title: gRNA enrichment library

city: Leuven

first: Bernard

last: Thienpont

address: ON4 Herestraat 49

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

description: 10x Genomics

data_processing:
Cell Ranger feature barcoding analysis (version 3.1.0) was used to perform raw reads (.fastq.gz) alignment and generate filtered matrix. R package Seurat (R version 4.2.0 and R package Seurat, version 4.1.0) was used to process filterd matrix and perform downstream analysis.
Assembly: GRCh38-3.0.0 from Cell Ranger website.
Supplementary files format and content: Filtered cell barodes and count matrix generated by CellRanger. Tab-separated values files and matrix files

source_name: Lung

growth_protocol: Lung adenocarcinoma cells, A549, were grown for 2 days under doxycycline (VWR, J60579.14) induction to allow for expression of Cas9. Cells were grown in DMEM high glucose (Thermo Fisher, 41965062) at 37  ̊C in 5% CO2 and passaged every 2 days with Trypsin-EDTA (Thermo Fisher, 25200056).

extract_protocol:
Cells were harvested and processed following the 10x Genomics demonstrated protocol for the preparation of single cell suspensions. See also 10x Genomics V3 Single Cell 3' Solution kit user guide. For the sgRNA enrichment libraries, briefly, 10% of the full length 10X cDNA was used as template for two consecutive PCRs aimed at enrichment of gRNA cassette and addition of sequencing adapters with Hifi HotStart ReadyMix (Roche, 7958935001).
For CROPseq library: 5000 cells were processed with Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead v3.1 kit (10X Genomics, 1000128) following the manufacturer’s instructions. For gRNA library: 10% of cDNA was used for sgRNA enrichment and creation of a specific gRNA library. For higher resolution and better cell assignments, gRNA sequences were amplified with Hifi HotStart ReadyMix (Roche, 7958935001) and gRNA cassette specific primers. gRNA cassette maps to CROPseq Guide-Puro vector (addgene plasmid #86708). Both libraries were sequenced on Illumina NovaSeq6000 with 28 cycles for read 1 and 91 cycles for read 2.

treatment_protocol: A lentiviral library was produced for the 120 sgRNAs cloned into the CROPseq Guide-Puro vector (addgene plasmid #86708). A549 cells with Cas9 under a doxycycline inducible promoter, were transduced with this lentiviral library at 0.3 multiplicity-of-infection (MOI). Cells were grown under puromycin (VWR, CAYM13884-100) selection for 10 to 14 days. Surviving cells were passaged under doxycyline induction for 2 days, after which they were grown for another 5 days and harvested for 10x single-cell RNA-sequencing library preparation.

tag: protocol

value: gRNA enrichment protocol

value: Lung

value: LUAD


title: control RV female (CTRL-f_3)

status: Public on Sep 29 2023

type: SRA

city: Bad Nauheim

first: Fatemeh

last: Khassafi

address: Parkstrasse

country: Germany

institute: Max Planck Institute

description:
processed-data-mct.xlsx
count matrix column name: CTRL-f_3

library_source: transcriptomic

data_processing:
Raw reads were assessed for quality, adapter content, and duplication rates using FastQC59. Trimmomatic version 0.39 was employed to trim reads following a quality drop (below a mean of Q15) in a window of five nucleotides
STAR mapping: mode: single-end, keep duplicates: no, keep multi-mapping: no, keep ribosomal: no, keep mitochondria: no --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignEndsProtrude 10 ConcordantPair --alignMatesGapMax 2000 --limitOutSAMoneReadBytes 10000000 --outMultimapperOrder Random --sjdbOverhang 100 --alignIntronMax 200000 --outFilterMultimapNmax 999 --outSAMmultNmax -1 --genomeDir rattus_norvegicus/104/index_star
FEATURE COUNT: The number of reads that aligned to genes was counted using featureCounts version 1.6.5 from the Subread package. Only reads mapping at least partially inside exons were aggregated and counted per gene. Reads aligning to multiple regions or genes were excluded. -t exon -g gene_id -s 2; multi-mapping: no; duplicates: no
Raw count values for each organism were normalized separately using DESeq2 version 1.30.0, then transformed into regularized logarithm values for further analysis. The normalized data were the basis of downstream analysis.
Assembly: Rn06/104/
Supplementary files format and content: excel file containing sheet 1: sample labels and mapping parameters
Supplementary files format and content: excel file containing sheet 2: BATCH 1. matrix of raw read counts for genes*samples
Supplementary files format and content: excel file containing sheet 2: BATCH 2. matrix of raw read counts for genes*samples

molecule: total RNA

organism: Rattus norvegicus

source_name: Right ventricle

extract_protocol:
MCT tissues from MCT-treated rats were harvested after RHC measurements and snap-frozen. Total RNA from each batch of RV samples were isolated separately using the RNeasy Mini Kit (or miRNeasy Micro Kit, when less sample provided-Qiagen) and snap-frozen. Purification of total RNA was performed as described in the RNeasy handbook, using DNase I digestion (RNase-Free DNase Set, Qiagen).
Following the RNA integrity measurement, approximately 2 µg of total RNA were used as starting material for library preparation using the VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme)

tag: tissue

value: Right ventricle

tag: Sex

value: F

tag: condition

value: control RV

tag: batch

value: batch 2


title: control RV female (CTRL-f_2)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-f_2


title: control RV female (CTRL-f_1)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-f_1


title: control RV male (CTRL-m_2)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-m_2

value: M


title: CROP-seq

description: 10x Genomics

library_source: transcriptomic single cell

organism: Homo sapiens

value: Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead v3.1 kit (10X Genomics, 1000128)

tag: cell line

tag: cell type


title: control RV female (CTRL-f_4)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-f_4


title: control RV male (CTRL-m_4)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-m_4


title: Tek-Cre tdTomato- 3

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hospital

description: TT tom- SCM - 2064737

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human (hg38) or mouse (mm10) genome assembly   (STAR v2.7.1a).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (human release 31  for human sampls or mouse release 22 for mouse samples).
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM text file

organism: Mus musculus

source_name: FACS sorted Tomato negative cells from the sternocleidomastoid muscle

extract_protocol:
For tumors, tumor samples were manually dissected from normal surrounding tissue.
For sorted cells, tissues were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
RNA from tumors was harvested using miRNeasy mini plus kit (Qiagen) and RNA from sorted cells was harvested using miRNeasy micro kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

tag: genotype

value: Tek-Cre;tdTom


title: PC3_RNAseq_siNON_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

molecule: polyA RNA

growth_protocol: LNCaP and PC-3 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using TriPure Isolation Reagent (Roche, cat. no. 11667165001) following manufacturer’s protocol.
mRNA was enriched using oligo(dT) beads and fragmented randomly by adding fragmentation buffer. The cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of terminal repair, ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: LNCaP and PC-3 cells were transfected with siRNA using Opti-MEM and Lipofectamine RNAiMAX reagent 48 h before extraction of RNA.

value: Bone Metastasis Prostate Cancer 3

tag: sirna treatment

value: non-targeting siRNA (siSCR, Dharmacon, cat. no. D-001810-01-05)

tag: sirna concentration

value: 25 nM

tag: sirna time


title: PC3_RNAseq_siFANCI_rep2

value: FANCI silencing RNA (siFANCI, Dharmacon, cat.no. L-022320-01-0005)


title: Control, DN3, ChIP

city: Shanghai

first: Mingyuan

last: Hu

address: 320, Yueyang Road

country: China

institute: Chinese Academy of Science

library_source: genomic

data_processing:
The sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to mm10 genome using the BWA algorithm with default settings.
Peaks were called using the MACS 2.1.0 algorithms with the following setting: band width = 200, model fold = [5, 50], pvalue cutoff = 1.00e-07, Broad region calling is off.
bigWig files were generated using Active Motive software.
The tag number of all samples (within a comparison group) is reduced by random sampling to the number of tags present in the smallest sample.
To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Active Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines the Active Region.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak (except for Input samples)

molecule: genomic DNA

source_name: double negative thymocytes

growth_protocol: Isolated HSCs  were co-cultured with OP9-DL1 cells in complete αMEM supplied with 5 ng/mL Flt-3L and 2 ng/mL IL-7. Cells are havested when developed into DN3 stage.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using a Active Motive ChIP-IT ChIP-Seq kit (Cat# 53041). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, dNTP mix, DNA polymerase I Klenow and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligate adapter to DNA fragments in a cocktail containing DNA, quick ligation buffer, adapter oligo mix and T4 DNA ligase for 20 minutes at room temperature. After adapter ligation DNA was PCR amplified with PCR primers mix for 18 cycles and library fragments of 200-300 bp were band isolated from an agarose gel.

treatment_protocol: HSCs were developed in the presence or absence of SCD1 inhibitor A939572

tag: strain

value: double negative thymocytes

tag: chip antibody

value: H3K79me2 (Active Motif, cat no. 39143)

tag: treatment

value: DMSO


title: late decompensated (DECOMP-MCT69-RV15)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-MCT69-RV15

value: late decompensated

value: batch 1


title: PC3_RNAseq_siFANCI_rep1


title: Tek-Cre tdTomato- 1

description: TT tom- SCM - 2064729

value: FACS sorted Tomato negative cells from the sternocleidomastoid muscle


title: Tek-Cre tdTomato+ 4

description: TT tom+ SCM - 2064739

source_name: FACS sorted Tomato positive cells from the sternocleidomastoid muscle


title: Tek-Cre tdTomato+ 2

description: TT tom+ SCM - 2064731

value: FACS sorted Tomato positive cells from the sternocleidomastoid muscle


title: PC3_RNAseq_siNON_rep1


title: late decompensated (DECOMP-MCT69-RV14)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-MCT69-RV14

value: Right ventricle


title: LNCaP_RNAseq_siFANCI_rep3

source_name: LNCaP

value: Lymph Node Carcinoma of the Prostate

value: LNCaP


title: late decompensated (DECOMP-MCT69-RV13)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-MCT69-RV13

value: M


title: PC3_RNAseq_siNON_rep3


title: LNCaP_RNAseq_siFANCI_rep2


title: CDF5_F

city: Vancouver

first: Angela

last: Devlin

state: British Columbia

address: 938 W 28th Ave

country: Canada

institute: University of British Columbia

description:
high_folate_vs_low_folate_in_chow_diet_females.csv
counts.csv

data_processing:
Sequenced reads were trimmed of adapter sequences/low quality sequences using Trimmomatic v0.39 (flags TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36)
Trimmed reads were aligned to mm10 (Gencode primary assembly vM25) using STAR v2.7.3a (default parameters)
Transcript abundance was estimated using Salmon v1.3.0
Transcript abundances were normalized and quantified, and comparison metrics were quantified, using DESeq2 v1.24 with apeglm method for effect size shrinkage
Assembly: mm10
Supplementary files format and content: high_folate_vs_low_folate_in_control_diet_males.csv: comma-delimited file showing metrics comparing rna expression in male offspring of dams on control diet with 10mg/kg folic acid or with 2mg/kg folic acid
Supplementary files format and content: high_folate_vs_low_folate_in_control_diet_females.csv: comma-delimited file showing metrics comparing rna expression in female offspring of dams on control diet with 10mg/kg folic acid or with 2mg/kg folic acid
Supplementary files format and content: high_folate_vs_low_folate_in_western_diet_males.csv: comma-delimited file showing metrics comparing rna expression in male offspring of dams on western diet with 10mg/kg folic acid or with 2mg/kg folic acid
Supplementary files format and content: high_folate_vs_low_folate_in_western_diet_females.csv: comma-delimited file showing metrics comparing rna expression in female offspring of dams on western diet with 10mg/kg folic acid or with 2mg/kg folic acid
Supplementary files format and content: counts.csv: comma-delimited file includes DESeq2-normalized gene counts for each sample

source_name: Female offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 5

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit (Qiagen)
One microgram of RNA per mouse was converted to cDNA libraries using the NEBNext Ultra II directional RNA library prep kit with poly(A) enrichment module (New England Biolabs); RNA-seq, directional and paired-end (43nt + 43nt)

value: Liver

value: female

tag: age

value: maternal diet:10% kcal fat, 10mg/kg diet folic acid


title: Tek-Cre tdTomato+ 3

description: TT tom+ SCM - 2064735

value: Tek-Cre;tdTom


title: Tek-Cre tdTomato- 2

description: TT tom- SCM - 2064733


title: CDF4_F

source_name: Female offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 4


title: CDF3_F

source_name: Female offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 3


title: CD5_F

source_name: Female offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 5

value: maternal diet:10% kcal fat, 2mg/kg diet folic acid


title: WD5_F

description:
high_folate_vs_low_folate_in_western_diet_females.csv
counts.csv

source_name: Female offspring of dam on western diet (45% fat), control  folic acid (2 mg/kg diet) replicate 5

value: maternal diet:45% kcal fat, 2mg/kg diet folic acid


title: MCP 3

description: CKIA 197 - 1955377

source_name: FACS sorted Tomato positive tumor cells

value: FACS sorted Tomato positive tumor cells


title: MCP 4

description: CKIA 205 - 1955378


title: LNCaP_RNAseq_siNON_rep3

value: non-targeting siRNA (siSCR, Dharmacon, cat. no. D-001810-01-05)

value: 25 nM


title: late decompensated (DECOMP-MCT69-RV09)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-MCT69-RV09

value: late decompensated


title: late decompensated (DECOMP-MCT69-RV04)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-MCT69-RV04

value: batch 1


title: MCP 2

description: CKIA 191 - 1955376


title: LNCaP_RNAseq_siFANCI_rep1

value: FANCI silencing RNA (siFANCI, Dharmacon, cat.no. L-022320-01-0005)


title: WD4_F

source_name: Female offspring of dam on western diet (45% fat), control  folic acid (2 mg/kg diet) replicate 4


title: CD4_F

source_name: Female offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 4


title: MCP 1

description: CKIA 25 - 1955375


title: LNCaP_RNAseq_siNON_rep2


title: Tek-Cre tdTomato+ 1

description: TT tom+ SCM - 2064727

value: FACS sorted Tomato positive cells from the sternocleidomastoid muscle


title: WDF5_F

source_name: Female offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet)  replicate 5

value: maternal diet:45% kcal fat, 10mg/kg diet folic acid


title: TCP 4

description: TPIT 87 - 1955374


title: LNCaP_RNAseq_siNON_rep1

value: Lymph Node Carcinoma of the Prostate


title: TCP 3

description: TPIT 76 - 1955373


title: WDF4_F

source_name: Female offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet)  replicate 4


title: early decompensated (DECOMP-FP-RV25)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-FP-RV25

value: Right ventricle

value: early decompensated


title: early decompensated (DECOMP-FP-RV07)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-FP-RV07

value: M


title: TCP 2

description: TPIT 56 - 1955372


title: early decompensated (DECOMP-FP-RV22)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-FP-RV22


title: WDF3_F

source_name: Female offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet)  replicate 3

value: Liver

value: female


title: Sample 36

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads are trimmed for adaptors and filtered by sequencing Phred quality (>= Q15) using fastp (Chen et al. 2018). The count table is generated by aligning reads to the human transcriptome (Ensembl version 98) using kallisto (Bray et al. 2016) and converting transcript counts to gene counts using tximport (Soneson, Love, and Robinson 2015). We adjust batch effects in the raw counts using ComBat-Seq (Johnson, Li, and Rabinovic 2007; Zhang, Parmigiani, and Johnson 2020).
Assembly: Ensembl human transcriptome version 98
Supplementary files format and content: CSV table with counts per gene (rows) per sample (columns)

source_name: Non-Sorted

growth_protocol: Approximately 20,000 islet equivalents were washed with DPBS and resuspended in TrypLE for single cell dispersion. The islets were dispersed into a single cell suspension in TrypLE for 12-15 min at 37 °C. Dissociated islet cells were washed with DMEM medium containing 10% FBS and resuspended in the Miami medium containing DA-ZP1 (80 nM) for 10 min at 37 °C. The cells were then filtered through a 30 um filter to remove any aggregates before FACS sorting. DA-ZP1 treated cells were sorted by FACSAria cell sorter (BD Biosciences, Joslin Flow Cytometry Core).

extract_protocol:
RNA extracted using Qiagen micro kit or Purelink RNA kit.
NovaSeq6000, 100PE, Low-input RNA seq, ~50M reads (25PR), SMARTer Stranded Total RNA-Seq kit-pico input mammalian kit v2
TruSeq Total pico RNA library

treatment_protocol: Sorted islet cells were spun at 250 g for 5 min, resuspended in Miami media, and immediately seeded in U-bottom low attachment 96 well plates (1000 cells/200 ul/well). Half of the medium was refreshed every other day for 10 days.

value: Sorted human islet cells

tag: day

tag: rna isolation method

value: Purelink RNA Kit

tag: modification

value: Batch #1


title: late decompensated (DECOMP-MCT69-RV07)

description:
processed-data-mct.xlsx
count matrix column name: DECOMP-MCT69-RV07

source_name: Right ventricle

tag: tissue


title: Sample 37

source_name: Whole islet


title: WDF2_F

source_name: Female offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet)  replicate 2

tag: Sex


title: TCP H3K27ac 3

description: TCP_H3K27ac_2 - 2379006

data_processing:
CUT&RUN libraries were sequenced on NovaSeq6000 sequencer and generated 50 bp paired-end reads
The reads were aligned to mouse mm10 genome reference and fruit fly dm6 genome reference by BWA (version 0.7.170.7.12, default parameter). Duplicated reads were marked by the bamsormadup from the biobambam tool (version 2.0.87) available at https://www.sanger.ac.uk/tool/biobambam/. Uniquely mapped reads were kept by samtools (parameter “-q 1 -F 1804,” version 1.14). Fragments < 2000 bp were kept for peak calling and bigwig files were generated for visualization.
macs2 (PMID: 18798982)   was used for peak calling
Assembly: mm10
Supplementary files format and content: narrowPeak,bw
Library strategy: CUT&RUN

extract_protocol:
Tumors were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
CUT&RUN libraries were prepared using the xGen ssDNA & Low-Input DNA Library Prep Kit (#10009859, IDT)

tag: antibody

value: H3K27ac (39133, Active Motif)


title: CDF2_F

source_name: Female offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 2

value: maternal diet:10% kcal fat, 10mg/kg diet folic acid


title: TCP 1

description: TPIT 48 - 1955371

value: FACS sorted Tomato positive tumor cells


title: Sample 34


title: Sample 35

source_name: Alpha


title: WD2_F

source_name: Female offspring of dam on western diet (45% fat), control  folic acid (2 mg/kg diet) replicate 2

value: maternal diet:45% kcal fat, 2mg/kg diet folic acid


title: TCP H3K27ac 2

description: TCP_H3K27ac_1 - 2376819


title: Compensated RV (COMP-ARN-RV08)

description:
processed-data-mct.xlsx
count matrix column name: COMP-ARN-RV08

tag: condition

value: Compensated RV

tag: batch

value: batch 1


title: TCP H3K27ac 1

description: TCP_25_H3K27ac - 267991

tag: cell type


title: Compensated RV (COMP-MCT66-RV07)

description:
processed-data-mct.xlsx
count matrix column name: COMP-MCT66-RV07


title: CD3_F

source_name: Female offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 3

tag: genotype

value: maternal diet:10% kcal fat, 2mg/kg diet folic acid


title: WD3_F

source_name: Female offspring of dam on western diet (45% fat), control  folic acid (2 mg/kg diet) replicate 3


title: Sample 32


title: Compensated RV (COMP-FP-RV14)

description:
processed-data-mct.xlsx
count matrix column name: COMP-FP-RV14


title: WD1_F

source_name: Female offspring of dam on western diet (45% fat), control  folic acid (2 mg/kg diet) replicate 1


title: MCP H3K27ac 6

description: MCP_H3K27ac_2 - 2379010


title: WDF1_F

source_name: Female offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet)  replicate 1

value: maternal diet:45% kcal fat, 10mg/kg diet folic acid


title: MCP H3K27ac 5

description: MCP_H3K27ac_1 - 2356937


title: Compensated RV (COMP-ARN-RV03)

description:
processed-data-mct.xlsx
count matrix column name: COMP-ARN-RV03


title: Compensated RV (COMP-FP-RV11)

description:
processed-data-mct.xlsx
count matrix column name: COMP-FP-RV11


title: CD2_F

source_name: Female offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 2


title: Compensated RV (COMP-FP-RV09)

description:
processed-data-mct.xlsx
count matrix column name: COMP-FP-RV09


title: Compensated RV (COMP-ARN-RV02)

description:
processed-data-mct.xlsx
count matrix column name: COMP-ARN-RV02


title: MCP H3K27ac 3

description: MCP_38_H3K27ac - 2428289


title: Sample 33


title: Control RV (CTRL-ARN-RV37)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-ARN-RV37

value: Control RV


title: Control RV (CTRL-ARN-RV36)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-ARN-RV36

value: Right ventricle


title: CDF1_F

description:
high_folate_vs_low_folate_in_chow_diet_females.csv
counts.csv

source_name: Female offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 1


title: WDF5_M

description:
high_folate_vs_low_folate_in_western_diet_males.csv
counts.csv

source_name: Male offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet) replicate 5

value: male


title: MCP H3K27ac 2

description: MCP_20_H3K27ac_2 - 2428289


title: Sample 26

value: Qiagen Microkit

value: Batch #2


title: Sample 29


title: Sample 28


title: Sample 24


title: Sample 25


title: CD5_M

description:
high_folate_vs_low_folate_in_chow_diet_males.csv
counts.csv

source_name: Male offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 5

value: Liver


title: Sample 23

value: Sorted human islet cells


title: Control RV (CTRL-Su28-RV04)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-Su28-RV04

value: M


title: TCP IgG 3

description: TCP 25 IgG - 2400058


title: TCP IgG 2

description: TCP IgG_2 - 2379004


title: WDF4_M

source_name: Male offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet) replicate 4


title: Control RV (CTRL-Su28-RV01)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-Su28-RV01


title: Sample 22


title: MCP H3K27ac 4

description: MCP_56_H3K27ac - 2428289


title: Sample 21


title: CD1_F

source_name: Female offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 1

value: female


title: WD5_M

source_name: Male offspring of dam on western diet (45% fat), control folic acid (2 mg/kg diet) replicate 5


title: TCP IgG 1

description: TCP IgG_1 - 2376816


title: CD4_M

source_name: Male offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 4


title: MCP H3K27ac 1

description: MCP_20_H3K27ac_1 - 2428288

value: H3K27ac (39133, Active Motif)


title: Sample 20

source_name: Whole islet


title: MCP IgG 3

description: MCP 20 IgG - 2400064


title: Control RV (CTRL-MCT62-RV22)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-MCT62-RV22

source_name: Right ventricle


title: Sample 19


title: WDF3_M

source_name: Male offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet) replicate 3


title: WD4_M

source_name: Male offspring of dam on western diet (45% fat), control folic acid (2 mg/kg diet) replicate 4


title: Control RV (CTRL-MCT62-RV21)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-MCT62-RV21


title: Control RV (CTRL-FP-RV04)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-FP-RV04


title: MCP IgG 2

description: MCP IgG_3 - 2379008


title: WD3_M

source_name: Male offspring of dam on western diet (45% fat), control folic acid (2 mg/kg diet) replicate 3


title: Sample 17

value: Batch #3


title: Sample 16

source_name: Alpha


title: Control RV (CTRL-Su28-RV06)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-Su28-RV06


title: MCP IgG 1

description: MCP IgG_2 - 2376821


title: TCP 130 tom+ tumor cells

data_processing:
Paired-end reads of 150 bp reads were processed by Juicer (v1.5, default parameters) based on mm10 and Arima fragment (cut sites GATC or GANTC).
Each replicate was processed separately using default parameters (every replicate got > 500M pairs as > 360M contacts). We required MAPQ score greater than 30 for generating .hic file and downstream analysis.
Loops were called by HiCCUPS from Juicer package (default parameters). Reproducibility have been confirmed by visual inspection.
Assembly: mm10(GRCm38.p6)
Supplementary files format and content: hic file

source_name: FACS sorted Tomato positive tumor cells

extract_protocol:
Tumors were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
Libraries were prepared using the Arima-HiC Kit (#A510008, Arima Genomics)

value: FACS sorted Tomato positive tumor cells


title: Control RV (CTRL-FP-RV01)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-FP-RV01


title: Sample 15

source_name: Non-Sorted

value: Batch #4


title: TCP 79 tom+ tumor cells


title: CDF4_M

source_name: Male offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 4

value: maternal diet:10% kcal fat, 10mg/kg diet folic acid


title: Fs+Cc total RNA EMBR

city: Santa Barbara

first: Kellie

last: Heom

state: California

address: UC Santa Barbara

department: Chemical Engineering

institute: University of California Santa Barbara

description: EMBR-seq

data_processing:
In the sequencing libraries, read 1 contains the sample barcode. Read 2 is mapped to the bacterial or fungal transcriptome. Prior to mapping, read 1 was trimmed to 25 bases, read 2 was trimmed to 51 bases, and only reads containing valid sample barcodes on read 1 were retained. Next, the reads were mapped to the appropriate reference transcriptome using Burrows-Wheeler Aligner (BWA) version 0.7.15 with default parameters.
Assembly: Escherichia coli K12 substr. MG1655 (ASM584v2); Geobacter metallireducens GS-15 (ASM1292v1); Fibrobacter succinogenes strain UWB7 (GCA_900142945.1); Anaeromyces robustus (Anaeromyces robustus v1.0); Caecomyces churrovis (Caecomyces churrovis A v1.0)
Supplementary files format and content: Text file where column 1 contains gene names or gene IDs and column 2 contains gene counts.

organism:
Fibrobacter succinogenes
Caecomyces churrovis

source_name: strain UWB7, C. churrovis

extract_protocol:
For E. coli and G. metallireducens monocultures, total RNA extractions were performed using Trizol according to the manufacturer’s protocol. RNA was extracted from F. succinogenes strain UWB7 monoculture & co-culture pellets using the RNeasy Mini Kit following the protocol for purification of total RNA from plant cells and tissues and filamentous fungi, using liquid N2 method of cell lysis, QIAshredder homogenization, on-column DNase I digestion, and elution in 30 µL of RNAse-free water.
(1) Overview: EMBR-seq libraries were prepared according to the protocol described in Wangsanuwat et al. 100 ng of total RNA were used as input material for all libraries. For the libraries denoted “EMBR-seq” and “EMBR-seq+”, blocking primers were added during the polyadenylation step and reverse transcription step. For the libraries denoted “No depletion” and “RNase H”, water was added instead of blocking primers during these two steps. In the libraries denoted “RNase H” and “EMBR-seq+”, the RNase H treatment was performed as described below. In the libraries denoted “No depletion” and “EMBR-seq”, the RNase H treatment was skipped; the amplified RNA (aRNA) product of in vitro transcription (IVT) was used directly for the library reverse transcription step as described in Wangsanuwat et al. (2) Polyadenylation: 2 μL of total RNA (50 ng/μL) was mixed with 1 μL of 5x first strand buffer [250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2, comes with Superscript II reverse transcriptase, Invitrogen Cat. # 18064014], 1 uL of blocking primer mix, 0.1 μL 10 mM ATP, and 0.1 μL E. coli poly-A polymerase (New England Biolabs, Cat. # M0276S). The samples were incubated at 37°C for 10 mins. In the “No depletion” and “RNase H” libraries, 1 μL of nuclease-free water was added instead of the blocking primer mix. (3) Reverse transcription: The polyadenylation product was mixed with 0.5 μL 10 mM dNTPs (New England Biolabs, Cat. # N0447L), 1 μL reverse transcription primers (25 ng/μL, Supplementary Table 2), and 1.3 μL blocking primer mix, and heated to 65°C for 5 mins, 58°C for 1 min, and then quenched on ice. In the “No depletion” and “RNase H” libraries, 1.3 μL of nuclease-free water was added instead of the blocking primer mix. This product was then mixed with 1.2 μL 5x first strand buffer, 1 μL 0.1 M DTT, 0.5 μL RNaseOUT (Thermo Fisher Scientific, Cat. #10777019), and 0.5 μL Superscript II reverse transcriptase, and then incubated at 42°C for 1 hr. Immediately afterwards, the samples were heat-inactivated at 70°C for 10 mins. (4) Second strand synthesis: The reverse transcription product was mixed with 33.5 μL nuclease-free water, 12 μL 5x second strand buffer [100 mM Tris-HCl (pH 6.9), 23 mM MgCl2, 450 mM KCl, 0.75 mM β-NAD, 50 mM (NH4)2SO4, Invitrogen, Cat. # 10812014], 1.2 μL 10 mM dNTPs, 0.4 μL E. coli ligase (Invitrogen, Cat. # 18052019), 1.5 μL DNA polymerase I (Invitrogen, Cat. # 18010025), and 0.4 μL RNase H (Invitrogen, Cat. # 18021071), and incubated at 16°C for 2 hrs. The cDNA was purified with 1x AMPure XP DNA beads (Beckman Coulter, Cat. # A63881) and eluted in 24 μL nuclease-free water that was subsequently concentrated to 6.4 μL. (5) In vitro transcription: The product from the previous step was mixed with 9.6 μL of in vitro transcription mix (1.6 μL of each ribonucleotide, 1.6 μL 10x T7 reaction buffer, 1.6 μL T7 enzyme mix, MEGAscript T7 Transcription Kit, Thermo Fisher Scientific, Cat. # AMB13345) and incubated at 37°C for 13 hrs. The IVT product was mixed with 6 μL ExoSAP-IT PCR Product Cleanup Reagent (Thermo Fisher Scientific, Cat. # 78200.200.UL) and incubated at 37°C for 15 mins. Next, it was treated with 5.5 μL fragmentation buffer (200 mM Tris-acetate (pH 8.1), 500 mM KOAc, 150 mM MgOAc) at 94°C for 3 mins and immediately quenched with 2.75 μL stop buffer (0.5 M EDTA) on ice. The fragmented aRNA was size-selected with 0.8x AMPure RNA beads (RNAClean XP Kit, Beckman Coulter, Cat. # A63987) and eluted in 18 μL nuclease-free water. In the libraries denoted “No depletion” and “EMBR-seq”, the fragmented and cleaned-up in vitro transcription product was used directly for Illumina library preparation by reverse transcription and PCR, as described previously (18, 30). In the “RNase H” and “EMBR-seq+” libraries, the RNase H treatment was performed before proceeding to Illumina library preparation. (6) RNase H treatment for monocultures: After ExoSAP treatment, RNA fragmentation, and bead-based size selection, the aRNA concentration was measured on a NanoDrop One spectrophotometer. 1000 ng of aRNA was mixed with 500 ng (3.2 μL) of RNase H probe mix, 3.2 μL of RNase H buffer mix, and nuclease-free water to reach a total volume of 15 μL for each reaction. This mixture was preheated at 65°C for 5 mins and quenched on ice. 1 μL of RNase H (Invitrogen, Cat. # 18021071) was added and the reaction was incubated at 16°C for 30 mins. Finally, the RNase H product was size-selected with 1x AMPure RNA beads and eluted in 15 μL nuclease-free water, and then concentrated to 5 μL volume for Illumina library preparation. (7) RNase H reaction for co-cultures: For co-culture samples, the RNase H probe mix was altered to include probes for depleting fungal rRNA along with bacterial rRNA. 1000 ng of aRNA derived from co-culture samples was mixed with 850 ng (5.5 μL) of co-culture RNase H probe mix, which consisted of: 100 ng each of the two fungal 28S probes with 50 ng each of the two fungal 18S, fungal 5.8S, and ten bacterial RNase H probes. The aRNA and probes were mixed with 3.2 μL RNase H buffer mix and nuclease-free water to reach a total volume of 15 μL for each reaction. The reactions were preheated at 65°C for 5 mins and quenched on ice. 1 μL of RNase H was added and the reaction was incubated at 16°C for 30 mins. The RNase H product was size-selected with 1x AMPure RNA beads and eluted in 15 μL nuclease-free water, and then concentrated to 5 μL volume for Illumina library preparation.
OTHER (EMBR-seq+). Method is detailed in Heom, Wangsanuwat et al.

tag: cell line

value: strain UWB7, C. churrovis

tag: input material_for_library_preparation

value: total RNA (RNeasy)


title: CDF5_M

source_name: Male offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 5


title: Sample 13


title: Fs+Cc RNase H Rep2

description: RNase H

value: total RNA (RNeasy), followed by poly-A depletion


title: Control RV (CTRL-MCT69-RV20)

description:
processed-data-mct.xlsx
count matrix column name: CTRL-MCT69-RV20

value: Control RV

value: batch 1


title: MCP 76 tom+ tumor cells


title: CDF3_M

source_name: Male offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 3

value: male


title: MCP 43 tom+ tumor cells


title: Fs+Cc EMBR Rep3

description: EMBR-seq


title: WDF2_M

source_name: Male offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet)  replicate 2

value: maternal diet:45% kcal fat, 10mg/kg diet folic acid


title: Sample 12

value: Qiagen Microkit


title: Fs+Cc EMBR Rep2

description: EMBR-seq


title: Mutant 3

city: Sydney

first: M. Mozammel

last: Hoque

state: NSW

address: 15 Broadway, Ultimo

department: Australian Institute for Microbiology & Infection (AIMI)

country: Australia

institute: University of Technology Sydney

data_processing:
The RNA sequencing reads were filtered to remove adapter contamination and low-quality bases (≤ Q20) using TrimGalore and were checked using FastQC before analysis.
Clean reads were aligned to the reference genome using Subread aligner.
The mapped reads per gene count were quantified using featureCount.
The count matrices were uploaded to R version 4.1.0 and differential expression analysis was performed using edgeR.
Assembly: Vibrio cholerae O1 El Tor strain N16961 (RefSeq accession numbers NC_002505 and NC_002506 for chromosome I and II respectively)
Supplementary files format and content: Count matrix

organism: Vibrio cholerae

growth_protocol: Acanthamoeba castellanii were infected with the V. cholerae A1552 wt strain and its isogenic flrA mutant at 100 MOI in marine minimal medium (2M) for 24 hours at room temperature before the extraction of total RNA.

extract_protocol:
The intracellular bacterial cells were recovered by lysing the amoeba with 1% Triton-X and total RNA was extracted using the RNeasy plus mini kit (Qiagen, Hilden, Germany). A combination of lysozyme and proteinase K was used to ensure complete lysis. RNeasy plus mini kit’s gDNA shearer column as well as RNase free DNase (Qiagen, Hilden, Germany) on column DNA digest were used to ensure sufficient degradation of the contaminant DNA in the sample.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA kit according to the manufacturer’s protocol (Illumina, San Diego, CA, USA).

value: ElTor

value: flrA


title: Sample 11

value: Sorted human islet cells


title: WD2_M

source_name: Male offspring of dam on western diet (45% fat), control folic acid (2 mg/kg diet) replicate 2

value: Liver

value: maternal diet:45% kcal fat, 2mg/kg diet folic acid


title: Mutant 2


title: Mutant 1


title: Sample 10

value: Batch #3


title: Fs+Cc EMBR Rep1

description: EMBR-seq


title: Wild type 2

value: Wild type


title: Sample 14

value: Batch #4


title: CDF1_M

source_name: Male offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 1

value: maternal diet:10% kcal fat, 10mg/kg diet folic acid


title: Sample 9


title: Fs+Cc Control Rep2

description: No depletion

value: strain UWB7, C. churrovis


title: Wild type 1


title: WD1_M

source_name: Male offspring of dam on western diet (45% fat), control folic acid (2mg/kg diet) replicate 1


title: Sample 7


title: Fs RNase H Rep2

description: RNase H

organism: Fibrobacter succinogenes

source_name: strain UWB7

value: strain UWB7

value: total RNA (RNeasy)


title: Sample 6


title: Ec EMBR+ Rep3

description: EMBR-seq+

organism: Escherichia coli

value: total RNA (Trizol)


title: CD3_M

source_name: Male offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 3

value: maternal diet:10% kcal fat, 2mg/kg diet folic acid


title: CD2_M

source_name: Male offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 2

value: male


title: Fs RNase H Rep1

description: RNase H


title: Ec EMBR+ Rep2

description: EMBR-seq+


title: WDF1_M

source_name: Male offspring of dam on western diet (45% fat), supplemental folic acid (10mg/kg diet) replicate 1

value: maternal diet:45% kcal fat, 10mg/kg diet folic acid


title: Sample 5

source_name: Whole islet

value: Qiagen Microkit


title: Ec EMBR+ Rep1

description: EMBR-seq+


title: Sample 4


title: CDF2_M

source_name: Male offspring of dam on supplemental folic acid diet (10% fat, 10mg / kg diet folic acid)  replicate 2


title: Fs+Cc Control Rep3

description: No depletion

value: total RNA (RNeasy), followed by poly-A depletion


title: Fs EMBR Rep2

description: EMBR-seq


title: Sample 8


title: Fs Control Rep3

description: No depletion


title: Sample 3


title: Ec RNaseH Rep2

description: RNase H


title: Fs Control Rep2

description: No depletion


title: Sample 2


title: control_sham_rep2

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.9
Alignment: STAR v2.7.9a
Post alignement QC assessment: sambamba v0.7.1, RSeQC and Picard tools v2.25.6
Gene transcripts assembly: featureCounts
Differentially expressed genes analysis: DESeq2
Assembly: GENCODE human genome model: GRCm39 v27
Supplementary files format and content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

source_name: Heart tissue

extract_protocol:
A conditional HIF2αfl/fl mice in the C57BL/6 background were purchased from Jackson laboratory. We bred Hif2αfl/fl mice to the transgenic mice expressing tamoxifen‐inducible Cre recombinase (CreERT2) under the control of the VE-cadherin promoter. To obtain experimental ecHif2α-/-( HIF2αfl/fx+Cre) and controls (Hif2α+l/- and Hif2α+/+Cre) mice were grouped and fed with or without tamoxifen containing food for two weeks. After determining the genotypes, We performed myocardial infarction (MI) in controls and ecHif2a-/- mice.  Heart tissues were harvested 28 days after MI Total RNA from controls and Hif2α-/- heart tissues was isolated 28 days after MI using RNeasy Fibrous Tissue Mini Kit (74704, Qiagen, MD) according to the manufacturer’s protocol. RNA integrity was confirmed using a Cytation3 microplate reader (BioTek, VT).
Library was performed according to the manufacter’s instructions  using Illumina TruSeq Small RNA Sample Preparation Kit (RS-930-1012, Illumina, CA).

value: Heart tissue

value: control sham

value: Control sham, replicate 2


title: control_sham_rep3

value: Control sham, replicate 3


title: Fs Control Rep1

description: No depletion


title: Ec RNaseH Rep1

description: RNase H


title: Fs+Cc Control Rep1

description: No depletion


title: Gm EMBR+ Rep2 Part2

description: EMBR-seq+

organism: Geobacter metallireducens


title: Gm EMBR Rep3

description: EMBR-seq+


title: Hif2α_MI_rep1

value: Hif2α-/-, replicate 1


title: Hi-C_mouse_sperm_WT_rep2

city: Nanjing

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
In situ Hi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
Assembly: mm9
Supplementary files format and content: .hic files

source_name: sperm

extract_protocol:
Briefly, collected sperm were fixed with 1% formaldehyde for 10 min (RT) and then quenched with glycine (at a final concentration of 0.2 M for 5 min RT). The cells were then washed with PBS, and added to 250 ml of lysis buffer (10 mM pH = 7.4 Tris-HCl, 10 mM NaCl, 0.1 mM EDTA, 0.5% NP-40, proteinase inhibitor), lysed on ice for > 15 min, and centrifuged at 2500 × g for 5 min. The pellet was washed once with 500 ml of precooled lysis buffer before centrifuging again at 2500 × g for 5 min. After the supernatant was discarded, adding 50 ml of 0.5% SDS was added to the pellet, which was incubated at 62 °C for 10min.
145 ml of ddH2O and 25 ml of 10% Triton X-100 were mixed, added to the detergent and pellet, and incubated at 37 °C for 15 min. Then, 25 ml 10XNEB buffer 2 and 100 U MboI were added to digest chromatin overnight at 37 °C. After digestion, MboI was inactivated at 62 °C for 20 min, and then, the mixture was cooled to RT. Biotins were then added to the DNA in the following reaction system: 20 ml of 0.4 mM biotin-14-dCTP, 0.8 of ml 10 mM dATP/dGTP/dTTP, and 8 ml of 5 U/ml Klenow. The reaction system and DNA were incubated at 37 °C for 1.5 h with rotation. Then, 900 ml of ligation master mix (663 ml of ddH2O, 120 ml of 10X NEB T4 DNA ligase buffer, 100 ml of 10% Triton X-100, 12 ml of 10 mg/ml BSA, 5 ml of 400 U/ml T4 DNA ligase) was added to the samples and incubated at RT for 4 h to ligate the fragments. After ligation, 50 ml of 20mg/ml proteinase K and 120 ml of 10% SDS were added to the mixture and incubated at 55 °C for 30 min. Following incubation, 130 ml of 5 M sodium chloride was added and incubated at 68 °C overnight. Finally, the DNA was purified and sheared into 300–500-bp fragments with a Covaris M220 ultrasonicator. The biotin-marked DNA was pulled down with Dynabeads MyOne Streptavidin C1 (Life Technology), and the library was constructed with the beads before sending for Illumina sequencing.

value: sperm

value: Wild type


title: control_sham_rep1

value: Control sham, replicate 1


title: Gm EMBR+ Rep1

description: EMBR-seq+


title: control_MI_rep2

value: control MI

value: control, replicate2


title: Hi-C_mouse_sperm_KO_rep2


title: Gm RNase H Rep1

description: RNase H


title: Hi-C_mouse_sperm_KO222_rep1


title: Gm RNase H Rep3

description: RNase H


title: Ec RNaseH Rep3

description: RNase H


title: Hi-C_mouse_sperm_KO206_rep1


title: Hi-C_mouse_sperm_WT_rep1


title: CD1_M

source_name: Male offspring of dam on control diet (10% fat, 2 mg/kg diet folic acid) replicate 1

value: Liver


title: CBD, scATACseq

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

description: 10x Genomics

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

source_name: tumor

extract_protocol:
After the tumor was removed, it was digested into single cell suspension with tumor tissue dissociation kit on ice, and 10x-RNA reagent and 10x-ATAC reagent were added
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cell suspension were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tumor cells,Stromal cells,Immune cells

value: tumor

value: 10 weeks old


title: Gm EMBR Rep3 Part1

description: EMBR-seq

value: total RNA (Trizol)


title: Gm EMBR Rep2 Part2

description: EMBR-seq


title: Gm RNase H Rep2

description: RNase H


title: PBS, scATACseq

description: 10x Genomics


title: mouse-3

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (for mouse), Rnor6 (for rat), OryCun2 (for rabbit),OchPri3 (for pika) whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38, Rnor6, OryCun2, OchPri3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: mouse fibroblast

growth_protocol: Cells were cultured under 5% CO2, 37 ℃ with DMEM (10% FBS, 1% PS)

extract_protocol:
After growing to 90% confluency, cells were lysed with TRIZOL directly and total RNA was extracted with chloroform and  isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epidermis


title: Gm EMBR Rep2 Part1

description: EMBR-seq


title: Sample 1

source_name: Alpha

value: Sorted human islet cells

value: Qiagen Microkit

value: Batch #4


title: Gm EMBR Rep1

description: EMBR-seq


title: Gm EMBR+ Rep2 Part1

description: EMBR-seq+


title: Gm Control Rep2

description: No depletion


title: mouse-1


title: control_MI_rep1

value: Heart tissue

value: control, replicate1


title: Gm Control Rep1

description: No depletion


title: PBS, scRNAseq

description: 10x Genomics


title: Arabidopsis thaliana col-0 mature leaf sRNA-seq r2

status: Public on Sep 28 2023

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
sRNA-seq; small RNA mapping in A.thaliana cells; Experiment SD180
A.thaliana-leaf-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.

organism: Arabidopsis thaliana

source_name: mature leaves

growth_protocol: A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).

extract_protocol: csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles.  Total RNA-Seq Library Preparation  Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Ribo-Zero Gold plant rRNA removal kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions.

value: mature leaves


title: Arabidopsis thaliana col-0 cells csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in A.thaliana cells; Experiment SD675
A.thaliana-cells-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Papaya1.0, Chlamydomonas_reinhardtii_v5.5, Drosophila melanogaster: dm6, ASM32608v1, Phypa V3, Selaginella moellendroffii: v1.0, Zea mays (rest): Zm-B73-REFERENCE-NAM-5.0, Zea mays : AGPv4.38 (STARR-seq)
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.
Library strategy: csRNA-Seq

source_name: cells

value: cells

tag: ecotype


title: Arabidopsis thaliana col-0 mature leaf csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in A.thaliana cells; Experiment SD177
A.thaliana-leaf-10.tss.txt


title: Gm EMBR Rep3 Part2

description: EMBR-seq


title: Arabidopsis thaliana col-0 mature leaf sRNA-seq r1

description:
sRNA-seq; small RNA mapping in A.thaliana cells; Experiment SD178
A.thaliana-leaf-10.tss.txt


title: Arabidopsis thaliana col-0 cells csRNA-seq r2

description:
csRNA-seq; nascent TSS mapping in A.thaliana cells; Experiment SD816
A.thaliana-cells-10.tss.txt


title: Gm Control Rep3

description: No depletion


title: Arabidopsis thaliana col-0 cells sRNA-seq r2

description:
sRNA-seq; small RNA mapping in A.thaliana cells; Experiment SD795
A.thaliana-cells-10.tss.txt


title: Arabidopsis thaliana col-0 cells sRNA-seq r1

description:
sRNA-seq; small RNA mapping in A.thaliana cells; Experiment SD723
A.thaliana-cells-10.tss.txt


title: ChIP-seq input for H3K27ac in propionate-treated NRVMs

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

data_processing:
Trim_galore (to remove sequencing adaptors)
Alignment to the genome (Bowtie2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads using Picard
Reference normalization by scaling read counts to mapped Drosophila reads (dm6) in IP and input samples
Assembly: rn6
Normalized bigWig generation using Homer v4.11

source_name: Neonatal rat ventricular myocytes (NRVMs)

growth_protocol: Primary neonatal rat ventricular myocytes were isolated from P1/P2 hearts of 1-2 day old Sprague-Dawley rats by enzymatic digestion, and a ‘pre-plating’ step was introduced to reduce fibroblasts in the myocyte-containing supernatant. Cells were plated onto fibronectin-coated TC culture dishes and cultured in M2 medium (80% DMEM medium containing 24 mM NaHCO3 and 20% M199 medium with 26mM NaHCO3) and incubated in a 5% CO2 atmosphere.  Initially, medium was supplemented with 10% horse serum, 5% newborn calf serum and penicillin/streptomycin mixture. Next day, cells were serum-starved, followed by incubation in either 3.05 mM (pH 6.4) or 24.4 mM (pH 7.4) NaHCO3 with addition of 0.05% DMSO, or 24.4mM NaHCO3 plus 3µM A485 (p300 inhibitor) for 48 h.

extract_protocol:
Cells were washed with PBS and fixed in 1% FA for 10 minutes. Cells were sonicated to give fragments of 200-300bp, then pooled with fixed, sonicated Drosophila S2 cells at a ratio of 4:1 rat:Drosophila, followed by IP.
DNA libraries were made using the NEBnext Ultra II DNA library preparation kit for Illumina (Cat no. E7645).

value: Serum-starved cells were incubated in 6mM sodium propionate for 48 h

value: input


title: H3K27ac ChIP-seq in propionate-treated NRVMs

value: Neonatal rat ventricular myocytes (NRVMs)


title: ChIP-seq input for H3K27ac in control NRVMs

value: Serum-starved cells were incubated for 48 h


title: H3K27ac ChIP-seq in control NRVMs


title: mouse-2

tag: strain


title: CBD, scRNAseq

description: 10x Genomics


title: Brain single cell 1152

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain single cell 1152

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

source_name: Brain

extract_protocol:
Fluorescent cells were sorted by FACS from Pdgfra-H2BGFP mice and Tagl-CREERT2;Ai14 mice as previously described (Vanlandewijck et al, 2018). Briefly, brain tissue from both males and females were mechanically and enzymatically digested and vascular fragments isolated using CD31 antibody coated Dynabeads and further digested into cell suspension.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: brain

value: adult mice


title: Brain single cell 1144

description: Brain single cell 1144


title: Brain single cell 1150

description: Brain single cell 1150


title: Brain single cell 1149

description: Brain single cell 1149


title: Brain single cell 1147

description: Brain single cell 1147


title: Brain single cell 1151

description: Brain single cell 1151


title: Brain single cell 1146

description: Brain single cell 1146


title: Brain single cell 1148

description: Brain single cell 1148


title: Brain single cell 1142

description: Brain single cell 1142


title: Brain single cell 1143

description: Brain single cell 1143


title: Brain single cell 1145

description: Brain single cell 1145


title: Brain single cell 1141

description: Brain single cell 1141


title: Brain single cell 1140

description: Brain single cell 1140


title: Brain single cell 1139

description: Brain single cell 1139


title: Brain single cell 1138

description: Brain single cell 1138


title: Brain single cell 1134

description: Brain single cell 1134


title: Brain single cell 1136

description: Brain single cell 1136


title: Brain single cell 1133

description: Brain single cell 1133


title: Brain single cell 1137

description: Brain single cell 1137


title: Brain single cell 1130

description: Brain single cell 1130


title: Brain single cell 1132

description: Brain single cell 1132


title: Brain single cell 1135

description: Brain single cell 1135


title: Brain single cell 1129

description: Brain single cell 1129


title: Brain single cell 1131

description: Brain single cell 1131


title: Arabidopsis thaliana col-0 mature leaf csRNA-seq r2

description:
csRNA-seq; nascent TSS mapping in A.thaliana cells; Experiment SD179
A.thaliana-leaf-10.tss.txt


title: Brain single cell 1127

description: Brain single cell 1127


title: Brain single cell 1124

description: Brain single cell 1124


title: Brain single cell 1128

description: Brain single cell 1128


title: Brain single cell 1125

description: Brain single cell 1125


title: Brain single cell 1123

description: Brain single cell 1123


title: Brain single cell 1122

description: Brain single cell 1122


title: Brain single cell 1119

description: Brain single cell 1119


title: Brain single cell 1117

description: Brain single cell 1117


title: Brain single cell 1121

description: Brain single cell 1121


title: Brain single cell 1114

description: Brain single cell 1114


title: Brain single cell 1115

description: Brain single cell 1115


title: Brain single cell 1110

description: Brain single cell 1110


title: Brain single cell 1112

description: Brain single cell 1112


title: Brain single cell 1111

description: Brain single cell 1111


title: Brain single cell 1113

description: Brain single cell 1113


title: Brain single cell 1116

description: Brain single cell 1116


title: Brain single cell 1126

description: Brain single cell 1126


title: Brain single cell 1109

description: Brain single cell 1109


title: Brain single cell 1108

description: Brain single cell 1108


title: Brain single cell 1118

description: Brain single cell 1118


title: Brain single cell 1105

description: Brain single cell 1105


title: Brain single cell 1106

description: Brain single cell 1106


title: Brain single cell 1101

description: Brain single cell 1101


title: Brain single cell 1104

description: Brain single cell 1104


title: Brain single cell 1102

description: Brain single cell 1102


title: Brain single cell 1120

description: Brain single cell 1120


title: Brain single cell 1098

description: Brain single cell 1098


title: Brain single cell 1097

description: Brain single cell 1097


title: Brain single cell 1099

description: Brain single cell 1099


title: Brain single cell 1100

description: Brain single cell 1100


title: Brain single cell 1096

description: Brain single cell 1096


title: Brain single cell 1094

description: Brain single cell 1094


title: Brain single cell 1095

description: Brain single cell 1095


title: Brain single cell 1092

description: Brain single cell 1092


title: Brain single cell 1093

description: Brain single cell 1093


title: Brain single cell 1091

description: Brain single cell 1091


title: Brain single cell 1090

description: Brain single cell 1090


title: Brain single cell 1089

description: Brain single cell 1089


title: Brain single cell 1086

description: Brain single cell 1086


title: Brain single cell 1085

description: Brain single cell 1085


title: Brain single cell 1083

description: Brain single cell 1083


title: Brain single cell 1088

description: Brain single cell 1088


title: Brain single cell 1087

description: Brain single cell 1087


title: Brain single cell 1084

description: Brain single cell 1084


title: Brain single cell 1082

description: Brain single cell 1082


title: Brain single cell 1081

description: Brain single cell 1081


title: Brain single cell 1103

description: Brain single cell 1103


title: Brain single cell 1078

description: Brain single cell 1078


title: Brain single cell 1079

description: Brain single cell 1079


title: Brain single cell 1080

description: Brain single cell 1080


title: Brain single cell 1077

description: Brain single cell 1077


title: Brain single cell 1107

description: Brain single cell 1107


title: Brain single cell 1075

description: Brain single cell 1075


title: Brain single cell 1073

description: Brain single cell 1073


title: Brain single cell 1076

description: Brain single cell 1076


title: Brain single cell 1074

description: Brain single cell 1074


title: Brain single cell 1071

description: Brain single cell 1071


title: Brain single cell 1072

description: Brain single cell 1072


title: Brain single cell 1070

description: Brain single cell 1070


title: Brain single cell 1066

description: Brain single cell 1066


title: Brain single cell 1069

description: Brain single cell 1069


title: Brain single cell 1063

description: Brain single cell 1063


title: Brain single cell 1068

description: Brain single cell 1068


title: Brain single cell 1064

description: Brain single cell 1064


title: Brain single cell 1062

description: Brain single cell 1062


title: Brain single cell 1061

description: Brain single cell 1061


title: Brain single cell 1060

description: Brain single cell 1060


title: Brain single cell 1059

description: Brain single cell 1059


title: Brain single cell 1057

description: Brain single cell 1057


title: Brain single cell 1056

description: Brain single cell 1056


title: Brain single cell 1055

description: Brain single cell 1055


title: Brain single cell 1058

description: Brain single cell 1058


title: Brain single cell 1054

description: Brain single cell 1054


title: Brain single cell 1052

description: Brain single cell 1052


title: Brain single cell 1067

description: Brain single cell 1067


title: Brain single cell 1044

description: Brain single cell 1044


title: Brain single cell 1048

description: Brain single cell 1048


title: Brain single cell 1053

description: Brain single cell 1053


title: Brain single cell 1047

description: Brain single cell 1047


title: Brain single cell 1040

description: Brain single cell 1040


title: Brain single cell 1042

description: Brain single cell 1042


title: Brain single cell 1051

description: Brain single cell 1051


title: Brain single cell 1049

description: Brain single cell 1049


title: Brain single cell 1065

description: Brain single cell 1065


title: Brain single cell 1045

description: Brain single cell 1045


title: Brain single cell 1043

description: Brain single cell 1043


title: Brain single cell 1039

description: Brain single cell 1039


title: Brain single cell 1050

description: Brain single cell 1050


title: Brain single cell 1038

description: Brain single cell 1038


title: Brain single cell 1037

description: Brain single cell 1037


title: Brain single cell 1041

description: Brain single cell 1041


title: Brain single cell 1036

description: Brain single cell 1036


title: Brain single cell 1035

description: Brain single cell 1035


title: Brain single cell 1034

description: Brain single cell 1034


title: Brain single cell 1033

description: Brain single cell 1033


title: Brain single cell 1031

description: Brain single cell 1031


title: Brain single cell 1032

description: Brain single cell 1032


title: Brain single cell 1046

description: Brain single cell 1046


title: Brain single cell 1030

description: Brain single cell 1030


title: Brain single cell 1029

description: Brain single cell 1029


title: Brain single cell 1027

description: Brain single cell 1027


title: Brain single cell 1028

description: Brain single cell 1028


title: Brain single cell 1024

description: Brain single cell 1024


title: Brain single cell 1026

description: Brain single cell 1026


title: Brain single cell 1022

description: Brain single cell 1022


title: Brain single cell 1023

description: Brain single cell 1023


title: Brain single cell 1025

description: Brain single cell 1025


title: Brain single cell 1016

description: Brain single cell 1016


title: Brain single cell 1014

description: Brain single cell 1014


title: Brain single cell 1020

description: Brain single cell 1020


title: Brain single cell 1017

description: Brain single cell 1017


title: Brain single cell 1013

description: Brain single cell 1013


title: Brain single cell 1009

description: Brain single cell 1009


title: Brain single cell 1015

description: Brain single cell 1015


title: Brain single cell 1008

description: Brain single cell 1008


title: Brain single cell 1012

description: Brain single cell 1012


title: Brain single cell 1018

description: Brain single cell 1018


title: Brain single cell 1006

description: Brain single cell 1006


title: Brain single cell 1019

description: Brain single cell 1019


title: Brain single cell 1010

description: Brain single cell 1010


title: Brain single cell 1011

description: Brain single cell 1011


title: Brain single cell 1005

description: Brain single cell 1005


title: Brain single cell 1001

description: Brain single cell 1001


title: Brain single cell 1004

description: Brain single cell 1004


title: Brain single cell 1002

description: Brain single cell 1002


title: Brain single cell 999

description: Brain single cell 999


title: Brain single cell 1021

description: Brain single cell 1021


title: Brain single cell 997

description: Brain single cell 997


title: Brain single cell 995

description: Brain single cell 995


title: Brain single cell 1000

description: Brain single cell 1000


title: Brain single cell 998

description: Brain single cell 998


title: Brain single cell 994

description: Brain single cell 994


title: Brain single cell 1007

description: Brain single cell 1007


title: Brain single cell 992

description: Brain single cell 992


title: Brain single cell 993

description: Brain single cell 993


title: Brain single cell 996

description: Brain single cell 996


title: Brain single cell 989

description: Brain single cell 989


title: Brain single cell 991

description: Brain single cell 991


title: Brain single cell 982

description: Brain single cell 982


title: Brain single cell 987

description: Brain single cell 987


title: Brain single cell 988

description: Brain single cell 988


title: Brain single cell 980

description: Brain single cell 980


title: Brain single cell 990

description: Brain single cell 990


title: Brain single cell 1003

description: Brain single cell 1003


title: Brain single cell 985

description: Brain single cell 985


title: Brain single cell 976

description: Brain single cell 976


title: Brain single cell 970

description: Brain single cell 970


title: Brain single cell 974

description: Brain single cell 974


title: Brain single cell 984

description: Brain single cell 984


title: Brain single cell 975

description: Brain single cell 975


title: Brain single cell 972

description: Brain single cell 972


title: Brain single cell 971

description: Brain single cell 971


title: Brain single cell 973

description: Brain single cell 973


title: Brain single cell 981

description: Brain single cell 981


title: Brain single cell 966

description: Brain single cell 966


title: Brain single cell 964

description: Brain single cell 964


title: Brain single cell 965

description: Brain single cell 965


title: Brain single cell 963

description: Brain single cell 963


title: Brain single cell 986

description: Brain single cell 986


title: Brain single cell 983

description: Brain single cell 983


title: Brain single cell 979

description: Brain single cell 979


title: Brain single cell 978

description: Brain single cell 978


title: Brain single cell 968

description: Brain single cell 968


title: Brain single cell 977

description: Brain single cell 977


title: Brain single cell 960

description: Brain single cell 960


title: Brain single cell 962

description: Brain single cell 962


title: Brain single cell 969

description: Brain single cell 969


title: Brain single cell 958

description: Brain single cell 958


title: Brain single cell 959

description: Brain single cell 959


title: Brain single cell 955

description: Brain single cell 955


title: Brain single cell 967

description: Brain single cell 967


title: Brain single cell 949

description: Brain single cell 949


title: Brain single cell 952

description: Brain single cell 952


title: Brain single cell 951

description: Brain single cell 951


title: Brain single cell 956

description: Brain single cell 956


title: Brain single cell 945

description: Brain single cell 945


title: Brain single cell 954

description: Brain single cell 954


title: Brain single cell 953

description: Brain single cell 953


title: Brain single cell 944

description: Brain single cell 944


title: Brain single cell 943

description: Brain single cell 943


title: Brain single cell 950

description: Brain single cell 950


title: Brain single cell 948

description: Brain single cell 948


title: Brain single cell 942

description: Brain single cell 942


title: Brain single cell 940

description: Brain single cell 940


title: Brain single cell 941

description: Brain single cell 941


title: Brain single cell 939

description: Brain single cell 939


title: Brain single cell 938

description: Brain single cell 938


title: Brain single cell 937

description: Brain single cell 937


title: Brain single cell 936

description: Brain single cell 936


title: Brain single cell 961

description: Brain single cell 961


title: Brain single cell 935

description: Brain single cell 935


title: Brain single cell 957

description: Brain single cell 957


title: Brain single cell 946

description: Brain single cell 946


title: Brain single cell 947

description: Brain single cell 947


title: Brain single cell 931

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