD4 DNA

label_protocol: Standard protocol

extract_protocol: Whole blood was collected from each previously recruited patient during clinic visits in vials containing EDTA. Peripheral blood mononuclear fractions were isolated using density centrifugation with Ficoll/Paque (GE Healthcare Life Sciences, Piscataway, NJ, USA).  CD4+ T cell were isolated using MACS magnetic bead CD4+ T-cell isolation kit (Miltenyi Biosystems, Auburn, CA). Genomic DNA was isolated from the CD4+ T cells using Qiagen DNEasy kit (Qiagen, Germantown, MD, USA). 250ng of DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo, Irvine, CA, USA) following the manufacturer’s instructions.

value: CD4+ T cell

tag: disease

value: SLE

tag: Sex

value: Male

tag: ancestry

value: European-American

tag: sledai score


title: CD4_SLE_P22_F

description: Patient 22 (Female)

value: Female


title: CD4_SLE_P16_M

description: Patient 16 (Male)


title: CD4_SLE_P20_M

description: Patient 20 (Male)


title: Early_2cell_WT_IP_S12

tag: strain

tag: developmental stage


title: CD4_SLE_P6_F

description: Patient 6 (Female)

tag: cell type


title: CD4_SLE_P17_M

description: Patient 17 (Male)


title: CD4_SLE_P19_F

description: Patient 19 (Female)


title: KO_1_Rep1

tag: genotype


title: CD4_SLE_P21_M

description: Patient 21 (Male)


title: CD4_SLE_P12_F

description: Patient 12 (Female)


title: CD4_SLE_P13_F

description: Patient 13 (Female)


title: CD4_SLE_P8_M

description: Patient 8 (Male)


title: Early_2cell_KI_Input_S14


title: CD4_SLE_P15_M

description: Patient 15 (Male)


title: Early_2cell_WT_Input_S9


title: Early_2cell_KI_IP_S8


title: CD4_SLE_P11_M

description: Patient 11 (Male)


title: WT_2_Rep1


title: CD4_SLE_P7_M

description: Patient 7 (Male)


title: CD4_SLE_P4_M

description: Patient 4 (Male)


title: CD4_SLE_P9_M

description: Patient 9 (Male)


title: Early_2cell_WT_IP_S11


title: M2_KI_IP_S7


title: M2_KI_IP_S6


title: CD4_SLE_P1_F

description: Patient 1 (Female)


title: U251_ZIKV3

city: Shenzhen

first: Qiqi

last: Chen

state: Guangdong Province

address: Guangming District, Shenzhen City, Guangdong Province

department: School of Public Health (Shenzhen)

country: China

institute: Sun Yat-sen University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Assembly: Homo sapiens, Ensembl v96
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Brain

growth_protocol: HTR8 cells and U251 cells were seeded in 24-well plates at 5 × 10^4 cells per well one day prior to infection.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard llumina protocols.

treatment_protocol: Cells were infected with ZIKV GZ01 with a multiplicity of infection (MOI) of 1 plaque-forming unit per cell and incubated for 1h at 37 °C. Next, the inoculum was removed and the cells were washed twice with phosphate-buffered saline (PBS) to eliminate the unbound virus. Complete culture medium was added to each well, and cells were incubated at 37 °C and 5% CO2.

tag: tissue

value: Brain

value: Pleomorphic/astrocytoid

tag: treatment

value: ZIKV


title: M2_KI_IP_S5


title: Early_2cell_KI_IP_S4


title: WT_1_Rep1

value: WT


title: U251_ZIKV1


title: CD4_SLE_P18_F

description: Patient 18 (Female)


title: U251_ZIKV2


title: WT_2_Rep2


title: CD4_SLE_P3_M

description: Patient 3 (Male)


title: M2_WT_Input_S18


title: M2_WT_IP_S3


title: M2_WT_IP_S2


title: M2_WT_IP_S1


title: HTR8_ZIKV3

source_name: Placenta

value: Placenta

value: trophoblast


title: CD4_SLE_P5_F

description: Patient 5 (Female)


title: HTR8_ZIKV2


title: CD4_SLE_P2_F

description: Patient 2 (Female)


title: WT_3_Rep1


title: CD4_SLE_P10_F

description: Patient 10 (Female)


title: U251_NF3

value: PBS


title: U251_NF2


title: HTR8_NF2


title: KO_3_Rep1


title: Late2Cell_KO_J9K_7

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file, then mapped to the reference genome using STAR ver. 2.7.6a. The reference genome contains sequences of GRCm38 and ERCC spike-ins.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 101) and from ERCC spike-in product page.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM, TPM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Zygotes were collected from 6-8-week-old female mice after hormone simulation and mating. The zygotes were cultured in vitro to collect embryos at different developmental stages. M2 eggs were collected from hormone simulated females without mating. M2 eggs or embryos were washed in PBS and transferred into acidic Tyrodes solution to remove zonae pellucidae. Single zona-free eggs or embryos were finally lysed and processed following the scNMT-seq protocol.
G&T-Seq protocol was used to construct single embryo RNA-Seq libraries.

value: Late 2-cell


title: HTR8_NF3


title: Late2Cell_KO_J9K_4


title: Late2Cell_KO_J9K_8


title: Late2Cell_KO_J9K_5


title: HTR8_NF1


title: Late2Cell_KO_J9K_6


title: Late2Cell_KO_J9K_2


title: Late2Cell_KO_J9K_3


title: U251_NF1


title: Late2Cell_KO_J9K_1


title: Late2Cell_KO_J8K_8


title: HAP1_WT_125nM_MZ1_rep2

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
read trimming: cutadapt (version 2.8)
read mapping: STAR (version 2.7.9a); reference genome annotation: Ensembl 98
read quantification: RSEM (version 1.3.2)
quality control: multiqc (version 1.11), FastQC (version 0.11.9), RSeQC (version 4.0.0)
Assembly: GRCh38.p13
Supplementary files format and content: count_table.tsv: tab-delimited text file with read counts per Ensembl Gene ID for each sample
Supplementary files format and content: tpm_table.tsv: tab-delimited text file with TPM values per Ensembl Gene ID for each sample

source_name: cell line

extract_protocol:
At the time of harvest, media is removed from cells and cells are washed once with 1 ml PBS buffer. After washing, 200 μl buffer RLT (Qiagen) is added directly to the cells. After complete cell lysis, lysates are transferred into matrix tubes and frozen at -80 °C until further treatment. For RNA purification, RNeasy 96 Kits (Qiagen) were used. DNA is removed by on-column DNase treatment as described in the manual. After purification, RNA is eluted in 60-80 μl RNase-free water and stored at -80 °C until further usage.
RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). Total RNA input of 250 ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 upstream and the NEBNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). The only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification, instead of the recommended SPRIselect Beads. The index PCR was performed with 12 cycles, while the final library was eluted in 35 μL. mRNA libraries were then quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). mRNA libraries were also assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 96-channel Fragment Analyzer (Agilent).
All sequencing libraries were normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina). The library pools were subsequently clustered on S4 Flow Cell and sequenced on a NovaSeq 6000 Sequencing System (Illumina) with dual index, paired-end reads at 2 x 50 bp length (Read parameters: Rd1: 51, Rd2: 8, Rd3: 8, Rd4: 51), aiming for an average depth of 25 million Pass-Filter reads per sample.

treatment_protocol: Drug-treated cell lines were grown in the presence of 125 or 500 mM MZ1 (and DMSO as control) for two weeks. During culture, cells were split every 2-3 days and fresh MZ1 was added each time.

value: cell line

value: HAP1 (RRID:CVCL_Y019)

value: Myeloid haploid karyotype cell line

value: 125nM MZ1 2 weeks


title: HAP1_WT_125nM_MZ1_rep3


title: Late2Cell_KO_J8K_7


title: HTR8_ZIKV1


title: Late2Cell_KO_J8K_6


title: HAP1_WT_500nM_MZ1_rep2

value: 500nM MZ1 2 weeks


title: Late2Cell_KO_J8K_5


title: HAP1_WT_500nM_MZ1_rep3


title: HAP1_WT_500nM_MZ1_rep1


title: Late2Cell_KO_J8K_4


title: Late2Cell_KO_J7K_7


title: Late2Cell_KO_J8K_3


title: HAP1_WT_DMSO_rep1

value: DMSO 2 weeks


title: Late2Cell_KO_J7K_6


title: Late2Cell_KO_J8K_1


title: HAP1-ABCB1-KO-c4_rep2

value: ABCB1 KO


title: Late2Cell_KO_J8K_2


title: HAP1-ABCB1-KO-c4_rep1


title: HAP1-ABCB1-KO-c1_rep2


title: Late2Cell_KO_J7K_5


title: HAP1_WT_125nM_MZ1_rep1


title: HAP1-ABCC1-KO-c5_rep1

value: ABCC1 KO


title: HAP1-ABCB1-KO-c1_rep1


title: Late2Cell_KO_J7K_4


title: HAP1-ABCC1-KO-c2_rep2


title: HAP1_WT_rep2


title: Late2Cell_KO_J7K_3


title: HAP1_WT_DMSO_rep3


title: HAP1-ABCC1-KO-c2_rep1


title: Late2Cell_KO_J7K_1


title: Late2Cell_KO_J7K_2


title: HAP1_WT_rep1


title: zebrafish cyproconazole treated from 4 hours post fertilization to 3 days post fertilization

city: Bloomington

first: Maria

last: Bondesson

state: IN

address: 2401 N Milo Sampson Ln

department: Department of Intelligent Systems Engineering

institute: Indiana University

data_processing:
Mapping: Reads were mapped with Tophat/2.0.4 to the Zebrafish genome assembly, build GRCz10.
Merging: Bamfiles from samples run on different lanes were merged with samtools.
Sorting and Marking duplicates: Merged bam files were sorted and duplicates removed using  picard-tools/1.29.
Counts for genes: Gene counts were generated using htseq/0.6.1 on bam files with duplicates included
FPKMs for genes and transcripts: FPKMs for genes and transcripts were generated using  cufflinks/2.1.1 on bamfiles with duplicates included.
Assembly: GRCz10
Supplementary files format and content: csv file includes FPKM values for each Sample, log2FoldChange, etc.

organism: Danio rerio

source_name: whole organism

growth_protocol: Natural breeding was used to produce embryos and the collected embryos were kept in Embryo media (E3; 5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) at 28.5oC with 14:10 day/night cycles

extract_protocol:
Forty pooled embryos were used to collect total RNA using Trizol (Invitrogen Corporation, Carlsbad, CA) and RNeasy spin columns (Qiagen, Chatsworth, CA) according to manufacturer’s protocols. Any DNA remaining in the column was removed using DNase I (Qiagen, Chatsworth, CA).
Library preparation: Illumina TruSeq RNA (poly-A-selection) on total RNA

treatment_protocol: 20 micromolar cyproconazole (CAS number: 94361-06-5) was added at 4 hours post fertilization to 3 days post fertilization

value: whole organism

value: embryo

value: SAGFF(LF)53A mitfab692/+

value: 20 micromolar cyproconazole


title: Late2Cell_KO_J7K_8


title: HAP1-Cas9-p2A-Blast-c3_rep2

value: Cas9-P2A-Blasticidin insertion


title: HAP1_WT_DMSO_rep2

value: WT


title: Late2Cell_KO_J6K_8


title: zebrafish untreated control 3 days post fertilization

value: untreated control


title: csm212-4

city: St. Louis

first: Dennis

last: Zhu

state: MO

address: 660 South Euclid Avenue

institute: Washington University

data_processing:
QC was performed using FastQC version 0.11.8 with default parameters
Adapter trimming and poor quality read filtering and was performed using Trimmomatic version 0.38.0 with the ILLUMINACLIP function targeting Illumina TruSeq3 paired-end adapter sequences and using a Sliding Window approach to trim reads with a quality <=20
Reads were aligned to the M. smegmatis MC2 155 reference genome using HISAT2 version 2.2.1 with default parameters for paired-end reads
Read counts aligning to annotated genes were quantified using featureCounts version 2.0.1
Differential expression analysis was performed using DESeq2 package version 1.30.1 implemented in Rstudio RStudio 2022.02.3+492 "Prairie Trillium" Release for macOS
Assembly: Mycobacterium smegmatis ASM1500v1
Supplementary files format and content: msmeg_countTable.csv - comma separated values table with results of featureCounts quantification of reads aligning to annotated genes
Supplementary files format and content: msmeg_differentialExpression.csv - comma separated values table with the results of differential expression analysis performed using DESeq2

organism: Mycolicibacterium smegmatis MC2 155

growth_protocol: Mycobacterium smegmatis cells were cultured in LB media supplemented with 0.5% (v/v) dextrose, 0.5% (v/v) glycerol, and 0.05% (v/v) tween-80 in 50mL glass flasks shaking at 150rpm at 37 C.

extract_protocol:
Mycobacterium smegmatis cells were lysed by bead-beating in Trizol reagent (Invitrogen) and then RNA was isolated by chloroform extraction.
RNA samples were treated with DNAse using the TURBO DNA-free kit (Invitrogen). Libraries were prepared with 500ng of total RNA. Ribosomal RNA was blocked using FastSelect reagents (Qiagen) during cDNA synthesis. RNA was fragmented in reverse transcriptase buffer with FastSelect reagent and heating to 94 degrees for 5 minutes, 75 degrees for 2 minutes, 70 degrees for 2 minutes, 65 degrees for 2 minutes, 60 degrees for 2 minutes, 55 degrees for 2 minutes, 37 degrees for 5 minutes, 25 degrees for 5 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags.

value: I27W CarD


title: HAP1-Cas9-p2A-Blast-c3_rep1


title: csm212-3


title: Late2Cell_KO_J6K_4

value: Late 2-cell


title: Late2Cell_KO_J6K_3


title: KO_2_Rep1

value: HEK 293T


title: Late2Cell_KO_J6K_2


title: Late2Cell_KO_J5K_7


title: H_siK2_input

city: Guangzhou

first: Zi-Qi

last: Zheng

state: Guangdong

address: No. 651 Dongfeng east road, Yuexiu district, Guangzhou

institute: Sun Yat-sen University Cancer Center

description:
All_sample_gene_expression_information.txt
H_siK_IPVSH_siK_input_peak.txt

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using fastp. We used HISAT2 to map reads to the genome of homo_sapiens (Version: homo_sapiens_ensembl_V90) with default parameters.
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software (http://www.igv.org/).
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house. Called peaks were annotated by intersection with gene architecture using ChIPseeker.
Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR.
Assembly: homo_sapiens_ensembl_V90)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was isolated from scrambled or VIRMA-silenced SUNE-1 and HONE-1 cells and analyzed using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, Santa Clara, CA, USA) with a RNA integrity number (RIN) number > 7.0.
After RNA purification and fragmentation, RNA samples were incubated with anti-m6A primary antibody (Synaptic Systems) for immunoprecipitation using a Magna MeRIPTM m6A kit (Millipore) according to the manufacturer’s instructions. Enriched m6A-modified RNA was then eluted and subjected to next-generation sequencing using the Illumina NovaseqTM 6000 platform (Illumina, San Diego, CA, USA) at LC-BIO Biotech Ltd (Hangzhou, China).

value: human nasopharyngeal carcinoma cells

value: VIRMA silenced


title: Late2Cell_KO_J5K_8


title: csm212-2


title: csm212-1


title: Late2Cell_KO_J6K_7


title: Late2Cell_KO_J6K_5


title: H_siK1_input


title: Late2Cell_KO_J5K_6


title: Late2Cell_KO_J6K_1


title: Late2Cell_KO_J5K_5


title: H_siK1_IP

tag: antibody


title: csm106-4

value: K125E CarD


title: H_NC2_IP

value: control


title: csm106-3


title: H_siK2_IP


title: Late2Cell_KO_J5K_2


title: Late2Cell_KO_J6K_6


title: Late2Cell_KO_J5K_1


title: Late2Cell_KO_J5K_3


title: Late2Cell_KO_J10K_7


title: H_NC2_input

description:
All_sample_gene_expression_information.txt
H_NC_IPVSH_NC_input_peak.txt


title: Late2Cell_KO_J10K_8


title: csm106-2


title: H_NC1_IP


title: Late2Cell_KO_J10K_6


title: mgm3044-4

value: R25E CarD


title: csm106-1


title: H_NC1_input


title: Late2Cell_KO_J5K_4


title: Late2Cell_KO_J10K_3


title: Late2Cell_KO_J10K_2


title: Late2Cell_KO_J10K_4


title: Late2Cell_KO_J10K_1


title: NHEM, CXCL1, SX682, rep1

city: Nashviile

first: Ann

last: Richmond

state: TN

address: 2220 Pierce Avenue

department: Department of Pharmacology and Dermatology

institute: Vanderbilt University School of Medicine

data_processing:
Cutadapt (https://github.com/marcelm/cutadapt) was used to trim adapters.
STAR was used to map reads to the human reference genome.
DESeq2 was used to detect differential expression between conditions.
Assembly: hg38
Supplementary files format and content: A count table that provides complete data with values for all features and all samples.

source_name: human epidermal melanocytes

growth_protocol: Normal human epidermal melanocytes (NHEM) cells were cultured in melanocyte growth medium containing vehicle or CXCL1 (100ng/ml), or CXCL1 (100ng/ml) with 5 µM SX-682.

extract_protocol:
RNA was extracted from cultured cells using the RNeasy Plus Mini Kit (Cat#74134, Qiagen) per manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NHEMs were treated with CXCL1 (100ng/ml) or vehicle, or with SX-682 and CXCL1 for 24 hours before RNA was extracted and processed for RNAseq analysis

value: human epidermal melanocytes

value: CXCL1 (100ng/ml) with 5 microM SX-682


title: mgm3044-3


title: NHEM, CXCL1, rep2

value: CXCL1 (100ng/ml)


title: mgm3044-2


title: NHEM, CXCL1, SX682, rep2


title: Late2Cell_Het_I8W_8

source_name: single embryo


title: NHEM, CXCL1, rep1


title: Late2Cell_Het_I8W_6


title: Late2Cell_Het_I8W_7


title: Late2Cell_Het_I8W_4


title: Late2Cell_Het_I8W_5


title: Late2Cell_Het_I8W_3


title: mgm3044-1


title: Early_2cell_WT_Input_S10

value: Early 2-cell


title: Late2Cell_KO_J10K_5


title: mgm3043-3

value: WT CarD


title: Late2Cell_Het_I8W_1


title: Late2Cell_Het_I8W_2


title: NHEM, rep2

value: Control


title: NHEM, rep1


title: Late2Cell_Het_I7W_8


title: mgm3043-2


title: Late2Cell_Het_I7W_5


title: Late2Cell_Het_I7W_7


title: mgm3043-1


title: Late2Cell_Het_I7W_4


title: Late2Cell_Het_I7W_6


title: R10-B

city: Trento

first: Erik

last: Dassi

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

data_processing:
Reads filtering (minimum base quality of Q30) and adapter trimming was performed with Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were aligned with meRanTK v1.2.1b (DOI: 10.1093/bioinformatics/btv647) using an index generated with the sequences of  5.8S, 18S, 28S, mt12S, and mt16S rRNAs obtained from the NCBI (https://www.ncbi.nlm.nih.gov/; #U13369.1:6623-6779, X03205.1, U13369.1:7935-12969, respectively.)). The meRanGs mode of meRanTK was used with default parameters.
The bisulfite-converted (RBS) and untreated samples (NBS) were then used as input for the ScorePseudouridinePosition tool of the RBSSeqTools v1.0 suite (23). For each RBS sample, the corresponding NBS sample was used as the non-bisulfite sample, using a threshold on the fraction of deletion reads at each position in the NBS sample of 10%. The per-position quantification and filtering produced by ScorePseudouridinePosition was used to analyze the fraction of modification of potential pseudouridine positions. The analysis on RBS samples consisted in filtering out positions not satisfying the following criteria: a) at least 10 reads in both RBS and NBS samples; b) at least 5 deletions in RBS; c) at least 5% of the reads with deletion on RBS samples; d) the percentage of deletion in NBS less than the threshold of 10%.
Assembly: hg38
Supplementary files format and content: tab-separated, fraction of modified reads at given position for each sample

source_name: breast

extract_protocol:
Total RNA was extracted from frozen specimens of 34 breast tumors using the mirVana miRNA isolation kit (ThermoFisher Scientific). Human total RNA (Human XpressRef Universal Total RNA, Qiagen) was used as normal reference samples for analysis.
RNA library construction was performed with the TruSeq Stranded mRNA kit (Illumina) with some modifications. In particular, 100 ng of each beads-purified aqueous RNA samples were submitted to a second round of RNACleanXP beads purification to substitute water with the FPF (Fragment, Prime, Finish Mix) solution included in the library kit. Then the manufacturer’s protocol was followed. The Unique-dual indexes (Illumina) were used in the adapters ligation step. Each individual library was then quantified and quality-controlled using Qubit Fluorometer (ThermoFisher Scientific) and LabChip GX (Perkin Elmer). An unbalanced pooling design was used to achieve a ratio of 1 to 8 between untreated and BS-treated samples. After libraries unbalanced pooling, the final pool was quality checked again with Qubit, LabChip GX, and qPCR (KAPA and BIORAD).

treatment_protocol: Bisulfite treatment was carried out as reported by Khoddami et al. Briefly, samples were incubated with 312 µl of freshly prepared 5M sodium bisulfite (pH 5) and 3 µl of freshly prepared 100mM hydroquinone at 50°C, rotating for 16 h. Desulfonation was performed adding 0.5 ml of 2M Tris buffer pH 9.0 at 37°C for 2 h. After ethanol purification, samples were resuspended in 20 mM MgCl2 and 50 mM Tris HCl pH 7 and incubated at 75°C for 15’.

value: breast

value: breast cancer

value: bisulfite


title: Digitalis lanata Root_6

city: BUFFALO

first: BARADWAJ

last: RAVI GOPAL

state: NEW YORK

address: 653 Cooke Hall

department: BIOLOGICAL SCIENCES

institute: STATE UNIVERSITY OF NEW YORK AT BUFFALO

data_processing:
Trinity assembler program (v2.8.4)
Trimmomatic tool embedded in the Trinity transcriptome assembler was used to remove Illumina sequencing adaptors, low-quality leading and trailing bases (below quality 5), cutting a sliding window of size 4 bp when their average quality drops below 5 and also filtering out reads below 25 bp.
De novo assembly of a single transcriptome (leaf and root) from the raw reads was done using the Trinity assembler program (v2.8.4) at the default k-mer value of 25
Bowtie2 (v2.3.4.3) was used to map raw reads to the assembled transcripts to ascertain completeness.
Trinity pipeline was used for differential expression (DE) analysis. As a prerequisite to DE analysis, abundance estimation of the transcripts was done using the alignment-based abundance estimation method, namely “RNA-Seq by Expectation-Maximization” (RSEM)
Assembly: mm10
Supplementary files format and content: File "Trinity_RSEM_trans.isoform.TMM.EXPR.matrix" is a tab-delimited text files include FPKM values for each sample
Supplementary files format and content: File "Dl_Transcriptome.fasta" is the transcriptome assembled by Trinity assembler program (v2.8.4) from all the samples

organism: Digitalis lanata

source_name: Root

growth_protocol: Digitalis lanata Ehrh seeds were procured from Strictly Medicinal (Williams, Oregon, USA). Seeds were germinated on the soil mix (57 g triple superphosphate, 85 g calcium hydroxide, 57 g bone meal, 369 g Osmocote (14-14-14), 99 g calcium carbonate, 25 L perlite, 50 L loosened peat and 25 L coarse vermiculite) and maintained in a growth chamber (Invitrogen, Clayton, Missouri, USA) under a light period of 16-hour at 25 ˚C and relative humidity of 60-80%.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Germantown, MD, USA).
The sequencing library was prepared from total RNA using the TrueSeq Ribo-Zero Plant RNA library prep kit (Illumina, San Diego, CA, USA) that removes ribosomal RNA. A quality check of the library was carried out with an Agilent 2100 bioanalyzer.

value: Root

value: WT


title: mgm3043-4


title: R10-A


title: Late2Cell_Het_I7W_3

value: Late 2-cell


title: Digitalis lanata Root_5


title: Late2Cell_Het_I7W_2


title: R-B


title: Late2Cell_Het_I6W_8


title: R-A


title: Digitalis lanata Root_4


title: Late2Cell_Het_I6W_7


title: Late2Cell_Het_I7W_1


title: Late2Cell_Het_I6W_6


title: Digitalis lanata Root_3


title: 9-NBS

value: untreated


title: Late2Cell_Het_I6W_5


title: R-NBS


title: Late2Cell_Het_I6W_3


title: Digitalis lanata Root_1


title: Late2Cell_Het_I6W_2


title: Digitalis lanata Root_2


title: 9-A


title: Late2Cell_Het_I2W_8


title: 8-NBS


title: Digitalis lanata Leaf_6

source_name: Leaf

value: Leaf


title: Late2Cell_Het_I2W_6


title: Late2Cell_Het_I2W_7


title: Digitalis lanata Leaf_5


title: Late2Cell_Het_I2W_5


title: 8-B


title: Digitalis lanata Leaf_4


title: Late2Cell_Het_I2W_3


title: 67-NBS


title: Digitalis lanata Leaf_3


title: 8-A


title: Late2Cell_Het_I2W_1


title: Late2Cell_Het_I2W_2


title: Late2Cell_Het_I12W_8


title: Digitalis lanata Leaf_2


title: Late2Cell_Het_I6W_4


title: 9-B


title: 67


title: Late2Cell_Het_I6W_1


title: Late2Cell_Het_I12W_7


title: Digitalis lanata Leaf_1


title: Late2Cell_Het_I12W_6


title: Late2Cell_Het_I12W_5


title: 61-NBS


title: HeLa-uninfected-mRNA

city: San Antonio

first: Yan

last: Xiang

state: TX

address: 7703 FLOYD CURL DR

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

description:
Homo sapiens
mRNA

data_processing:
for ribo-seq and rna-seq, The adaptor AAAAAAAAAAAA was trimmed by Cutadapt. The reads with length <15 nt were not included.  The trimmed reads were aligned to human and VACV transcriptome, using STAR with default parameters. The uniquely mapped reads were used for analysis.
Assembly: GRCh38，VACV-WR(NC_006998)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
For mRNA-seq, total cellular RNA was extracted with Trizol, and 5 μg of the total RNA was used for isolation of mRNA with the Poly(A) mRNA magnetic isolation module (NEB). For Ribo-seq, ribosome protected fragments were purified after RNase I treatment and ribosome recovery.
For mRNA-seq, the mRNA was heat fragmented with RNA Fragmentation Reagents (Thermo Fisher Scientific), and the cDNA library was constructed with NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). For Ribo-seq, 3’adaptor ligation, rRNA depletion, reverse transcription, circularization, and PCR amplification were performed

value: HeLa cells

value: uninfected


title: Late2Cell_Het_I12W_4

first: Guanghui

last: Yang


title: HeLa-WT-VACV-early-mRNA

description:
Homo sapiens+VACV
mRNA

value: infection with WT VACV with AraC


title: Late2Cell_Het_I2W_4


title: Late2Cell_Het_I12W_2


title: Late2Cell_Het_I12W_3


title: Late2Cell_Het_I12W_1


title: 60


title: Late2Cell_Het_I11W_8


title: Late2Cell_Het_I11W_7


title: 60-NBS


title: 61


title: Late2Cell_Het_I11W_5


title: Late2Cell_Het_I11W_6


title: Late2Cell_Het_I11W_4


title: HeLa-mut-VACV-mRNA

description:
Homo sapiens+VACV
mRNA

value: infection with vK1-C7- VACV


title: 58T


title: HeLa-mut-VACV-early-mRNA

description:
Homo sapiens+VACV
mRNA

value: infection with vK1-C7- VACV with AraC


title: 58T-NBS


title: HeLa-uninfected-RPF

description:
Homo sapiens
Ribosome protected fragment


title: 56-NBS


title: HeLa-WT-VACV-mRNA

description:
Homo sapiens+VACV
mRNA

value: infection with WT VACV


title: Late2Cell_Het_I11W_1


title: Late2Cell_Het_I11W_2


title: Late2Cell_Het_I11W_3


title: Early2Cell_KO_H7K_8

value: Early 2-cell


title: 56


title: Early2Cell_KO_H7K_7


title: HeLa-WT-VACV-early-RPF

description:
Homo sapiens+VACV
Ribosome protected fragment


title: Early2Cell_KO_H7K_6


title: Early2Cell_KO_H7K_5


title: HeLa-WT-VACV-RPF


title: 52-NBS


title: Early2Cell_KO_H7K_4


title: Early2Cell_KO_H7K_3


title: HeLa-mut-VACV-RPF


title: 52


title: HeLa-mut-VACV-early-RPF


title: Early2Cell_KO_H6K_6


title: Early2Cell_KO_H7K_2


title: 50-NBS


title: Early2Cell_KO_H6K_7


title: 3D 3T3-L1 DIF+ (2)

city: Sapporo

first: Tatsuya

last: Sato

state: Hokkaido

address: South-1, West-17, Chuo-ku

department: Department of Cellular Physiology and Signal Transduction

institute: Sapporo Medical University School of Medicine

data_processing:
The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7)
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0).
The HISAT2-resultant files were used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file

source_name: 3D cultured 3T3L-1 cells

growth_protocol: 3T3-L1 preadipocytes were cultured in planar 2D culture dishes at 37 °C in a high-glucose (HG)-DMEM medium supplemented with 8 mg/L d-biotin, 4 mg/L calcium pantothenate, 100 U/mL penicillin, 100 μg/mL streptomycin (b.p. HG-DMEM), 10% calf serum (CS) and methylcellulose (Methocel A4M).

extract_protocol:
Total RNA was extracted using an RNeasy mini kit (Qiagen, Valencia, CA). Reverse transcription was performed with the SuperScript IV kit (Invitrogen) according to the manufacturer’s instructions.
Libraries were prepared for sequencing using library creation kits (NEBNext Ultra Directional RNA Library Prep Kit, Illumina, San Diego, CA, USA)

treatment_protocol: After reaching approximately 90% confluence, the cells were divided into planar 2D cultures and 3D spheroid cultures using a hanging droplet spheroid 3D culture system. Under these conditions, the 2D planar cultured 3T3-L1 cells were maintained with medium changes daily until Day 7. Alternatively, in the 3D 3T3-L1 spheroid cultures, each well of the drop culture plate (#HDP1385, Sigma-Aldrich) was seeded with approximately 20,000 cells in 28 μL of the medium (3D/Day 0) and thereafter maintained by exchanging half of the culture medium each day until Day 7. To induce adipogenic differentiation, addition of 250 nM dexamethasone and 10 nM triiodothyronine (T3) during the initial two days, and addition of 10 μM troglitazone and 1 μg/ml insulin each day for 7 days was performed.

value: 3D cultured 3T3L-1 cells

value: preadiopcyte

value: 3D adipogenic differentiation


title: Early2Cell_KO_H6K_3

address: 50 South Drive

institute: National Institutes of Health


title: 49-NBS

value: breast

value: breast cancer


title: 3D 3T3-L1 DIF+ (1)


title: 50

value: bisulfite


title: Early2Cell_KO_H6K_4


title: 3D 3T3-L1 DIF- (2)


title: 3D 3T3-L1 DIF- (1)


title: Early2Cell_KO_H6K_5


title: 2D 3T3-L1 DIF+ (2)

source_name: 2D cultured 3T3L-1 cells

value: 2D cultured 3T3L-1 cells

value: 2D adipogenic differentiation


title: 48-NBS

value: untreated


title: 49


title: Early2Cell_KO_H4K_6


title: Early2Cell_KO_H6K_2


title: Early2Cell_KO_H4K_7


title: Early2Cell_KO_H6K_1


title: Early2Cell_KO_H4K_8


title: 48


title: Early2Cell_KO_H7K_1


title: Early2Cell_KO_H4K_4


title: 2D 3T3-L1 DIF- (2)


title: Early2Cell_KO_H4K_2


title: 47-NBS


title: 47


title: Early2Cell_KO_H4K_1


title: Early2Cell_KO_H3K_8


title: Early2Cell_KO_H3K_7


title: 46-NBS


title: Early2Cell_KO_H3K_3


title: Early2Cell_KO_H3K_5


title: Early2Cell_KO_H3K_4


title: 46-B


title: 45


title: 46-A


title: P3_ONC_1

city: Shantou

first: Ling-Ping

last: Cen

address: North Dongxia Road

institute: JSIEC

data_processing:
Illumina Casava1.8 software used for basecalling.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Files include gene counts and FPKM values for each Sample

source_name: retina

extract_protocol:
Retinas were removed and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: retina

tag: age

value: postnatal day (P) 3

value: wild type

value: optic nerve crush injury


title: 2D 3T3-L1 DIF+ (1)

tag: cell line


title: Early2Cell_KO_H3K_1

city: Bethesda


title: Early2Cell_KO_H3K_2


title: P3_ONC_4


title: P3_ONC_2


title: Early2Cell_KO_H4K_3


title: Early2Cell_KO_H2K_6


title: P3_ONC_3


title: P3_NTC_4

value: naïve control


title: 2D 3T3-L1 DIF- (1)


title: 42-NBS


title: P3_NTC_3


title: Early2Cell_KO_H2K_8


title: Early2Cell_KO_H2K_5


title: Early2Cell_KO_H4K_5


title: Early2Cell_KO_H3K_6


title: Early2Cell_KO_H2K_4


title: 42


title: P3_NTC_2


title: 45-NBS


title: Early2Cell_KO_H2K_2


title: Early2Cell_KO_H2K_7


title: 36-NBS


title: P3_NTC_1


title: Early2Cell_KO_H2K_1


title: Early2Cell_KO_H1K_8


title: 36


title: Early2Cell_KO_H1K_6


title: P1_ONC_4

value: postnatal day (P) 1


title: 35-NBS


title: Early2Cell_KO_H1K_5


title: Early2Cell_KO_H1K_7


title: 34-NBS


title: Early2Cell_KO_H1K_2


title: Early2Cell_KO_H1K_1


title: 35


title: Early2Cell_KO_H1K_4


title: P1_NTC_4


title: Early2Cell_KO_H1K_3


title: P1_ONC_2


title: P1_ONC_1


title: Early2Cell_Het_G9W_7


title: Early2Cell_Het_G9W_8


title: Early2Cell_KO_H2K_3


title: P1_NTC_3


title: 34-A


title: 34-B


title: Early2Cell_Het_G9W_5


title: P1_NTC_2


title: Early2Cell_Het_G9W_4


title: 33-NBS


title: Early2Cell_Het_G9W_3


title: P1_NTC_1


title: Early2Cell_Het_G9W_2


title: 33


title: Early2Cell_Het_G9W_1


title: Early2Cell_Het_G7W_7


title: E20_ONC_3

value: embryonic day (E) 20


title: Early2Cell_Het_G7W_8

value: Early 2-cell


title: 32-NBS


title: E20_ONC_2


title: 32


title: E20_ONC_1


title: 31-NBS


title: Early2Cell_Het_G7W_3


title: 31


title: E20_NTC_2


title: Early2Cell_Het_G9W_6


title: Early2Cell_Het_G6W_8


title: 28T-NBS


title: Early2Cell_Het_G7W_2


title: Early2Cell_Het_G7W_6


title: Early2Cell_Het_G7W_1


title: Early2Cell_Het_G6W_7


title: 28T


title: Early2Cell_Het_G6W_6


title: E20_NTC_1


title: Early2Cell_Het_G6W_4


title: PWK_0-2

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

description: 10x Visium RNA probes

data_processing:
spaceranger mkfastq v2.0.0
spaceranger count v2.0.0
Seurtat 4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

growth_protocol: SARS-CoV-2 (USA_WA1/2020) from University of Texas Medical Branch (Vero passage 4) was propagated on Vero cells cultured in DMEM supplemented with 10% fetal bovine serum, 1 mM L-glutamine, 50U/ml penicillin and 50ug/ml streptomycin.  Culture supernatants were collected at 72 hours post-inoculation, at stored at -80 C. Mice were inoculated by the intranasal routh with 10^3 plaque forming units of SARS-CoV-2 in a volume of 50 ul phosphate buffered saline.

extract_protocol:
Formalin-fixed paraffin-embedded tissues were sectioned directly onto 10X Visium Spatial slides and processed using 10X Visium spatial protocols.
RNA libraries were prepared for sequencing using the 10X Visium Spatial for FFPE Gene Expression protocols.

treatment_protocol: Mouse lung was insufflated with phosphate buffered saline to collect bronchoalveolar lavage fluid followed by insufflation with 10% formalin.  Samples were fixed in 10% formalin for at least 7 days and paraffin embedded.

value: lung

tag: time

value: naive

value: PWK/PhJ x K18 hACE2

value: uninf ctrl


title: Early2Cell_Het_G6W_5


title: Early2Cell_Het_G6W_2


title: B6_0-2

description: 10x Visium RNA probes

value: B6 x K18-ACE2


title: 28-B

value: breast

value: breast cancer

value: bisulfite


title: 28-NBS

value: untreated


title: PWK_0-1

description: 10x Visium RNA probes


title: Early2Cell_Het_G7W_4


title: Early2Cell_Het_G7W_5


title: E20_NTC_3

value: retina


title: B6_0-1

description: 10x Visium RNA probes


title: Early2Cell_Het_G6W_1


title: Mt4_NKX1

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
Sequencing reads were mapped using STAR against the Mus musculus genome (UCSC mm10), and gene level quantification was performed with featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file with featureCounts for all the samples combined

growth_protocol: All cell lines used in this study were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
ribosomal RNA depletion was performed using KAPA RiboErase kit (Roche) and libraries were prepared using KAPA Hyperprep kit (Roche) following manufacturer's protocols.

value: IPMN-associated cancer cells

value: Nkx6-2 overexpression


title: Mt4_NKX3


title: B6_6-3

description: 10x Visium RNA probes


title: 26-NBS


title: Mt4_NKX2


title: Mt4_control3

value: Control (WT)


title: 27-NBS


title: Early2Cell_Het_G5W_8


title: Early2Cell_Het_G5W_7


title: 28-A


title: PWK_3-3

description: 10x Visium RNA probes


title: Early2Cell_Het_G5W_6


title: Mt4_control2


title: Early2Cell_Het_G6W_3


title: PWK_6-3

description: 10x Visium RNA probes


title: Early2Cell_Het_G5W_5


title: B6_3-3

description: 10x Visium RNA probes


title: Mt4_control1


title: Early2Cell_Het_G5W_4


title: KPCt_NKX3

source_name: KPCt

value: KPCt


title: PWK_3-2

description: 10x Visium RNA probes


title: Early2Cell_Het_G5W_3


title: KPCt_NKX2


title: 27


title: B6_3-2

description: 10x Visium RNA probes


title: 23-B


title: KPCt_NKX1


title: KPCt_control3


title: 22-NBS


title: Early2Cell_Het_G4W_8


title: B6_6-2

description: 10x Visium RNA probes


title: KPCt_control2


title: Early2Cell_Het_G4W_7


title: Early2Cell_Het_G4W_6


title: 22


title: 26


title: PWK_6-1

description: 10x Visium RNA probes


title: 21-NBS


title: Early2Cell_Het_G4W_5


title: B6_6-1

description: 10x Visium RNA probes


title: PWK_3-1

description: 10x Visium RNA probes


title: 21-A


title: 23-A


title: Early2Cell_Het_G5W_2


title: 23-NBS


title: B6_3-1

description: 10x Visium RNA probes


title: Control_Brain

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

institute: Beijing Tiantan Hospital, Capital Medical University

description: 10x Genomics

data_processing:
Raw files (FASTQ format) were processed with Cell Ranger software (v5.0.1), which performed mapping to the mm10 transcriptome, filtering, barcode counting and UMI counting and finally generated feature-by-barcode UMI matrix. Scrublet software was employed to remove potential doublets for individual samples. Seurat (v3.1.5) was used for downstream analysis. Low-quality cells, <500 genes expressed or with <2500 UMIs, were excluded at the initial quality-control step. Cells >15% mitochondrial UMIs were removed. Library-size normalization was performed on the UMI-collapsed gene expression values for each cell barcode, by scaling the total number of transcripts and multiplying by 10,000. Data were then log-transformed for further downstream analysis.
Assembly: mm10
Supplementary files format and content: tab-separated values files

extract_protocol:
Single-cell suspensions were prepared from pooled mouse spleen and brain tissues at 72 h after ICH induced by autologous blood injection or sham operations.CD45+ cells were isolated at 4°C using flow-cytometry.As there are few T cells in sham brain, we optimized the  FACS-sorting and also isolated the the CD45hi cells in the sham brain. This allows us to obtain enough CD4+ T cells in sham brains for sub-clustering and data processing.
Library was performed according to the manufacter’s instructions (single-cell 3' v.2 kit, 10× Genomics). Cell viability was ≥90% for all samples. Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel beads-in- emulsion (GEM), which were used to reverse-transcribe mRNA and amplify the derived cDNA. Specifically, gel beads work as delivery system of millions of oligo primers each containing (a) a partial Read 1 primer sequence used for sequencing on the flow cell, (b) a 16-bp cell barcode called 10× barcode that serves as the unique molecular address for that particular bead, (c) the unique molecular identifier (UMI) which is a 10-bp randomer different for each oligo of a bead used for digital mRNA counting, and (d) a 30-bp poly dT tail which allows the primers to hybridize to mature mRNAs for first-strand cDNA synthesis. Once partitioned with the cells and reverse transcription (RT) reagents, the gel bead dissolves and its oligo primers are released into the aqueous environment of the GEM. The cell captured in the GEM is also lysed and the content of the GEM (oligos, lysed cell components, and master mix) is incubated in an RT reaction to generate full-length, barcoded cDNA from the poly A-tailed mRNA transcripts. The RT reaction is primed by the barcoded gel bead oligo and the reverse transcriptase incorporates a template switch oligo via a template switching reaction at the 50 end of the transcript. The GEMs are then broken and single-stranded barcoded cDNAs from thousands of cells are pooled. A bulk cDNA PCR amplification follows to generate enough material for library generation. During library preparation after an enzymatic fragmentation, Read 2 is added by adapter ligation, and finally paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Brain

value: CD45+ cells

value: Sham induction


title: Early2Cell_Het_G4W_3

value: Early 2-cell


title: Early2Cell_Het_G4W_4


title: Early2Cell_Het_G4W_2


title: 19-NBS


title: PWK_6-2

description: 10x Visium RNA probes

value: lung


title: BMMCs, PMA Ionomycin, 1

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

country: Switzerland

institute: Institute for Research in Biomedicine

data_processing:
Reads were de-multiplexed based on the experimental barcode and adapter sequences were removed from the read ends (Flexbar v3.5.0). UMIs were trimmed and added to the read names. Individual samples were mapped to the respective genome (assembly version GRCm38.p6 for all mouse samples) and its annotation (GENCODE release M25 for all mouse samples) using STAR (v2.7.6a). Reads were de-duplicated if they had identical UMIs. Significant crosslink sites at single-nucleotide resolution were called using PureCLIP (v.1.3.1) with default parameters, and individual crosslink sites within a distance of 8 bp of each other were merged into wider binding regions (peaks). For assigning a host gene to each PureCLIP peak, transcript annotations were taken from GENCODE release M32, mm39.
Assembly: GRCm39
Supplementary files format and content: Bigwig files were generated usingbed GraphToBigWig.

source_name: BMMCs

extract_protocol: Total RNA was isolated with TRIzol. For mRNA purification, two rounds of poly(A) selection were perfomed using Dynabeads mRNA purification kit (Ambion) according to the manufacturer’s instructions, which was followed by fragmentation using RNA fragmentation reagents (Invitrogen). To verify the size of fragmented mRNAs, the mRNA samples were analyzed with the Agilent RNA 6000 pico kit on an Agilent 2100 Bioanalyzer System. The fragmented mRNA samples were incubated with anti-m6A antibody (Synaptic Systems) and cross-linked twice with 150 mJ/cm2 UV light (254 nm) in a Stratalinker. After cross-linking, the solution was further incubated with protein A beads. After stringent washing, RNA 3’ ends were dephosphorylated with T4 PNK and subsequentlys the 3’ adaptor was ligated. The samples were radioactively end-labled and were subjected to NuPAGE gel electrophoresis and tranferred onto Nitrocellulose Membrane. The RNA was isolated from the membrane by treatment with proteinase K. After phonol/chloroform extraction and precipitation, the RNA was reversed transcribed and cDNA was purified with Dynabeads MyOne Silane (Invitrogen). The 5’ adaptor was ligated. First-strand cDNA was synthesized with 6 cycles and size-selected using ProNex Size-Selective Purification System (Promega). Libraries were PCR amplified for 8–13 cycles and sequencing was performed on an Illumina sequencer.

value: BMMCs

value: wild type

value: PMA Ionomycin

value: anti-m6A antibody (SynapticSystem)


title: 19-B

value: breast

value: breast cancer


title: 21-B

value: bisulfite


title: BMMCs, PMA Ionomycin, 3


title: Early2Cell_Het_G4W_1

state: Maryland

department: National Institute of Diabetes and Digestive and Kidney Diseases


title: KPCt_control1


title: 19-A


title: Male_low

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

data_processing:
Paired-end (150 + 150) FASTQ files were subjected to trimGalore pre-processing to remove Illumina adaptor sequences and low quality reads (Q<30).
Trimmed FASTQ files were analyzed using the Bismark toolkit to examine CpG methylation. Bismark aligned FASTQ data to the mm10 mouse reference genome using Bowtie2.
Bismark generated .begGraph files reporting CpG site coordinates and their degree of DNA methylation (0-100%).
CpG sites were classified based on their degree of methylation and linked to known mouse repetitive sequences registered in the RepeatMasker file of mm10.
Assembly: mm10
Supplementary files format and content: BedGraph files include coordinates and methylation of CpG sites.

source_name: embryonic gonad

extract_protocol:
Genomic DNA was isolated from FACS-enriched mouse primordial germ cells (20,000 - 30,000 cells) using AllPrep Micro Kit (QIAGEN) and subjected to bisulfite conversion using EZ DNA Methylation-Gold Kit (Zymo Research) following manurfacturers' instructions.
Illumina libraries were synthesized using Accel-NGS Methyl-seq DNA Library Kit (Swift Biosciences) following manufacturer's instructions.

value: embryonic gonad

tag: generation

value: primordial germ cell

value: M

value: Exposed to 0.033 mg/kg/day BaP


title: Male_oil

value: Exposed to vehicle control


title: BMMCs, unstimulated, 2

value: unstimulated


title: 18-NBS

value: untreated


title: Early2Cell_Het_G1W_6


title: BMMCs, unstimulated, 1


title: Early2Cell_Het_G1W_7


title: Male_high

value: Exposed to 2 mg/kg/day BaP


title: 18-B


title: Female_oil

value: F


title: BMMCs, PMA Ionomycin, 2


title: Early2Cell_Het_G1W_5

value: Early 2-cell


title: BMMCs, Input, 2

value: BMMCs

value: Input


title: BMMCs, Input, 3

value: wild type


title: Female_low


title: BMMCs, unstimulated, 3

value: anti-m6A antibody (SynapticSystem)


title: 18-A

value: breast


title: Early2Cell_Het_G1W_4


title: 15-NBS

value: breast cancer


title: 15

value: bisulfite


title: Early2Cell_Het_G1W_3


title: Female_high

value: embryonic gonad


title: 13-NBS


title: 13-B


title: liver, patient11, week24

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

description: Viral reads were identified using Viral-Track from the 10X Genomics scRNA-Seq of fine needle aspirates from the liver of patients treated with Tenofovir Alafenamide

data_processing:
The viral read filtering and alignment were performed using Viral-Track(https://github.com/PierreBSC/Viral-Track)using the viruSITE database (http://www.virusite.org/index.php)
Assembly: viruSITE database (release2020.3)
Supplementary files format and content: Alignment files for Hepatitis B viral reads in BAM format
Supplementary files format and content: Viral read coverage matrix files in text format

organism: Hepatitis B virus

source_name: liver

extract_protocol:
After taking FNAs from the patients, samples were maintained on ice and immediately processed. After quality control steps, red blood cells were removed by 5 min incubation with Red Blood Cell Lysis Buffer (BioLegend) and subsequent 10x dilution with PBS. Cells were washed, counted, and subjected to scRNAseq.
Samples were prepared as outlined by the 10x Genomics Single Cell 5’ Reagent Kit user guide.
The molarity of each library was calculated based on library size as measured by the Bioanalyzer (Agilent Technologies) and qPCR amplification data. Samples were pooled and adjusted to 10 nM, then diluted to 2 nM. Each 2 nM pool was denatured. Library pools were further diluted to a final loading concentration of 14 pM. 150 μl were loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on the HiSeq 2500 (Illumina) system.

tag: disease state

value: Hepatitis B

value: liver

value: Tenofovir Alafenamide


title: liver, patient11, week0


title: liver, patient11, week12


title: Early2Cell_Het_G1W_1

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file, then mapped to the reference genome using STAR ver. 2.7.6a. The reference genome contains sequences of GRCm38 and ERCC spike-ins.
StringTie ver. 2.1.4 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 101) and from ERCC spike-in product page.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM, TPM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Zygotes were collected from 6-8-week-old female mice after hormone simulation and mating. The zygotes were cultured in vitro to collect embryos at different developmental stages. M2 eggs were collected from hormone simulated females without mating. M2 eggs or embryos were washed in PBS and transferred into acidic Tyrodes solution to remove zonae pellucidae. Single zona-free eggs or embryos were finally lysed and processed following the scNMT-seq protocol.
G&T-Seq protocol was used to construct single embryo RNA-Seq libraries.

tag: female mouse donor genotype


title: liver, patient10, week12


title: Early2Cell_Het_G1W_2


title: E2C_KO_Ribo2

description: Ribosome protected RNA fragments, S12

library_source: other

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using cutadapt by indicating “AAAAAAAAAA” as the adapter sequence file, then mapped to the reference genome using STAR ver. 2.7.6a. The reference contained annotation of GRCm38 and rDNA.
Bam files containing only uniquely mapped reads were extracted and StringTie ver. 2.1.4 was used to generate counts of genes in the reference. deepTools ver. 3.5.1 was used to normalize the bam files by RPKM and generate the bigWig files.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM, TPM values for each sample.
Supplementary files format and content: bigWig file of uniquely mapped reads for each sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Library strategy: Ribo-seq

molecule: other

source_name: Early 2-cell embryos

extract_protocol:
~200 oocytes or zygote, or ~100 early 2-cell embryos were used as one group for low input ribo-seq. Collected samples were washed with PBS and transferred into 1.5 ml nuclease free centrifuge tubes with a minimal volume of PBS. The tubes were frozen immediately in dry ice and stored at -80 until use.
The EZ-Manga RIP kit (Millipore 17-701) and anti-HA beads (Pierce 88836) were used for the low input ribo-seq experiment. Samples were first lysed following the RIP kit manual and then 100U RNase I (Ambion AM2294) was added to each tube for RNA digestion. The digestion was done at room temperature for 45 min. After digestion, anti-HA magnetic beads were added to each tube to finish IP at 4 degrees for 4h following the manual. 7ul ultrapure water supplied with 0.25 ul RNase inhibitor from the SMARTer smRNA-Seq Kit (Takara 635029) was added to each tube and the tubes were heated for 15min at 70 degrees to denature the proteins and RNAs inside. The tubes were transferred to ice immediately after heating and the remaining part of the manual was followed to finish library construction. 22 PCR cycles were used for indexing of libraries and the finial PCR products were purified with AMPure XP beads (Bechman A63881) for 2 time at 1:1.5 ratio.

value: Early 2-cell embryos

tag: female mice donor genotype

value: Eif4e1b KO; Rpl22 HA


title: PN5_KO_Ribo3

description: Ribosome protected RNA fragments, S14

source_name: PN5 zygotes

value: PN5 zygotes


title: E2C_Het_Ribo3

description: Ribosome protected RNA fragments, S15

value: Eif4e1b Het; Rpl22 HA


title: PN5_KO_F8K_8


title: PN5_KO_F8K_7


title: PN5_Het_Ribo3

description: Ribosome protected RNA fragments, S13


title: 10-NBS

value: untreated


title: liver, patient10, week0


title: PN5_KO_F8K_6


title: E2C_KO_Ribo1

description: Ribosome protected RNA fragments, S11

value: Early 2-cell


title: 10-B


title: BMMCs, Input, 1

value: BMMCs


title: PN5_KO_F8K_5


title: 10-A


title: liver, patient9, week0


title: E2C_Het_Ribo1

description: Ribosome protected RNA fragments, S9


title: PN5_KO_F8K_4


title: liver, patient8, week24


title: PN5_KO_Ribo2

description: Ribosome protected RNA fragments, S8


title: PN5_KO_Ribo1

description: Ribosome protected RNA fragments, S7


title: liver, patient8, week12


title: PN5_KO_F8K_2


title: PN5_KO_F8K_3


title: liver, patient8, week0


title: PN5_Het_Ribo2

description: Ribosome protected RNA fragments, S6


title: PN5_KO_F8K_1


title: 16HBE14o- CFTRlow #12 rep2 [RNA-seq]

city: Cleveland

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.7 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using DAVID 2021.
Assembly: hg19
Supplementary files format and content: CSV file includes normalized count values for each sample

growth_protocol: Cells were grown in DMEM + 10% FBS using standard methods

extract_protocol:
Confluent 16HBE14o- cells were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and Bioanalyzer. Samples stored at -80oC under ethanol.
Oligo-dt mRNA directional

value: human bronchial epithelial cells

value: CFTRlow


title: 16HBE14o- CFTRlow #12 rep1 [RNA-seq]


title: 16HBE14o- CFTRlow #3 rep3 [RNA-seq]


title: liver, patient4, week24


title: PN5_Het_Ribo1

description: Ribosome protected RNA fragments, S5


title: 16HBE14o- CFTRlow #12 rep3 [RNA-seq]


title: liver, patient4, week0


title: PN5_KO_F7K_8


title: 16HBE14o- CFTRlow #3 rep2 [RNA-seq]


title: liver, patient9, week24


title: E2C_Het_Ribo2

description: Ribosome protected RNA fragments, S10


title: M2_KO_Ribo2

description: Ribosome protected RNA fragments, S4

source_name: M2 eggs

value: M2 eggs


title: 16HBE14o- CFTRlow #3 rep1 [RNA-seq]


title: PN5_KO_F7K_7


title: M2_KO_Ribo1

description: Ribosome protected RNA fragments, S3


title: ∆ntrC xylX::pPTM057-3xFLAG-ntrC output DNA

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Paired-end reads were mapped to the C. crescentus NA1000 reference genome (GenBank accession number CP001340) with CLC Genomics Workbench 20 (Qiagen). Peak calling was performed with the Genrich tool (https://github.com/jsh58/Genrich) on Galaxy; peaks are presented in Table S2. Briefly, PCR duplicates were removed from mapped reads, replicates were pooled, input reads were used as the control dataset, and peak were called using the default peak calling option [Maximum q-value: 0.05, Minimum area under the curve (AUC): 20, Minimum peak length: 0, Maximum distance between significant sites: 100].     To identify promoters that contained NtrC peaks, promoters were designated as 300 bp upstream and 100 bp downstream of the transcription start sites (TSS) annotated for each operon (65, 66). For genes/operons that did not have an annotated TSS, the +1 nucleotide of the first gene in the operon was designated as the TSS. Promoters were defined as containing an NtrC peak if there was any overlap between the NtrC ChIP-seq peak and the indicated promoter. To compare the relative location of NtrC binding sites with various cell cycle regulators, ChIPpeakAnno (67) was used to determine distance from the summit of the NtrC peaks to the nearest CtrA, SciP, MucR1, and GapR peak summit. To compare the relative location of NtrC binding sites with various cell cycle regulators, ChIPpeakAnno (67) was used to determine distance from the summit of the NtrC peaks to the nearest CtrA, SciP, MucR1, and GapR peak summit. ChIP-seq peaks (50 bp windows) for CtrA, SciP, and MucR1 were derived from (17) and the summits were considered the center of the 50 bp window. ChIP-seq summits for GapR were derived from (16). For motif discovery, sequences of the ChIP-seq peaks were submitted to MEME suite (68). Sequences were scanned for enriched motifs between 6 and 30 bp in length that had any number of occurrences per sequence.
Assembly: NA1000 Caulobacter crescentus
Supplementary files format and content: Processed data file contains log2 fold enrichment of reads (output DNA/input DNA) (SCD_346/SCD_345)

organism: Caulobacter vibrioides NA1000

source_name: cultures

growth_protocol: The ∆ntrC xylX::pPTM057-3xFLAG-ntrC strain was grown overnight in PYE at 30˚C. The overnight culture was diluted to OD660 0.1 in PYE and outgrown for 2 h at 30˚C. This culture was back-diluted to OD660 0.1 in PYE supplemented with 50 µM cumate and grown for 3.25 h at 37˚C to induce 3xFLAG-ntrC during log-phase growth.

extract_protocol:
To crosslink 3xFLAG-NtrC to DNA, formaldehyde was added to 125 ml of culture to a final concentration of 1% (w/v) and shaken at 37˚C for 10 min. The crosslinking was quenched using a final concentration of 125 mM glycine and shaken at 37˚C for 5 min. Cells were pelleted by centrifugation at 7,196 x g for 5 min at 4˚C. Supernatant was removed and the pellet was washed 4 times with ice-cold PBS pH 7.5. To lyse the cells, the washed pellet was resuspended in 1 ml lysis buffer [10 mM Tris pH 8, 1 mM EDTA, protease inhibitor tablet (Roche), 1 mg/ml lysozyme].  After a 30 min incubation at 37˚C for 0.1% (w/v) sodium dodecyl sulfate (SDS) was added. To shear the genomic DNA to 300-500 bp fragments, the lysate was sonicated on ice for 10 cycles (20% magnitude for 20 sec on/off pulses using a Branson Sonicator). Cell debris was cleared by centrifugation (15,000 x g for 10 min at 4°C). Supernatant was transferred to a clean tube and Triton X-100 was added to a final concentration of 1% (v/v). The sample was pre-cleared via incubation with 30 µl of SureBeads Protein A magnetic agarose beads (BioRad) for 30 min at RT. The supernatant was transferred to a clean tube and 5% of the total lysate was saved as the input DNA reference sample.  Pulldown was performed as previously described (58). Briefly, 100 ul magnetic agarose anti-FLAG beads (Pierce / Thermo) were pre-equilibrated in binding buffer [10 mM Tris pH 8 at 4°C, 1 mM EDTA, 0.1% (w/v) SDS, 1% (v/v) Triton X-100] supplemented with 1% (w/v) bovine serum albumin (BSA) overnight at 4˚C, washed with binding buffer and incubated in the lysate for 3 hours at room temperature.  Beads were cleared from the lysate with a magnet, and washed with a low-salt buffer [50 mM HEPES pH 7.5, 1% (v/v) Triton X-100, 150 mM NaCl], followed by a high-salt buffer [50 mM HEPES pH 7.5, 1% (v/v) Triton X-100, 500 mM NaCl], and then LiCl buffer [10 mM Tris pH 8 at 4°C, 1 mM EDTA, 1% (w/v) Triton X-100, 0.5% (v/v) IGEPAL CA-630, 150 mM LiCl].  Finally, beads were incubated with 100 ul elution buffer [10 mM Tris pH 8 at 4°C, 1 mM EDTA, 1% (w/v) SDS, 100 ng/μl3xFLAG peptide] for 30 minutes at room temperature.  After pulldown, the input sample was brought to equal volume as the output/pulldown sample using elution buffer [10 mM Tris pH 8, 1 mM EDTA pH 8, 1% SDS, 100 ng/µl 3xFLAG peptide]. Input and output samples were supplemented with 300 mM NaCl and 100 µg/ml RNAse A and incubated at 37°C for 30 min. Proteinase K was added to samples at a final concentration of 200 µg/ml and samples were incubated overnight at 65°C to reverse crosslinks. Samples were purified using the Zymo ChIP DNA Clean & Concentrator kit.  ChIP DNA was sequenced at SeqCenter (Pittsburgh, PA).  Briefly, sequencing libraries were prepared using the Illumina DNA prep kit and sequenced (150 bp paired end reads) on an Illumina Nextseq 2000.
Library preparation was performed using the Illumina DNA prep kit and 10bp UDI indices

value: cultures


title: PN5_KO_F7K_6

source_name: single embryo


title: M2_Het_Ribo2

description: Ribosome protected RNA fragments, S2


title: ∆ntrC xylX::pPTM057-3xFLAG-ntrC input DNA


title: PN5_KO_F7K_5


title: 16HBE14o- CFTRhigh #7 rep3 [RNA-seq]

value: CFTRhigh


title: 16HBE14o- CFTRhigh #7 rep2 [RNA-seq]


title: 13-A

source_name: breast

value: breast

value: breast cancer

value: bisulfite


title: PN5_KO_F7K_4


title: 16HBE14o- CFTRhigh #7 rep1 [RNA-seq]


title: M2_Het_Ribo1

description: Ribosome protected RNA fragments, S1


title: PN5_KO_F7K_3


title: WT dsDNA+anti-IFNARab, 4 biol replicates (cell culture), scRNA-seq

city: La Jolla

first: Kevin

middle: Robert

last: King

email: krking@health.ucsd.edu, krking@ucsd.edu

state: CA

address: 9500 Gilman Dr

department: Bioengineering; Medicine

institute: University of California San Diego

description: 10X Genomics

data_processing:
The alignments, filtering, and demultiplexing of generated fastq files were run with the 10X Genomics Cell Ranger analysis pipeline using standard configurations (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Variations in sequencing depth were accounted for by scaling each cell's total transcript count to 10,000 molecules and normalizing raw counts for each gene to the total transcript count for that cell followed by natural log transformation. Cells with between 200 and 2000 uniquely expressed genes and < 1% mitochondrial counts were retained for analysis. Highly variable genes were identified using the FindVariableFeatures method from seurat R package (version 3.0) to select 3000 genes with the highest variance after variance-stabilizing transformations.
Multiple single-cell RNA-seq datasets were integrated in Seurat to allow harmonized clustering and downstream analysis across conditions. Anchoring cell pairs between the datasets were identified with Canonical Correlation Analysis (CCA) and Mutual Nearest Neighbors (MNN) methods with the Seurat FindIntegrationAnchors function.
After scaling and centering expression values for each variable gene, the integrated data underwent linear dimensionality reduction using principal component analysis (PCA). Clustering was performed through the Shared Nearest Neighbor (SNN) clustering algorithm with Louvain method for modularity optimization using the Seurat FindNeighbors and FindClusters functions. Two-dimensional data visualization was done by performing Uniform Manifold Approximation and Projection (UMAP) demensional reduction, and differentially expressed genes (DEGs) between clusters were identified with the Wilcoxon Rank Sum test. Wherever specified, subsets of cells were bioinformatically isolated and reclustered to identify DEGs.
Assembly: GRCm38.p5
Supplementary files format and content: Tab-separated values files and counts matrix files consisting of matrix.mtx, features.tsv, barcodes.tsv

source_name: Bone Marrow

extract_protocol:
Femurs and tibia were harvested from C57BL6 or IFNAR-/- mice. Bone marrow cells were flushed from femurs with ice-cold PBS and filtered through a 40 µm nylon mesh. The filtered solution was treated with red blood cell (RBC) lysis buffer (BioLegend). Bone marrow cells were flushed from femurs with ice-cold PBS and filtered through a 40 µm nylon mesh. The filtered solution was treated with red blood cell (RBC) lysis buffer (BioLegend).
Single cell libraries were prepared according to standard 10X Genomics protocols
Dual index Illumina single cell RNA sequencing

value: Bone Marrow

value: Bone marrow derived monocytes

value: M-CSF (Peprotech), HT DNA (Invivogen), MAR1-5A3 IFNAR neutralizing antibody (BioXCell)


title: PN5_KO_F7K_1


title: 16HBE14o- CFTRhigh #4 rep3 [RNA-seq]


title: IFNAR KO Control, 3 biol replicates (cell culture), scRNA-seq

description: 10X Genomics

value: M-CSF (Peprotech)


title: PN5_KO_F7K_2


title: ∆ntrC PglnBA::IS3 PYE log phase - rep 1

data_processing:
Reads were mapped to NA1000 Caulobacter crescentus genome and normalized using default settings for RNA-seq workflow in CLC Genomics Workbench v 21
Assembly: NA1000 Caulobacter crescentus
Supplementary files format and content: processed data file contains normalized counts (counts per million (CPM)) for each annotated gene in NA1000 Caulobacter crescentus genome

growth_protocol: Starter cultures were grown for 18 hours at 30˚C in PYE or PYE plus 9.3mM (final concentration) glutamine. Cultures were then diluted to OD660 0.1 in their respective medium and grown for 2 h to get the cultures in similar (logarithmic) phase of growth. Once again, cultures were diluted to OD660 0.1 in their respective medium and grown another 3.25 h (OD660 < 0.4) to capture mRNA in similar log-phase growth.

extract_protocol:
6 ml of each culture were pelleted via centrifugation (1 min at 17,000 x g). Pellets were immediately resuspended in 1ml TRIzol and stored at -80˚C until RNA extraction. To extract RNA, thawed samples were incubated at 65˚C for 10 min. After addition of 200 µl of chloroform, samples were vortexed for 20 s and incubated at RT for 5 min. Phases were separated by centrifugation (10 min at 17,000 x g). The aqueous phase was transferred to a fresh tube and an equal volume of isopropanol was added to precipitate the nucleic acid. Samples were stored at 80˚C (1 h to overnight), then thawed and centrifuged at 17,000 x g for 30 min at 4˚C to pellet the nucleic acid.  Pellets were washed with ice-cold 70% ethanol then centrifuged for at 17,000 x g for 5 min at 4˚C.  After discarding the supernatant, pellets were air-dried at RT, resuspended in 100 µl RNAse-free water, and incubated at 60˚C for 10 min. Samples were treated with TURBO DNAse (Invitrogen) following manufactures protocol for 30 min at RT and then column purified using RNeasy Mini Kit (Qiagen).  RNA samples were sequenced at SeqCenter (Pittsburgh, PA). Briefly, sequencing libraries were prepared using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and custom rRNA depletion probes.  50 bp paired end reads were generated using the Illumina NextSeq 2000 platform (Illumina).
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices

treatment_protocol: For glutamine treatment conditions, 9.3 mM (final concentration) glutamine was added to growth medium


title: WT dsDNA, 4 biol replicates (cell culture), scRNA-seq

description: 10X Genomics

value: M-CSF (Peprotech), HT DNA (Invivogen)


title: ∆ntrC PYE + 9.3 mM gln log phase - rep 3

value: 9.3 mM (final concentration) glutamine


title: 16HBE14o- CFTRhigh #4 rep1 [RNA-seq]


title: WT Isotype Control, 3 biol replicates (cell culture), scRNA-seq

description: 10X Genomics

value: M-CSF (Peprotech), Isotype Antibody Control (BioXCell)


title: ∆ntrC PYE + 9.3 mM gln log phase - rep 2


title: PN5_KO_F6K_7


title: ∆ntrC PYE + 9.3 mM gln log phase - rep 1


title: PN5_KO_F6K_8