title: Control_C4

status: Public on Jan 06 2021

first: Jin

last: Li

address: 99 Shangda Road

institute: Shanghai University

description: gastrocnemius muscles from mice that without denervation of the right sciatic nerve, which is control

hyb_protocol: The purified cRNA were hybridized for 17 hr at 65°C on Agilent Mouse lncRNA array（4*180K，Design ID：049801）.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies)was used to analyze array images to get raw data. Genespring were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis.
Differentially expressed genes were then identified through fold change as well as P value calculated with t-test.

label_protocol: Total RNA were reverse transcribed into cDNA, labeled with Cyanine-3-CTP, and then synthesized to cRNA.

growth_protocol: All mice maintained in specific pathogen-free (SPF) laboratory animal facility of Shanghai University (Shanghai, China). All procedures with animals followed guidelines on the use and care of laboratory animals for biomedical research published by National Institutes of Health (No. 85-23, revised 1996), and approved by the committee on the Ethics of Animal Experiments of Shanghai University.

extract_protocol: Total RNA were isolated using mirVanaTM RNA Isolation Kit according to the manufacturer's instructions.

treatment_protocol: The model of denervation-induced muscle atrophy was achieved through cutting a small section of the sciatic nerve by micro clipping and ensuring no docking of the severed nerve. Mice that had not severed the sciatic nerve were used as controls. gastrocnemius muscles samples were harvested 7 days post denervation and snap frozen in liquide nitrogen.

tag: mouse model

value: Male

value: 10 week

value: gastrocnemius muscles


title: K562_4sUchr_ONT_5b

type: SRA

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

description: K562 4sU labeled chromatin-associated RNA with rRNA depletion, poly(I) tail addition and direct RNA sequencing rep 5b

library_source: transcriptomic

data_processing:
Library strategy: nano-COP
Raw signal fast5 files were basecalled during sequencing with MINKNOW. RNA sequences that pass basecalling thresholds were converted into DNA by substituting U to T bases before sequence alignment. Sequences were aligned to the reference genomes using minimap2 (version 2.10-r764-dirty) with recommended parameters for Oxford Nanopore Technologies direct RNA sequencing (-ax splice -uf -k14) or cDNA sequencing (-ax splice). All analyses were performed using reads that pass the MINKNOW sequencing threshold (QC>7) and align uniquely to the genome.
The splice_df datasets were generated by first intersecting reads with constitutively spliced introns. Constitutively spliced introns with “medium stringency” included in this dataset have at least 20 reads total RNA-seq dataset that span either splice junction by at least 4 nt overlap and more than 80% of the spanning reads are spliced. For reads mapping to constitutive introns, the features of read cigar strings were extracted for the 50 nt around the intron 5’ and 3’ splice sites and the entirety of the intron. Reads were called as ‘not spliced’ if the alignment file shows no indication of splicing within the 50 nt around each splice site, mapped portions of the read (rather than deletions) represent greater than 50% of the 50 nt around each splice site, and at least 75% of the read within the intron is aligned to the reference. Reads were called as ‘spliced’ if the alignment file displays the start or end of a splicing event within the 50nt around both splice sites and the size of the aligned splicing event is within 90-110% and 100 nt of the intron size. If aligned reads that map to introns do not meet these qualifications, the splicing event is characterized as ‘undetermined’ and not used in subsequent analyses. Other information included in this file include the soft clipped length at the start of the read alignment, the distance between the read start (or aligned RNA end) and the 3’SS of the intron, and whether or not the read start (or aligned RNA end) is close to the poly(A) site of a gene (within 150 nt upstream or any distance downstream of the annotated poly(A) site of the gene)
The polyA_polyI_estimates datasets were obtained with nanopolish_polyI using default parameters
Genome_build: hg38

molecule: total RNA

organism: Homo sapiens

source_name: K562 cells

growth_protocol: K562 cells (ATCC, CCL-243) were maintained at 37°C and 5% CO2 in RPMI 1640 medium containing 10% FBS, 100 U/ml penicillin and 100 ug/ml streptomycin

extract_protocol: Oxford Nanopore Technologies direct RNA sequencing with SQK-RNA002 kit

tag: cell line

tag: rna preparation

value: 4-thiouridine (4sU) labeling (500 uM, 8 minutes), cellular fractionation and purification of chromatin-associated RNA, 4sU biotinylation and streptavidin pulldown


title: K562_4sUchr_cDNA_2

description: K562 4sU labeled chromatin-associated RNA with rRNA depletion, poly(I) tail addition and direct cDNA sequencing

extract_protocol: Oxford Nanopore Technologies direct cDNA sequencing with SQK-DCS109 kit


title: K562_mRNA_polyI

description: K562 total RNA with polyA+ RNA selection, poly(I) tail addition and direct RNA sequencing

value: total RNA extraction with Qiagen miRNeasy kit, polyA+ RNA selection with oligodT beads


title: K562_chr_RNA_2

description: K562 chromatin-associated RNA with rRNA depletion, poly(I) tail addition and direct RNA sequencing

value: cellular fractionation and purification of chromatin-associated RNA


title: K562_chr_RNA_1

description: K562 chromatin-associated RNA with rRNA depletion, poly(A) tail addition and direct RNA sequencing


title: Enok_Input_1

status: Public on Jan 07 2021

city: Taipei

first: Fu

last: Huang

address: 128, Academia Road Sec. 2, Nankang

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

library_source: genomic

data_processing:
Adapter trimming was done with Trimmomatic. (Bolger et al., 2014. PMID: 24695404)
Fastq files were aligned to UCSC dm3 with Bowtie2-2.2.1. (Langmead et al., 2012. PMID: 22388286)
MACS2 was used to call peaks with default settings (callpeak), additional parameters (--p-value 5e-2), and PCR duplicates were removed. An additional cutoff of p-value less than 1e-15 was applied. (Zhang et al., 2008. PMID: 18798982)
Genome_build: UCSC dm3
Supplementary_files_format_and_content: The tab-delimited text files include peak information (position, -LOG10(pvalue) and -LOG10(qvalue), and fold enrichment) of Enok_IP_1 and Enok_IP_2.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were grown at 25C. Females were collected after 24-48 hr after eclosure and conditioned with wet yeast paste for 24 hr before ovary dissection.

extract_protocol:
Lysates were prepared from sonicated nuclei and Enok-DNA complexes were isolated with the anti-Enok antibody.
Libraries were prepared according to Illumina's instructions. Barcodes used for each sample are as follows: Enok_IN_1—AGTTCC, Enok_IN_2—ATCACG, Enok_IP_1—GTGGCC, Enok_IP_2—TAGCTT

tag: tissue

value: ovary

tag: developmental stage

value: 2-3 day old adult

tag: genotype

value: Oregon-R

tag: antibody


title: Denervation_D5

type: RNA

city: Shanghai

country: China

description: gastrocnemius muscles from mice that have undergone denervation of the right sciatic nerve,which is muscle atrophy model

organism: Mus musculus

value: denervation of the right sciatic nerve; muscle atrophy model

tag: Sex

tag: age


title: Denervation_D7

source_name: gastrocnemius muscles from mice that have undergone denervation of the right sciatic nerve


title: run1_CC5390_Fe_neg

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

country: USA

institute: UCLA

data_processing:
Libraries were sequenced by Illumina NextSeq500 and NovaSeq Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to the Chlamydomonas reference genome (Chlamydomonas reinhardtii v5.5) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: Chlamydomonas reinhardtii v5.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Chlamydomonas reinhardtii

source_name: run1 no cell wall Fe–

growth_protocol: We used the Chlamydomonas reinhardtii strains CC-5390 (cw15 arg7-8::ARG7 MT+) and CC-4532 (CW MT-), which we procured from laboratory stocks. We grew all pre-cultures in Tris Acetate Phosphate (TAP) medium supplemented with micronutrients  at 24 ºC in constant light (~50 µmol/m2/s) and under constant agitation (180 rpm) in an Innova-44R incubator.

extract_protocol: Single-cell RNAseq libraries were prepared by using the Chromium single cell 3′ library and gel bead kit v3 (10x Genomics).

value: Cultured Chlamydomonas cells


title: run1_CC5390_Fe_pos

source_name: run1 no cell wall Fe+


title: Control_C3

source_name: gastrocnemius muscles from mice that without denervation of the right sciatic nerve


title: Denervation_D1


title: iPSC WGBS

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

data_processing:
We used trim-galore (v.0.4.0) to trim off the adapter sequences or low-quality reads. Trimmed sequences were then aligned to the human reference genome (hg19) using Bismark (0.14.4) with –bowtie2 option. Duplicated reads were removed using Picard markduplicate (1.141). Methylated value (Beta value, the ratio of intensities between methylated and un-methylated alleles) for all the covered CpG sites were calculated using bismark_methylation_extractor (0.14.4) “–no_overlap –comprehensive –bedgraph”.
Raw reads were aligned to the human reference (hg19) using STAR (v2.6.0a) with the support of transcriptome reference (GRCh37, UCSC). From the mapped reads, we further calculated the TPM (Transcripts per Million) using RSEM (v1.2.31) at the gene level. To reduce any technical bias among the samples, we further quantile normalized using R library, preprocesscore.
For read alignment, we used BWA (0.7.7) to map reads to the human genome sequence (hg19). We further removed duplicated reads using Picard MarkDuplicate (1.141). For peak calling, we used MACS2 (2.1.0) to call the significantly enriched ChIP region compare to the input IgG control “q -0.01 (FDR <0.01%)”
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements
Supplementary_files_format_and_content: peak calling data

source_name: induced pluripotent stem cell

growth_protocol: Human iPS Cell line were kindly provided from Yonsei University College of Medicine. First, STO fibroblast (American Type Culture Collection (ATCC)) was cultured and inactivated by mitomycin C (10μg/ml, Sigma-Aldrich) for feeder cell preparation. iPSCs were cultured on feeder cell layers and maintained using hiPSC maintain medium consist of DMEM/F12 (Invitrogen, Carlsbad, CA, USA), 20% knockoutserum replacement (Invitrogen), 1% penicillin-streptomycin (Invitrogen), 1×non-essential amino acid (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), and 10ng/ml basic fibroblast growth factor (bFGF) (Peprotech).

extract_protocol:
Genomic DNA was extracted by PureLink™ Genomic DNA Kit according to manufacturer’s protocol. Total RNA of each cell type was extracted by TRIzol™ Reagent (Invitrogen) and RNA integrity (RIN) was assessed by Agilent Bioanalyzer (RIN>=8). 1 million cells were crosslinked in crosslinking buffer (100 mM NaCl, 0.1mM EDTA, 5mM Hepes, pH 8.0, 1% formaldehyde) for 10 min at 25°C. The crosslinking was quenched with 125 mM glycine in 25°C for 5 min with rotation and washed twice with ice-cold PBS. The cross-linked cells were re-suspended in SDS lysis buffer (1% SDS, 50 mM Tris-HCl, pH8.0, 10mM EDTA) with protease inhibitor (Roche). Mono- and di-nucleosome size chromatin was obtained through sonication (Covaris, S220)
Total 300ng of genomic DNA was used for bisulfite conversion (EZ DNA Methylation-Gold Kit, Zymo research) and library preparation (TruSeq DNA Methylation, Illumina). We sequenced the bisulfite converted genomic library (2x150bp) using HiseqX. 200ng of total RNA was used for library preparation with TruSeq rapid SBS kit or Truseq SBS Kit v4 according to the kit guidelines. We sequenced the paired-end RNA-sequencing library (2x101bp) using HiSeq 2500 system. The immunoprecipitated DNA was recovered using AMPure XP beads (Beckman Coulter) and ChIP-seq libraries were prepared using NEBNext Ultra II DNA library Prep Kit following the manufacturer’s instruction. The ChIP-seq libraries were sequenced in 150 bp paired-end mode using Illumina NovaSeq 6000 platform.

treatment_protocol: For neuronal differentiation, an embryoid body (EB) was generated by culturing human iPSCs for 5-6 days on non-adherent Petri dishes in hiPSC maintain medium absence of bFGF. To guide differentiation of EBs into neuroectodermal fate, additional supplement of 5μM dorsomorphin (DM) (Sigma-Aldrich) and 5μM SB431542 (Sigma-Aldrich) were added to the hiPSC medium during EB formation. EBs were then attached to the culture dish coated with Matrigel (BD Biosciences) and were cultured in neural induction medium consist of DMEM/F12 medium (Invitrogen), 1×N2 supplement (Invitrogen), 1×nonessential amino acids (Invitrogen) for 6 days10-12. When neural rosettes appear in the center of the EBs, then NPCs were collected through manipulated Pasteur pipet. Collected NPCs were re-plated on Matrigel coated plate for neuronal maturation and cultured for 14 days in Neurobasal medium (Invitrogen) containing 1X B27 supplement without vitamin A (Invitrogen), 1x Glutamax (Invitrogen) supplemented with 10 ng/ml brain-derived neurotrophic factor (BDNF, Peprotech), 10 ng/ml glial cell-derived neurotrophic factor (GDNF, Peprotech), 10 ng/ml neurotrophin-3 (NT3, Peprotech). Early neurons were collected by Accutase (Invitrogen) treatment.

tag: cell type

value: Human induced pluripotent stem cell

value: Stem cell


title: Control_C1

value: without denervation of the right sciatic nerve


title: run1_CC5390_Mix

source_name: run1 no cell wall Mixed of Fe+ and Fe–


title: Nr4a1KO-isoalloLCA rep2

city: Boston

first: Huh

last: lab

state: MA

address: 77 Avenue Louis Pasteur

department: Department of Immunology

institute: Harvard Medical School

data_processing:
ATAC-seq reads were first filtered based on quality using sickle (default settings for either single-end or paired-end reads based on the library type; v1.33)
The adapter sequences were trimmed using Cutadapt (-e 0.1, -m 20; v1.14)
Reads were aligned to the mouse reference genome (mm10) using Bowtie 2 (v2.3.4.3)
Mapped reads which have multiple alignments were removed using SAMtools (v1.3.1). PCR duplicates were removed by using Picard (v2.8.0)
The final output bam file was converted to bigwig format using deepTools (bamCoverage --normalizeUsing RPKM; v3.0.2)
To identify ATAC-seq peaks for individual replicates, MACS2 (2.1.1.20160309) was used. Reproducible peaks among replicates were retained (IDR<0.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for each sample

source_name: Naïve CD4+ T cell

growth_protocol: Naive CD4+ T cells were purified from dissociated spleens of C56/bL6N mice or Nr4a1-KO mice by fluorescence-associated cell sorting (FACS) (CD4+ CD62LhiCD44lo). Purified cells were cultured under TH0 condition stimulated with anti-CD3e (2 μg/mL, clone 145- 2C11, eBioscience), anti-CD28 (5 μg/mL, clone 37.51, eBioscience), and human IL-2 (100 U/mL, Peprotech).

extract_protocol:
20,000 cells were sorted in 1.5ml DNA lo-bind tubes, wash with PBS, and then lysed as well as tagging by Tn5 transposase mixture: 1x Tagment DNA Buffer, 0.5uL Tagment DNA Enzyme (Nextera DNA Library Preparation Kit, Illumina) and 0.2mg/ml digitonin (#G9441, Promega) on ice. Cells were incubated at 37°C for 30 minutes with agitation followed by DNA purification using the MinElute Reaction Cleanup Kit (QIAGEN, Hilden, Germany).
ATAC-seq libraries were constructed through first-round PCR using the NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, MA, USA) with primers (0.5uM each) from (Buenrostro et al., 2015) with the following thermal cycles: 5 minutes at 72°C, 30 s at 98°C, followed by 7 cycles [98°C for 10 s, 63°C for 30 s and 72°C for 60 s] and a final extension at 72°C for 5 minutes. PCR products went through 2 rounds of size selection by Agencourt AMPure XP beads (Beckman Coulter) (0.65x and 1.8x volume to remove long and short fragments respectively) and eluted in 18uL of EB (QIAGEN). Second-round PCR was performed using the NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, MA, USA) with primers (1.25uM each) with the following thermal cycles: 30 s hot-start at 98°C, followed by 7∼13 cycles [98°C for 10 s, 63°C for 30 s and 72°C for 60 s] and a final extension at 72°C for 5 minutes. The final PCR products were purified by Agencourt AMPure XP beads (x1.8 vol.), quantified by tapestation and qPCR, pooled and sequenced as paired-end (38+37bp) on an Illumina NextSeq 500 instrument in high-output mode.

treatment_protocol: DMSO or isoalloLCA were added on day 0. IsoalloLCA dissolved in DMSO were sonicated before adding to the culture. Cells were harvested at 48 hourshrs for ATACseq.

tag: strain

value: spleen + LN

value: 4-6 weeks

value: Nr4a1 KO

value: CD4+ T cell

tag: treatment

value: isoalloLCA


title: NPC WGBS

value: Human induced pluripotent stem cell derived

value: Neuronal progenitor cell


title: Nr4a1KO-isoalloLCA rep1


title: Nr4a1KO-DMSO rep2

value: DMSO


title: Control_C2

value: Male

value: 10 week

value: gastrocnemius muscles


title: CTL-isoalloLCA rep4

value: wild type


title: CTL-isoalloLCA rep3


title: CTL-isoalloLCA rep2


title: Denervation_D6

value: denervation of the right sciatic nerve; muscle atrophy model


title: CTL-isoalloLCA rep1


title: K562_4sUchr_cDNA_1

description: K562 4sU labeled chromatin-associated RNA with rRNA depletion, poly(A) tail addition and direct cDNA sequencing

value: 4-thiouridine (4sU) labeling (500 uM, 8 minutes), cellular fractionation and purification of chromatin-associated RNA, 4sU biotinylation and streptavidin pulldown


title: EN WGBS

value: Early Neuron


title: CTL-DMSO rep4


title: Nr4a1KO-DMSO rep1


title: isoalloLCA rep2

data_processing:
Low quality reads were first removed by using sickle (default settings for either single-end or paired-end reads based on the library type; v1.33)
Reads were then mapped to the mm10 reference genome using the TopHat (v2.1.1) splice-junction mapper. Duplicated reads were removed using Picard
The HTSeq (htseq-count; v0.12.4) was used to count the number of reads overlapping genes
TPM values of genes were calculated using kallisto (v0.45.1)
DESeq2 was then used to identify differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

growth_protocol: Naive CD4+ T cells were purified from dissociated spleens of C56/b6N mice by fluorescence-associated cell sorting (FACS) (CD4+ CD62LhiCD44lo). Purified cells were cultured under TH0 condition stimulated with anti-CD3e (2 μg/mL, clone 145- 2C11, eBioscience), anti-CD28 (5 μg/mL, clone 37.51, eBioscience), and human IL-2 (100 U/mL, Peprotech). Additional TGFβ (0.5 ng/mL, Peprotech) were added for Treg polarization condition.

extract_protocol:
RNA isolation were performed with Qiagen RNAeasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO, isoalloLCA or TGFb were added on day 0. IsoalloLCA dissolved in DMSO were sonicated before adding to the culture. Cells were harvested at 48 hourshrs for RNAseq.


title: DMSO rep2


title: TGFb rep1

value: TGFb


title: DMSO rep1


title: PBS rep3

city: Chicago

first: Stephen

last: Henrich

state: IL

address: 540 West Briar Place, Apt 2M

department: Urology

institute: Northwestern Unversity

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: CD11b+ mouse bone marrow cells

extract_protocol:
Bone marrow was harvested from mouse femurs and tibias, RBCs were lysed, CD11b+ cells were isolated using EasySep Mouse CD11b Positive Selection Kit II, and RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All mice were subjected to tail vein injections of either PBS (100 µl) or EnzR exosomes (100 µl, 10 µg exosomal protein) on Days 1, 3, and 5.  Mice in the HDL NP + EnzR exosomes group were also treated with tail vein injections of HDL NPs (100 µl, 1 µM) on Days 0, 2, and 4.

value: CD11b+ mouse bone marrow cells

tag: cell isolation method

value: EasySep Mouse CD11b+ Positive Selection Kit II


title: EnzR exosome rep1


title: EnzR exosome + HDL NP rep3


title: EnzR exosome + HDL NP rep2


title: CTL-DMSO rep1

value: spleen + LN

value: 4-6 weeks


title: PBS rep1


title: Liver_youngRBC9

city: Pittsburgh

first: Zeyu

last: Xiong

state: Pennsylvania

address: 3459 5th Ave, MUH W631

department: Medicine

institute: University of Pittsburgh

data_processing:
Sequence data were acquired using Illumina standard procedures, and analyzed with CLC Genomics Workbench version 12
Sequenced reads were trimmed for adaptor sequences and low-quality sequence
The sequence data were mapped to Mus Musculus Ensembl Version 80 for sequence, ensembl Version 86 for gene and mRNA
Genome_build: Mus Musculus Ensembl V80
Supplementary_files_format_and_content: Tab-delimited text files include Total counts, RPKM, TPM, CPM values for each sample

source_name: Liver

extract_protocol:
Frozen mouse liver were homogeized in Qiazol, and total RNA were purified with RNeasy Plus Universal Mini kit following the instrucition of the kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6J mice were anesthetized with isoflurane and 10^3 CFU of KP in a total volume of 100 µL was administered intratracheally under direct visualization using a sterile 200 µL pipet with filtered tip positioned just above the vocal cords. One hour following KP inoculation, 200 µL of washed stressed RBC (11-13 days old) or young RBC (1 day old) was transfused via retro-orbital vein. At 24 hours time point, mice were euthanized and livers were snap frozen in liquid nitrogen.

value: Liver

value: 8 weeks


title: Liver_youngRBC11


title: Liver_youngRBC10


title: PBS rep2


title: Liver_youngRBC15


title: isoalloLCA rep1

value: CD4+ T cell

value: isoalloLCA


title: EnzR exosome + HDL NP rep1


title: Liver_stressedRBC1


title: CTL-DMSO rep3

value: DMSO


title: Liver_stressedRBC2


title: Liver_stressedRBC4


title: Liver_stressedRBC3


title: CTL-DMSO rep2


title: DMSO rep3


title: EnzR exosome rep3


title: TGFb rep2


title: isoalloLCA rep3


title: EnzR exosome rep2


title: RPB3_DKO

city: New York

first: Miki

last: JIshage

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 (v2.3.5) with default parameters.
Peak calling was analyzed by Homer (v4.10) with the default setting for factors or histone.
Peaks were filtered for significance (p-value < 1.00E-10).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bigwig files were generated by Homer (v4.10).

extract_protocol:
Lysates were clarified from MNase-treated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using DNA SMART ChIP-seq kits (Takara Bio) according to the manufacturer’s instructions.

tag: strain/background

tag: genotype/variation

value: 7 weeks

value: TAM

tag: chip antibody

value: RPB3 (Bethyl #A303-771A)


title: RPB3_p53KO


title: Gdown1_DKO

value: Gdown1 (in-house)


title: Input_DKO


title: Gdown1_p53KO


title: Input_p53KO


title: RPB3_KO


title: Gdown1_KO


title: Gdown1_FF


title: Input_KO


title: p53KO2_TAM24h_No467

data_processing:
Basecalls performed using CASAVA version 1.82.
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
RNA-seq reads were aligned to the mm10 genome assembly using hisat2 with default parameters.
Transcript abundances were estimated reported as raw read counts using featureCounts.
Differential expression was analyzed using R script.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include read counts for each sample.

extract_protocol:
Liver tissue samples were homogenized in TRIZOL and purified by RNA Clean & concentrator (Zymo research).
RNA libraries were generated using SMARTer® Stranded Total RNA Sample Prep Kits (Takara Bio) according to the manufacturer’s instructions.


title: p53KO1_TAM24h_No466


title: KO1_7W_No100


title: KO2__7W_No356


title: DKO2_TAM24h_No459


title: DKO3_8W


title: FF1_7W_No97


title: p53KO1_8W


title: DKO2_8W


title: p53KO2_8W


title: RPB3_FF


title: Input_FF


title: 1383D6_MHG

city: Chuo-ku

first: Keisuke

last: Sekine

state: Tokyo

address: 5-1-1 Tsukiji

department: Graduate School of Medicine

country: Japan

institute: National Cancer Center Research Institute, Japan

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Genome_build: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary_files_format_and_content: read counts (RPM)

source_name: iPSC derived mid-hindgut endoderm cells

growth_protocol: Ff-I01s04 (Ff01), 1383D6, and 1231A3 hiPSCs were kindly provided by Center for iPS Cell Research and Application (CiRA) . TkDA3-4 (TkDA) hiPSC was kindly provided by University of Tokyo . HiPS-RIKEN-2A (2A), HiPS-RIKEN-12A (12A), and Nips-B2 (B2) hiPSCs were kindly provided by RIKEN BioResource Research Center (RIKEN BRC) . The characteristics of the hiPSCs used in this study were summarized in Table S1. The hiPSCs were maintained on Laminin 511 E8-fragment-coated (iMatrix-511, kindly provided by Nippi) dishes with StemFit AK02N medium (Ajinomoto). On day0, the Accutase-treated (Innovative Cell Technologies) hiPSCs were seeded at a density of 2.2 × 105 cells/well on Laminin 511 E8-fragment-coated 24-well plates with RPMI-1640 (Wako) supplemented with 2% (v/v) B-27 Supplement, serum free (Gibco), 1% (v/v) Pen Strep (Gibco), and the designated cell signaling modifiers shown in column “Day0” of Tables S2 or S4. The culture medium was changed daily following the aforementioned protocols for 13 days. The use of human iPSC was approved by the ethical committee at Yokohama City University and the University of Tokyo.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen).
RNA libraries were prepared using 100 ng of total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific).

value: iPSC derived mid-hindgut endoderm cells

tag: iPSc type


title: 2A_Pancreatic

source_name: iPSC derived pancreatic cells

value: iPSC derived pancreatic cells


title: 1231A3_Pancreatic


title: B2_MHG


title: 2A_MHG


title: TkDA_Pancreatic


title: 1231A3_MHG


title: 1383D6_Pancreatic


title: TkDA_MHG


title: 12A_Pancreatic

value: HiPS-RIKEN-12A (12A)


title: 12A_MHG


title: B2_Pancreatic


title: Ff01_MHG


title: DKO1_TAM24h_No458


title: 12A_Hepatic

source_name: iPSC derived hepatic cells

value: iPSC derived hepatic cells


title: FF2_7W_No355


title: Ff01_Pancreatic


title: B2_Hepatic


title: TkDA_Hepatic


title: 1231A3_Hepatic


title: 1383D6_Hepatic


title: Ff01_Hepatic


title: B2_AFG

source_name: iPSC derived anterior foregut endoderm cells


title: 12A_AFG

value: iPSC derived anterior foregut endoderm cells


title: 2A_AFG


title: TkDA_AFG


title: 1383D6_AFG


title: 1231A3_AFG


title: Ff01_AFG


title: 2A_Hepatic


title: ELOX38-08L1

city: Delft

first: Raúl

middle: Antonio

last: Ortiz-Merino

address: van der Maasweg 9

department: Biotechnology

country: Netherlands

institute: Delft University of Technology

data_processing:
RNAseq reads were mapped to the genome using bowtie v1.2.1.1 with parameters  -v 0 -k 10 --best -M 1
Alignments were filtered and sorted using samtools (v1.3.1)
Read counts were obtained with featureCounts (v1.6.0) using parameters -B -C t
Differential gene expression analysis was performed using edgeR (v3.28.1). Genes with 0 read counts in all conditions were filtered out from the analysis, same as genes with less than 10 counts per million
Counts were normalized using the TMM method, and dispersion was estimated using generalized linear models
Differentially expressed genes were then calculated using a log ratio test adjusted with the Benjamini-Hochberg method. Absolute log2 fold-change values > 2, false discovery rate < 0.5, and P value < 0.05 were used as significance cutoffs.
Genome_build: GCA_002571405.2 (scer)
Genome_build: (kmar)
Supplementary_files_format_and_content: raw gene counts in text format
Supplementary_files_format_and_content: differential gene expression data in text format

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Bioreactor cell culture sample

extract_protocol:
Cells were flash frozen on liquid nitrogen, and RNA was harvested using acidic phenol chloroform extraction. Illumina TruSeq stranded mRNA LT protocol (#15031047) with polyA enrichment was used with approximately 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild-type

value: Chemostat anaerobic, 20 g/L glucose, SM urea medium, D = 0.1 h-1, anaerobic, pH=6, antifoam pluronic acid, 420 mg/L Tween 80, 0 mg/L ergosterol


title: ELOX24-10R3

value: Chemostat anaerobic, 20 g/L glucose, SM urea medium, D = 0.1 h-1, anaerobic, pH=6, antifoam pluronic acid, 0 mg/L Tween 80, 0 mg/L ergosterol


title: ELOX24-10R1

value: Chemostat anaerobic, 20 g/L glucose, SM urea medium, D = 0.1 h-1, anaerobic, pH=6, antifoam pluronic acid, 420 mg/L Tween 80, 10 mg/L ergosterol


title: ELOX39-10L1

value: Chemostat aerobic, 7.5 g/L glucose, SM urea medium, D = 0.1 h-1, aerobic, pH=6, antifoam pluronic acid, 0 mg/L Tween 80, 10 mg/L ergosterol


title: ELOX38-08R1


title: ELOX23-08L1

value: Chemostat O-limited, 20 g/L glucose, SM urea medium, D = 0.1 h-1, micro-aerobic, pH=6, antifoam pluronic acid, 420 mg/L Tween 80, 10 mg/L ergosterol


title: ELOX24-10L3


title: ELOX24-10L1


title: F0 PAIII rep3

city: Tampa

first: Conor

last: Lynch

state: FL

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center

description: rat.raw.counts.txt

data_processing:
BlueBee Data Analysis Pipeline were used for data processing. See details at www.bluebee.com/lexogen
Aligned with STAR v2.5.2a; Gene read counting with HTSeq-count v0.6.0
Genome_build: GRCh38; Rnor6
Supplementary_files_format_and_content: TXT files contain gene IDs and their raw gene counts of human and rat samples, respectively

organism: Rattus norvegicus

source_name: Prostate Cancer

growth_protocol: Cell lines grown in DMEM with 10% FBS

extract_protocol:
RNeasy kit (Qiagen Cat# 74104)
Libraries were prepared using LEXOGEN QuantSeq 3' mRNA-Seq Library PrepKit FWD for Illumina. https://www.lexogen.com/quantseq-3mrna-sequencing/
QuantSeq

treatment_protocol: F2 cell lines were treated with two rounds of MSC conditioned media 72 hours each

value: Prostate Cancer

value: PAIII

value: Parental


title: F2 PaIII rep3

description: rat.raw.counts.txt

value: MSC Educated


title: syd-5_H3K27me3 rep2

city: London

first: YUHAI

last: CUI

state: ON

address: 1391 Sandford Street

department: London Research and Development Centre

institute: Agriculture and Agri-Food Canada

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie2
Mapped reads were filted by removing PCR duplications and unmapped reads
unique mapped reads were converted to bed file by bedtools2
Reads were mapped to genome using TopHat v2.0.4 with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4000 bp were used. Calculations to identify differentially expressed genes were carried out as described (Trapnell et al., 2012)
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for WT and syd-5

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates for 14 days under 16h light/ 8h dark condition.

extract_protocol:
Lysates were clarified from sonicated nuclei and the associated complexes were isolated with antibodies.
14-day-old seedlings were  frozen with liquid nitrogen. Total RNA was isolated from   ̴50 mg of in vitro-grown seedlings using the RNeasy Plant Mini kit (Qiagen) according to supplier’s instructions. Total RNA was treated with RNase-free DNaseI kit (Life Techologies).
5 ng of ChIP DNAs were used for library construction per sample.
Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol.

value: seedlings

tag: developmental

value: 14 days

tag: ecotype and genotype

value: Col-0 (syd-5)


title: syd-5_H3K27me3 rep1


title: ELOX23-08R1


title: ELOX39-09R1


title: AGS _Control-3, Biological Replicate 3

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

country: India

institute: Madurai Kamaraj University

description: Gene expression data of AGS gastric cancer cell line treated with DMSO - Replicate 3

hyb_protocol: The fragmented and labelled cDNA were hybridized for 16 hr at 45°C with GeneChip® Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip® Scanner 3000.

data_processing: Gene level normalized expression signal intensity data of the HTA 2.0 arrays were calculated from CEL files using Gene Level-SST-RMA method which performs GCCN and SST prior to RMA in Affymetrix Expression Console (v1.4.1.46) .

label: biotin

source_name: DMSO treated AGS gastric cancer cells - Replicate 3

label_protocol: 500 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (Affymetrix).

growth_protocol: AGS gastric cancer cell line were seeded in 6 well culture plates and maintained in DMEM-F12 media with 10% FBS in a humidified incubator at 37˚C and 5% CO2.

extract_protocol: 48 Hrs after treatment, the total RNA was isolated from the cells using RNeasy mini kit (Qiagen) following manufacture's standard protocol. All RNA samples had both 18S and 28S bands with RIN (RNA integrity number) value as 10 and free of DNA and protein contamination.

treatment_protocol: Upon reaching 80-90% confluency, the cells were treated with 5µM of doxycycline or with 0.01% of DMSO.

tag: cell line

value: AGS

value: gastric adenocarcinoma cell line


title: AGS _Control-1, Biological Replicate 1

description: Gene expression data of AGS gastric cancer cell line treated with DMSO - Replicate 1

source_name: DMSO treated AGS gastric cancer cells - Replicate 1

tag: tissue


title: syd-5_H3K27me3 input


title: F2 PaIII rep2

description: rat.raw.counts.txt


title: hiPSC-derived_microglia_RNA-seq_rep4

first: Alison

last: Goate

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads were filtered by the thresholds for complexity (40) and the number of uncalled bases (1), respectively, and base corrected in fastp (v 0.20.0).
In STAR (v 2.7.0e), filtered reads were mapped to the hg19 genome and counted using the refernce gene annotation (ENSEMBL release95 basic).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts

source_name: hiPSC-derived microglia

growth_protocol: Isolated CD43+ iHPCs were washed using iMGL base differentiation medium and centrifuged at 300 x g for 5 min at room temperature. After centrifugation, supernatant was aspirated to waste and iHPCs were gently suspended in complete differentiation medium: M-CSF (25 ng/ml), IL-34 (100 ng/ml; PeproTech), and TGFb-1 (50 ng/ml; Militenyi) added fresh each time. Cell density was adjusted to seed at 2 x10^5 cells in 2mL of complete medium per well in growth factor-reduced Matrigel-coated 6-well plates. Every two days: Each well was supplemented with 1 mL per well of complete differentiation medium. Day (12; or day 22 from iPSC): Early iMGLs were collected (300x g for 5 min at room temperature) and a 50% media change was performed. After 25 days of microglial differentiation, iMGLs were cultured in complete differentiation media supple- mented with CD200 (100 ng/ml, Novoprotein) and CX3CL1 (100 ng/ml; PeproTech) for an additional three days.

extract_protocol:
Cells were harvested, stored in RNAlater, and RNA subsequently extracted from all cell types using RNeasy Mini (Qiagen) following manufacturer’s guidelines. RNA sequencing was performed by UCI GHTF.  The Illumina TruSeq mRNA stranded protocol was used to isolate poly-A mRNA from RNA (RNA integrity score ≥ 9)
200 ng was used to construct libraries that were quantified and normalized using the Library Quantification Kit (Kapa Biosystems) and sequenced as paired-end 100 bp reads on the Illumina HiSeq 4000

value: hiPSC-derived microglia


title: AGS _Doxycycline-1, Biological Replicate 1

description: Gene expression data of AGS gastric cancer cell line treated with Doxycycline - Replicate 1

source_name: Doxycycline treated AGS gastric cancer cells - Replicate 1


title: AGS _Doxycycline-3, Biological Replicate 3

description: Gene expression data of AGS gastric cancer cell line treated with Doxycycline - Replicate 3

source_name: Doxycycline treated AGS gastric cancer cells - Replicate 3


title: AGS _Control-2, Biological Replicate 2

description: Gene expression data of AGS gastric cancer cell line treated with DMSO - Replicate 2

source_name: DMSO treated AGS gastric cancer cells - Replicate 2


title: AGS _Doxycycline-2, Biological Replicate 2

description: Gene expression data of AGS gastric cancer cell line treated with Doxycycline - Replicate 2

source_name: Doxycycline treated AGS gastric cancer cells - Replicate 2


title: hiPSC-derived_microglia_RNA-seq_rep3


title: F2 PaIII rep1

description: rat.raw.counts.txt


title: WT_H3K27me3 rep2

value: Col-0 (wild type)


title: AB_Head_sib3

city: Wuhan

first: Jingzhen

address: Wuhan, Hubei 430074, PR China

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz11 genome assembly using HISAT version 2.0.4.
HTSeq v0.9.1 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced, considers the effect of sequencing depth and gene length  for the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels (Trapnell, Cole, et al., 2010)
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: Head

extract_protocol:
Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent (Life Technologies). 35 heads were used for each RNA sample
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

value: AB

value: Head

value: 36 hours post fertilization

value: wild type


title: WT_H3K27me3 rep1


title: F0 PAIII rep2

description: rat.raw.counts.txt


title: AB_Head_mt 2


title: SYD input

value: Col-0 (syd-5 pSYD::SYDΔC-GFP)


title: reference [ID-005507-Grad_11_Fraction_20]

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

country: Germany

institute: Würzburg University

data_processing:
library strategy: Grad-seq
READemption analysis, for details see https://reademption.readthedocs.io/en/latest/example_analysis.html, after gene-quantification the reads were normalized to the ERCC spike-in
Supplementary_files_format_and_content: wig files were generated using READemption; Scores represent 'coverage-tnoar_min_normalized', tdf files were generated with igvtools

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial culture

growth_protocol: Pseudomonas aeruginosa cells were grown in LB media to an OD600 of 0.3

extract_protocol:
500 µl gradient fractionation samples were deproteinized with 1% SDS and extracted with an equal volume acidic phenol:chloroform:isoamylalcohol (PCI), and precipitated with ethanol and 1:30 volume NaOAc pH 5.2 with 1 µl glycoblue
Samples were solubilized in 50 µl, 5 µl were diluted with 45 µl water, 10 µl were mixed with 10 µl 1:100 diluted ERCC RNA spike-in mix1. RNA samples were prepared as described in Hör et al. 2020 NAR.

treatment_protocol: Cells were optionally infected with an MOI of 15 with ΦKZ bacteriophage and incubated for 10 min

value: none (no infection)


title: reference [ID-005506-Grad_11_Fraction_19]


title: reference [ID-005505-Grad_11_Fraction_18]


title: hiPSC-derived_microglia_ATAC-seq_rep3

data_processing:
FASTQ files were aligned to hg19 human reference genome using Bowtie2 (v2.4.1).
Uniquely mapped reads were obtained using SAMtools(v1.9). Reads were filtered for MAPQ score of 5. Bam files were sorted and indexed.
Coverage tracks (at 1 bp resolution and normalized to RPKM) was generated from reads in BAM files using the bamCoverage utility of deepTools (v 3.3.2).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: microglia

growth_protocol: Isolated CD43+ iHPCs were washed using iMGL base differentiation medium and centrifuged at 300 x g for 5 min at room temperature. After centrifugation, supernatant was aspirated to waste and iHPCs were gently suspended in complete differentiation medium: M-CSF (25 ng/ml), IL-34 (100 ng/ml; PeproTech), and TGFb-1 (50 ng/ml; Militenyi) added fresh each time. Cell density was adjusted to seed at 2 x10^5 cells in 2mL of complete medium per well in growth factor-reduced Matrigel-coated 6-well plates. Every two days: Each well was supplemented with 1 mL per well of complete differentiation medium. Day (12; or day 22 from iPSC): Early iMGLs were collected (300x g for 5 min at room temperature) and a 50% media change was performed. After 25 days of microglial differentiation, iMGLs were cultured in complete differentiation media supple- mented with CD200 (100 ng/ml, Novoprotein) and CX3CL1 (100 ng/ml; PeproTech) for an additional three days.

extract_protocol:
ATAC-seq reactions were performed using an established protocol (Buenrostro et al PMID: 25559105)
hiPSC-derived microglia (50K cells) from each patient line were collected and processed as previously described (Abud et al. 2017). Samples were either processed at New York Genome Center or at UCI’s Genomics High-Throughput Facility and sequenced as 50 bp paired-end reads on a HiSeq 2500 and 100 bp paired-end reads on a HiSeq 4000, respectively.


title: F0 PAIII rep1

description: rat.raw.counts.txt

value: Prostate Cancer


title: WT_H3K27me3 input


title: reference [ID-005508-Grad_11_Fraction_21P]


title: AB_Head_mt 3


title: hiPSC-derived_microglia_RNA-seq_rep2


title: AB_Head_mt 1


title: SYD rep1

value: anti-GFP


title: AB_Head_sib2


title: AB_Head_sib1


title: NPC Hi-C_rep1

description: iNPC.txt

data_processing:
Prior to mapping, quality control steps were executed. We assessed reads by ‘FastQC’ for read quality control and adapter removing process was done by ‘Cutadapt’ (cutadapt -a CTGTCTCTTATACACATCT -q 10 --minimum-length 36 -o sample_1_trimmed.fastq -p sample_2_trimmed.fastq sample_1.fastq sample_2.fastq). Processed reads were aligned by ‘Bowtie2’ (bowtie2 --very-sensitive -x <genomeIndexName> -X 2000 -1 sample_1_trimmed.fastq -2 sample_2_trimeed.fastq). We next removed duplicated reads using Picard MarkDuplicate (1.141) for elimination of technical bias. iPSC and NPC chromatin accessible peaks were determined by MACS2 with specific option (macs2 callpeak --verbose 3 --treatment sample.bam -g hs -B -q 0.05 --extsize 200 –nomodel --shift -100 --nolambda --keep-dup all -f BAMPE --outdir dir --call-summits). To identify the confident stage-specific ATAC peaks, we employed a strategy that confirming background signal of each iPSC and NPC ATAC peaks. We first listed stage-specific peaks based macs2 peak calling results by selecting peaks which was not defined in other cell types. To define cell type-specific accessible regions, we further manipulated macs2 peak calling results. For each stage-specific peak, we plotted normalized ATAC peak intensity (log2RPKM) distribution graph of corresponding cell types and another cell types simultaneously. We observed crossing point of two distribution plot and defined this point as background signal. Finally, we defined revised stage-specific ATAC peaks. For data visualization on genome browser, we used bamCoverage tool with following options; --normalizeUsing CPM --effectiveGenomeSize 2864785220.
We utilized H3K4me3 and H3K27me3 ChIP-seq data for iPSC and NPC in GEO (GSE156723). For read alignment, we used BWA (0.7.7) to map reads to the human genome sequence (hg19). We further removed duplicated reads using Picard MarkDuplicate (1.141). We further inspected the quality of the ChIP-seq experiment by measuring FRiP (fraction of reads in peaks) using ChIPQC (3.3). For peak calling, we used MACS2 (2.1.0) to call the significantly enriched ChIP region compare to the input IgG control “q -0.01 (FDR <0.01%)”. For the ATAC peak intensity comparison, we generated the normalized RPKM values by counting the number of reads for 50bp bins then dividing by the total sequencing depth.
Hi-C data processing is executed by described method in Yang et al. Raw reads were aligned to hg19 human reference genome. To focus on cis-chromosomal interactions, invalid Hi-C reads were removed by criteria which defined in previous studies; inter-chromosomal interactions, putative self-ligations, and non-restriction site specific ligations. Valid cis-interactions were collected to build raw interaction frequency matrix with 5 kb resolution. A negative binomial model-based normalization pipeline removed biases of the interaction frequency matrix. Finally, distance dependent background signal was used to normalization for emphasizing biologically significant long-range chromatin interactions.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq: peak calling data
Supplementary_files_format_and_content: ChIP-seq: RPKM with 50bin; peak calling data
Supplementary_files_format_and_content: Hi-C: Interaction contact map

source_name: induced pluripotent stem cell

extract_protocol:
For ATAC-seq, 50000 cells were washed with cold-PBS and resuspended by cell lysis buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged (10min, 2000g at 4°C). For H3K27ac ChIP-seq, CCells were washed with DPBS and crosslinked by crosslinking buffer (100mM NaCl, 0.1mM EDTA, 5mM HEPES (pH8.0), 1% formaldehyde) for 10min at room temperature. The crosslinking process was halted with 125mM glycine in room temperature for 5 min with rotation and washed twice with cold DPBS. Crosslinked samples were resuspended in SDS lysis buffer (1%SDS, 50mM Tris-HCl (pH8.0), 10mM EDTA) with protease inhibitor. For Hi-C, about 1 million cells were used for crosslinking with 1% formaldehyde. Crosslinked cells were lysed (10nM Tris-HCl (pH8.0), 10mM NaCl, and 0.2% IGEPAL CA630) and digested with 100U MboI.
For ATAC-seq, the nuclei pellet were resuspended with Transposase mixture in Illumina Nextera Kit (FC-121-1031) and incubated for 30min at 37°C. Tagmented DNA fragments were puriﬁed using MinElute PCR purification kit following manufacturer’s protocol. For eluted DNA samples, we executed small scale qPCR to determine adequate PCR amplification cycles for library preparation. We checked Ct value for qPCR sample mix (5ul 2×KAPA HiFi HotStart Ready Mix, 0.1ul 100x SYBR green, 0.3ul Nextera Ad1.2 (25uM), 0.3ul Nextera Ad2.X (25uM), 2.3ul Nuclease-free water and 2ul eluted DNA) and determined PCR amplification cycles with value of Ct+1. We then executed large scale PCR (25ul 2×KAPA HiFi HotStart Ready Mix, 1.5ul Nextera Ad1.2 (25uM), 1.5ul Nextera Ad2.X (25uM), 2ul Nuclease-free water and 20ul eluted DNA). After PCR step, we cleaned library samples and performed size selection (200~400bp) by AMPure XP beads (Beckman Coulter, A63881) following manufacturer’s instruction. For H3K27ac ChIP-seq, sonicated chromatin samples were incubated with H3K27ac antibody and magnetic bead for 4 hours in 4°C with rotation. At the same time, input chromatin was stored from sonicated samples to be used as input control. After incubation, the bead complex was washed by RIPA-α (140mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 10mM Tris pH8) with 4 times. The chromatin immunoprecipitated complex was treated with RNaseA and executed overnight reverse-crosslinking at 68°C. The chromatin immunoprecipitated DNA was extracted using AMPure XP beads and libraries were prepared using NEB Next Ultra II DNA library Prep Kit. For Hi-C library, digested fragments were labelled with biotin-14-dCTP and proximally ligated with T4 DNA Ligase, followed by reverse-crosslinking. The fragments were then subjected to sonication and purified with AMPure XP beads. The final ligated DNA was pulled down with Dynabeads MyOne streptavidin T1 beads.

value: Human induced pluripotent stem cell derived

tag: developmental stage

value: Neuronal progenitor cell


title: SYD rep2

value: seedlings


title: reference [ID-005504-Grad_11_Fraction_17]


title: NPC Hi-C_rep2

description: iNPC.txt


title: hiPSC-derived_microglia_RNA-seq_rep1


title: CWRU205 ALIW5

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.6 (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 the Panther database (http://pantherdb.org/)  and gProfiler.
RNAseq was integrated with ATACseq results with BETA (http://cistrome.org/BETA/).
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include normalized count values for each Sample

source_name: CWRU205 iPSC line

growth_protocol: iPSC to ALI differentiation was carried out as described in the manuscript. HBE ALI cells were cultured according to Fulcher et al. 2005

extract_protocol:
For each stage of differentiation, confluent cells were harvested for RNA extraction using TRIzol. HBE-ALI cells were harvested similarly. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80oC under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

treatment_protocol: No Treatment

value: Air-Liquid Interface (week 5)


title: iPSC Hi-C_rep2

description: iPSC.txt

value: Human induced pluripotent stem cell

value: Stem cell


title: reference [ID-005501-Grad_11_Fraction_14]


title: reference [ID-005503-Grad_11_Fraction_16]


title: reference [ID-005500-Grad_11_Fraction_13]


title: Healthy donor 5

first: Min-Seok

last: Rha

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Otorhinolaryngology

institute: Yonsei University College of Medicine

data_processing:
Trimming using BBDuk (> average Q20)
Mapping: Bowtie2
Abundance measurements: DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized counts for every sample

source_name: Vγ9+Vδ2+ T cells

extract_protocol:
Cells were cryopreserved in Trizol reagent and RNA extracted according to the manufacturer’s instructions. Total RNA quality was assessed with the Agilent 2100 Bioanalyzer System. RNA quantification was performed using ND-2000 Spectrophotometer.
Extracted RNA samples were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Vienna)

value: liver perfusate

tag: disease state

value: healthy donor


title: HBV-CLD 4

value: hepatitis B virus-related chronic liver disease


title: HBV-CLD 2


title: ND2.0 ALIW5

source_name: CR0000008 (ND2.0 iPSC line)


title: B173_depleted

city: Houston

first: Karina

last: Vazquez-Arreguin

state: TX

address: 1881 East Rd

department: Cancer Biology

institute: MD Anderson Cancer Center

data_processing: none provided by the submitter

source_name: colon tumor

extract_protocol:
Total RNA was extracted using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 19.7 weeks

tag: genotype

value: Villin-Cre-ERT2; APCflox/flox; p53flox/flox; tetO-LSL-KrasG12D; Rosa26-LSL-Luc; Rosa26-LSL-rtTA-GFP; alpha-SMA-TK+


title: reference [ID-005499-Grad_11_Fraction_12]


title: HBV-CLD 5


title: HBV-CLD 3


title: HBV-CLD 1


title: CWRU205 ALIW3

value: Air-Liquid Interface (week 3)


title: reference [ID-005497-Grad_11_Fraction_10]


title: reference [ID-005498-Grad_11_Fraction_11]


title: Healthy donor 4


title: B154_depleted


title: ND2.0 ALIW3


title: B148_depleted


title: iPSC Hi-C_rep1

description: iPSC.txt


title: reference [ID-005496-Grad_11_Fraction_09]


title: CWRU205 LP3b

value: Lung Progenitor Cells 3b


title: Healthy donor 3


title: ND2.0 LP3b


title: CWRU205 LP3a

value: Lung Progenitor Cells 3a


title: B155_control

value: Villin-Cre-ERT2; APCflox/flox; p53flox/flox; tetO-LSL-KrasG12D; Rosa26-LSL-Luc; Rosa26-LSL-rtTA-GFP; alpha-SMA-TK-


title: reference [ID-005494-Grad_11_Fraction_07]

value: none (no infection)


title: Healthy donor 1


title: reference [ID-005493-Grad_11_Fraction_06]


title: B149_control


title: Healthy donor 2


title: ND2.0 LP3a


title: F2 DU145 rep3

description: human.raw.counts.txt

source_name: Prostate Cancer

value: Prostate Cancer

value: MSC Educated


title: B136_control


title: CWRU205 AFE

value: Anterior Foregut Endoderm


title: B189_WT

source_name: colon

value: WT


title: reference [ID-005491-Grad_11_Fraction_04]


title: B181_WT


title: CWRU205 DE

value: Definitive Endoderm


title: F0 DU145 rep3

description: human.raw.counts.txt

value: Parental


title: reference [ID-005490-Grad_11_Fraction_03]


title: F2 DU145 rep2

description: human.raw.counts.txt


title: reference [ID-005489-Grad_11_Fraction_02]


title: F2 DU145 rep1

description: human.raw.counts.txt


title: F0 DU145 rep2

description: human.raw.counts.txt


title: reference [ID-005488-Grad_11_Fraction_01]


title: reference [ID-005495-Grad_11_Fraction_08]


title: B180_WT


title: AH760: HBE_ALI_6wk (DD0780)

data_processing:
Libraries were sequenced on Illumina HiSeq 4000 machines.
Data was analyzed using ENCODE pipeline https://github.com/kundajelab/atac-seq-pipeline
Genome_build: hg19

source_name: HBE_ALI_6wk (DD0780)

growth_protocol: Cells were grown in indicated medias using standard methods

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were construced using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purfied with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion

value: Primary Human Bronchial Epithelium


title: AH759: HBE_ALI_6wk (DD0760)

source_name: HBE_ALI_6wk (DD0760)


title: ND2.0 DE


title: reference [ID-005487-Grad_11_Fraction_00L]


title: F0 DU145 rep1

description: human.raw.counts.txt


title: ND2.0 AFE


title: reference [ID-005492-Grad_11_Fraction_05]


title: reference [ID-005502-Grad_11_Fraction_15]


title: s7

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

data_processing:
Trim Galore
TopHat (v2.0.9)
HTSeq (v0.5.4p5), Ensembl v74 annotation
Genome_build: hg19
Supplementary_files_format_and_content: raw counts from HTSeq with Ensembl v74 annotation

source_name: Endometrium

extract_protocol:
EZ-RNA Total RNA Isolation Kit
NeoPrep Automated Library Prep System

tag: source

value: biopsy

value: npreg

tag: sequencing batch

value: frozen


title: AH727: LP3b CWRU205

source_name: LP3b CWRU205


title: s6

value: preg


title: s44


title: H2

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

description:
mRNA-Seq
Processed_file_hwj.xls

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2 (v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed_file_hwj.xls: Excel file includes FPKM values for each Sample.

source_name: Liver, treatment

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shaken vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB), which had more than 300 copies of one molecular. DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: The liver of mice which were administered Chebulae Fructus hydrosoluble extract ethyl acetate fraction (1 g/kg/day) or water by gastric irrigation for 1 week for transcriptome sequencing.

value: ICR

value: Liver

value: Chebulae Fructus hydrosoluble extract ethyl acetate fraction (1g/kg/day) by gastric irrigation for 1 week


title: H3

description:
mRNA-Seq
Processed_file_hwj.xls


title: Unstimulated T cells (Un-TC1)

city: New Delhi

first: Ashima

last: Bhaskar

state: Delhi

address: Aruna Asaf Ali Marg

institute: National Institute of Immunology

description: Un-TC vs Pep-TC

data_processing:
The raw reads generated for unstimulated DCs and peptide pool pulsed DCs and unstimulated Co-cultured T cells and T cells co-cultured with peptide pool pulsed DCs were subjected to quality check using Fast QC (version 0.11.5, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) using the parameters like base quality score distribution, sequence quality score distribution, average base content per read and GC distribution in the reads. Illumina Adapters (AGATCGGAAGAGC) was removed using Trim Galore (version 0.4.1), a wrapper script to automate quality and adapter trimming as well as quality control. Clean reads were mapped on reference Mus-musculus_GRCm38.p6 using TopHat v2.1.0. Differential analysis was performed on counted mapped reads in range of positions on a chromosome for (Un-DC) vs (Pep-DC), and (Un-TC) vs (Pep-TC) combinations, predicted using htseq-count software and then differential gene expression was found using DeSeq, a bio-conductor R package that estimate variance-mean dependence in count data and implements a range of statistical methodology based on the negative binomial distributions. Functional annotation for combination was performed using Uniprot database, and DAVID.
Genome_build: mm9
Supplementary_files_format_and_content: excel files with raw counts, fold change and p values

source_name: Splenic T cells

growth_protocol: C57BL/6 Mice were euthanized, and the femurs were isolated. Bone marrow was flushed out with RPMI 1640 medium using a 2.0-ml syringe (26.5 gauge). The cells were washed twice with PBS and then cultured in complete RPMI 1640 medium (Gibco, In-vitrogen, UK) supplemented with GM-CSF (40 ng/ml) and IL-4 (10 ng/ml) on 12-well plates (one million cells/ml). On the 3rd day, 75% of the medium was replaced with fresh DC culture medium. On day 5th, the suspended cells were removed, and the loosely adherent cells were collected as immature DCs (CD11c- positive cells were >90%). For mature DCs, immature DCs were stimulated with lipopolysaccharide (LPS, 1 mg/ml) for 24 h. FACS analysis using anti-CD11c, -CD80, -CD86, and -MHC class II antibodies suggested that >90% of the cells were conventional DCs. DCs were either left untreated or treated overnight with 20 µg/ml of CSA or 0.2 µg/ml of each peptide followed by co-culture with CD3+ T cells isolated from M.tb infected and DOTS treated animals for 48h.

extract_protocol: Total RNA was isolated from unstimulated Dendritic cells (Un-DC) and DCs pulsed with peptide pool (Pep-DC) as well as from unstimulated co-cultured T cells (Un-TC) and co-cultured T cells (Pep-TC) along with DCs pulsed with peptide pool using an RNeasy RNA isolation kit (Qiagen, USA).

tag: organ

value: spleen

tag: protocol

value: Unstimulated


title: Unstimulated T cells (Un-TC2)

description: Un-TC vs Pep-TC

treatment_protocol: DCs were either left untreated or treated overnight with 20 µg/ml of CSA or 0.2 µg/ml of each peptide followed by co-culture with CD3+ T cells isolated from M.tb infected and DOTS treated animals for 48h.

tag: strain


title: Unstimulated T cells (Un-TC3)

description: Un-TC vs Pep-TC


title: Peptide stimulated T cells (Pep-TC1)

description: Un-TC vs Pep-TC

value: Peptide stimulated


title: Peptide stimulated T cells (Pep-TC2)

description: Un-TC vs Pep-TC


title: H1

description:
mRNA-Seq
Processed_file_hwj.xls

tag: treatment


title: Peptide pulsed dendritic cells (Pep-DC3)

description: Un-DC vs Pep-DC

source_name: mouse derived dendritic cells

value: peritoneum

value: Peptide pulsed


title: AH726: LP3a CWRU205

source_name: LP3a CWRU205

value: Lung Progenitor Cells 3a


title: C3

description:
mRNA-Seq
Processed_file_hwj.xls

source_name: Liver, control

value: Water (10ml/kg) by gastric irrigation for 1 week


title: AH720: LP3a ND2.0

source_name: LP3a ND2.0


title: s39

value: fresh


title: AH723: iPSC CWRU205

source_name: iPSC CWRU205

value: CWRU205 iPSC line


title: Peptide pulsed dendritic cells (Pep-DC2)

description: Un-DC vs Pep-DC


title: AH717: iPSC ND2.0

source_name: iPSC ND2.0

value: CR0000008 (ND2.0 iPSC line)


title: C2

description:
mRNA-Seq
Processed_file_hwj.xls


title: s37

value: biopsy


title: s35

value: npreg


title: Peptide pulsed dendritic cells (Pep-DC1)

description: Un-DC vs Pep-DC


title: C1

description:
mRNA-Seq
Processed_file_hwj.xls


title: AH724: DE CWRU205

source_name: DE CWRU205

value: Definitive Endoderm


title: Unstimulated dendritic cells (Un-DC3)

description: Un-DC vs Pep-DC


title: s32

value: preg


title: AH721: LP3b ND2.0

source_name: LP3b ND2.0

value: Lung Progenitor Cells 3b


title: H358_M2 rep2

city: nantong

first: mangze

last: hu

address: qixiu street 19

institute: nantong university

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12)
differential expression analysis was performed using the DESeq2(v1.4.5) with Q value smaller than 0.05. To take insight to the change of phenotype, GO and KEGG enrichment analysis of annotated different expressed gene was performed by Phyper based on Hypergeometric test .
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Gene Count values for each Sample.

source_name: H358 cell line (NSCLC)

extract_protocol:
mRNA was harvested using Trizol reagent according to RNA Extraction SOP For Cell protocol (SOP-SMM-J007)
RNA libraries were prepared for sequencing using RNA-seq library prepration protocol (SOP-SS-027)

tag: cell type

value: non-small cell lung cancer (NSCLC)

value: ARS-1620 treat for 24 hours with M2-type macrophage conditional medium


title: H358_M2 rep3


title: AH718: DE ND2.0

source_name: DE ND2.0


title: s23


title: H358_M2 rep1


title: s41


title: Unstimulated dendritic cells (Un-DC1)

description: Un-DC vs Pep-DC


title: AH736: ALI w5 ND2.0

source_name: ALI w5 ND2.0

value: Air-Liquid Interface (week 5)


title: H358_M1 rep3

value: ARS-1620 treat for 24 hours with M1-type macrophage conditional medium


title: AH740: ALI w5 CWRU205

source_name: ALI w5 CWRU205


title: KO+2KR-HA-Zbtb20_mm_rna_sr_MTirard_D_6

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
FastQ files were aligned to mouse genome using STAR version 2.5.2a
Read counting within genes was performed using featureCounts version 1.5.0-p1
Differential expression analysis was performed using DESeq2 version 1.24.0
Promoter analysis was performed to find which transcription factors were enriched for the deregulated genes in each differential expression analysis. This was done using the function findMotifs.pl (using default parameters) within HOMER version 4.11
Genome_build: mm10 version gene version 96
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: DIV5 primary hippocampal neurons from E18 pregnant female infected with HA-Zbtb20-2KR virus after 1DIV

growth_protocol: Primary hippocampal cultures were generated as previously reported (Daniel et al. 2017, Tirard et al. 2012, Tirard & Brose 2016). Briefly, the hippocampi of 18-days old mouse embryos (E18) or newborn (P0) pups were isolated and digested for 45 min at 37°C in DMEM (Gibco) containing 2.5 units/ml papain (Worthington Biomedical Corporation), 0.2 mg/ml L-cystein (Sigma), 1 mM CaCl2, and 0.5 mM EDTA. After papain digestion, hippocampi were incubated for 15 min at 37°C in DMEM supplemented with 10% (vol/vol) heat-inactivated FBS, 2.5 mg/ml albumin, and 2.5 mg/ml trypsin inhibitor, and then mechanically dissociated via repeated pipetting. Cells were seeded on poly-L-lysine-coated 12 mm glass coverslips (Sigma-Aldrich) for immunocytochemical analysis or on 35 mm culture dishes for RNA extraction experiments. Neurons were maintained at 37°C and 5% CO2 in Neurobasal medium (Gibco) supplemented with 2% B27 (Gibco), penicillin (100 U/ml) and streptomycin (100 μg/ml).

extract_protocol: At DIV5, primary hippocampal neurons were lysed in TRI Reagent (Zymo, R2050), snap frozen, and kept at -80°C until needed. RNAs were extracted using the Direct-zol Zymo RNA extraction kit following the manufacturer's instructions (Zymo Research, R20270).

value: Zbtb20 kncok-out line RRID:MGO:5693950

value: KO


title: s25

source_name: Endometrium


title: s20


title: KO+2KR-HA-Zbtb20_mm_rna_sr_MTirard_D_5


title: H358_M1 rep2


title: KO+2KR-HA-Zbtb20_mm_rna_sr_MTirard_D_4


title: s2

value: frozen


title: AH739: ALI w3 CWRU205

source_name: ALI w3 CWRU205

value: Air-Liquid Interface (week 3)


title: H358_M1 rep1


title: AH735: ALI w3 ND2.0

source_name: ALI w3 ND2.0


title: KO+WT-HA-Zbtb20_mm_rna_sr_MTirard_C_6

source_name: DIV5 primary hippocampal neurons from E18 pregnant female infected with HA-Zbtb20-WT virus after 1DIV


title: KO+2KR-HA-Zbtb20_mm_rna_sr_MTirard_D_3


title: H358_ARS rep3

value: ARS-1620 treat for 24 hours


title: s18

value: fresh


title: KO+WT-HA-Zbtb20_mm_rna_sr_MTirard_C_5


title: Unstimulated dendritic cells (Un-DC2)

description: Un-DC vs Pep-DC

source_name: mouse derived dendritic cells

value: peritoneum

value: Unstimulated


title: s19

value: biopsy


title: AH725: AFE CWRU205

source_name: AFE CWRU205

value: Anterior Foregut Endoderm


title: AH719: AFE ND2.0

source_name: AFE ND2.0


title: s15


title: H358_ARS rep2


title: KO+WT-HA-Zbtb20_mm_rna_sr_MTirard_C_3


title: H358 DMSO rep3

value: DMSO


title: H358_ARS rep1


title: s11

value: preg


title: s14


title: KO+WT-HA-Zbtb20_mm_rna_sr__MTirard_C_1


title: KO+WT-HA-Zbtb20_mm_rna_sr_MTirard_C_2


title: s13

value: npreg


title: H358-R rep3

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using the DESeq2 (v1.4.5) with Q value smaller than 0.05. To take insight to the change of phenotype, GO and KEGG enrichment analysis of annotated different expressed gene were performed by Phyper based on Hypergeometric test.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include gene count values for each Sample.

extract_protocol:
mRNA was harvested using Trizol reagent according to RNA Extraction SOP For Cell protocol (SOP-SMM-J007).
RNA libraries were prepared for sequencing using RNA-seq library preparation protocol (SOP-SS-027).

treatment_protocol: H358-P (H358 cell treated with ARS-1620 for 0 hour), ARS-24H (H358 cell treated with ARS-1620 for 24 hours), ARS-48H (H358 cell treated with ARS-1620 for 48 hours), and H358-R (H358 cell treated with ARS-1620 for long period until it is resistant to ARS1620).

value: NSCLC cell line

tag: genotype/variation

value: ARS-1620 until resistant


title: H358 DMSO rep2

value: non-small cell lung cancer (NSCLC)


title: KO_mm_rna_sr_MTirard_B_6

source_name: DIV5 primary hippocampal neurons from E18 pregnant female infected with eGFP virus after 1DIV


title: H358-R rep2


title: H358 DMSO rep1


title: s10


title: ATACseq_D4pDOXRep2

city: Madison

first: Igor

middle: I.

last: Slukvin

address: 1220 Capitol Court

institute: University of Wisconsin

data_processing:
ATAC-seq fragments were mapped to human genome by BWA with default settings.  Human genome were divided into 32 bp bins and the number of reads in each bin was counted.  In order to smooth the data, reads were extended to 200 bp.  To normalize signals across ATAC-seq datasets, the number of reads in each dataset was reduced by random sampling to the smallest number of reads present in the datasets.   ATAC-seq peaks were called by MACS2.
ChIP-seq fragments were aligned by BWA (version 0.7.15) with quality threshold at 5 for read trimming and all the other options in default settings.  Normalized SOX17 ChIP-seq signals were calculated by MACS2 by using all the tags at the same loci.
RNA-seq fragments were aligned by STAR (version 2.5.2b) to human genome with gene annotations from GENCODE (version 27).  Transcript expression levels were quantified by RSEM (version 1.3.0).
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq BED files contain peaks called by MACS2
Supplementary_files_format_and_content: ATAC-seq bigWig files contain normalized ATAC-seq signals as described in ATAC-seq data processing step
Supplementary_files_format_and_content: ChIP-seq bigWig files contain normalized SOX17 fold enrichment over IgG control calculated by MACS2
Supplementary_files_format_and_content: RNA-seq TSV files contain gene expression levels quantified by RSEM

source_name: Primordial hemogenic endothelium from H9

growth_protocol: Inducible SOX17 H9 ESC s were differentiated in ColIV coating plate. Singular Cells were plated 5,000 cells/cm2 to 10cm plates coated with ColIV (Sigma-Aldrich). After 1 day, media was changed to IF9S media with 50 ng/ml FGF, 2 mM LiCl, 15 ng/ml Activin A, and 50 ng/ml BMP4. On day 2, media was changed to IF9S media with 50 ng/ml VEGF, 2.5 uM SB431542 and 50 ng/ml FGF and D4 PHE cells were collected (1 X 106 cells).

extract_protocol:
D4 PHE cell were CD31 MACs, and then cells were frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay.
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems).

value: Inducible SOX17 H9 ESC

value: DOX+

tag: replicate

tag: description

value: CD31 MACs cell at D4


title: PMH_Chrebp-KO_Fructose

city: Ann Arbor

first: Deqiang

last: Zhang

state: MI

address: 1137 Catherine Street

department: Molecular & Integrative Physiology

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on the Affymetrix Mouse Gene 2.1 ST Array and were washed and stained using the Affymetrix Gene Atlas system (software version 2.0.0.460).

scan_protocol: Peg Arrays were scanned using the Affymetrix Gene Atlas system (software version 2.0.0.460).

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.4.0.

source_name: Chrebp KO Primary mouse hepatocytes treated with fructose

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: Primary mouse hepatocytes were isolated from 2-month-old wildtype or Chrebp-KO male mice.

extract_protocol: Liver total RNA were extracted with RNeasy Mini kit from Qiagen.

treatment_protocol: Primary hepatocytes were treated with/without 25mM fructose for 16 hrs in serum free medium.

value: Primary mouse hepatocytes

value: Chrebp-KO

tag: Sex

value: Male

tag: age

value: 2 months

value: Fructose


title: s1

value: frozen


title: KO_mm_rna_sr_MTirard_B_3

tag: cell line

value: Zbtb20 kncok-out line RRID:MGO:5693950

value: KO


title: Mus_Musculus_SmoM2_Cdk6_koko_Tumor_6

city: San Francsico

first: David

last: Raleigh

address: 1450 3rd Street Rm 402

department: Department of Radiation Oncology

institute: University of California, San Francisco

description: genomically engineered mouse medulloblastoma model with constitutively active Smoothened under Math1-Cre promoter, Cdk6-/-

data_processing:
50 base pair single-ended sequencing on Illumina HiSeq 4000, basecalling with
Quality control performed by FASTQC
Reads were trimmed using Trimmomatic, removing leading and trailing bases with quality scores below 28, as well as any base that did not have an average quality score of 28 within a sliding window of 4 bases. Any read shorter than 37 bases was removed
Reads were mapped to GRCm38.p6, using HISAT2 default paramters
Differential analysis was performed using DESeq2 with "apeglm" parameters with a FDR of 0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Medulloblastoma

extract_protocol:
Medulloblastomas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Illumina 20020594) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain (targeted mutation)


title: Mus_Musculus_SmoM2_Cdk6_koko_Tumor_5


title: PMH_Chrebp-KO_Control

source_name: Chrebp KO Primary mouse hepatocytes

value: Control


title: KO_mm_rna_sr_MTirard_B_2


title: ATACseq_D4pDOXRep1


title: ATACseq_D4mDOXRep2

value: DOX-


title: PMH_WT_Fructose

source_name: Wildtype Primary mouse hepatocytes treated with fructose

value: WT


title: KO_mm_rna_sr_MTirard_B_1


title: KO_mm_rna_sr_MTirard_B_4


title: PMH_WT_Control

source_name: Wildtype Primary mouse hepatocytes


title: ARS-24H rep3

source_name: H358 cell line (NSCLC)

value: NSCLC cell line

value: ARS-1620 for 24 hours


title: WT_mm_rna_sr_MTirard_A_4


title: Mus_Musculus_SmoM2_Cdk6_koko_Tumor_4


title: H358-R rep1

value: ARS-1620 until resistant


title: Mus_Musculus_SmoM2_Cdk6_koko_Tumor_3


title: ARS-48H rep3

value: ARS-1620 for 48 hours


title: ARS-24H rep2


title: PC9-BrM3 shHSF1 clone 7480 Rep 1

city: Durham

first: Ann Marie

last: Pendergast

state: North Carolina

address: 308 Research Drive LSRC

department: Pharmacology and Cancer Biology

institute: Duke University

data_processing:
Libraries were sequences on an Illumina HiSeq 2000 sequencing system using 50-bp single-ended reads by the Duke University Genome Sequencing facility.
RNA-seq data was processed using the TrimGalore toolkit under default parameters
Reads were mapped to the GRCh37 version of the human genome and transcriptome using the HISAT2 RNA-seq alignment tool.
Reads were used for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the FeatureCounts tool. Normalization and differential expression were carried out using the DESeq2 package in the R statistical programming environment.
Genome_build: GRCh37
Supplementary_files_format_and_content: featureCounts

source_name: non-small cell lung adenocarcinoma

growth_protocol: Cells were cultured in RPMI 1640 medium containing 10% FBS + 10 mM HEPES, 1 mM Sodium Pyruvate and 0.2% glucose

extract_protocol:
RNA was harvested using the Qiagen RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols by the Duke University Sequencing and Genomic Technologies core facility.

treatment_protocol: PC9-BrM3 cells were lentivirally-transduced with dox-inducible Tet-pLKO-shNTC or Tet-pLKO-shHSF1 (clone 7480) plasmids. Transduced cells were selected with puromycin for 5 days. Expression of shRNAs was induced by treating sub-confluent monolayers of cells with 500 ng/mL doxycycline for 48 hrs prior to total RNA harvest. For samples comparing PC9 parental versus PC9-BrM3 cells, sub-confluent monolayers were cultured for 48 hrs prior to total RNA harvest.

value: cell line:PC9-BrM3 shHSF1 clone 7480

tag: shRNA

value: Tet-pLKO-shHSF1 (clone 7480)


title: ARS-48H rep2


title: Mus_Musculus_SmoM2_Cdk6_koko_Tumor_2


title: KO_mm_rna_sr_MTirard_B_5


title: PC9-BrM3 shNTC Rep 2

value: Tet-pLKO-shNTC


title: Mus_Musculus_SmoM2_Tumor_1

description: genomically engineered mouse medulloblastoma model with constitutively active Smoothened under Math1-Cre promoter, Cdk6+/+


title: WT_mm_rna_sr_MTirard_A_1


title: PC9-BrM3 shNTC Rep 1


title: ARS-24H rep1


title: ATACseq_D4mDOXRep1

value: Inducible SOX17 H9 ESC

value: CD31 MACs cell at D4


title: H358 P rep3

value: DMSO


title: H358 P rep2


title: GVHD_HSC.1

city: Philadelphia

first: Yi

state: PA

address: 3500 N Broad Street

department: Microbiology and Immunology

institute: Temple University

data_processing:
Raw sequence reads were aligned to the mouse genome (mm10) using the Tophat algorithm
 Cufflinks  was implemneted to assemble transcripts and estimate their abundance.
Cuffdiff was used to statistically assess expression changes in quantified genes in different conditions
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Sample ...

source_name: Lin-c-kithiSca1+CD135-cells  in GVHD Mice

extract_protocol:
Total RNA was isolated from cells using an RNAeasy mini kit
RNA-seq libraries were prepared using SureSelect RNA Library Preparation kits


title: H358 P rep1


title: PC9-BrM3 Rep 1


title: PC9 Parental Rep 2

value: PC9 Parental


title: E24Am

city: Columbia

first: Wipawee

last: Winuthayanon

state: Missouri

address: 1030 Hitt Street

department: OB/GYN & Women's Health

institute: University of Missouri

description: 10x Chemistry: Single Cell 3’ v2

data_processing:
Both mouse and human data, processing of the raw sequencing data (mkfastq files) was carried out using Cell Ranger v3.1.0 to generate fastq files with default settings.
Fastq files were then processed through Velocyto v0.1.24 to produce loom files with spliced and unspliced mRNA information. Velocyto was run using the command run10x with default setting and a repeat masker gtf file from UCSC Genome Browser for mouse with an assembly for GRCm38/mm10 to mask expressed repeated elements. Generated loom files were then read in scanpy v1.6.0 using JupyterLab for analyses and saved in an h5ad format. For subsequent data analysis and visualization, a virtual machine (Docker) was used to create the analysis environment. Analysis packages including scanpy v1.6.0, anndata v0.7.5, umap v0.4.6, numpy v1.19.4, scipy v1.5.3, pandas v1.1.4, scikit-learn v0.23.2, statsmodels v0.12.1, python-igraph v0.8.3, louvain v0.7.0, and leidenalg v0.8.2 were installed on the Docker.
Genome_build: Reference genomes, mm10-3.0.0 and GRCh38-3.0.0, were used for sequence alignment in mouse and human samples, respectively.
Supplementary_files_format_and_content: Cell Ranger output

source_name: Mouse oviduct

extract_protocol:
For mouse samples, oviducts were collected 24 hrs after Veh or E2 treatment (n=5-6 mice/group) or at estrus (n=5 mice). Oviducts were pooled and collected in Leibovitz-15 media supplement with 1% fetal bovine serum (L15+1%FBS) and placed on ice. For Veh and E2-treated samples, the oviduct was dissected into distal (infundibulum with ampulla, referred to as InfAmp) or proximal (isthmus with UTJ, referred to as IsthUTJ) regions. To isolate oviductal cells, oviducts were quickly uncoiled by trimming the mesosalpinx in order to locate the ampulla-isthmus junction (AIJ). Then, the tissues were dissected at the AIJ region for subsequent InfAmp and IsthUTJ cell isolation. For estrus samples, the entire length of the oviduct was used. After dissection, 0.25% trypsin-EDTA was injected into the oviduct using a blunted 30-gauge needle until the trypsin was visibly flushed out from the other end of the oviduct. The tissues were then placed in a tube containing 500 µL of trypsin and incubated on ice for 30 min and at 37°C for another 30 min. After the incubation, 500 uL of FBS was added to stop the enzymatic activity of trypsin. Oviductal cells were then flushed out from oviductal tubes with 4°C L15+10%FBS. At this stage, the epithelial, stromal, and parts of muscle cell layers were visibly flushed out. Only translucent longitudinal muscle cells were left intact. Cell clumps and tissue debris were strained twice through 40-µm cell strainers. Cells were then spun down and resuspended in 0.04% bovine serum albumin in phosphate-buffered saline. The final cell concentration was targeted for 8,000 cells/run. For human sample, To obtain cell singlets, the Fallopian tubes were transected so that the luminal portion of the tube was exposed. The mucosal lining of the tubes was gently dissected with a scalpel and enzymatically digested in a solution of 0.05% Trypsin (Sigma, T1426) dissolved in HBSS (Gibco) for 30 minutes, followed by incubation in Collagenase (5 mg/ml, Sigma C5138) and DNAse I (200 µg/ml, Sigma DN25) solution for 20 minutes. The cells were filtered through a 40 µm filter, collected by centrifugation and resuspended in DMEM/F12 (Gibco, 11-330-057) supplemented with 10% FBS (Sigma, F2442) and antibiotics (Gibco, 15-240-096). Live cells were sorted on a BD FACS Aria II at the Cytometry and Cell Sorting Core Laboratory at Baylor College of Medicine (BCM) and submitted for single cell sequencing at the Single Cell Genomics Core Laboratory at BCM.
For mouse samples, scRNA-seq libraries were performed using manufacturer’s protocol (10X Genomics Inc, Pleasanton, CA). Single Cell 3’ v2 chemistry was used. Briefly, individual cells (~8,000 cells/run) were separated into droplets by Gel bead in EMulsion (GEM) technology using 10X Chromium Controller. Emulsion beads were broken and barcoded cDNAs were pooled for amplification. For human sample, scRNA-seq libraries were also performed using 10X Chromium Controller with Single Cell 3’ v3 chemistry.
For mouse samples, libraries generated were sequenced using an Illumina HiSeq4000, targeting 400M reads/run, paired-end, and 100bp read length. For human sample, libraries generated were sequenced using an Illumina NovaSeq 6000, targeting 300M reads/run, paired-end, 50bp read length.

treatment_protocol: Female mice were ovariectomized and left for 14 days to recover and eliminate endogenous steroid hormones. Sesame oil (100 µL) was used as a negative (Vehicle or Veh) control group. 17beta-estradiol (E2) at a dose of 0.25 µg was diluted in 100 µL of 10% ethanol and sesame oil. Ovariectomized females were subcutaneously injected with Veh or E2. Twenty-four hrs after injection, the oviduct was collected for scRNA-seq analysis. Vaginal washes were collected from adult female mice (between 8-12 weeks old) to determine the stage of estrous cycle21. At 11:00 h, oviducts from females in estrus were collected for subsequent scRNA-seq analysis. For human sample, the tissue was collected from an individual without underlying gynecological diseases who underwent post-partum bilateral salpingectomy for sterilization.

tag: tissue

value: oviduct

tag: region

value: infundibulum, ampulla

value: 17beta-estradiol 24 hrs


title: Naive_HSC.1

source_name: Lin-c-kithiSca1+CD135-cells  in Normal Mice


title: Mus_Musculus_SmoM2_Cdk6_koko_Tumor_1

state: CA

tag: genotype


title: PC9-BrM3 shHSF1 clone 7480 Rep 2


title: Naive_HSC.0


title: WT_mm_rna_sr_MTirard_A_2

value: Zbtb20 kncok-out line RRID:MGO:5693950


title: WT_mm_rna_sr_MTirard_A_5


title: S14 refeed

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
trimgalore with options '-p --illumina' to trim reads
HISAT2 align with options '-p --no-mixed --no-discordant' to align to GRCh38 + GRCm38 combined reference genome
Sambamba view to reformat aligned reads from .sam to .bam and sambamba sort to sort reads by coordinate
subread featureCounts with options '-p -P -s2' using Gencode H29 reference annotation to generate raw gene counts for aligned files
Genome_build: GRCh38 + GRCm38
Supplementary_files_format_and_content: tab delimited text file includes raw gene counts for each sample

organism:
Homo sapiens
Mus musculus

source_name: Liver

extract_protocol:
Whole livers were removed from the humanized mice either with ad libitum, a 24h fasting, or a 24h fasting followed by a 4h refeeding. The livers were flash frozen and powdered in liquid nitrogen, and the RNA was harvested using Trizol reagent.  Strand specific sequencing libraries were constructed using illumine TruSeq RNA sample Prep kit.
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

treatment_protocol: TK-NOG mice, in which a herpes simplex virus type 1 thymidine kinase (TK) transgene under a mouse albumin promoter is expressed within the liver of highly immune-deficient NOG mice, were obtained from Taconic Biosciences. The TK converts an antiviral medication ganciclovir (GCV) into a toxic product that allows selective elimination of TK positive cells in vivo. The cryopreserved primary human hepatocytes were obtained from Thermo Fisher Scientific. The humanized TK-NOG mice were prepared as previously described (Hasegawa, M. et al.). Briefly, The TK-NOG mice at 8-9 weeks old received an i.p. injection of GCV at a dose of 25 mg/kg. One week later, 50ul volume of 1 106 human primary hepatocytes suspended in HBSS solution were transplanted via intra-splenic injection. 8-12 weeks after transplantation, the serum human albumin in the mice were measured as an index of the extent of human hepatocytes replacement. Humanized TK-NOG mice with serum human albumin levels above 0.5 mg/ml were used for experiments, in which human hepatic genes could be reliably detected by q-PCR. Reference paper PMID: 21238430.

tag: condition

value: fast 24h then refed for another 4h, from 9:00am to 13:00pm

value: Human Liver cells xenografted into TKNOG mice


title: GVHD_HSC.0


title: Mus_Musculus_SmoM2_Tumor_3


title: Estrus

description: 10x Chemistry: Single Cell 3’ v2

value: infundibulum, ampulla, isthmus, uterotubal junction

value: estrus stage


title: KO_MTX_3

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCm38

source_name: white adipose tissue

extract_protocol: Trizol (Invitrogen) was used for RNA isolation from white adipose tissue.

treatment_protocol: miR-181a2b2-/- (KO) and miR-181a2b2flox/flox (flox) mice were placed on a 60% high fat diet for 12 weeks. Each group of mice was weekly i.p. injected with vehicle control or methotrexate (1 mg/kg).

value: methotrexate

value: white adipose


title: PC9-BrM3 Rep 2


title: E24Is

description: 10x Chemistry: Single Cell 3’ v2

value: isthmus, uterotubal junction


title: ARS-48H rep1

value: NSCLC cell line

value: ARS-1620 for 48 hours


title: run2_CC4532_Fe_pos

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced by Illumina NextSeq500 and NovaSeq Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to the Chlamydomonas reference genome (Chlamydomonas reinhardtii v5.5) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: Chlamydomonas reinhardtii v5.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: run2 cell wall Fe+

growth_protocol: We used the Chlamydomonas reinhardtii strains CC-5390 (cw15 arg7-8::ARG7 MT+) and CC-4532 (CW MT-), which we procured from laboratory stocks. We grew all pre-cultures in Tris Acetate Phosphate (TAP) medium supplemented with micronutrients  at 24 ºC in constant light (~50 µmol/m2/s) and under constant agitation (180 rpm) in an Innova-44R incubator.

extract_protocol: Single-cell RNAseq libraries were prepared by using the Chromium single cell 3′ library and gel bead kit v3 (10x Genomics).

value: Cultured Chlamydomonas cells


title: Mus_Musculus_SmoM2_Tumor_2


title: Naive_HSC.2


title: run2_CC5390_N_neg_rep2

source_name: run2 no cell wall N– replicate 2


title: PC9 Parental Rep 1


title: KO_MTX_2


title: S12 refeed


title: S13 refeed


title: FLOX_MTX_4

value: miR-181a2b2flox/flox (flox)


title: V24Am

description: 10x Chemistry: Single Cell 3’ v2

value: Vehicle 24 hrs


title: run2_CC5390_Fe_pos

source_name: run2 no cell wall Fe+


title: run2_CC4532_Fe_neg

source_name: run2 cell wall Fe–


title: run2_CC5390_Fe_neg

source_name: run2 no cell wall Fe–