title: 701

last: Bryant

address: 72 E Concord St

institute: Boston University School of Medicine

data_processing:
We used the R/Bioconductor package “scruff” to conduct demultiplexing, read alignment, read counting, quality checking and data visualization (Wang et al., 2019).
Reads were trimmed for quality using Trimmomatic (Bolger et al., 2014).
Trimmed reads were then aligned to the mm10 mouse reference genome (Ensembl) to generate BAM files for alignment using STAR (Dobin et al., 2013)
For differential gene analysis in the spinal cord, the featureCounts read summarization program was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl (GRCm38).
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts from featureCounts.

tag: cpp treatment

value: SALINE

value: M


title: 705

status: Public on Feb 11 2022

type: SRA

city: Boston

first: Camron

middle: D

state: Massachusetts

department: Pharmacology

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
RNA was extracted in RNAlater-preserved tissue using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide free water (Yazdani et al., 2015) and diluted to 100 ng/ul.
RNA library preparation (poly-A selection) and RNA-seq was conducted at the University of Chicago Genomics Facility on an Illumina NovaSEQ6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. ~30M clusters/sample, 60M PE reads/sample.

tag: strain

tag: Sex

value: F

tag: rna extraction cohort

tag: tissue

value: Hippocampus


title: Male brain

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
The base call (BCL) files generated from the Illumina sequencing were processed by Cell Ranger (v. 3.0.1) and converted to FASTQ files by the ‘mkfastq’ function.
The reads were mapped to the Ae. aegypti reference genome Aaegl5 using STAR aligner
The Cell Ranger pipeline was used to perform background filtration based on UMI (unique molecular identities) versus barcode counts, and to generate feature-barcode matrices from the libraries
The read count data of genes of single cells, generated by the Cell Ranger pipeline, was analyzed using the R package ‘Seurat’.
Genome_build: Aaegl5
Supplementary_files_format_and_content: Three processed data files (tsv.gz) were generated per library that included information of barcodes, features and read counts.

molecule: total RNA

organism: Aedes aegypti

source_name: Adult brain

growth_protocol: 7-day old Ae. aegypti (LVP strain) males and females were used in the study.

extract_protocol:
Brain was dissected from 30 males and females, resuspended in Schneider’s Drosophila Medium on ice, and subjected to single nucleus isolation using the Pure Prep Nuclei Isolation kit (Sigma, St. Louis, MO, USA). Complete brain tissue was resuspended in Schneider’s Drosophila Medium on ice.
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 protocol

value: Male

value: brain

tag: developmental stage

value: 7 day old adult


title: 190726_BBB_snRNA-G8

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

description: brain.BBB.humanHD.counts.rds

data_processing:
Raw sequencing reads were aligned to the pre-mRNA annotated  Homo sapiens reference genome version GRCh38.
Counts were estimated using Cellranger 3.0.1 (10x Genomics, Pleasanton CA)
The generated cell-by-gene unique molecular identifier (UMI) count matrix was analyzed using the Seurat R package v.3.2.021.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.rds, meta.rds

molecule: nuclear RNA

organism: Homo sapiens

source_name: post mortem tissue

growth_protocol: Not applicable

extract_protocol:
Tissue was homogenized in media followed by either enrichment (BVE)/nuclei extraction or only nuclei extraction. Nuclei were processed through the 10X Single Cell Gene Expression platform per manufacturer's protocol
Libraries were constructed using the 10X Genomics Chromium Single Cell 3′ Reagent Kit v3

treatment_protocol: Not applicable

tag: disease state

value: Pathologically Normal

tag: protocol

value: Blood Vessel Enrichment


title: 190726_BBB_snRNA-G12

description: brain.BBB.humanHD.counts.rds

value: Huntington's


title: canine cortisol-secreting adrenocortical tumor 25

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

data_processing:
reads were demultiplexed and aligned to canine cDNA reference using the BWA
Genome_build: CanFam3.1
Supplementary_files_format_and_content: raw counts

organism: Canis lupus familiaris

source_name: cortisol-secreting adrenocortical tumor

extract_protocol:
cells were trypsinized and stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using CEL-Seq2

tag: disease


title: 190726_BBB_snRNA-G11

description: brain.BBB.humanHD.counts.rds


title: D_4

city: Beijing

first: Feng

last: Wan

address: No. 8 Xishiku Street

country: China

institute: Peking University First Hospital

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
A FDR corrected p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNAs were extracted from samples using TRIzol (Invitrogen) following the methods by Chomczynski et al. DNA digestion was carried out after RNA extraction by DNaseI
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: treatment

value: LCWE-induced


title: canine cortisol-secreting adrenocortical tumor 24


title: D_2


title: canine cortisol-secreting adrenocortical tumor 23


title: C_4

value: PBS


title: canine cortisol-secreting adrenocortical tumor 22


title: SAMPLE 24

type: RNA

city: Moscow

first: Anastasia

middle: A

last: Sadova

state: Russian Federation

address: Khoroshevskoe Shosse 76a

country: Russia

institute: Institute of Biomedical Problems of RAS

description: Test

data_processing:
Analysis of the fold difference in the expression of target genes was performed with StepOne Software v2.3 (Thermo Fisher Scientific, USA)
For the normalization it uses the expression of a housekeeping gene TBP
Target gene signals normalized to the housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The StopOne Software package automatically performs all deltadeltaCt based fold-change calculations from the raw threshold cycle data.
Fold Change file reports test/control (i.e., CD14+monocytes on day 7/CD14+ monocytes on day -7) ratios.

label: SYBR Green

source_name: CD14+ monocytes extracted on day 7 of recovery period

label_protocol: PCR assays were performed on AB StepOnePlus Real-Time PCR system (Thermo Fisher Scientific, Carlsbad, CA, USA) using SYBR Green reagent qPCRmix-HS SYBR+HighROX (Evrogen, Moscow, Russia). Reverse transcription was performed from 500 ng total RNA using the MMLV RT kit (Evrogen, Moscow, Russia). The run protocol consisted of 40 cycles of 95 °C for 15s, 60 °C for 15s, and 72 °C for 30s, with fluorescence intensity measurement performed after the elongation stage.

extract_protocol: Total RNA was extracted using phenol-chlorophorm extraction followed by DNase I treatment.

tag: cell type

value: CD14+ monocytes

tag: volunteer

tag: time

value: +7 days


title: D_1


title: 190726_BBB_snRNA-G10

description: brain.BBB.humanHD.counts.rds


title: D20-169016

description: brain.BBB.human.counts.rds

source_name: ex vivo resection

value: intractable epilepsy


title: canine cortisol-secreting adrenocortical tumor 20


title: C_3


title: SAMPLE 22

description: Test

source_name: CD14+ monocytes extracted on day 7 of confinement

value: 7 days


title: SAMPLE 21

description: Control

source_name: CD14+ monocytes extracted 7 days before confinement

value: -7 days


title: SAMPLE 23

description: Test

source_name: CD14+ monocytes extracted on day 14 of confinement

value: 14 days


title: canine cortisol-secreting adrenocortical tumor 21


title: C_2


title: D20-169017

description: brain.BBB.human.counts.rds

value: Standard Nuclei Extraction


title: D20-169015

description: brain.BBB.human.counts.rds


title: B_4

source_name: small intestine

value: small intestine


title: SAMPLE 19

description: Test


title: canine cortisol-secreting adrenocortical tumor 19


title: SAMPLE 20

description: Test


title: canine cortisol-secreting adrenocortical tumor 18


title: D20-169014

description: brain.BBB.human.counts.rds


title: B_2


title: SAMPLE 18

description: Test


title: D20-169013

description: brain.BBB.human.counts.rds


title: SAMPLE 17

description: Control


title: B_1


title: canine cortisol-secreting adrenocortical tumor 17


title: D20-169012

description: brain.BBB.human.counts.rds


title: canine cortisol-secreting adrenocortical tumor 16


title: SAMPLE 16

description: Test


title: A_4


title: D20-169011

description: brain.BBB.human.counts.rds


title: A_3


title: canine cortisol-secreting adrenocortical tumor 15


title: D20-169010

description: brain.BBB.human.counts.rds


title: canine cortisol-secreting adrenocortical tumor 14


title: canine cortisol-secreting adrenocortical tumor 13


title: A_2


title: D20-125073

description: brain.BBB.human.counts.rds


title: D20-125072

description: brain.BBB.human.counts.rds


title: D20-125071

description: brain.BBB.human.counts.rds


title: canine cortisol-secreting adrenocortical tumor 12


title: SAMPLE 13

description: Control


title: SAMPLE 14

description: Test


title: SAMPLE 12

description: Test


title: canine cortisol-secreting adrenocortical tumor 11


title: FST+LIN28B-2

city: Baltimore

first: Angelika

last: Doetzlhofer

state: MD

address: 855 North Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

data_processing:
Basecalling using Illumina NovaSeq 6000 RTA3
RNAseq reads were aligned to the GRCm38 mouse transcriptome using Kallisto v0.46.1
RNAseq read abundance quantifications were performed using Kallisto v0.46.1
Genome_build: GRCm38 mouse transcriptome
Supplementary_files_format_and_content: h5 abundance files

source_name: cochlea

growth_protocol: Dissociated cochlear epithelial cells isolated from 5-day old mice were cultured at high density within a drop of Matrigel matrix in expansion medium prepared with DMEM/F12 , N2 supplement , B-27 supplement, EGF, FGF2, CHIR99021, VPA, and penicillin.

extract_protocol:
Organoids were washed once with 1x PBS, after which they were treated with Cell Recovery solution to dissolve Matrigel matrix. Organoids were pelleted and total RNA was extracted using the miRNeasy Micro Kit (Qiagen, no. 217084).
Samples were processed using Illumina's TruSeq stranded Total RNA kit, per manufacturer's recommendations, using the UDI indexes.  The samples were sequenced on the Illumina NovaSeq 6000, paired end, 2x50 bp reads

treatment_protocol: To induce and maintain FST and or LIN28B transgene expression, expansion media contained doxycycline hyclate (0.5 μg/mL)

value: cochlear epithelial cell

value: FST and LIN28B overexpression

tag: time point

value: expansion for 7 days


title: FST+LIN28B-1


title: D20-125070

description: brain.BBB.human.counts.rds

value: brain


title: LIN28B-3

value: LIN28B overexpression


title: LIN28B-2


title: SAMPLE 15

description: Test


title: D20-125068

description: brain.BBB.human.counts.rds

value: Blood Vessel Enrichment


title: SAMPLE 10

description: Test


title: SAMPLE 9

description: Control


title: canine cortisol-secreting adrenocortical tumor 10


title: SAMPLE 11

description: Test


title: SAMPLE 8

description: Test


title: D20-125067

description: brain.BBB.human.counts.rds


title: LIN28B-1


title: canine cortisol-secreting adrenocortical tumor 7


title: FST-3

value: FST overexpression


title: SAMPLE 7

description: Test


title: D20-125066

description: brain.BBB.human.counts.rds


title: canine cortisol-secreting adrenocortical tumor 6


title: FST+LIN28B-3


title: SAMPLE 6

description: Test


title: FST-1


title: D20-125065

description: brain.BBB.human.counts.rds


title: canine cortisol-secreting adrenocortical tumor 4


title: FST-2


title: D20-125069

description: brain.BBB.human.counts.rds


title: canine cortisol-secreting adrenocortical tumor 5


title: D20-125064

description: brain.BBB.human.counts.rds


title: Control-3

value: control


title: SAMPLE 5

description: Control


title: canine cortisol-secreting adrenocortical tumor 9


title: Control-2


title: SAMPLE 4

description: Test


title: canine cortisol-secreting adrenocortical tumor 3


title: D20-125062

description: brain.BBB.human.counts.rds


title: D20-125063

description: brain.BBB.human.counts.rds


title: canine cortisol-secreting adrenocortical tumor 8


title: canine cortisol-secreting adrenocortical tumor 2


title: SAMPLE 2

description: Test


title: D20-125061

description: brain.BBB.human.counts.rds


title: Control-1


title: SAMPLE 1

description: Control


title: Ezh2 K307R rep2

status: Public on Feb 10 2022

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical University

data_processing:
SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard BGI protocols

value: Liver

tag: genotype


title: Ezh2 K307R rep1


title: NK_Bach2 cKO rep3

first: Shasha

last: Li

state: MO

address: 660 S Euclid Avenue

department: Rheumatology

institute: Washington University in St.Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a (Dobin, A et al., Bioinformatics, 2013).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5 (Liao Y et al., Bioinformatics, 2014).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *gene_counts.txt: Tab-delimited text files include gene counts, CPM and RPKM values for each Sample.
Supplementary_files_format_and_content: all.gene_counts.tsv: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Differential_gene_expression_in_NK_cells_between_Bach2_cKO_and_control_mice.txt: Tab-delimited text file with differential gene expression between Bach2 cKO and control samples.

source_name: Natural Kill cells

growth_protocol: Fresh NK cell were enriched from spleen by EasySep Mouse NK cell isolation kit (STEMCELL Technologies). CD3-CD19-NK1.1+NKp46+ NK cells were then sorted from enriched cells.

extract_protocol:
Total RNA were isolated by PureLink RNA Mini Kit (Ambion).
The library was generated using low input Clontech method.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: No treatment

value: spleen

value: CD3-CD19-NK1.1+NKp46+ NK cells

value: Bach2 conditional knockout


title: WT rep2

value: WT


title: WT rep1


title: SAMPLE 3

description: Test

value: CD14+ monocytes


title: NK_Bach2 cKO rep4


title: NK_Bach2 cKO rep1


title: NK_Bach2 control rep4

value: wild type


title: D.4 [16]

source_name: Spinal Cord

value: BALB/cByJ

value: F

tag: testing cohort

value: Spinal Cord


title: C.1 [13]

value: M


title: A.2 [09]

value: BALB/cJ


title: 3.2 [05]


title: NK_Bach2 control rep3


title: 3.3 [06]


title: 4.1 [07]


title: NK_Bach2 control rep2


title: NK_Bach2 cKO rep2


title: Non-invasive

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

description: Non-invasive

hyb_protocol: The labeled circRNAs were hybridized onto the human circular RNA Array V2.0, and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 1 out of 2 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

source_name: primary human CRC cells

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNAs were isolated from CRC cells using Trizol reagent. The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

treatment_protocol: Cells were isolated from human CRC samples

value: Non-invasive CRC cell


title: Invasive

description: Invasive

value: Invasive CRC cell


title: C.3 [14]


title: NK_Bach2 control rep1


title: 1.2 [01]


title: 2.1 [03]


title: D.1 [15]


title: canine cortisol-secreting adrenocortical tumor 1


title: B.4 [12]


title: 2.3 [04]


title: 4.4 [08]


title: 1.4 [02]


title: WT1 H3K9me3 ChIP

city: Guangzhou

first: Bo

last: Yang

state: Guangdong

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University

library_source: genomic

data_processing:
150-bp paired-end reads per ChIP-seq were mapped to the mouse (mm9) genome using Bowtie2 (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0) with default parameters.
Peaks were called by model-based analysis of ChIP-seq (MACS2 Galaxy toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6) using GFP input as control and calling p value 1e-6.
Consensus target motif was derived from peak regions by using MEME-ChIP tool (http://meme-suite.org/tools/meme-ChIP).
Heatmap and profile plots then were generated by plotHeatmap or plotProfile (Galaxy toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.0.0.1, toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0) using calculated matrix generated by ComputeMatrix.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using bigwig

molecule: genomic DNA

source_name: Zfp961-GFPflox/flox ESCs

growth_protocol: Zfp961 GFPflox/flox mouse ROSA-cre-ERT2 ESCs were cultured in ESM medium containing DMEM (Gibco), 15% fetal bovine serum (FBS; Hyclone), 10mM NEAA, 100 μM β-mercaptoethanol, 2 mM L-glutamine, 10ng/mL LIF, 2i (3μM CHIR-99021, 1μM PD0325901, Selleck).

extract_protocol:
Crosslinked chromatin from 2-4X107 cells fragmented on a Covaris to ~100-300bp was immunoprecipitated with GFP (Invitrogen A-6455) or H3K9me3 (Abcam ab8898) antibodies.
library construction using the KAPA Hyper Prep Kit (Roche)

treatment_protocol: ROSA-Cre-ERT2 ESCs were treated with 4-OHT or vehicle for 48 hours, then feed with normal culture medium for another 72 hours before experiments.

value: mouse ESCs

value: Zfp961 WT

value: EtOH

tag: antibody

value: H3K9me3 (Abcam ab8898)


title: WT2 H3K9me3 ChIP


title: KO1 GFP ChIP

value: Zfp961 KO

value: GFP (Invitrogen A-6455)


title: A.3 [10]


title: AGM niche (live, Ter119-)

first: Edroaldo

last: Lummertz da Rocha

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Single-cell RNA-sequencing of AGM niche cells (live, Ter119-)

data_processing:
Raw sequencing files were processed using CellRanger pipeline
Quality control, normalization, graph-based clustering, identification of gene signatures and trajectory analysis were performed using CellRouter
Intercellular communication analysis was performed using CellComm
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression counts

source_name: E10.5 AGM region

growth_protocol: Embryos were harvested at E10.5 and somites were counted, only processing embryos between 28 and 32 somite pairs. AGM regions were dissected, pooled and dissociated following Chen et al., 2020. Cells were filtered (40 µm filter) and stained in PBS/2%FBS on ice using antibodies provided in the manuscript. Cells were sorted at 15 psi pressure using a 100 µm nozzle on a MoFlo Astrios EQ Cell Sorter (Beckman Coulter). Sorted cells were collected into 1.5 ml Eppendorf tubes containing 300 µl PBS/50%FBS.

extract_protocol:
Following sorting, each cell population was divided across two lanes on a 10X Genomics scRNA-Seq chip as independent technical replicates to encapsulate cells into droplets.
scRNA-Seq libraries were  prepared per the 10X scRNA-Seq v2 protocol. Cells were loaded into 10X lanes at cell concentrations to maintain an estimated doublet rate below 5%. Final 10X libraries were assayed via an Agilent High Sensitivity dsDNA Bioanalyzer, normalized, pooled and shallow sequenced on a MiniSeq, identifying 10,000 high confidence cell barcodes in total across all conditions. 10X libraries were then renormalized per the distribution of reads/library from the MiniSeq run and deep sequenced on a NovaSeq S4 to a depth of 50,000 reads per cell barcode.

value: aorta-gonad-mesonephros region (AGM)

value: AGM niche


description: Single-cell RNA-sequencing of T1-preHSCs (Ter119-CD31+VCad+CD41lowcKit+)


title: KO1 H3K9me3 ChIP


title: peripheral blood mononuclear cells_CLP

first: Li

last: Jiaxin

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

data_processing:
Transcriptome data were demultiplexed and mapped to the mm39 transcriptome with Cell Ranger Software Suite 5.0.1
The Seurat package 4.0.6 was used for integration in R 4.0.3 after obtaining the expression matrix for each sample. From this, all cells were removed that had over 5,000 or below 200 expression genes, over 30,000 UMIs, over 15% UMIs derived from mitochondrial genes, over 50% UMIs derived from the ribosome genome, or over 0.01% UMIs derived from the hemoglobin genome.
Doublet cell and cell-free mRNA were also removed. From the remaining 26,337 cells, gene expression matrices were normalized by using Normalize Data function in the Seurat package.
To visualize and explore this data set, the first 5 principal components were further summarized using UMAP dimensionality reduction using the default setting of the RunUMAP function. Cell clusters in the resulting two-dimensional representation were annotated to known biological cell types using canonical marker genes.
Different periods were extracted, and KEGG enrichment analysis was performed using the clusterprofile package 3.18.1. Pathway analyses were predominantly performed on the KEGG subset of Canonical pathways in curated gene sets described in the molecular signature database, analyzed by using the Gene Set Variation Analysis (GSVA) package 1.42.0
Genome_build: mm39
Supplementary_files_format_and_content: Marix table with raw gene counts for every gene and every cell

source_name: peripheral blood mononuclear cells

extract_protocol:
The bood was incubated in dissociation buffer containing 1 mg/ml hyaluronidase（sigma,H3506） and 20,000U/ml DNase I（sigma,DN25） for 15 min at 37 C. Enzymatic digestion was quenched with Dulbecco’s Modifified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, 10270106, Gibco). Cells were resuspended at a concentration of 1 million cells per ml and stained with PBST containing 1% FCS
The Chromium Single Cell 3′Library & Gel Bead Kit v3 (10X Genomics, 1000075) was used for single-cell barcoding, cDNA synthesis and library preparation，following manufacturer’s instructions as previously described. Libraries were sequenced on Illumina novaseq 6000 using paired-end 150 bp.

value: peripheral blood mononuclear cells

value: CMC-treated +CLP for 12h


title: WT1 GFP ChIP


title: peripheral blood mononuclear cells_Sham

value: Sham for 12h


title: KO2 GFP ChIP


title: WT2 GFP ChIP


title: MA-104 cells, Control (48hpi), L1

city: Wuhan

first: Gehad

last: Elkady

state: Hubei

address: Huazhong Agricultural University, No.1,Shizishan Street, Hongshan District,Wuhan

department: Virology

institute: HZAU

description: miRNA

data_processing:
Raw sequence data obtained by high-throughput sequencing were analyzed by Base Calling and transformed into Sequenced Reads, which are called Raw Data or Raw Reads.
The results were stored in FASTQ format, which contains sequence information of sequencing sequences (reads) and their corresponding sequencing quality information.
Clean reads of each sample were screened, sRNA within a certain length was selected for subsequent analysis, and the length distribution statistics of sRNA was made; the length range of animal sRNA is 18-35nt (Bartel, 2018).
The small RNAs were aligned and analyzed in comparison to the reference genome sequence in the Sanger miRBase 21.0 database (http://www.mirbase.org/) (Langmead et al., 2009). The expression levels of known and novel miRNAs in each sample were counted, and TPM was used to normalize the expression levels (Zhou et al., 2010). For the samples with biological duplication, DESeq2 (Love et al., 2014) based on negative binomial distribution was used for analysis. For samples without biological duplication, DEGseq (Wang et al., 2010) based on TMM algorithm was used to standardize read count data and then conduct difference analysis, the differences of miRNAs filter condition is: padj < 0.05 & |log2 (foldchange) | > 1. Additionally, the differentialy expressed miRNAs which linked between the different time points of the BRV infection were identified.
Moreover, animal miRNA target gene were predicted by miRanda (http://www. microrna.org/) (Enright et al., 2003) and RNAhybrid (http://bibiserv.techfak.uni-bielefeld. de/rnahybrid/) (Krüger and Rehmsmeier, 2006).After obtaining the differentially expressed miRNAs among each group, we conducted Gene Ontology and KEGG enrichment analysis for the collection of differentially expressed miRNA target genes in each group according to the corresponding relationship between miRNA and its target genes. Gene Ontology (GO), (http://www.geneontology.org/) is the international standard classification system Gene function, was used to study the target mRNA function, GO enrichment analysis method is Goseq (Young et al., 2010), is based on Wallenius non-central hyper-geometric distribution. Besides, KEGG (Kyoto Encyclopedia of Genes and Genomes) (Kanehisa et al., 2008) was adopted to study the biochemical metabolic pathways and signal transduction pathways (protein-protein interaction) involved by the target genes candidates, pathway significance enrichment analysis was conducted by using KEGG pathway (KOBAS 2.0 annotation tool) (http://kobas.cbi.pku.edu.cn/help.do), it is using hypergeometric test / Fisher's exact test to find out which pathway was significantly enriched in candidate target genes compared with the whole genome background.
Supplementary_files_format_and_content: 10.Readcount_TPM.xls, 11.TPM_interval.xls

organism: Macaca mulatta

growth_protocol: MA-104 cell line was purchased from Procell Life Sciences& Technology Co., Ltd. China.The cells were sub-cultured in six-well tissue culture plates (Corning, Inc., Cat. No.002019). Dulbecco’s Modified Eagle’s Media (DMEM,  Gibco ™, Cat. No 11965092)) complemented with 5% -10% fetal bovine serum (Gibco ™, Cat. No 26140–079) and antibiotic (1000 IU of penicillin-1000 μg streptomycin per ml) (Sigma Aldrich, Cat. No 15140122) were used.

extract_protocol:
The infected and control cell samples were collected from six-well plate in triplicate for each of the following time points: 0 hpi (just after adsorption time (90 min), 6 hpi, 12 hpi, 24 hpi, 36 hpi and 48 hpi. Three replicates of virus- and mock-infected cultures were prepared at each time point. Total RNA was purified from the cells using TRIzol (Ambion® (life technology, USA), 15596-026). Then strict quality control was carried out on the RNA samples. The quality control criteria included the following three aspects: Agarose gel electrophoresis: analyze the integrity of sample RNA and whether there is DNA contamination, nanodrop: preliminary quantification, detection of RNA concentration and purity (OD260/280 and OD260/230) and Agilent 2100 Bioanalyzer for accurate Detection of RNA integrity.
The small RNA-SEQ technology process mainly consists of two parts: database building sequencing and bioinformatics analysis. After the qualified samples were detected, Small RNA Sample Pre-Kit was used to construct the small RNA library. Illumina deep sequencing was performed

treatment_protocol: The cells were used for infection when grown to 80–90% confluence, they infected with 100TCID50 of bovine rotavirus strain G8P[7]. Uninfected cells were used as the mock-infected group. Morphological changes of the infected cells were observed at 0, 6, 12, 24, 36, 48, and 72 hours post-infection (hpi) in comparison to the uninfected one.

tag: cell line

tag: cell source

value: established from rhesus fetal kidney

tag: infection

value: Bovine rotavirus G8P[7]

value: Control (48hpi)


title: MA-104 cells, Control (48hpi), L2

description: miRNA


title: MA-104 cells, Control (48hpi), L3

description: miRNA


title: MA-104 cells, Infected (48hpi), K2

description: miRNA

value: Infected (48hpi)


title: MA-104 cells, Control (36hpi), J2

description: miRNA

value: Control (36hpi)


title: MA-104 cells, Infected (48hpi), K3

description: miRNA


title: MA-104 cells, Control (36hpi), J3

description: miRNA


title: peripheral blood mononuclear cells_HDCA+CLP

tag: strain

value: HDCA-reated +CLP for 12h


title: MA-104 cells, Infected (48hpi), K1

description: miRNA


title: MA-104 cells, Infected (36hpi), I2

description: miRNA

value: Infected (36hpi)


title: MA-104 cells, Control (24hpi), H3

description: miRNA

value: Control (24hpi)


title: MA-104 cells, Infected (36hpi), I3

description: miRNA


title: Endothelial cells (Ter119-CD31+VCad+CD41-cKit+)

description: Single-cell RNA-sequencing of endothelial cells (Ter119-CD31+VCad+CD41-cKit+)

tag: tissue

value: Endothelial cells


title: KO2 H3K9me3 ChIP

value: mouse ESCs

value: H3K9me3 (Abcam ab8898)


title: MA-104 cells, Control (24hpi), H1

description: miRNA


title: MA-104 cells, Control (12hpi), F3

description: miRNA

value: Control (12hpi)


title: MA-104 cells, Infected (24hpi), G1

description: miRNA

value: Infected (24hpi)


title: B.2 [11]

value: BALB/cJ

tag: Sex

value: F

value: Spinal Cord


title: MA-104 cells, Control (12hpi), F2

description: miRNA


title: MA-104 cells, Infected (12hpi), E2

description: miRNA

value: Infected (12hpi)


title: MA-104 cells, Infected (12hpi), E1

description: miRNA

value: established from rhesus fetal kidney


title: MA-104 cells, Control (6hpi), D2

description: miRNA

value: Bovine rotavirus G8P[7]

value: Control (6hpi)


title: MA-104 cells, Infected (36hpi), I1

description: miRNA


title: MA-104 cells, Infected (12hpi), E3

description: miRNA


title: MA-104 cells, Control (12hpi), F1

description: miRNA


title: MA-104 cells, Control (24hpi), H2

description: miRNA


title: MA-104 cells, Control (6hpi), D3

description: miRNA


title: MA-104 cells, Infected (6hpi), C2

description: miRNA

value: Infected (6hpi)


title: MA-104 cells, Control (0hpi), B2

description: miRNA

value: Control (0hpi)


title: MA-104 cells, Infected (6hpi), C3

description: miRNA


title: MA-104 cells, Infected (6hpi), C1

description: miRNA


title: MA-104 cells, Control (6hpi), D1

description: miRNA


title: MA-104 cells, Control (36hpi), J1

description: miRNA

value: Control (36hpi)


title: MA-104 cells, Infected (24hpi), G3

description: miRNA


title: MA-104 cells, Infected (0hpi), A1

description: miRNA

value: Infected (0hpi)


title: MA-104 cells, Infected (0hpi), A2

description: miRNA


title: MA-104 cells, Control (0hpi), B1

description: miRNA


title: MA-104 cells, Infected (0hpi), A3

description: miRNA


title: MA-104 cells, Infected (24hpi), G2

description: miRNA


title: XZ1515_GZ_B8_I6_GZpool_03_2019

city: Evanston

first: Gaotian

last: Zhang

address: 2205 Tech Drive

department: Department of Molecular Biosciences

institute: Northwestern University

data_processing:
fastp (v0.20.0) was used to trim raw FASTQ files
Kallisto (v0.44.0) was used for alignment and expression quantification
Genome_build: Caenorhabditis elegans N2 reference genome (WS276)
Supplementary_files_format_and_content: Matrix tables with raw  counts and raw TPM for every transcript and every sample

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Animals were cultured at 20°C on modified nematode growth medium (NGMA) containing 1% agar and 0.7% agarose to prevent burrowing and fed Escherichia coli (E. coli) strain OP50.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen)
For each sample, mRNA was purified and enriched from 1 µg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog no. E7490L). RNA libraries were constructed with the NEBNext Ultra II RNA Library Prep with Sample Purification Beads (New England Biolabs, catalog no. E7775L). The cDNA libraries were adapter-ligated using adapters and unique dual indexes in the NEBNext Multiplex Oligos for Illumina (New England Biolabs, catalog no. E6440, E6442) and amplified using 12 PCR cycles. All procedures were performed according to the manufacturer’s protocols.

tag: developmental stage

value: young adult

value: hermaphrodite


title: XZ1516_GZ_B2_C5_GZpool_01_2019


title: XZ1516_GZ_B2_G5_GZpool_03_2019


title: XZ1515_GZ_B8_I9_GZpool_07_2020


title: XZ1515_GZ_B8_I8_GZpool_05_2019


title: MA-104 cells, Control (0hpi), B3

description: miRNA


title: XZ1516_GZ_B5_A8_GZpool_05_2019


title: XZ1513_GZ_B8_I5_GZpool_07_2020


title: XZ1513_GZ_B8_D5_GZpool_03_2019


title: WN2050_GZ_B8_A5_GZpool_06_2019


title: RC301_GZr_B5_I8_GZpool_08_2020


title: XZ1513_GZ_B8_F6_GZpool_05_2019


title: WN2050_GZ_B6_H8_GZpool_04_2019


title: RC301_GZ_B7_G3_GZpool_06_2019


title: WN2050_GZr_B6_F2_GZpool_08_2020


title: QX1793_GZ_B8_F5_GZpool_05_2019


title: QX1793_GZ_B8_I4_GZpool_07_2020


title: QX1793_GZ_B8_D4_GZpool_03_2019


title: QX1792_GZ_B7_E1_GZpool_06_2019


title: QX1791_GZ_B9_E3_GZpool_08_2020


title: QX1792_GZr_B5_I7_GZpool_08_2020


title: QX1791_GZ_B9_C7_GZpool_08_2020


title: QX1233_GZ_B9_E2_GZpool_08_2020


title: QX1233_GZ_B9_C6_GZpool_08_2020


title: QX1212_GZ_B5_G2_GZpool_06_2019


title: QW947_GZ_B9_E1_GZpool_08_2020


title: QX1212_GZ_B3_C8_GZpool_03_2019


title: QG2075_GZr_B3_I1_GZpool_08_2020


title: QG556_GZ_B7_B4_GZpool_04_2019


title: RC301_GZ_B7_E2_GZpool_04_2019


title: QG556_GZr_B5_G1_GZpool_08_2020


title: QX1794_GZ_B4_E5_GZpool_05_2019


title: QX1794_GZm_B1_C8_GZpool_0108_2020


title: QX1212_GZr_B3_A2_GZpool_07_2020


title: QG2075_GZ_B6_H7_GZpool_06_2019


title: QX1794_GZm_B3_I2_GZpool_0307_2020


title: QW947_GZ_B9_C5_GZpool_08_2020


title: QG556_GZ_B7_D9_GZpool_06_2019


title: PX179_GZ_B5_F9_GZpool_06_2019


title: PX179_GZr_B3_C7_GZpool_07_2020


title: PS2025_GZm_B8_D3_GZpool_0307_2020


title: QX1792_GZ_B7_B5_GZpool_04_2019


title: NIC529_GZ_B7_G2_GZpool_06_2019


title: PS2025_GZ_B8_F4_GZpool_05_2019


title: NIC528_GZr_B5_F8_GZpool_08_2020


title: PS2025_GZ_B8_I3_GZpool_07_2020


title: QG2075_GZ_B6_F1_GZpool_04_2019


title: NIC529_GZ_B7_B3_GZpool_04_2019


title: NIC527_GZr_B5_F7_GZpool_08_2020


title: NIC528_GZ_B7_B2_GZpool_04_2019


title: NIC527_GZ_B7_D7_GZpool_06_2019


title: NIC528_GZ_B7_D8_GZpool_06_2019


title: NIC527_GZ_B7_B1_GZpool_04_2019


title: NIC526_GZ_B9_D9_GZpool_08_2020


title: PX179_GZ_B3_H9_GZpool_03_2019


title: NIC526_GZ_B9_C4_GZpool_08_2020


title: NIC523_GZ_B5_D5_GZpool_06_2019


title: NIC523_GZ_B2_C9_GZpool_01_2019


title: NIC515_GZ_B1_H1_GZpool_01_2019


title: NIC523_GZ_B2_G4_GZpool_03_2019


title: NIC514_GZ_B5_D4_GZpool_06_2019


title: NIC529_GZr_B5_I6_GZpool_08_2020


title: NIC514_GZ_B2_G3_GZpool_03_2019


title: NIC514_GZ_B2_C4_GZpool_01_2019


title: NIC511_GZ_B6_E8_GZpool_04_2019


title: NIC511_GZ_B6_H5_GZpool_06_2019


title: NIC511_GZm_B1_G9_GZpool_0107_2020


title: NIC513_GZ_B2_A2_GZpool_01_2019


title: NIC501_GZ_B6_C3_GZpool_04_2019


title: NIC513_GZ_B6_C4_GZpool_04_2019


title: NIC501_GZ_B6_E7_GZpool_06_2019


title: NIC3_GZ_B4_H1_GZpool_04_2019


title: NIC3_GZ_B7_H7_GZpool_06_2019


title: NIC501_GZ_B1_G8_GZpool_01_2019


title: NIC3_GZ_B1_E8_GZpool_01_2019


title: NIC277_GZ_B4_G9_GZpool_04_2019


title: NIC277_GZ_B7_I1_GZpool_06_2019


title: NIC276_GZ_B5_D3_GZpool_06_2019


title: NIC515_GZ_B6_H6_GZpool_06_2019


title: NIC275_GZm_B1_E7_GZpool_0108_2020


title: NIC275_GZ_B4_E4_GZpool_04_2019


title: NIC276_GZ_B2_G2_GZpool_01_2019


title: NIC275_GZ_B4_G8_GZpool_05_2019


title: NIC276_GZ_B3_C6_GZpool_03_2019


title: NIC274_GZ_B4_E3_GZpool_04_2019


title: NIC271_GZr_B3_A1_GZpool_07_2020


title: NIC271_GZ_B3_C5_GZpool_03_2019


title: NIC268_GZr_B5_I5_GZpool_08_2020


title: NIC271_GZ_B5_D2_GZpool_05_2019


title: NIC268_GZ_B7_G1_GZpool_06_2019


title: NIC274_GZ_B4_G7_GZpool_05_2019


title: NIC267_GZ_B7_D5_GZpool_06_2019


title: NIC266_GZ_B9_C3_GZpool_08_2020


title: NIC515_GZ_B6_C5_GZpool_04_2019


title: NIC274_GZm_B1_C5_GZpool_0108_2020


title: NIC266_GZ_B9_D8_GZpool_08_2020


title: NIC277_GZr_B4_B6_GZpool_08_2020


title: NIC265_GZ_B5_D1_GZpool_05_2019


title: NIC265_GZ_B3_F5_GZpool_03_2019


title: NIC265_GZr_B3_C4_GZpool_07_2020


title: NIC261_GZ_B4_E2_GZpool_05_2019


title: NIC267_GZr_B5_F6_GZpool_08_2020


title: NIC268_GZ_B7_D6_GZpool_04_2019


title: NIC261_GZ_B1_E6_GZpool_01_2019


title: NIC267_GZ_B7_A9_GZpool_04_2019


title: NIC261_GZ_B3_H8_GZpool_03_2019


title: NIC260_GZ_B4_B5_GZpool_04_2019


title: NIC260_GZ_B4_E1_GZpool_05_2019


title: NIC513_GZ_B6_E9_GZpool_06_2019


title: NIC260_GZ_B1_C4_GZpool_01_2019


title: NIC259_GZ_B6_E6_GZpool_06_2019


title: NIC259_GZ_B6_C2_GZpool_04_2019


title: NIC259_GZ_B1_G7_GZpool_01_2019


title: NIC258_GZ_B7_F9_GZpool_06_2019


title: NIC258_GZ_B7_D4_GZpool_04_2019


title: NIC256_GZ_B4_D9_GZpool_05_2019


title: NIC256_GZ_B1_E5_GZpool_01_2019


title: NIC255_GZ_B5_C9_GZpool_05_2019


title: NIC255_GZ_B2_G1_GZpool_01_2019


title: NIC252_GZ_B4_B3_GZpool_04_2019


title: NIC255_GZ_B3_F4_GZpool_03_2019


title: NIC252_GZ_B4_D8_GZpool_05_2019


title: NIC256_GZ_B4_B4_GZpool_04_2019


title: NIC242_GZ_B5_C7_GZpool_05_2019


title: NIC251_GZ_B5_C8_GZpool_05_2019


title: NIC242_GZr_B3_C3_GZpool_07_2020


title: NIC251_GZ_B3_F3_GZpool_03_2019


title: NIC242_GZ_B3_F2_GZpool_03_2019


title: NIC252_GZ_B2_A1_GZpool_01_2019


title: NIC236_GZ_B1_A7_GZpool_01_2019


title: NIC231_GZ_B7_D3_GZpool_06_2019


title: NIC258_GZr_B5_I4_GZpool_08_2020


title: NIC236_GZ_B5_F5_GZpool_06_2019


title: NIC251_GZr_B2_I9_GZpool_07_2020


title: NIC207_GZr_B2_I7_GZpool_07_2020


title: NIC231_GZ_B7_A8_GZpool_04_2019


title: NIC207_GZ_B5_C6_GZpool_05_2019


title: NIC2_GZr_B4_B2_GZpool_08_2020


title: NIC2_GZ_B5_A6_GZpool_05_2019


title: NIC2_GZ_B4_G6_GZpool_04_2019


title: NIC199_GZ_B1_A2_GZpool_01_2019


title: NIC199_GZr_B4_B1_GZpool_07_2020


title: NIC199_GZr_B1_C3_GZpool_08_2020


title: NIC1_GZ_B1_I9_GZpool_01_2019


title: NIC166_GZ_B5_F3_GZpool_06_2019


title: NIC166_GZ_B3_E9_GZpool_03_2019


title: NIC236_GZ_B2_I8_GZpool_03_2019


title: N2_GZr_B6_E4_GZpool_08_2020


title: NIC231_GZr_B5_F4_GZpool_08_2020


title: NIC1_GZ_B4_G5_GZpool_05_2019


title: NIC1_GZ_B4_D7_GZpool_04_2019


title: MY920_GZ_B2_F9_GZpool_03_2019


title: N2_GZ_B7_A7_GZpool_06_2019


title: NIC207_GZm_B3_F1_GZpool_0307_2020


title: N2_GZm_B6_H3_GZpool_0408_2020


title: NIC166_GZr_B2_I6_GZpool_07_2020


title: MY920_GZ_B2_C3_GZpool_01_2019


title: MY795_GZ_B6_H2_GZpool_06_2019


title: MY795_GZ_B6_C1_GZpool_04_2019


title: MY772_GZ_B6_H1_GZpool_06_2019


title: MY920_GZ_B5_A5_GZpool_05_2019


title: MY518_GZ_B6_G9_GZpool_06_2019


title: MY795_GZ_B1_G5_GZpool_01_2019


title: MY518_GZ_B6_B8_GZpool_04_2019


title: MY772_GZ_B1_G4_GZpool_01_2019


title: MY772_GZ_B6_B9_GZpool_04_2019


title: MY2713_GZ_B6_B7_GZpool_04_2019


title: MY2585_GZ_B8_A7_GZpool_06_2019


title: MY23_GZ_B6_G6_GZpool_06_2019


title: MY2585_GZ_B6_G7_GZpool_04_2019


title: MY2573_GZ_B2_F8_GZpool_01_2019


title: MY2713_GZ_B6_G8_GZpool_06_2019


title: MY23_GZm_B6_E3_GZpool_0407_2020


title: MY2585_GZr_B6_B6_GZpool_08_2020


title: MY518_GZ_B1_G3_GZpool_01_2019


title: MY2713_GZ_B1_G2_GZpool_01_2019


title: MY2573_GZ_B2_I5_GZpool_03_2019


title: MY2573_GZ_B5_A4_GZpool_05_2019


title: MY2212_GZ_B2_C8_GZpool_01_2019


title: MY18_GZr_B3_C2_GZpool_07_2020


title: MY23_GZ_B1_F9_GZpool_01_2019


title: MY1_GZ_B4_G4_GZpool_05_2019


title: MY2212_GZ_B5_A3_GZpool_05_2019


title: MY2212_GZ_B2_F7_GZpool_03_2019


title: MY18_GZ_B5_F2_GZpool_06_2019


title: MY2147_GZ_B6_E2_GZpool_06_2019


title: MY2147_GZ_B6_B5_GZpool_04_2019


title: MY2147_GZ_B1_F8_GZpool_01_2019


title: MY1_GZ_B4_D6_GZpool_04_2019


title: MY16_GZ_B6_G5_GZpool_06_2019


title: MY10_GZ_B9_D7_GZpool_08_2020


title: MY16_GZ_B6_B4_GZpool_04_2019


title: MY16_GZ_B1_F7_GZpool_01_2019


title: MY10_GZ_B9_C2_GZpool_08_2020


title: MY18_GZ_B3_E8_GZpool_03_2019


title: MY1_GZ_B1_C2_GZpool_01_2019


title: LKC34_GZ_B6_B2_GZpool_04_2019


title: LKC34_GZ_B6_E1_GZpool_06_2019


title: KR314_GZ_B3_H7_GZpool_03_2019


title: KR314_GZ_B4_D5_GZpool_05_2019


title: KR314_GZm_B1_C1_GZpool_0108_2020


title: JU847_GZ_B5_C5_GZpool_05_2019


title: JU830_GZ_B4_D4_GZpool_05_2019


title: JU830_GZ_B3_H6_GZpool_03_2019


title: JU847_GZr_B2_I4_GZpool_07_2020


title: JU847_GZr_B3_E7_GZpool_07_2020


title: JU792_GZ_B5_F1_GZpool_06_2019


title: JU778_GZr_B3_B9_GZpool_07_2020


title: JU782_GZ_B9_C1_GZpool_08_2020


title: JU778_GZ_B5_C4_GZpool_05_2019


title: JU778_GZ_B3_E6_GZpool_03_2019


title: JU775_GZ_B6_G4_GZpool_06_2019


title: JU792_GZ_B3_C1_GZpool_03_2019


title: JU782_GZ_B9_D6_GZpool_08_2020


title: JU775_GZ_B6_D9_GZpool_04_2019


title: JU642_GZr_B5_I2_GZpool_08_2020


title: JU642_GZ_B7_A6_GZpool_04_2019


title: JU642_GZ_B7_D2_GZpool_06_2019


title: JU775_GZ_B1_F6_GZpool_01_2019


title: JU774_GZ_B4_D3_GZpool_05_2019


title: JU774_GZ_B4_A9_GZpool_04_2019


title: JU774_GZm_B1_E3_GZpool_0108_2020


title: JU440_GZ_B4_G3_GZpool_05_2019


title: LKC34_GZ_B1_I7_GZpool_01_2019


title: JU792_GZr_B2_I3_GZpool_07_2020


title: JU440_GZ_B4_A8_GZpool_04_2019


title: JU440_GZ_B1_I6_GZpool_01_2019


title: JU406_GZr_B3_B8_GZpool_07_2020


title: JU397_GZ_B7_D1_GZpool_04_2019


title: JU397_GZ_B7_F8_GZpool_06_2019


title: JU394_GZ_B5_E8_GZpool_06_2019


title: JU830_GZ_B1_E4_GZpool_01_2019


title: JU394_GZ_B3_E4_GZpool_03_2019


title: JU397_GZr_B5_I1_GZpool_08_2020


title: JU360_GZm_B1_E2_GZpool_0108_2020


title: JU360_GZ_B4_G2_GZpool_05_2019


title: JU360_GZ_B4_A7_GZpool_04_2019


title: JU367_GZr_B2_I1_GZpool_07_2020


title: JU346_GZr_B4_A6_GZpool_08_2020


title: JU367_GZm_B3_E3_GZpool_0307_2020


title: JU346_GZ_B7_H9_GZpool_06_2019


title: JU323_GZ_B1_E1_GZpool_01_2019


title: JU367_GZ_B3_H5_GZpool_05_2019


title: JU406_GZ_B5_E9_GZpool_06_2019


title: JU3144_GZ_B2_F6_GZpool_03_2019


title: JU3144_GZ_B5_A2_GZpool_05_2019


title: JU3140_GZ_B5_A1_GZpool_05_2019


title: JU3140_GZ_B2_F5_GZpool_03_2019


title: JU323_GZ_B4_A5_GZpool_03_2019


title: JU406_GZ_B3_E5_GZpool_03_2019


title: JU3134_GZ_B9_D5_GZpool_08_2020


title: JU3128_GZ_B4_I9_GZpool_05_2019


title: JU3132_GZr_B2_F4_GZpool_07_2020


title: JU3140_GZ_B2_C7_GZpool_01_2019


title: JU3128_GZ_B2_F3_GZpool_03_2019


title: JU323_GZ_B4_F9_GZpool_05_2019


title: JU3132_GZr_B1_I5_GZpool_07_2020


title: JU3144_GZ_B2_C2_GZpool_01_2019


title: JU311_GZ_B4_D2_GZpool_04_2019


title: JU394_GZr_B2_I2_GZpool_07_2020


title: JU346_GZ_B4_G1_GZpool_04_2019


title: JU3128_GZ_B1_F5_GZpool_01_2019


title: JU2907_GZr_B2_B9_GZpool_08_2020


title: JU310_GZ_B8_I2_GZpool_07_2020


title: JU311_GZ_B1_B8_GZpool_01_2019


title: JU310_GZ_B8_D2_GZpool_03_2019


title: JU310_GZ_B8_F3_GZpool_05_2019


title: JU2907_GZ_B1_F4_GZpool_01_2019


title: JU2906_GZm_B2_F1_GZpool_0307_2020


title: JU2906_GZ_B2_B8_GZpool_01_2019


title: JU3134_GZ_B9_B9_GZpool_08_2020


title: JU2879_GZr_B8_A9_GZpool_08_2020


title: JU2906_GZ_B4_I8_GZpool_05_2019


title: JU2866_GZ_B2_B6_GZpool_01_2019


title: JU2879_GZ_B2_E9_GZpool_03_2019


title: JU311_GZ_B4_F8_GZpool_05_2019


title: JU2879_GZ_B4_I7_GZpool_04_2019


title: JU2907_GZr_B2_F2_GZpool_07_2020


title: JU2866_GZ_B5_C3_GZpool_05_2019


title: JU2862_GZ_B4_I6_GZpool_05_2019


title: JU2862_GZ_B2_B5_GZpool_01_2019


title: JU2862_GZ_B2_E7_GZpool_03_2019


title: JU2853_GZm_B1_F3_GZpool_0107_2020


title: JU3132_GZr_B2_C1_GZpool_08_2020


title: JU2853_GZr_B2_C6_GZpool_08_2020


title: JU2841_GZ_B4_I5_GZpool_05_2019


title: JU2841_GZ_B2_B4_GZpool_01_2019


title: JU2841_GZ_B2_E5_GZpool_03_2019


title: JU2838_GZ_B7_G6_GZpool_06_2019


title: JU2838_GZ_B2_E4_GZpool_03_2019


title: JU2811_GZ_B1_F2_GZpool_07_2020


title: JU2811_GZm_B6_D8_GZpool_0408_2020


title: JU2838_GZ_B2_B3_GZpool_01_2019


title: JU2811_GZ_B6_G3_GZpool_06_2019


title: JU2800_GZ_B9_D4_GZpool_08_2020


title: JU2619_GZm_B6_G2_GZpool_0408_2020


title: JU2866_GZm_B2_E8_GZpool_0307_2020


title: JU2610_GZ_B7_C9_GZpool_06_2019


title: JU2619_GZ_B7_F7_GZpool_06_2019


title: JU2610_GZr_B5_H8_GZpool_08_2020


title: JU2610_GZ_B7_A5_GZpool_04_2019


title: JU2600_GZ_B2_E3_GZpool_03_2019


title: JU2600_GZ_B2_B2_GZpool_01_2019


title: JU2853_GZr_B2_E6_GZpool_07_2020


title: JU2586_GZ_B7_C7_GZpool_06_2019


title: JU2586_GZ_B7_A3_GZpool_04_2019


title: JU2592_GZ_B7_C8_GZpool_06_2019


title: JU2581_GZ_B7_F6_GZpool_06_2019


title: JU2586_GZr_B5_H6_GZpool_08_2020


title: JU2592_GZr_B5_H7_GZpool_08_2020


title: JU2592_GZ_B7_A4_GZpool_04_2019


title: JU2581_GZr_B5_H5_GZpool_08_2020


title: JU2578_GZ_B5_C2_GZpool_05_2019


title: JU2578_GZr_B2_E2_GZpool_08_2020


title: JU2578_GZ_B2_B1_GZpool_01_2019


title: JU2619_GZr_B5_H9_GZpool_08_2020


title: JU2576_GZr_B5_H4_GZpool_08_2020


title: JU2576_GZ_B7_F5_GZpool_06_2019


title: JU2581_GZ_B7_A2_GZpool_04_2019


title: JU2575_GZ_B7_C6_GZpool_06_2019


title: JU2575_GZr_B5_E7_GZpool_08_2020


title: JU2576_GZ_B7_A1_GZpool_04_2019


title: JU2575_GZ_B6_I9_GZpool_04_2019


title: JU2572_GZr_B6_G1_GZpool_08_2020


title: JU2572_GZ_B6_I8_GZpool_04_2019


title: JU2570_GZ_B7_F4_GZpool_06_2019


title: JU2570_GZ_B6_I7_GZpool_04_2019


title: JU2600_GZ_B4_I4_GZpool_05_2019


title: JU2566_GZ_B9_D3_GZpool_08_2020


title: JU2565_GZ_B4_I3_GZpool_07_2020


title: JU2566_GZ_B9_B7_GZpool_08_2020


title: JU2565_GZ_B2_H9_GZpool_03_2019


title: JU2565_GZ_B2_E1_GZpool_01_2019


title: JU2522_GZ_B4_D1_GZpool_05_2019


title: JU2526_GZ_B9_B5_GZpool_08_2020


title: JU2522_GZr_B2_H8_GZpool_07_2020


title: JU2526_GZ_B9_D1_GZpool_08_2020


title: JU2534_GZ_B9_D2_GZpool_08_2020


title: JU2522_GZ_B3_H2_GZpool_03_2019


title: JU2534_GZ_B9_B6_GZpool_08_2020


title: JU2519_GZ_B1_A1_GZpool_01_2019


title: JU2519_GZ_B3_H1_GZpool_03_2019


title: JU2513_GZ_B3_E2_GZpool_03_2019


title: JU2519_GZ_B4_C9_GZpool_05_2019


title: JU2513_GZr_B2_H7_GZpool_07_2020


title: JU2478_GZ_B6_A9_GZpool_04_2019


title: JU2466_GZm_B1_D9_GZpool_0107_2020


title: JU2572_GZ_B7_C5_GZpool_06_2019


title: JU2464_GZ_B5_C1_GZpool_05_2019


title: JU2570_GZr_B6_F9_GZpool_08_2020


title: JU2466_GZ_B4_C8_GZpool_05_2019


title: JU2513_GZ_B5_E6_GZpool_06_2019


title: JU2466_GZ_B3_G9_GZpool_03_2019


title: JU2478_GZ_B6_D6_GZpool_06_2019


title: JU2257_GZr_B2_H6_GZpool_07_2020


title: JU2257_GZ_B3_G7_GZpool_05_2019


title: JU2257_GZ_B3_E1_GZpool_03_2019


title: JU2534_GZ_B9_E4_GZpool_08_2020


title: JU2464_GZ_B3_G8_GZpool_03_2019


title: JU2464_GZr_B3_B7_GZpool_07_2020


title: JU2250_GZr_B2_H5_GZpool_07_2020


title: JU2478_GZr_B5_E5_GZpool_08_2020


title: JU2234_GZr_B2_D9_GZpool_08_2020


title: JU2234_GZ_B5_B9_GZpool_05_2019


title: JU2234_GZ_B2_A8_GZpool_01_2019


title: JU2250_GZ_B3_B6_GZpool_03_2019


title: JU2250_GZ_B7_G5_GZpool_06_2019


title: JU2141_GZ_B2_A7_GZpool_01_2019


title: JU2141_GZ_B4_I1_GZpool_07_2020


title: H6 Osteogenic + C6 Osteogenic

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

description:
HOU_meta.csv
HOU_count.csv

data_processing:
10X cell barcodes were bioinformatically reassigned to their species of origin using standard Cell Ranger pipelines (cellranger 3.1.0), with the exception that reads were aligned to both the human genome (hg38) and chimpanzee genome (panTro6) and that a curated set of orthologous exons was used for transcriptome alignment. Briefly, Cell Ranger aligns reads to each genome, retaining only those reads that specifically align to one genome and discarding reads that align to both genomes. Instead of using the default Cell Ranger species assignments, which call human and chimpanzee cells based on which genome has a more aligned UMI counts and call multiplets if the human UMI counts and the chimpanzee UMI counts exceed the 10th percentile of each species’ distribution, we assigned cells as either human or chimpanzee based on the ratio of human-aligned UMIs to the total number of aligned UMIs within each cell. Specifically, cells with a ratio greater than or equal to 0.9 were assigned as human, and cells with a ratio less than or equal to 0.1 were assigned as chimpanzee.
Data in fastq files corresponding to human cells were processed into count matrices (genes x cells) using cellranger 3.1.0 by aligning reads to the human genome (hg38) and a curated set of orthologous exons.
Data in fastq files corresponding to chimpanzee cells were processed into count matrices (genes x cells) using cellranger 3.1.0 by aligning reads to the chimpanzee  genome (panTro6) and a curated set of orthologous exons.
Genome_build: hg38
Genome_build: panTro6
Supplementary_files_format_and_content: CSV table with the raw UMI counts for every gene and every cell from every sample; cell names include the 10X barcode preceded by a character string unique to each 10X batch that corresponds with the initital fastq files
Supplementary_files_format_and_content: CSV table with metadata details for each cell/sample in the raw UMI counts file

organism:
Pan troglodytes
Homo sapiens

source_name: induced pluripotent stem cell-derived osteogenic cells

growth_protocol: induced pluripotent stem cells: Feeder-free iPSCs were maintained on Matrigel Growth Factor Reduced Matrix (354230, Corning) at a 1:100 dilution and in mTeSR™1 Medium (85851, STEMCELL Technologies) supplemented with 1% Penicillin/Streptomycin (30-002-CI, Corning). Cells were cultured at 37˚C in 5% CO2 and atmospheric O2 and passaged every 3-4 days using a dissociation reagent (0.25mM EDTA, 150mM NaCl in PBS).

extract_protocol:
differentiation protocol - mesenchymal stem cells (2B): iPSCs were seeded at approximately 30% confluency in Matrigel-coated culture dishes and cultured in mTeSR™1 (85851, STEMCELL Technologies) until cells fully adhered to the plate (at least 3 hours). Following this, the medium was replaced with MSC medium, which consisted of DMEM (10567-014, ThermoFisher Scientific) supplemented with 20% FBS (FB5001, Thomas Scientific) and 1% Penicillin/Streptomycin (30-002-CI, Corning). Cells were cultured at 37˚C in 5% CO2 and atmospheric O2 with daily MSC medium changes until 80-100% confluent (2-5 days). Cells were subsequently detached from the Matrigel-coated culture dishes using 0.05% Trypsin 0.53mM EDTA (25-052-CI, Corning) and passaged to uncoated polystyrene culture dishes. Cells continued to be cultured at 37˚C in 5% CO2 and atmospheric O2 with MSC medium changes every 2-3 days, and cells were sub-cultured at an approximately 1:3 ratio until at least passage 4 when cells began to display characteristic MSC morphologies (3-9 weeks).
differentiation protocol - mesenchymal stem cells (3B): iPSCs were seeded at approximately 30% confluency in Matrigel-coated culture dishes and cultured in mTeSR™1 (85851, STEMCELL Technologies) until cells fully adhered to the plate (at least 3 hours). Following this, the medium was replaced with MSC medium, which consisted of DMEM (11330-032, ThermoFisher Scientific) supplemented with 20% FBS (FB5001, Thomas Scientific) and 1% Penicillin/Streptomycin (30-002-CI, Corning). Cells were cultured at 37˚C in 5% CO2 and atmospheric O2 with daily MSC medium changes until 80-100% confluent (2-5 days). Cells were subsequently detached from the Matrigel-coated culture dishes using 0.05% Trypsin 0.53mM EDTA (25-052-CI, Corning) and passaged to uncoated polystyrene culture dishes. Cells continued to be cultured at 37˚C in 5% CO2 and atmospheric O2 with MSC medium changes every 2-3 days, and cells were sub-cultured at an approximately 1:3 ratio until at least passage 4 when cells began to display characteristic MSC morphologies (3-9 weeks).
differentiation protocol - osteogenic cells: iPSC-derived MSCs were seeded at 4.2 x 104 cell/cm2 in culture dishes (4-10cm diameter) that were coated in 5ug/cm2 Type I Collagen (sc-136157, Santa Cruz Biotechnology). After culturing cells for 1 day in MSC medium, this medium was replaced with osteogenic medium that contained DMEM (11965-092, ThermoFisher Scientific) supplemented with 10% FBS (FB5001, Thomas Scientific), 1% Penicillin/Streptomycin (30-002-CI, Corning), 50ug/mL Vitamin C (A8960, Sigma-Aldrich), 100nM Dexamethasone (D4902, Sigma-Aldrich), 10mM β-glycerophosphate (G9422, Sigma-Aldrich), and 1uM Vitamin D (D1530, Sigma-Aldrich). Cells were cultured at 37˚C in 5% CO2 and atmospheric O2, and medium was changed every 2-3 days for 3 weeks.
PolyA RNA was extracted from single cells using the Chromium Single Cell 3' Reagent Kit (version 3, 10X Genomics) and following standard manufacture instructions. Each 10X run included a mixture human cells and chimpanzee cells.
Libraries were prepared for sequencing using standard protocols from 10X Genomics and Illumina.

tag: human cell line id

tag: human cell line sex

value: male

tag: human cell line age at reprogramming

tag: chimpanzee cell line id

tag: chimpanzee cell line sex

tag: chimpanzee cell line age at reprogramming

tag: protocol


title: JU2131_GZ_B2_D7_GZpool_01_2019


title: JU2131_GZ_B4_H9_GZpool_07_2020


title: JU2106_GZ_B5_B8_GZpool_05_2019


title: H6 iPSC + C6 iPSC

description:
HOU_meta.csv
HOU_count.csv

source_name: induced pluripotent stem cells

value: growth protocol - induced pluripotent stem cells


title: JU2017_GZr_B3_B4_GZpool_07_2020


title: JU2017_GZ_B5_E4_GZpool_06_2019


title: H5 MSC + C5 MSC

description:
HOU_meta.csv
HOU_count.csv

source_name: induced pluripotent stem cell-derived mesenchymal stem cells

value: female

value: differentiation protocol - mesenchymal stem cells (2B)


title: H5 Osteogenic + C5 Osteogenic

description:
HOU_meta.csv
HOU_count.csv

value: differentiation protocol - osteogenic cells


title: H4 Osteogenic + C4 Osteogenic

description:
HOU_meta.csv
HOU_count.csv


title: JU2016_GZr_B1_D8_GZpool_08_2020


title: JU2016_GZ_B2_H3_GZpool_05_2019


title: H4 iPSC + C4 iPSC

description:
HOU_meta.csv
HOU_count.csv


title: JU2141_GZr_B2_D8_GZpool_08_2020


title: H3 Osteogenic + C3 Osteogenic

description:
HOU_meta.csv
HOU_count.csv


title: JU2016_GZ_B1_A4_GZpool_01_2019


title: H3 MSC + C3 MSC

description:
HOU_meta.csv
HOU_count.csv

value: differentiation protocol - mesenchymal stem cells (3B)


title: JU2106_GZr_B3_B5_GZpool_07_2020


title: JU2007_GZ_B4_C7_GZpool_05_2019


title: JU2007_GZ_B4_A4_GZpool_03_2019


title: JU2106_GZ_B3_D9_GZpool_03_2019


title: JU2007_GZm_B1_I3_GZpool_0107_2020


title: H2 MSC + C2 MSC

description:
HOU_meta.csv
HOU_count.csv


title: H4 MSC + C4 MSC

description:
HOU_meta.csv
HOU_count.csv


title: JU2001_GZ_B5_B7_GZpool_05_2019


title: JU2001_GZr_B3_B3_GZpool_07_2020


title: JU1934_GZr_B2_D6_GZpool_08_2020


title: JU2001_GZ_B3_D8_GZpool_03_2019


title: H1 Chondrogenic + C1 Chondrogenic

source_name: induced pluripotent stem cell-derived chondrogenic cells

growth_protocol:
induced pluripotent stem cells: Feeder-free iPSCs were maintained on Matrigel Growth Factor Reduced Matrix (354230, Corning) at a 1:100 dilution and in mTeSR?1 Medium (85851, STEMCELL Technologies) supplemented with 1% Penicillin/Streptomycin (30-002-CI, Corning). Cells were cultured at 37?C in 5% CO2 and atmospheric O2 and passaged every 3-4 days using a dissociation reagent (0.25mM EDTA, 150mM NaCl in PBS).
differentiation protocol - mesenchymal stem cells (3B): iPSCs were seeded at approximately 30% confluency in Matrigel-coated culture dishes and cultured in mTeSR?1 (85851, STEMCELL Technologies) until cells fully adhered to the plate (at least 3 hours). Following this, the medium was replaced with MSC medium, which consisted of DMEM (11330-032, ThermoFisher Scientific) supplemented with 20% FBS (FB5001, Thomas Scientific) and 1% Penicillin/Streptomycin (30-002-CI, Corning). Cells were cultured at 37?C in 5% CO2 and atmospheric O2 with daily MSC medium changes until 80-100% confluent (2-5 days). Cells were subsequently detached from the Matrigel-coated culture dishes using 0.05% Trypsin 0.53mM EDTA (25-052-CI, Corning) and passaged to uncoated polystyrene culture dishes. Cells continued to be cultured at 37?C in 5% CO2 and atmospheric O2 with MSC medium changes every 2-3 days, and cells were sub-cultured at an approximately 1:3 ratio until at least passage 4 when cells began to display characteristic MSC morphologies (3-9 weeks).
differentiation protocol - chondrogenic cells: iPSC-derived MSCs were seeded at 5.0 x 104 cell/cm2 in culture dishes (4-10cm diameter) that were coated in 5ug/cm2 Type I Collagen (sc-136157, Santa Cruz Biotechnology). After culturing cells for 1 day in MSC medium, this medium was replaced with chondrogenic medium that contained DMEM (11965-092, ThermoFisher Scientific) supplemented with 1% Penicillin/Streptomycin (30-002-CI, Corning), 50ug/mL Vitamin C (A8960, Sigma-Aldrich), 50mg/mL L-Proline (P5607, Sigma), 200mM GlutaMax (35050061, Gibco), 11g/L Sodium pyruvate (11360070, Gibco), 5mM Dexamethasone (D4902, Sigma), 1X ITS Premix (CB40352, Fisher), and 10ng/mL TGF-?3 (243-B3-010, R&D Systems). Cells were cultured at 37?C in 5% CO2 and atmospheric O2, and medium was changed every 2-3 days for 3 weeks.
differentiation protocol - osteogenic cells: iPSC-derived MSCs were seeded at 4.2 x 104 cell/cm2 in culture dishes (4-10cm diameter) that were coated in 5ug/cm2 Type I Collagen (sc-136157, Santa Cruz Biotechnology). After culturing cells for 1 day in MSC medium, this medium was replaced with osteogenic medium that contained DMEM (11965-092, ThermoFisher Scientific) supplemented with 10% FBS (FB5001, Thomas Scientific), 1% Penicillin/Streptomycin (30-002-CI, Corning), 50ug/mL Vitamin C (A8960, Sigma-Aldrich), 100nM Dexamethasone (D4902, Sigma-Aldrich), 10mM ?-glycerophosphate (G9422, Sigma-Aldrich), and 1uM Vitamin D (D1530, Sigma-Aldrich). Cells were cultured at 37?C in 5% CO2 and atmospheric O2, and medium was changed every 2-3 days for 3 weeks.

extract_protocol:
PolyA RNA was extracted from single cells using the Chromium Single Cell 3' Reagent Kit (version 3, 10X Genomics) and following standard manufacture instructions. Each 10X run included a mixture human cells and chimpanzee cells.
Libraries were prepared for sequencing using standard protocols from 10X Genomics and Illumina.


title: H2 Osteogenic + C2 Osteogenic

description:
HOU_meta.csv
HOU_count.csv


title: JU1934_GZm_B1_D7_GZpool_0108_2020


title: H1 Osteogenic (replicate 2) + C1 Osteogenic (replicate 2)

description:
HOU_meta.csv
HOU_count.csv


title: JU2131_GZ_B2_H4_GZpool_03_2019


title: JU1896_GZ_B9_C9_GZpool_08_2020


title: H1 MSC + C1 MSC


title: JU1896_GZ_B9_B4_GZpool_08_2020


title: H1 MSC (replicate 2) + C1 MSC (replicate 2)

description:
HOU_meta.csv
HOU_count.csv


title: JU1934_GZ_B3_D7_GZpool_05_2019


title: JU1808_GZr_B2_D5_GZpool_08_2020


title: noDOX_NO3d_8

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Sequencing was performed on a HiSeq 4000 (Illumina, San Diego, CA) to obtain 50 bases per single end read (52 bases actual). Base calling was performed using Casava (Illumina).
Reads were trimmed using Trimmomatic v0.36 (Bolger et al. Bioinformatics, 2014) with parameters ILLUMINACLIPTruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:25 SLIDINGWINDOW:4:15.
Single-end alignments and gene level counts were obtained using RSEM v1.3.1 (Li and Dewey. BMC Bioinformatics, 2011). STAR v2.5.2a was the aligner called by RSEM and the default parameters were used (Dobin et al. Bioinformatics, 2013).
The mouse reference sequence mm10/GRCm38 and annotations, including gene IDs, were obtained from GENCODE v. M10 (Frankish et al. Nucleic Acids Res. 2018).
Supplementary files: sample expression matrices (tab-delimited text with headers) with counts, FPKM, and TPM are provided for both genes and transcript isoforms. The first two columns contain gene IDs.
Genome_build: mm10
Supplementary_files_format_and_content: Quantification files for both genes and transcript isoforms are provided for each sample in tab-delimited text files containing headers.  See RSEM documentation for more detail on contents.

source_name: bone marrow-derived macrophage

growth_protocol: Bone marrow was isolated from the femurs of C57B6/J mice as described17 and maintained in macrophage differentiation media (high-glucose DMEM with 10% FBS, penicillin/streptomycin (Gibco), sodium pyruvate (Gibco), and 30% L929 conditioned media) for five days. Media was refreshed on day three, and naïve macrophages were polarized on day five.

extract_protocol:
Polarized BMDMs were lysed with RLT Plus buffer with beta-mercaptoethanol, lysates were homogenized using a Qiashredder, and RNA samples were isolated according to the RNeasy Plus Mini Kit (Qiagen) protocol, which included gDNA eliminator spin columns. All RNA samples were tested for concentration and purity via NanoDrop (Thermo Scientific). RNA samples were stored at -80ºC.
Libraries were constructed with the TruSeq mRNA kit (Illumina) using the manufacturer's protocol.

treatment_protocol: BMDMs were polarized with either 10ng/mL murine macrophage colony-364 stimulating factor (M-CSF) (Peprotech), 10ng/mL lipopolysaccharide (LPS) (Enzo), 10ng/mL murine interleukin-4 (IL4) (Peprotech), 2ng/mL murine granulocyte-macrophage colony-stimulating factor (GM-366 CSF), or 75% Kras-On or Kras-Off PDA cell conditioned media. In certain conditions, macrophages were spiked with 5mM lactic acid to assess the effects of extracellular lactate and acidic pH on macrophage gene expression. Each macrophage subtype was polarized from matched biological replicates. Macrophages were maintained in the presence of polarization factors for 48 hours.

tag: treatment

value: Kras-Off PDA media (3 days)

tag: cell type

value: bone marrow-derived macrophage


title: H1 iPSC (replicate 2) + C1 iPSC (replicate 2)

description:
HOU_meta.csv
HOU_count.csv


title: H3 iPSC + C3 iPSC

description:
HOU_meta.csv
HOU_count.csv


title: H2 iPSC + C2 iPSC

description:
HOU_meta.csv
HOU_count.csv


title: H1 iPSC + C1 iPSC


title: noDOX_NO3d_7


title: JU1808_GZ_B4_H8_GZpool_07_2020


title: JU1808_GZ_B2_A6_GZpool_01_2019


title: noDOX_5d_4

value: Kras-Off PDA media (5 days)


title: noDOX_NO3d_6


title: JU1793_GZr_B2_D4_GZpool_08_2020


title: JU1793_GZ_B4_H7_GZpool_05_2019


title: noDOX_5d_2


title: JU1793_GZ_B2_A5_GZpool_01_2019


title: H1 Osteogenic + H1 Osteogenic


title: noDOX_5d_1


title: JU1792_GZ_B7_I4_GZpool_06_2019


title: JU1792_GZr_B7_H1_GZpool_08_2020


title: plusDOX_1

value: Kras-On PDA media


title: plusDOX_4


title: plusDOX_2


title: JU1792_GZ_B7_H5_GZpool_04_2019


title: M1_LPS_4

value: LPS


title: JU1666_GZ_B3_B2_GZpool_05_2019


title: JU1666_GZ_B1_A5_GZpool_01_2019


title: JU1666_GZr_B1_I2_GZpool_08_2020


title: JU1652_GZ_B6_D5_GZpool_04_2019


title: M1_LPS_2


title: M2_IL4_4


title: M1_LPS_1


title: M2_IL4_1


title: M2_IL4_2


title: JU1586_GZ_B8_I1_GZpool_07_2020


title: JU1652_GZr_B5_H3_GZpool_08_2020


title: JU1586_GZ_B8_F2_GZpool_05_2019


title: H6 MSC + C6 MSC

description:
HOU_meta.csv
HOU_count.csv


title: MSCF_2

value: M-CSF


title: JU2017_GZ_B3_G5_GZpool_03_2019


title: JU1586_GZ_B8_D1_GZpool_03_2019


title: MCSF_1


title: JU1581_GZ_B4_F7_GZpool_05_2019


title: JU1581_GZ_B1_D6_GZpool_01_2019


title: JU1581_GZm_B4_A3_GZpool_0307_2020


title: JU1652_GZ_B7_G7_GZpool_06_2019


title: JU1568_GZr_B3_G4_GZpool_08_2020


title: JU1568_GZ_B6_D4_GZpool_06_2019


title: ME11_50um_H3K27ac_2

city: New Haven

first: Yanxiang

last: Deng

state: CT

address: 55 Prospect Street

department: Biomedical Engineering

institute: Yale University

data_processing:
Read 1 was first filtered by two constant linker sequences (linker 1 and linker 2). Then filtered sequences were processed to cellranger atac format (10x Genomics), where the new Read 1 was genome sequences and the new Read 2 includes barcodes A and barcodes B. Resulting fastq files were aligned to the mouse genome (mm10), filtered for duplicates and counted using cellranger atac, which generated the BED like fragments file for downstream analysis. The fragments file contains tissue location info (barcode A x barcode B) and fragments info on the genome. We developed a preprocessing pipeline using Snakemake workflow management system, which is shared at https://github.com/dyxmvp/spatial-CUT-Tag
Genome_build: mm10
Supplementary_files_format_and_content: BED like fragments file for downstream analysis. The fragments file contains tissue location info (barcode A x barcode B) and fragments info on the genome.

source_name: Mouse embryo E11

extract_protocol: First, a tissue section on a standard aminated glass slide was lightly fixed with formaldehyde. Antibody binds to the target histone modification was added, followed by a secondary antibody binding to enhance the tethering of pA-Tn5 transposome. By adding Mg++ to activate the transposome in tissue, adapters containing a ligation linker were inserted to genomic DNA at the histone mark antibody recognition sites. Then, a set of DNA barcode A solutions were introduced to perform in situ ligation for appending a distinct spatial barcode Ai (i = 1-50). Afterwards, a second set of barcodes Bj (j = 1-50) were flowed on the tissue surface in microchannels perpendicularly to those in the first flow barcoding step. These barcodes were then ligated at the intersections, resulting in a mosaic of tissue pixels, each of which contains a distinct combination of barcodes Ai and Bj (i = 1-50, j = 1-50). The tissue slide being processed could be imaged during each flow or afterward such that the tissue morphology can be correlated with spatial epigenomics map. After forming a spatially barcoded tissue mosaic, DNA fragments were collected by cross-link reversal and amplified by PCR to complete library construction. NGS sequencing was then performed using a HiSeq sequencer with pair-end 150 bp mode with custom read 1 primer.

value: Embryo

tag: spatial resolution

value: 50 um

tag: antibody


title: Brain_20um_H3K4me3

source_name: Mouse brain P21

value: Mouse brain

value: 20 um

value: H3K4me3 (Active Motif, 39159)


title: MSCF_4


title: JU1568_GZ_B6_A7_GZpool_04_2019

value: young adult

value: hermaphrodite


title: JU1543_GZ_B2_H2_GZpool_03_2019


title: RNA-seq from Lrh1 Dhh-Cre knockout replicate 3 [p3_testis_DhhCre_rep3]

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
KA11
Stranded mRNA-seq library from whole Mouse gonad

data_processing:
Reads were trimmed using Trim Galore (v0.6.0) and cutadapt (v1.18) and assessed for quality with FastQC (v0.11.8). Trimmed reads were mapped with STAR (v2.7.2a) to the GRCm38 (mm10) genome.
The GENCODE M25 gene annotation set was used to estimate strand-specific gene expression data with the Bioconductor package RSubread (v1.28.1).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig

source_name: RNA-seq from Lrh1 Dhh-Cre knockout

growth_protocol: Mice were of mixed genetic background (129Sv and C57Bl/6J) and maintained in conventional housing facilities.  Presence of a copulation plug in the morning was recorded as day E0.5.  Experimental protocols and euthanasia protocols were approved by the University of Minnesota Animal Care and Use Committee.

extract_protocol:
P1/P3 gonads were harvested into Trizol reagent and stored at -80o C.  Total RNA was prepared according to Trizol reagent manufacturer’s protocols and further cleaned up using RNAeasy kit protocols and reagents (Qiagen).
RNA was quantified via Qubit RNA assay, and 400-500ng total RNA (see sample details) were used in stranded mRNA-seq library preparation (KAPA Biosystems, KK8481) for Illumina sequencing.

treatment_protocol: None.

value: testis

tag: age

value: Postnatal Day 3

tag: genotype

value: Lrh1 flox/flox; Dhh-Cre

tag: strain background

value: Mixed 129Sv and C57Bl/6J

tag: total rna input


title: RNA-seq from Lrh1 Dhh-Cre knockout replicate 4 [p3_testis_DhhCre_rep4]

description:
KA12
Stranded mRNA-seq library from whole Mouse gonad

tag: tissue


title: JU1543_GZ_B5_B6_GZpool_05_2019

tag: strain

tag: developmental stage

tag: Sex


title: RNA-seq from Control Testis at P3 replicate 4 [p3_testis_noCre_rep4]

description:
KA9
Stranded mRNA-seq library from whole Mouse gonad

source_name: RNA-seq from Control Testis at P3

value: Lrh1 flox/flox


title: JU1543_GZ_B2_D3_GZpool_01_2019


title: JU1530_GZr_B2_H1_GZpool_07_2020


title: JU1530_GZ_B5_B5_GZpool_05_2019


title: RNA-seq from Control Testis at P3 replicate 2 [p3_testis_noCre_rep2]

description:
KA6
Stranded mRNA-seq library from whole Mouse gonad


title: RNA-seq from Control Testis at P3 replicate 3 [p3_testis_noCre_rep3]

description:
KA8
Stranded mRNA-seq library from whole Mouse gonad


title: JU1530_GZ_B3_B1_GZpool_03_2019


title: RNA-seq from Control Testis at P3 replicate 1 [p3_testis_noCre_rep1]

description:
KA5
Stranded mRNA-seq library from whole Mouse gonad


title: Brain_20um_H3K27me3

value: H3K27me3 (Cell Signaling Technology, 9733)


title: RNA-seq from Lrh1 Nanos3-Cre knockout replicate 4 [p1_testis_Nanos3Cre_rep4]

description:
KA1
Stranded mRNA-seq library from whole Mouse gonad

source_name: RNA-seq from Lrh1 Nanos3-Cre knockout

value: Postnatal Day 1

value: Lrh1 flox/-; Nanos3-Cre


title: JU1491_GZr_B5_H2_GZpool_08_2020


title: JU1491_GZ_B7_C4_GZpool_06_2019


title: RNA-seq from Lrh1 Nanos3-Cre knockout replicate 3 [p1_testis_Nanos3Cre_rep3]

description:
bardwell-RNA-seq-03-21-5
Stranded mRNA-seq library from whole Mouse gonad


title: RNA-seq from Lrh1 Nanos3-Cre knockout replicate 2 [p1_testis_Nanos3Cre_rep2]

description:
bardwell-RNA-seq-03-21-4
Stranded mRNA-seq library from whole Mouse gonad


title: RNA-seq from Lrh1 Nanos3-Cre knockout replicate 1 [p1_testis_Nanos3Cre_rep1]

description:
bardwell-RNA-seq-03-21-1
Stranded mRNA-seq library from whole Mouse gonad


title: RNA-seq from Lrh1 Dhh-Cre knockout replicate 2 [p3_testis_DhhCre_rep2]

description:
KA10
Stranded mRNA-seq library from whole Mouse gonad


title: RNA-seq from Lrh1 Dhh-Cre knockout replicate 1 [p3_testis_DhhCre_rep1]

description:
KA7
Stranded mRNA-seq library from whole Mouse gonad


title: RNA-seq from Control Testis at P1 replicate 4 [p1_testis_noCre_rep4]

description:
KA2
Stranded mRNA-seq library from whole Mouse gonad

source_name: RNA-seq from Control Testis at P1

value: Lrh1 flox/-


title: JU1440_GZ_B7_H2_GZpool_06_2019


title: JU1440_GZ_B1_B7_GZpool_01_2019


title: RNA-seq from Control Testis at P1 replicate 3 [p1_testis_noCre_rep3]

description:
bardwell-RNA-seq-03-21-10
Stranded mRNA-seq library from whole Mouse gonad


title: RNA-seq from Control Testis at P1 replicate 2 [p1_testis_noCre_rep2]

description:
bardwell-RNA-seq-03-21-3
Stranded mRNA-seq library from whole Mouse gonad


title: JU1409_GZm_B4_A1_GZpool_0308_2020


title: JU1409_GZ_B1_I1_GZpool_01_2019


title: ME11_20um_H3K27ac


title: JU1491_GZ_B6_I6_GZpool_04_2019


title: ME11_20um_H3K4me3


title: JU1395_GZ_B7_F3_GZpool_06_2019


title: OB_20um_H3K27me3

source_name: Olfactory bulb_Coronal

value: Olfactory bulb


title: JU1395_GZr_B5_H1_GZpool_08_2020


title: ME11_20um_H3K27me3

value: Embryo


title: JU1409_GZ_B4_F5_GZpool_05_2019


title: JU1395_GZ_B7_C3_GZpool_04_2019


title: JU1246_GZr_B3_A9_GZpool_07_2020


title: ME11_50um_H3K27ac

value: 50 um


title: JU1246_GZ_B3_G3_GZpool_03_2019


title: ME11_50um_H3K4me3


title: JU1246_GZ_B5_E3_GZpool_06_2019


title: ME11_50um_H3K27me3


title: JU1242_GZ_B4_F4_GZpool_05_2019


title: JU1242_GZ_B4_C6_GZpool_04_2019


title: JU1440_GZ_B4_F6_GZpool_04_2019


title: coi1_8h_1

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

data_processing:
Sequencing reads were cleaned with Trim Galore v0.5.0,  including removing bases with low quality score (<20)  and cutting sequencing adaptors followed by filtering short reads.
For bulk RNA-seq, the paired-end reads of RNA-seq data were mapped to Arabidopsis thaliana genome (TAIR10) using STAR v2.7.2b. Gene abundance was determined using RSEM v1.3.2 . Differentially expressed genes were detected by EBSeq
Supplementary_files_format_and_content: tab-delimited text files include TPM for each gene

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedings

growth_protocol: Arabidopsis seeds (Col-0 and the coi1-2 mutant) were germinated and grown on 1/2 MS medium with 1% sucrose at 22°C under a 16-h light/8-h dark photoperiod for 12 d.

extract_protocol:
The whole leaf explants were harvested and frozen in liquid nitrogen. RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The first pair of rosette leaves were cut at the junction of the blade and petiole, and the detached blades were cultured on sucrose-free B5 medium at 22°C under 24-h light conditions for 0 (t0), 10 min, 30 min, 1 h, 2 h, 4 h, 8 h and 12 h .

value: the entire tissues of leaf explants

tag: Stage

value: 8 h after detachment


title: RNA-seq from Control Testis at P1 replicate 1 [p1_testis_noCre_rep1]

description:
bardwell-RNA-seq-03-21-2
Stranded mRNA-seq library from whole Mouse gonad


title: JU1242_GZ_B1_B6_GZpool_01_2019


title: coi1_4h_2

value: 4 h after detachment


title: JU1213_GZr_B3_G2_GZpool_07_2020

value: young adult


title: coi1_4h_1


title: coi1_30min_2

value: 30 min after detachment


title: JU1213_GZ_B6_F8_GZpool_06_2019

value: hermaphrodite


title: JU1212_GZ_B5_B4_GZpool_05_2019


title: JU1212_GZr_B3_A8_GZpool_07_2020


title: coi1_1h_2

value: 1 h after detachment


title: coi1_2h_2

value: 2 h after detachment


title: coi1_1h_1


title: coi1_2h_1


title: JU1212_GZ_B3_D6_GZpool_03_2019


title: JU1200_GZ_B5_B3_GZpool_05_2019


title: coi1_12h_2

value: 12 h after detachment


title: JU1200_GZr_B2_G9_GZpool_07_2020


title: coi1_30min_1


title: JU1200_GZ_B3_D5_GZpool_03_2019


title: coi1_12h_1


title: coi1_10min_2

value: 10 min after detachment


title: JU1172_GZ_B7_H8_GZpool_06_2019


title: coi1_T0_2

value: 0 min after detachment


title: coi1_10min_1


title: JU1172_GZ_B4_C5_GZpool_04_2019


title: JU1172_GZm_B1_D5_GZpool_0107_2020


title: JU1088_GZ_B4_C4_GZpool_05_2019


title: coi1_T0_1


title: JU1088_GZ_B3_I9_GZpool_03_2019


title: JU1088_GZ_B1_D4_GZpool_01_2019


title: WT_8h_1

value: wild type col-0


title: JU1213_GZ_B6_A6_GZpool_04_2019


title: WT_30min_1


title: GXW1_GZr_B5_G9_GZpool_08_2020


title: JT11398_GZr_B6_A5_GZpool_08_2020


title: JT11398_GZ_B6_I5_GZpool_06_2019


title: WT_2h_1


title: coi1_8h_2


title: WT_1h_1


title: ME11_50um_H3K4me3_2

value: H3K4me3 (Active Motif, 39159)


title: GXW1_GZ_B7_C2_GZpool_04_2019


title: WT_12h_1


title: EG4946_GZ_B9_B3_GZpool_08_2020


title: EG4724_GZ_B6_I4_GZpool_04_2019


title: WT_10min_1


title: EG4724_GZ_B7_F1_GZpool_06_2019


title: JT11398_GZm_B6_F7_GZpool_0407_2020


title: 4dpi Inhib 5 S10

city: Woods hole

first: Karen

last: Echeverri

address: 7 MBL ST

department: Eugene Bell Center for Regeneration Biology and Tissue Engineering

institute: MARINE BIOLOGICAL LAB

data_processing:
RNA-seq data were comprised of 2 ×126 bp paired-end reads. The RNA-seq reads from all samples were combined and then assembled by using Trinity (Grabherr et al., 2011) (v2.3.2) with default parameters. We used cd-hit-est (v4.6) (Fu et al., 2012) with parameter “-c 1” to remove shorter contigs with 100% identity with aligned longer contigs. These non-redundant contigs were mapped to Ensembl human proteins (v85) by BLASTX (v2.2.18). Contigs were assigned to human proteins by taking the best BLASTX hit with E-value < 10-5.    We used Bowtie (v0.12.1) (Langmead et al., 2009) to map the reads against all non-redundant contigs. Quantification of each contig was performed by RSEM v1.1.6 (Boido et al., 2011). RSEM employs an expectation maximization algorithm, so that for reads that match to multiple contigs, RSEM assigns a fraction of each read to each contig based on estimated abundances of contigs based on unique reads (Boido et al., 2011).  RNA-seq data were comprised of 2 ×126 bp paired-end reads. The RNA-seq reads from all samples were combined and then assembled by using Trinity (Grabherr et al., 2011) (v2.3.2) with default parameters. We used cd-hit-est (v4.6) (Fu et al., 2012) with parameter “-c 1” to remove shorter contigs with 100% identity with aligned longer contigs. These non-redundant contigs were mapped to Ensembl human proteins (v85) by BLASTX (v2.2.18). Contigs were assigned to human proteins by taking the best BLASTX hit with E-value < 10-5.    We used Bowtie (v0.12.1) (Langmead et al., 2009) to map the reads against all non-redundant contigs. Quantification of each contig was performed by RSEM v1.1.6 (Boido et al., 2011). RSEM employs an expectation maximization algorithm, so that for reads that match to multiple contigs, RSEM assigns a fraction of each read to each contig based on estimated abundances of contigs based on unique reads (Boido et al., 2011).
Relative abundances, in terms of transcripts per million (TPM), for genes were computed by first normalizing each gene’s fragment count by the sum of the “effective lengths” (weighted average of contigs’ length based on contigs’ abundance) of the contigs mapped to that gene and then scaling the resulting values such that they summed to one million over all genes. To identify differentially expressed genes the normalized counts from RSEM were imported into DESeq2 (version 1.16.1) (Love et al., 2014) as integers to determine moderated estimates of Log2 fold changes and Benjamini-Hochberg adjusted p-values between conditions.

organism: Ambystoma mexicanum

source_name: spinal cord

extract_protocol:
Trizol RNA extraction
Illumina

treatment_protocol: All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota or at the MBL under the IACUC protocols #1710-35242A, #18-49. Axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.      Experimental Design: miR-200 inhibitor or control inhibitor  s pressure injected into the central canal of the spinal cord, and this was visualized by the addition of Fast Green into the solution. Directly after injection, a portion of the spinal cord was surgically removed and the animals were placed back into water in individual containers. Four days post injury (4dpi) animals were anesthetized again and the area of the injury was removed. Tissue from 10 animals were pooled for each RNA sample.

value: spinal cord

tag: sample type

value: 4 days post injury miR-200 inhibitor


title: 4dpi Inhib 6 S11


title: 4dpi Inhib 7 S12


title: Uninj Inhib 7 S9

value: uninjured miR-200 inhibitor injected


title: Uninj Inhib 6 S8


title: EG4347_GZ_B7_E9_GZpool_06_2019


title: Uninj Inhib 5 S7


title: WT_4h_1


title: GXW1_GZ_B7_F2_GZpool_06_2019


title: WT_T0_1


title: EG4347_GZr_B5_G7_GZpool_08_2020


title: 4dpi Cntl 6 S6

value: 4 days post injury spinal cord


title: EG4347_GZ_B6_I3_GZpool_04_2019


title: T0_2

description: rsemv2.all.genes.tpm_B5.results.txt,rsemv2.all.genes.tpm_NPA.results.txt

growth_protocol: Arabidopsis Col-0 were germinated and grown on 1/2  MS medium with 1% sucrose at 22°C under a 16-h light/8-h dark photoperiod for 12 d.

extract_protocol:
The wounded region of leaf explants were harvested and frozen in liquid nitrogen. RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The first pair of rosette leaves were cut at the junction of the blade and petiole, and the detached blades were cultured on sucrose-free B5 medium without (mock) or with NPA at 22°C under 24-h light conditions for t0, 6 h, 12 h, 1 d, 2 d, 3 d, 4 d, and 5 d .

value: the wounded region of leaf explants


title: 4dpi Cntl 5 S5


title: EG4946_GZ_B9_C8_GZpool_08_2020


title: ED3077_GZm_B3_A7_GZpool_0308_2020


title: ED3077_GZ_B2_D2_GZpool_01_2019


title: EG4724_GZr_B5_G8_GZpool_08_2020


title: ED3077_GZ_B5_B1_GZpool_05_2019


title: ED3073_GZr_B2_G7_GZpool_07_2020


title: NPA_6h_1

value: 6 h after detachment


title: ED3073_GZ_B5_E2_GZpool_06_2019


title: ED3073_GZ_B3_A6_GZpool_03_2019


title: 4dpi Cntl 1 S4


title: Cntl Uninj 5 S3

value: uninjured spinal cord


title: NPA_5d_2

value: 5 d after detachment


title: ED3052_GZ_B1_B5_GZpool_01_2019

value: young adult


title: NPA_4d_2

value: 4 d after detachment


title: ED3049_GZ_B4_F2_GZpool_05_2019

value: hermaphrodite


title: ED3049_GZ_B3_I7_GZpool_03_2019


title: Cntl Uninj S2


title: ED3052_GZ_B4_F3_GZpool_05_2019


title: Cntl Uninj 1 S1


title: ED3048_GZ_B7_I3_GZpool_06_2019


title: NPA_6h_2


title: ED3049_GZ_B1_D3_GZpool_01_2019


title: ED3048_GZ_B1_D2_GZpool_01_2019


title: ED3048_GZ_B4_H6_GZpool_04_2019


title: ED3040_GZm_B1_D1_GZpool_0108_2020


title: NPA_3d_1

value: 3 d after detachment


title: NPA_3d_2


title: Starved_Surface2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
RNA-seq: Reads were aligned to UCSC genome astMex_2.0 with STAR aligner (version STAR_2.6.1c ), using Ensembl 94 gene models. TPM values were generated using RSEM (version v1.3.0 ).
ChIP-seq: Reads were aligned to UCSC genome astMex_2.0 with Bowtie2 aligner with default parameters. Bigwig files were generated using R package rtracklayer.
Genome_build: AstMex_2.0
Supplementary_files_format_and_content: TPM gene expression in csv file for RNA-seq data, bigwig files for ChIPseq data

organism: Astyanax mexicanus

source_name: liver

growth_protocol: For all fish populations, embryos were collected and cultured in E2 embryo media containing methylene blue at 28 °C. When they were 6 dpf, 25 fry were housed in one 3 L tank on the circulating system. The fry were fed twice per day with live artemia. At the age of two months, fish were housed at a density of 2 fish per liter and fed ad libitum with artemia, frozen mysis shrimp, and GEMMA (Skretting, USA) three times per day.

extract_protocol:
Total RNA was extracted using Trizol reagent (Ambion). For ChIP-seq, livers from eight juvenile fish (4-month-old) were pooled together and snap frozen. Then the frozen tissues were grinded into powder, followed by 1% pfa (diluted from 16% pfa, Thermo Fisher, PI28906) fixation for 10 min at room temperature. The cross link was quenched with 0.125 M glycine. Chromatin shearing was performed by using a Bioruptor sonication system with following parameters: 30 s on and 30 s off per cycle, 10 cycles in total. DNA fragments were collected and purified with MAGnify™ Chromatin Immunoprecipitation System (ThermoFisher, 492024) according to the kit instruction.
Libraries for RNA-seq were prepared according to manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina). The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies). Libraries for ChIP-seq were prepared using the KAPA HTP Library Prep Kit (Roche, Cat No. KK8234) with 15 cycles of PCR and using 1:125 dilution of NEXTflex DNA barcodes (Perkin Elmer, Cat No. NOVA-514104). The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies). Post amplification size selection was performed on all libraries using a PippinHT (Sage Science).
Libraries for RNA-seq were re-quantified, normalized, pooled and sequenced on an Illumina HiSeq 2500 using v4 High Output chemistry, single read 50bp, RTA v1.18.64, and bcl2fastq2 v2.20 for demultiplexing and FASTQ file generation. Libraries for ChIP-seq were performed high throughput sequencing on the Illumina NextSeq platform.

treatment_protocol: For RNA-seq, each fish was fed 10mg Gemma twice per day for at least one week to allow the fish acclimate to the new environment. Once the fish were used to the new feeding regime, they were all fasted after one feeding (10mg Gemma per fish) for 4 days. These fish were termed as the fasted group. Half of the fish (3 surface and 3 Pachón cavefish) were refed 10mg Gemma after 4 days fasting and were termed the refed group. Fasted fish and refed fish (3 hours after feeding) were dissected quickly. For ChIP-seq, fish were fed everyday and dissected for liver collection at 3 hours after feeding.

tag: FISH population

value: surface fish

value: 4 month old

value: Starved

value: liver


title: Starved_Surface3


title: Starved_Surface1


title: NPA_5d_1

value: wild type col-0


title: ED3040_GZ_B4_E9_GZpool_05_2019


title: NPA_2d_2

value: 2 d after detachment


title: ED3017_GZ_B6_D2_GZpool_06_2019


title: Starved_Pachón3

value: Pachón cavefish


title: ED3052_GZ_B3_I8_GZpool_03_2019


title: ED3040_GZ_B3_I6_GZpool_03_2019


title: NPA_2d_1


title: ED3017_GZ_B6_A4_GZpool_04_2019


title: NPA_24h_2

value: 24 h after detachment


title: NPA_4d_1


title: Starved_Pachón2


title: ED3017_GZ_B1_H8_GZpool_01_2019


title: ED3012_GZr_B5_E1_GZpool_08_2020


title: NPA_12h_2

value: 12 h after detachment


title: NPA_24h_1

value: the wounded region of leaf explants


title: ED3012_GZ_B6_I2_GZpool_04_2019


title: Refed_Surface3

value: Refed


title: ED3005_GZ_B3_D3_GZpool_03_2019


title: ED3005_GZ_B5_D9_GZpool_06_2019


title: NPA_12h_1


title: Refed_Surface2


title: Refed_Surface1


title: B5_6h_2

value: 6 h after detachment


title: Refed_Pachón3


title: ED3005_GZ_B2_G6_GZpool_01_2019


title: B5_6h_1


title: ECA923_GZ_B8_C6_GZpool_03_2019


title: ECA923_GZ_B8_H3_GZpool_07_2020


title: ECA812_GZ_B8_H2_GZpool_07_2020


title: ECA812_GZm_B8_C5_GZpool_0307_2020


title: Refed_Pachón2


title: ECA923_GZ_B8_F1_GZpool_05_2019


title: ED3012_GZ_B7_E8_GZpool_06_2019


title: ECA812_GZ_B8_E9_GZpool_05_2019


title: Refed_Pachón1


title: ECA777_GZ_B8_E8_GZpool_05_2019


title: ECA745_GZ_B8_G9_GZpool_07_2020


title: B5_4d_2


title: IP-Surface-2

tag: chip antibody

value: Pparγ


title: B5_5d_1

value: 5 d after detachment


title: ECA745_GZ_B8_E7_GZpool_05_2019

value: young adult


title: ECA743_GZ_B8_E6_GZpool_05_2019

value: hermaphrodite


title: ECA743_GZ_B8_G8_GZpool_07_2020


title: B5_4d_1

value: 4 d after detachment


title: IP-Surface-1

value: surface fish


title: ECA743_GZ_B8_C2_GZpool_03_2019


title: B5_3d_2

value: 3 d after detachment


title: Input-Surface

value: 4 month old


title: B5_3d_1


title: B5_2d_2


title: ME11_bulk_H3K27me3_2

value: Embryo

value: bulk

value: H3K27me3 (Cell Signaling Technology, 9733)


title: IP-Pachón-2

value: Pachón cavefish

value: liver


title: ECA738_GZ_B8_G7_GZpool_07_2020


title: IP-Pachón-1


title: B5_5d_2

value: wild type col-0


title: ECA777_GZm_B8_C4_GZpool_0308_2020


title: ECA738_GZ_B8_E5_GZpool_05_2019


title: ECA777_GZ_B8_H1_GZpool_07_2020


title: Input-Pachón


title: B5_2d_1

value: the wounded region of leaf explants

value: 2 d after detachment


title: B5_24h_2

value: 24 h after detachment


title: ECA738_GZ_B8_C1_GZpool_03_2019


title: SF7 WT

city: Oxford

first: Mathilda

middle: TM

last: Mommersteeg

state: Oxfordshire

address: Sherrington Building

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

data_processing:
FASTQ files were generated using Cellranger mkfastq (v3.0.2)
To enable the maximum capture of transcripts during data exploration pending the availability of a better genome annotation, a terminal exon extension algorithm was ap-plied to extend the 3’UTR annotation. The extension algorithm used a full-length poly(A) RNA-seq sample as a reference and applied the following heuristic:     1. Identify transcripts without 3'UTR annotation in the Ensembl GTF file     2. Compare fragment coverage over 100bp flanking the terminal exon     3. If median 3' coverage > median 5' coverage, extend last exon 100bp in the 3' direction and repeat steps 2 & 3 until no further extension occurs.
The raw reads were mapped to Astyanax mexicanus v1.0.2 and v2.0 genome assemblies using cellranger count with the corresponding 3'UTR-extended annotations and two filtered feature matrices were produced
Supplementary_files_format_and_content: surface_E103e_SF7_barcodes.tsv: v2 assembly_10X Genomics Chromium Filtered Feature BC Barcodes
Supplementary_files_format_and_content: surface_E103e_SF7_features.tsv: v2 assembly_10X Genomics Chromium Filtered Feature BC Genes
Supplementary_files_format_and_content: surface_E103e_SF7_matrix.mtx: v2 assembly_ 10X Genomics Chromium Filtered Feature BC Matrix
Supplementary_files_format_and_content: pachon_E103e_SF7_barcodes.tsv: v102 assembly_10X Genomics Chromium Filtered Feature BC Barcodes
Supplementary_files_format_and_content: pachon_E103e_SF7_features.tsv: v102 assembly_10X Genomics Chromium Filtered Feature BC Genes
Supplementary_files_format_and_content: pachon_E103e_SF7_matrix.mtx: v102 assembly_ 10X Genomics Chromium Filtered Feature BC Matrix

source_name: cardiac ventricle

extract_protocol:
Hearts were isolated and tissue digestion was based on a protocol previously described by Sander et al (2013). Hearts were digested in 500µL Perfusion Buffer. Perfusion Buffer was made fresh every digestion and consisted of: 1X PBS, 30mM Taurine (Sigma, cat. no. T8691), 5.5mM Glucose (Sigma, cat. no. G7528), 10mM 2,3-Butanedione Monoxime (Sig-ma, cat. no. B0753), 10mM HEPES (Sigma, cat. no. H3393), 12.5uM CaCl2 (Sigma, cat. no. C4901), 5mg/mL Collagenase II (Gibco, cat. no. 17101-015), 5mg/mL Collagenase IV (Gib-co, cat. no. 17104-019) and 30mg DNAse I (Sigma, cat. no. 10104159001). [CaCl2] concen-tration was kept at 12.5µM to ensure adequate cell survival of all cell types present in the heart. Ventricles were collected on ice, minced into small pieces, and digested in an Ep-pendorf tube with 500µL of digestion buffer. Samples were incubated at 32°C on an Ep-pendorf thermomixer at 800rpm. Supernatants were collected every 15 minutes, neutral-ised using 1% sheep serum (Sigma, cat. no. S3772) and samples were replenished with fresh digestion buffer until all tissue had been digested (approx. 1-2 hours). Dissociated cells were filtered through 100µm filters, spun down (300g for 5 mins at 4°C), counted and spun down again before resuspension. Cells were suspended at 2000 cells/µL in DMEM (Life Technologies, cat. no. 22320-022) plus 10% fetal bovine serum (ThermoFisher, cat.no. A3840001) before loading onto 10X Chromium Chip B (10x Genomics, cat. no. 1000073).
Single Cell RNAseq libraries were generated using the 10X Chromium Next GEM Single Cell 3’ v3.1 kit (10x Genomics, cat. no. 1000092) and sequenced using the Illumina NextSeq® 500/550 High Output Kit v2 (cat.no. FC-404-2005) in 4 runs.

value: ventricular cardiac cells

value: Surface fish morph

value: heart


title: B5_12h_1

value: 12 h after detachment


title: H5 iPSC + C5 iPSC

description:
HOU_meta.csv
HOU_count.csv

tag: human cell line id

tag: human cell line sex

value: female

tag: human cell line age at reprogramming

tag: chimpanzee cell line id

tag: chimpanzee cell line sex

tag: chimpanzee cell line age at reprogramming

tag: protocol

value: growth protocol - induced pluripotent stem cells


title: Starved_Pachón1

tag: age

tag: treatment

value: Starved


title: T0_1

tag: tissue

tag: genotype

value: 0 min after detachment


title: B5_24h_1


title: AT12_scRNA-seq

data_processing:
For single cell RNA-seq, raw data was mapped to Arabidopsis thaliana genome (TAIR10) using Cell Ranger v3.1.0 with parameter “expect-cells=5,000”. gene expression matrix from Cell Ranger was input to R package Seurat v3.0.2 which was used for cell clustering and dimensionality reduction analysis.
Supplementary_files_format_and_content: tab-delimited text files include UMI for each gene in each cell

growth_protocol: Arabidopsis Col-0 were germinated and grown on 1/2 MS medium with 1% sucrose at 22°C under a 16-h light/8-h dark photoperiod for 12 d.

extract_protocol:
The base region of ~50 leaves at 4 d after detachment were harvested and digested for 2 h at room temperature in RNase-free enzyme solution (1.5% cellulase R10, 1.2% macerozyme R10, 0.4 M mannitol, 3 mM -mercaptoethanol, 10 mM CaCl2 and 0.3% BSA). The protoplast solution was strained through a 40-mm filter and a 30-mm filter. The filtered solution was centrifuged at 500 g for 3 min, and washed twice with 8% mannitol at room temperature. The protoplast pellet was resuspended in 50 μl of 8% mannitol with 0.04% BSA. About 94% cell viability was confirmed by trypan blue staining. Then the single cell suspension was counted using the hemocytometer and the concentration was adjusted to 500 cells/μl.
Single-cell suspension was loaded to 10× Chromium to capture 8,000 single cells according to the manufacturer’s instructions of 10× Genomics Chromium Single-Cell 3’ kit (V3, 10× Genomics, USA) .The library was constructed according to the standard protocol and deep sequencing was performed by Illumina NovaSeq 6000 sequencing (paired-end multiplexing run,150 bp) (LC-Bio Technology, China).

treatment_protocol: The first pair of rosette leaves were cut at the junction of the blade and petiole, and the detached blades were cultured on sucrose-free B5 medium at 22°C under 24-h light conditions for 4 d .

value: 4 d after detachment


title: B5_12h_2


title: ECA710_GZ_B8_E4_GZpool_04_2019

source_name: whole animals

tag: strain

tag: developmental stage

value: young adult

value: hermaphrodite


title: ECA705_GZ_B8_G5_GZpool_07_2020

tag: Sex


title: ECA710_GZ_B8_B9_GZpool_03_2019


title: ECA710_GZ_B8_G6_GZpool_07_2020


title: ECA705_GZ_B8_E3_GZpool_04_2019


title: ECA705_GZ_B8_B8_GZpool_03_2019


title: ECA703_GZ_B8_I7_GZpool_07_2020