title: RNA-seq 20220730_mesc_ssea1_NANOG_be_ssea1_neg_rep1

description:
Library name: 20220730_mesc_ssea1_NANOG_be_ssea1_neg_rep1
RNA-seq sample NANOG_be_ssea1_neg_rep1


title: experiment:poolsize2_920 condition:1_1 sample[6]

status: Public on Feb 26 2026

type: SRA

city: Martinsried

first: Wolfgang

last: Enard

state: Bavaria

address: Grossshaderner Str.2, Anthropology Human Genomics, AG Enard

department: Anthropology and human genomics

country: Germany

institute: LMU Munich

description: Library name: poolsize2_920_1_1_sample6

library_source: transcriptomic

data_processing:
Quality assessment of the fastq data files was conducted using fastqc (v 0.11.5) [2], followed by polyA trimming using cutadapt (v 4.1) [3]. Subsequent read filtering, mapping, and counting were performed using the zUMIs pipeline (v 2.9.7) [4], with reads mapped to the mouse genome (mm10). Fastq files were sample-demultiplexed using deML [5].
2 Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
3 Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), 10-12.
4 Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2018). zUMIs- A fast and flexible pipeline to process RNA sequencing data with UMIs. GigaScience, 7(6), giy059.
5 Gabriel Renaud, Udo Stenzel, Tomislav Maricic, Victor Wiebe, Janet Kelso (2015) deML: robust demultiplexing of Illumina sequences using a likelihood-based approach, Bioinformatics, Volume 31, Issue 5, March 2015, Pages 770–772, https://doi.org/10.1093/bioinformatics/btu719
Assembly: GRCm39
Supplementary files format and content: processed data files contain the Barcode (BC) of each sample with the associated counts (N) per feature (type), e.g. Intergenic, Intron, Exon, Ambiguity and Unmapped.

molecule: polyA RNA

organism: Mus musculus

source_name: brain

extract_protocol:
prime-seq - tissue lysis and homogenization in RLT+ buffer + 1 % B-Mercaptoethanol
prime-seq, the prime-seq original protocol  [1] , the original protocol with adaptions and the new, improved protocol  version (Pförtner et al, this study)
1 Janjic, A., Wange, L.E., Bagnoli, J.W. et al. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 23, 88 (2022). https://doi.org/10.1186/s13059-022-02660-8

tag: tissue

value: brain


title: RNA-seq 20220730_mesc_ssea1_NANOGSE_be_ssea1_neg_rep1

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

country: China

institute: Tsinghua University

description:
Library name: 20220730_mesc_ssea1_NANOGSE_be_ssea1_neg_rep1
RNA-seq sample NANOGSE_be_ssea1_neg_rep1

data_processing:
RNA-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to the reference genome using STAR (version 2.5.3a) with parameters "--twopassMode Basic --outSAMstrandField introMotif --quantMode TranscriptomeSAM".
The STAR index was constructed using the Gencode annotation gtf file (version 32 for human or version m23 for mouse) and its corresponding genome reference (hg38 for human and mm10 for mouse).
Post alignment, RSEM (version 1.3.0) was used to extract the final read count from the aligned bam file, with parameters "--no-bam-output --paired-end".
Assembly: mm10/hg38
Supplementary files format and content: raw count matrix (RSEM)
Supplementary files format and content: tpm matrix (RSEM)

source_name: mESC

extract_protocol:
Dynabeads M-280 sheep anti-Rabbit IgG (Invitrogen, 11201D) were diluted 1:10 in 1× PBS (Invitrogen, AM9624), magnetically washed, and incubated with Nesprin1 antibody (abcam, ab192234) at room temperature for 30 minutes. Antibody-coupled beads were washed and resuspended in cell lysis buffer containing 10 mM HEPES (Gibco, 15630106), 2.5 mM MgCl2 (Invitrogen, AM9530G), 10 mM KCl (Sigma, P9333), 1 mM DTT (ThermoFisher, 707265ML), 0.5% Triton X-100 (Sigma, 93443), and 2 U recombinant RNase inhibitor (Takara, 2313A). A population of 500 GFP-positive cells per sample was sorted into 10 µL lysis buffer in 96-well plates, centrifuged at 700 g for 1 minute, and incubated at 4°C with shaking (300 rpm) for 30 minutes. After magnetic separation, the supernatant was transferred to a new plate for RNA-seq workflow, while nuclei were retained for ATAC-side tagmentation workflow in AR-seq. RNA in the supernatant was purified using 2.2× VAHTS RNA Clean Beads (Vazyme, N412-03) and reverse-transcribed using SMART-seq2.
RNA-seq library construction was performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501), following the manufacturer's manual. Libraries were generated from SMART-seq2-derived cDNA and sequenced in paired-end mode on short-read sequencing platforms.

tag: cell line

value: mESC

tag: batch


title: experiment:poolsize2_920 condition:1_1 sample[3]

description: Library name: poolsize2_920_1_1_sample3


title: ATAC-seq 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep2

description:
Library name: 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep2
ATAC-seq sample pft-a_cas9_only_vector_rep2

library_source: genomic

data_processing:
ATAC-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to hg38 (human) or mm10 (mouse) using bowtie2 (version 2.4.4) with parameters -X2000 --mm -t -q -N1 -L 25 --no-mixed --no-discordant.
Aligned reads were filtered using samtools (version 1.13) to exclude unmapped reads, unmapped mates, non-primary alignments, vendor/quality-fail reads, and duplicates (SAM flag 1804).
Standard samtools sort and fixmate operations were applied. PCR duplicates were removed using picard MarkDuplicates (version 2.20.4), followed by samtools view filtering (-F1804 -f2). ENCODE blacklist regions were removed in the final alignment set.
For uploaded processed bigWig files, bamCoverage was used with -p 8 --normalizeUsing RPKM --binSize 100.
Assembly: mm10/hg38
Supplementary files format and content: ATAC-seq coverage bigWig

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Cells were collected and washed with ice-cold PBS. Cell pellets were resuspended in ATAC-seq RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 10 minutes. ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL-630 or digitonin) was then added for washing. Nuclei were pelleted in a pre-chilled centrifuge. Nuclei were incubated with Tn5 transposase and tagmentation buffer at 37°C for 30 minutes. Stop buffer and Proteinase K were added, and samples were incubated at 55°C for 30 minutes to terminate tagmentation and remove proteins.
PCR was performed to amplify the ATAC library for 5 cycles using KAPA HiFi PCR kit. To determine additional amplification cycles for each sample, qPCR was performed, and the additional cycle number was determined as the cycle reaching one-third of maximal abundance in the qPCR amplification curve. All samples were then amplified for another N+3 cycles, followed by final extension. Libraries were purified with DNA clean beads and sequenced as paired-end libraries on Illumina platforms.


title: ATAC-seq 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep1

description:
Library name: 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep1
ATAC-seq sample pft-a_cas9_only_vector_rep1


title: experiment:poolsize2_920 condition:1_1 sample[4]

description: Library name: poolsize2_920_1_1_sample4


title: ATAC-seq 20250831_hek293t_cas12a_EMX1-1_rep1

description:
Library name: 20250831_hek293t_cas12a_EMX1-1_rep1
ATAC-seq sample EMX1-1_rep1


title: ATAC-seq 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep3

description:
Library name: 20210630_hek293t_cas9_p53_pft-a_cas9_only_vector_rep3
ATAC-seq sample pft-a_cas9_only_vector_rep3


title: RNA-seq 20250731_hek293t_rnp_ZSWIM3_rep1

description:
Library name: 20250731_hek293t_rnp_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: RNA-seq 20220730_mesc_ssea1_NANOGSE_be_ssea1_neg_rep3

description:
Library name: 20220730_mesc_ssea1_NANOGSE_be_ssea1_neg_rep3
RNA-seq sample NANOGSE_be_ssea1_neg_rep3


title: RNA-seq 20220730_mesc_ssea1_EMX1_be_ssea1_pos_rep3

description:
Library name: 20220730_mesc_ssea1_EMX1_be_ssea1_pos_rep3
RNA-seq sample EMX1_be_ssea1_pos_rep3


title: experiment:poolsize2_920 condition:1_1 sample[2]

description: Library name: poolsize2_920_1_1_sample2


title: RNA-seq 20250731_hek293t_rnp_EMX1_rep2

description:
Library name: 20250731_hek293t_rnp_EMX1_rep2
RNA-seq sample EMX1_rep2


title: RNA-seq 20220730_mesc_ssea1_NANOGSE_be_ssea1_neg_rep2

description:
Library name: 20220730_mesc_ssea1_NANOGSE_be_ssea1_neg_rep2
RNA-seq sample NANOGSE_be_ssea1_neg_rep2


title: ATAC-seq 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep3
ATAC-seq sample ZSWIM3_pft-a_editing_rep3


title: RNA-seq 20250731_hek293t_rnp_EMX1_rep1

description:
Library name: 20250731_hek293t_rnp_EMX1_rep1
RNA-seq sample EMX1_rep1


title: experiment:poolsize2_920 condition:1_1 sample[16]

description: Library name: poolsize2_920_1_1_sample16


title: RNA-seq 20250731_hek293t_cas12a_ZSWIM3-2_rep2

description:
Library name: 20250731_hek293t_cas12a_ZSWIM3-2_rep2
RNA-seq sample ZSWIM3-2_rep2


title: experiment:poolsize2_920 condition:1_1 sample[15]

description: Library name: poolsize2_920_1_1_sample15


title: RNA-seq 20220730_mesc_ssea1_EMX1_be_ssea1_pos_rep2

description:
Library name: 20220730_mesc_ssea1_EMX1_be_ssea1_pos_rep2
RNA-seq sample EMX1_be_ssea1_pos_rep2


title: RNA-seq 20220730_mesc_ssea1_EMX1_be_ssea1_pos_rep1

description:
Library name: 20220730_mesc_ssea1_EMX1_be_ssea1_pos_rep1
RNA-seq sample EMX1_be_ssea1_pos_rep1


title: RNA-seq 20250731_hek293t_cas12a_ZSWIM3-2_rep1

description:
Library name: 20250731_hek293t_cas12a_ZSWIM3-2_rep1
RNA-seq sample ZSWIM3-2_rep1


title: ATAC-seq 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep2
ATAC-seq sample ZSWIM3_pft-a_editing_rep2


title: experiment:poolsize2_920 condition:1_1 sample[13]

description: Library name: poolsize2_920_1_1_sample13


title: ATAC-seq 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_pft-a_editing_rep1
ATAC-seq sample ZSWIM3_pft-a_editing_rep1


title: RNA-seq 20220730_mesc_ssea1_EMX1_be_ssea1_neg_rep3

description:
Library name: 20220730_mesc_ssea1_EMX1_be_ssea1_neg_rep3
RNA-seq sample EMX1_be_ssea1_neg_rep3


title: RNA-seq 20250731_hek293t_cas12a_ZSWIM3-1_rep2

description:
Library name: 20250731_hek293t_cas12a_ZSWIM3-1_rep2
RNA-seq sample ZSWIM3-1_rep2


title: experiment:poolsize2_920 condition:1_1 sample[14]

description: Library name: poolsize2_920_1_1_sample14


title: RNA-seq 20250731_hek293t_cas12a_ZSWIM3-1_rep1

description:
Library name: 20250731_hek293t_cas12a_ZSWIM3-1_rep1
RNA-seq sample ZSWIM3-1_rep1


title: RNA-seq 20220730_mesc_ssea1_EMX1_be_ssea1_neg_rep1

description:
Library name: 20220730_mesc_ssea1_EMX1_be_ssea1_neg_rep1
RNA-seq sample EMX1_be_ssea1_neg_rep1


title: ATAC-seq 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep1
ATAC-seq sample ZSWIM3_dmso_editing_rep1


title: RNA-seq 20250731_hek293t_cas12a_EMX1-2_rep1

description:
Library name: 20250731_hek293t_cas12a_EMX1-2_rep1
RNA-seq sample EMX1-2_rep1


title: ATAC-seq 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep3
ATAC-seq sample ZSWIM3_dmso_editing_rep3


title: experiment:poolsize2_920 condition:1_1 sample[11]

description: Library name: poolsize2_920_1_1_sample11


title: RNA-seq 20250731_hek293t_cas12a_EMX1-2_rep2

description:
Library name: 20250731_hek293t_cas12a_EMX1-2_rep2
RNA-seq sample EMX1-2_rep2


title: experiment:poolsize2_920 condition:1_1 sample[12]

description: Library name: poolsize2_920_1_1_sample12


title: RNA-seq 20210727_mesc_se_ZFP42_rep3

description:
Library name: 20210727_mesc_se_ZFP42_rep3
RNA-seq sample ZFP42_rep3


title: ATAC-seq 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep3
ATAC-seq sample TYR_pft-a_editing_rep3


title: RNA-seq 20220730_mesc_ssea1_EMX1_be_ssea1_neg_rep2

description:
Library name: 20220730_mesc_ssea1_EMX1_be_ssea1_neg_rep2
RNA-seq sample EMX1_be_ssea1_neg_rep2


title: RNA-seq 20210727_mesc_se_ZFP42_rep2

description:
Library name: 20210727_mesc_se_ZFP42_rep2
RNA-seq sample ZFP42_rep2


title: RNA-seq 20250731_hek293t_cas12a_EMX1-1_rep1

description:
Library name: 20250731_hek293t_cas12a_EMX1-1_rep1
RNA-seq sample EMX1-1_rep1


title: RNA-seq 20250731_hek293t_cas12a_EMX1-1_rep2

description:
Library name: 20250731_hek293t_cas12a_EMX1-1_rep2
RNA-seq sample EMX1-1_rep2


title: ATAC-seq 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_ZSWIM3_dmso_editing_rep2
ATAC-seq sample ZSWIM3_dmso_editing_rep2


title: ATAC-seq 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep2
ATAC-seq sample TYR_pft-a_editing_rep2


title: experiment:poolsize2_920 condition:1_1 sample[10]

description: Library name: poolsize2_920_1_1_sample10


title: ATAC-seq 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_TYR_pft-a_editing_rep1
ATAC-seq sample TYR_pft-a_editing_rep1


title: ATAC-seq 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep3
ATAC-seq sample TYR_dmso_editing_rep3


title: experiment:poolsize2_80 condition:1_1 sample[7]

description: Library name: poolsize2_80_1_1_sample7


title: experiment:poolsize2_920 condition:1_1 sample[1]

description: Library name: poolsize2_920_1_1_sample1


title: RNA-seq 20210727_mesc_se_SOX2_rep2

description:
Library name: 20210727_mesc_se_SOX2_rep2
RNA-seq sample SOX2_rep2


title: RNA-seq 20210727_mesc_se_SOX2_rep1

description:
Library name: 20210727_mesc_se_SOX2_rep1
RNA-seq sample SOX2_rep1


title: SP_array2

city: Luzhou

first: Fengtian

last: Li

address: Zhongshan Road

institute: Southwest Medical University

description: Library name: SP_PT6+PT14

data_processing:
The FASTQ files were processed and aligned to human reference genome using MobiVision software (version 3.2) with unique molecular identifier (UMI) counts  ummarized for each barcode.  The sequencing and bioinformatics analysis were provided by OE Biotech Co., Ltd. (Shanghai, China).
Assembly: GRCh38
Supplementary files format and content: Seurat RDS data including barcode, count, cell type and sample ID for each sample from the Single cell RNA-seq. Rdata file including count, sample ID, image, RCTD resluts for each sample from Spatial transcriptomics.
Library strategy: Spatial Transcriptomics

molecule: total RNA

source_name: OSCC tumor

extract_protocol:
The experimental procedure of the MobiNova high-throughput single-cell sequencing solution consists of three steps. The first step involves dissociating the tissue sample using the MobiSoultionTM Tissue Dissociation Kit to prepare a single-cell suspension. The second step utilizes the MobiNova-100 library construction system in combination with the MobiCube single-cell nucleic acid capture.
Using the MobiNova-100 library construction system, combined with the MobiCube single-cell nucleic acid capture and library construction kit, single-cell nucleic acid capture and sequencing library construction are completed.

value: OSCC tumor


title: RNA-seq 20210727_mesc_se_SALL4_rep3

description:
Library name: 20210727_mesc_se_SALL4_rep3
RNA-seq sample SALL4_rep3


title: OSCC_16

description: Library name: PT16

library_source: transcriptomic single cell

data_processing:
The FASTQ files were processed and aligned to human reference genome using MobiVision software (version 3.2) with unique molecular identifier (UMI) counts  ummarized for each barcode.  The sequencing and bioinformatics analysis were provided by OE Biotech Co., Ltd. (Shanghai, China).
Assembly: GRCh38
Supplementary files format and content: Seurat RDS data including barcode, count, cell type and sample ID for each sample from the Single cell RNA-seq. Rdata file including count, sample ID, image, RCTD resluts for each sample from Spatial transcriptomics.


title: experiment:poolsize2_80 condition:1_1 sample[4]

description: Library name: poolsize2_80_1_1_sample4


title: RNA-seq 20210727_mesc_se_ZFP42_rep1

description:
Library name: 20210727_mesc_se_ZFP42_rep1
RNA-seq sample ZFP42_rep1


title: RNA-seq 20210727_mesc_se_SOX2_rep3

description:
Library name: 20210727_mesc_se_SOX2_rep3
RNA-seq sample SOX2_rep3


title: experiment:poolsize2_80 condition:1_1 sample[8]

description: Library name: poolsize2_80_1_1_sample8


title: SP_array3

description: Library name: SP_PT11+PT13


title: ATAC-seq 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep2
ATAC-seq sample TYR_dmso_editing_rep2


title: ATAC-seq 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep3
ATAC-seq sample EMX1_pft-a_editing_rep3


title: ATAC-seq 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep2
ATAC-seq sample EMX1_pft-a_editing_rep2


title: ATAC-seq 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_TYR_dmso_editing_rep1
ATAC-seq sample TYR_dmso_editing_rep1


title: RNA-seq 20210727_mesc_se_SALL4_rep2

description:
Library name: 20210727_mesc_se_SALL4_rep2
RNA-seq sample SALL4_rep2


title: experiment:poolsize2_80 condition:1_1 sample[3]

description: Library name: poolsize2_80_1_1_sample3


title: experiment:poolsize2_80 condition:1_1 sample[6]

description: Library name: poolsize2_80_1_1_sample6


title: ATAC-seq 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_pft-a_editing_rep1
ATAC-seq sample EMX1_pft-a_editing_rep1


title: experiment:poolsize2_80 condition:1_1 sample[2]

description: Library name: poolsize2_80_1_1_sample2


title: experiment:poolsize2_80 condition:1_1 sample[5]

description: Library name: poolsize2_80_1_1_sample5


title: SP_array1

description: Library name: SP_PT2+PT5


title: OSCC_13

description: Library name: PT13


title: RNA-seq 20210727_mesc_se_SALL4_rep1

description:
Library name: 20210727_mesc_se_SALL4_rep1
RNA-seq sample SALL4_rep1


title: OSCC_14

description: Library name: PT14


title: OSCC_15

description: Library name: PT15


title: RNA-seq 20210727_mesc_se_NANOGSE_rep2

description:
Library name: 20210727_mesc_se_NANOGSE_rep2
RNA-seq sample NANOGSE_rep2


title: RNA-seq 20210727_mesc_se_NANOGSE_rep1

description:
Library name: 20210727_mesc_se_NANOGSE_rep1
RNA-seq sample NANOGSE_rep1


title: experiment:poolsize2_80 condition:1_1 sample[1]

description: Library name: poolsize2_80_1_1_sample1


title: ATAC-seq 20210218_hek293t_be_ZSWIM3_rep2

description:
Library name: 20210218_hek293t_be_ZSWIM3_rep2
ATAC-seq sample ZSWIM3_rep2


title: ATAC-seq 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep3

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep3
ATAC-seq sample EMX1_dmso_editing_rep3


title: OSCC_6

description: Library name: PT6


title: experiment:alt_Liver condition:old sample[7]

description: Library name: alt_Liver_old_sample7

source_name: Liver

value: Liver


title: experiment:alt_Liver condition:old sample[8]

description: Library name: alt_Liver_old_sample8


title: ATAC-seq 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep2

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep2
ATAC-seq sample EMX1_dmso_editing_rep2


title: RNA-seq 20210727_mesc_se_POU5F1SE_rep3

description:
Library name: 20210727_mesc_se_POU5F1SE_rep3
RNA-seq sample POU5F1SE_rep3


title: OSCC_12

description: Library name: PT12


title: experiment:alt_Liver condition:old sample[5]

description: Library name: alt_Liver_old_sample5


title: ATAC-seq 20210218_hek293t_be_TYR_rep6

description:
Library name: 20210218_hek293t_be_TYR_rep6
ATAC-seq sample TYR_rep6


title: ATAC-seq 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep1

description:
Library name: 20210630_hek293t_cas9_p53_EMX1_dmso_editing_rep1
ATAC-seq sample EMX1_dmso_editing_rep1


title: OSCC_11

description: Library name: PT11


title: RNA-seq 20210727_mesc_se_POU5F1SE_rep2

description:
Library name: 20210727_mesc_se_POU5F1SE_rep2
RNA-seq sample POU5F1SE_rep2


title: OSCC_10

description: Library name: PT10


title: experiment:alt_Liver condition:old sample[4]

description: Library name: alt_Liver_old_sample4


title: RNA-seq 20210727_mesc_se_POU5F1SE_rep1

description:
Library name: 20210727_mesc_se_POU5F1SE_rep1
RNA-seq sample POU5F1SE_rep1


title: OSCC_7

description: Library name: PT7


title: RNA-seq 20210727_mesc_se_MYC_rep3

description:
Library name: 20210727_mesc_se_MYC_rep3
RNA-seq sample MYC_rep3


title: OSCC_9

description: Library name: PT9


title: ATAC-seq 20210218_hek293t_be_ZSWIM3_rep1

description:
Library name: 20210218_hek293t_be_ZSWIM3_rep1
ATAC-seq sample ZSWIM3_rep1


title: experiment:alt_Liver condition:old sample[3]

description: Library name: alt_Liver_old_sample3


title: RNA-seq 20210727_mesc_se_MYC_rep2

description:
Library name: 20210727_mesc_se_MYC_rep2
RNA-seq sample MYC_rep2


title: ATAC-seq 20210218_hek293t_be_ZSWIM3_rep3

description:
Library name: 20210218_hek293t_be_ZSWIM3_rep3
ATAC-seq sample ZSWIM3_rep3


title: experiment:alt_Liver condition:old sample[6]

description: Library name: alt_Liver_old_sample6


title: RNA-seq 20210727_mesc_se_NANOGSE_rep3

description:
Library name: 20210727_mesc_se_NANOGSE_rep3
RNA-seq sample NANOGSE_rep3


title: OSCC_8

description: Library name: PT8


title: ATAC-seq 20210218_hek293t_be_TYR_rep5

description:
Library name: 20210218_hek293t_be_TYR_rep5
ATAC-seq sample TYR_rep5


title: OSCC_5

description: Library name: PT5


title: ATAC-seq 20210218_hek293t_be_TYR_rep4

description:
Library name: 20210218_hek293t_be_TYR_rep4
ATAC-seq sample TYR_rep4


title: RNA-seq 20210727_mesc_se_MYC_rep1

description:
Library name: 20210727_mesc_se_MYC_rep1
RNA-seq sample MYC_rep1


title: OSCC_4

description: Library name: PT4


title: experiment:alt_Liver condition:old sample[1]

description: Library name: alt_Liver_old_sample1


title: RNA-seq 20210727_mesc_se_KLF4_rep2

description:
Library name: 20210727_mesc_se_KLF4_rep2
RNA-seq sample KLF4_rep2


title: experiment:alt_Liver condition:PTO sample[5]

description: Library name: alt_Liver_PTO_sample5


title: experiment:alt_Liver condition:PTO sample[7]

description: Library name: alt_Liver_PTO_sample7


title: ATAC-seq 20210218_hek293t_be_TYR_rep1

description:
Library name: 20210218_hek293t_be_TYR_rep1
ATAC-seq sample TYR_rep1


title: RNA-seq 20210727_mesc_se_KLF4_rep3

description:
Library name: 20210727_mesc_se_KLF4_rep3
RNA-seq sample KLF4_rep3


title: experiment:alt_Liver condition:old sample[2]

description: Library name: alt_Liver_old_sample2


title: RNA-seq 20210727_mesc_se_FGFR1_rep3

description:
Library name: 20210727_mesc_se_FGFR1_rep3
RNA-seq sample FGFR1_rep3


title: RNA-seq 20210727_mesc_se_FGFR1_rep2

description:
Library name: 20210727_mesc_se_FGFR1_rep2
RNA-seq sample FGFR1_rep2


title: experiment:alt_Liver condition:PTO sample[8]

description: Library name: alt_Liver_PTO_sample8


title: Overexpressed ncRNA-182  grown on GMM media, biol rep 2

city: Riverside

first: Jason

last: Stajich

state: CA

address: 900 University Ave

department: Microbiology and Plant Pathology

country: USA

institute: University of California-Riverside

description:
Library name: OE_182_GMM_2
Growth on GMM media, grown as stationary cultures for 48 hours.

data_processing:
Reads were quality controlled with fastp
Trimmed reads were aligned with STAR v2.7.11a to the A1163 genome
Alignments were transformed to BAM file and processed with featureCounts (subread package v 2.0.6) to obtain per gene read counts
DESeq analysis of the treatment to produced the normalized read counts
Assembly: Aspergillus_fumigatus_A1163 EuPathDB release 68 // GCA_000150145.1
Supplementary files format and content: tab delimited file with read counts per experiment by gene
Supplementary files format and content: tab delimited FPM normalized

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: Fungal strains were grown at 37°C for 48 hours  glucose minimal medium.

extract_protocol:
AGPC method, followed by silica membrane based column purification, DNAse treatment and magnetic beads purification
Illumina’s TruSeq-stranded-mRNA sample preparation protocol

treatment_protocol: GMM vs GMM + 0.15µg/ml voriconazole

value: mycelium

tag: strain

tag: genotype

value: pyrG-; gpdA(p)::afu-182:trpC(T)::pyrG

tag: treatment

value: GMM

tag: replicate


title: experiment:alt_Liver condition:PTO sample[4]

description: Library name: alt_Liver_PTO_sample4


title: OSCC_3

description: Library name: PT3


title: ATAC-seq 20210218_hek293t_be_EMX1_rep6

description:
Library name: 20210218_hek293t_be_EMX1_rep6
ATAC-seq sample EMX1_rep6


title: Overexpressed ncRNA-182  grown on GMM media, biol rep 3

description:
Library name: OE_182_GMM_3
Growth on GMM media, grown as stationary cultures for 48 hours.


title: ATAC-seq 20210218_hek293t_be_TYR_rep2

description:
Library name: 20210218_hek293t_be_TYR_rep2
ATAC-seq sample TYR_rep2


title: OSCC_1

description: Library name: PT1


title: OSCC_2

description: Library name: PT2


title: RNA-seq 20210727_mesc_se_KLF4_rep1

description:
Library name: 20210727_mesc_se_KLF4_rep1
RNA-seq sample KLF4_rep1


title: experiment:alt_Liver condition:PTO sample[3]

description: Library name: alt_Liver_PTO_sample3


title: RNA-seq 20210727_mesc_se_FGFR1_rep1

description:
Library name: 20210727_mesc_se_FGFR1_rep1
RNA-seq sample FGFR1_rep1


title: experiment:alt_Liver condition:PTO sample[6]

description: Library name: alt_Liver_PTO_sample6


title: ATAC-seq 20210218_hek293t_be_EMX1_rep5

description:
Library name: 20210218_hek293t_be_EMX1_rep5
ATAC-seq sample EMX1_rep5


title: Overexpressed ncRNA-182  grown on GMM media, biol rep 1

description:
Library name: OE_182_GMM_1
Growth on GMM media, grown as stationary cultures for 48 hours.


title: ATAC-seq 20210218_hek293t_be_EMX1_rep4

description:
Library name: 20210218_hek293t_be_EMX1_rep4
ATAC-seq sample EMX1_rep4


title: RNA-seq 20210531_mesc_cas9_ZSWIM3_rep3

description:
Library name: 20210531_mesc_cas9_ZSWIM3_rep3
RNA-seq sample ZSWIM3_rep3


title: experiment:alt_Liver condition:PTO sample[2]

description: Library name: alt_Liver_PTO_sample2


title: ATAC-seq 20210218_hek293t_be_EMX1_rep3

description:
Library name: 20210218_hek293t_be_EMX1_rep3
ATAC-seq sample EMX1_rep3


title: RNA-seq 20210531_mesc_cas9_ZSWIM3_rep2

description:
Library name: 20210531_mesc_cas9_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2


title: RNA-seq 20210531_mesc_cas9_ZSWIM3_rep1

description:
Library name: 20210531_mesc_cas9_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: Runx3-2_CUTnRUN

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

description:
Library name: Runx3-2
CUT&RUN data generated using an antibody recognizing RUNX3

data_processing:
Fastq files were aligned using bowtie2 (v.2.5.3) and converted to sorted bam files and BED files via Samtools (v.1.21).
EaSeq software (v.1.2) was used to call differential peaks-finding, IgG normalization, and trackplot visualization (Lerdrup and Hansen 2020).
Assembly: Mouse GRCm39 (mm39)
Supplementary files format and content: .bed files contain peaks aligned to the mouse mm39 genome
Library strategy: CUT&Run

source_name: testis

extract_protocol:
Single-cell suspensions of postnatal day 6 Nanos2-Cre and Rosa26-tdTomatofl/+ testes were prepared and germ cells isolated using fluorescence activated cell sorting by gating for tdTomato+ cells. Next, cells were lysed to isolate nuclei following the manufacturer recommendations and CUT&RUN was performed using the CUTANA™ ChIC/CUT&RUN Kit (EpiCypher 14-1048, v.3.5). Approximately 1 μg of antibody was used for each CUT&RUN reaction, including a rabbit anti- CBF (Ichiro Taniuchi), rabbit anti-RUNX1 (Abcam, ab23980), rabbit anti-RUNX3 (Cell Signaling Technology, 9647), H3K4me3 (EpiCypher; positive control), and IgG (EpiCypher; negative control).
Genomic libraries were generated using CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, v.1.3).

value: testis

tag: cell type

value: Germ Cell

value: WT

tag: age


title: ATAC-seq 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep3

description:
Library name: 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep3
ATAC-seq sample ZSWIM3_editing_72h_rep3


title: delta afu-182 grown on GMM media, biol rep 1

description:
Library name: GMM_182_1
Growth on GMM media, grown as stationary cultures for 48 hours.

value: pyrG-;delta afu-182::pyrG


title: delta afu-182 grown on GMM media, biol rep 3

description:
Library name: GMM_182_3
Growth on GMM media, grown as stationary cultures for 48 hours.


title: delta afu-182 grown on GMM media, biol rep 2

description:
Library name: GMM_182_2
Growth on GMM media, grown as stationary cultures for 48 hours.


title: RNA-seq 20210531_mesc_cas9_TCF19_rep2

description:
Library name: 20210531_mesc_cas9_TCF19_rep2
RNA-seq sample TCF19_rep2


title: Overexpressed ncRNA-182  grown on Azole media, biol rep 1

description:
Library name: OE_182_Azole_1
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.

value: Azole


title: ATAC-seq 20210218_hek293t_be_EMX1_rep1

description:
Library name: 20210218_hek293t_be_EMX1_rep1
ATAC-seq sample EMX1_rep1


title: ATAC-seq 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep3

description:
Library name: 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep3
ATAC-seq sample ZSWIM3_editing_48h_rep3


title: ATAC-seq 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep1

description:
Library name: 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep1
ATAC-seq sample ZSWIM3_editing_72h_rep1


title: RNA-seq 20210531_mesc_cas9_SOX2_rep3

description:
Library name: 20210531_mesc_cas9_SOX2_rep3
RNA-seq sample SOX2_rep3


title: Overexpressed ncRNA-182  grown on Azole media, biol rep 3

description:
Library name: OE_182_Azole_3
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: ATAC-seq 20210218_hek293t_be_EMX1_rep2

description:
Library name: 20210218_hek293t_be_EMX1_rep2
ATAC-seq sample EMX1_rep2


title: RNA-seq 20210531_mesc_cas9_TCF19_rep1

description:
Library name: 20210531_mesc_cas9_TCF19_rep1
RNA-seq sample TCF19_rep1


title: experiment:alt_Liver condition:PTO sample[1]

description: Library name: alt_Liver_PTO_sample1


title: Runx3-1_CUTnRUN

description:
Library name: Runx3-1
CUT&RUN data generated using an antibody recognizing RUNX3


title: NegCon_CUTnRUN

description:
Library name: NegCon
CUT&RUN data generated using an antibody recognizing IgG Control


title: ATAC-seq 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep2

description:
Library name: 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_72h_rep2
ATAC-seq sample ZSWIM3_editing_72h_rep2


title: Runx1-1_CUTnRUN

description:
Library name: Runx1-1
CUT&RUN data generated using an antibody recognizing RUNX1


title: Overexpressed ncRNA-182  grown on Azole media, biol rep 2

description:
Library name: OE_182_Azole_2
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: Complemented ncRNA-182 grown on GMM media, biol rep 3

description:
Library name: Comp_GMM_3
Growth on GMM media, grown as stationary cultures for 48 hours.


title: RNA-seq 20210531_mesc_cas9_TCF19_rep3

description:
Library name: 20210531_mesc_cas9_TCF19_rep3
RNA-seq sample TCF19_rep3


title: Runx1-2_CUTnRUN

description:
Library name: Runx1-2
CUT&RUN data generated using an antibody recognizing RUNX1


title: ATAC-seq 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep2

description:
Library name: 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep2
ATAC-seq sample ZSWIM3_editing_48h_rep2


title: RNA-seq 20210531_mesc_cas9_SOX2_rep2

description:
Library name: 20210531_mesc_cas9_SOX2_rep2
RNA-seq sample SOX2_rep2


title: Complemented ncRNA-182 grown on GMM media, biol rep 2

description:
Library name: Comp_GMM_2
Growth on GMM media, grown as stationary cultures for 48 hours.


title: Cbfb-2_CUTnRUN

description:
Library name: Cbfb-2
CUT&RUN data generated using an antibody recognizing CBFB


title: ATAC-seq 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep1

description:
Library name: 20201230_hek293t_cas9_timeseries_ZSWIM3_editing_48h_rep1
ATAC-seq sample ZSWIM3_editing_48h_rep1


title: Cbfb-1_CUTnRUN

description:
Library name: Cbfb-1
CUT&RUN data generated using an antibody recognizing CBFB


title: Sp FO5

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 30

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.3.3) and GRCm38 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Assembly: Mouse GRCm10
Supplementary files format and content: RSEM count file in text format

source_name: Spleen

extract_protocol:
Total RNA was subsequently isolated using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions. Quality control checks were conducted on all samples using an Agilent 2100 Bioanalyzer to ensure RNA integrity.
Library was prepared using Illumina HT DNA Sequencing - HiSeq2500 and sequenced at at the Weill Cornell Genomics Resources core facility.

value: Spleen

value: primary cell

value: Dendritic cells

value: wildtype

value: no treatment


title: Complemented ncRNA-182 grown on GMM media, biol rep 1

description:
Library name: Comp_GMM_1
Growth on GMM media, grown as stationary cultures for 48 hours.


title: ATAC-seq 20201230_hek293t_cas9_timeseries_TYR_editing_72h_rep3

description:
Library name: 20201230_hek293t_cas9_timeseries_TYR_editing_72h_rep3
ATAC-seq sample TYR_editing_72h_rep3


title: RNA-seq 20210531_mesc_cas9_SOX2_rep1

description:
Library name: 20210531_mesc_cas9_SOX2_rep1
RNA-seq sample SOX2_rep1


title: ATAC-seq 20210218_hek293t_be_TYR_rep3

description:
Library name: 20210218_hek293t_be_TYR_rep3
ATAC-seq sample TYR_rep3


title: RNA-seq 20210531_mesc_cas9_SLC2A3_rep3

description:
Library name: 20210531_mesc_cas9_SLC2A3_rep3
RNA-seq sample SLC2A3_rep3


title: RNA-seq 20210531_mesc_cas9_SLC2A3_rep2

description:
Library name: 20210531_mesc_cas9_SLC2A3_rep2
RNA-seq sample SLC2A3_rep2


title: BMDC CO4

description: Library name: 28

source_name: Bone marrow

value: Bone marrow


title: ATAC-seq 20201230_hek293t_cas9_timeseries_TYR_editing_72h_rep2

description:
Library name: 20201230_hek293t_cas9_timeseries_TYR_editing_72h_rep2
ATAC-seq sample TYR_editing_72h_rep2


title: Complemented ncRNA-182 grown on Azole media, biol rep 3

description:
Library name: Comp_Azole_3
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: Sp FO1

description: Library name: 29


title: Complemented ncRNA-182 grown on Azole media, biol rep 2

description:
Library name: Comp_Azole_2
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: Complemented ncRNA-182 grown on Azole media, biol rep 1

description:
Library name: Comp_Azole_1
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: WT CEA10 grown GMM media, biol rep 2

description:
Library name: CEA10_GMM_2
Growth on GMM media, grown as stationary cultures for 48 hours.


title: ATAC-seq 20201230_hek293t_cas9_timeseries_TYR_editing_72h_rep1

description:
Library name: 20201230_hek293t_cas9_timeseries_TYR_editing_72h_rep1
ATAC-seq sample TYR_editing_72h_rep1


title: ATAC-seq 20201230_hek293t_cas9_timeseries_TYR_editing_48h_rep3

description:
Library name: 20201230_hek293t_cas9_timeseries_TYR_editing_48h_rep3
ATAC-seq sample TYR_editing_48h_rep3


title: RNA-seq 20210531_mesc_cas9_NANOG_rep3

description:
Library name: 20210531_mesc_cas9_NANOG_rep3
RNA-seq sample NANOG_rep3

value: mESC


title: Sp FO4

description: Library name: 25


title: RNA-seq 20210531_mesc_cas9_SLC2A3_rep1

description:
Library name: 20210531_mesc_cas9_SLC2A3_rep1
RNA-seq sample SLC2A3_rep1


title: RNA-seq 20210531_mesc_cas9_NANOG_rep2

description:
Library name: 20210531_mesc_cas9_NANOG_rep2
RNA-seq sample NANOG_rep2


title: BMDC CO3

description: Library name: 26


title: WT CEA10 grown GMM media, biol rep 3

description:
Library name: CEA10_GMM_3
Growth on GMM media, grown as stationary cultures for 48 hours.


title: ATAC-seq 20201230_hek293t_cas9_timeseries_TYR_editing_48h_rep2

description:
Library name: 20201230_hek293t_cas9_timeseries_TYR_editing_48h_rep2
ATAC-seq sample TYR_editing_48h_rep2


title: RNA-seq 20210531_mesc_cas9_NANOG_rep1

description:
Library name: 20210531_mesc_cas9_NANOG_rep1
RNA-seq sample NANOG_rep1


title: Sp FO3

description: Library name: 24


title: WT CEA10 grown GMM media, biol rep 1

description:
Library name: CEA10_GMM_1
Growth on GMM media, grown as stationary cultures for 48 hours.


title: ATAC-seq 20201230_hek293t_cas9_timeseries_TYR_editing_48h_rep1

description:
Library name: 20201230_hek293t_cas9_timeseries_TYR_editing_48h_rep1
ATAC-seq sample TYR_editing_48h_rep1


title: RNA-seq 20210531_mesc_cas9_NANOGSE_rep3

description:
Library name: 20210531_mesc_cas9_NANOGSE_rep3
RNA-seq sample NANOGSE_rep3


title: RNA-seq 20210531_mesc_cas9_NANOGSE_rep2

description:
Library name: 20210531_mesc_cas9_NANOGSE_rep2
RNA-seq sample NANOGSE_rep2


title: ATAC-seq 20201230_hek293t_cas9_timeseries_EMX1_editing_72h_rep3

description:
Library name: 20201230_hek293t_cas9_timeseries_EMX1_editing_72h_rep3
ATAC-seq sample EMX1_editing_72h_rep3


title: WT CEA10 grown Azole media, biol rep 2

description:
Library name: CEA10_Azole_2
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: RNA-seq 20210531_mesc_cas9_NANOGSE_rep1

description:
Library name: 20210531_mesc_cas9_NANOGSE_rep1
RNA-seq sample NANOGSE_rep1


title: ATAC-seq 20201230_hek293t_cas9_timeseries_EMX1_editing_72h_rep2

description:
Library name: 20201230_hek293t_cas9_timeseries_EMX1_editing_72h_rep2
ATAC-seq sample EMX1_editing_72h_rep2


title: WT CEA10 grown Azole media, biol rep 3

description:
Library name: CEA10_Azole_3
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: ATAC-seq 20201230_hek293t_cas9_timeseries_EMX1_editing_72h_rep1

description:
Library name: 20201230_hek293t_cas9_timeseries_EMX1_editing_72h_rep1
ATAC-seq sample EMX1_editing_72h_rep1


title: RNA-seq 20210531_mesc_cas9_KLF4_rep3

description:
Library name: 20210531_mesc_cas9_KLF4_rep3
RNA-seq sample KLF4_rep3


title: Sp FO2

description: Library name: 23


title: Sp CO5

description: Library name: 22


title: RNA-seq 20210531_mesc_cas9_KLF4_rep2

description:
Library name: 20210531_mesc_cas9_KLF4_rep2
RNA-seq sample KLF4_rep2


title: ATAC-seq 20201230_hek293t_cas9_timeseries_EMX1_editing_48h_rep2

description:
Library name: 20201230_hek293t_cas9_timeseries_EMX1_editing_48h_rep2
ATAC-seq sample EMX1_editing_48h_rep2


title: ATAC-seq 20201230_hek293t_cas9_timeseries_EMX1_editing_48h_rep3

description:
Library name: 20201230_hek293t_cas9_timeseries_EMX1_editing_48h_rep3
ATAC-seq sample EMX1_editing_48h_rep3


title: WT CEA10 grown Azole media, biol rep 1

description:
Library name: CEA10_Azole_1
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: Sp CO4

description: Library name: 21


title: Sp CO1

description: Library name: 18


title: delta afu-182 grown on Azole media, biol rep 3

description:
Library name: Azole_182_3
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: RNA-seq 20210531_mesc_cas9_KLF4_rep1

description:
Library name: 20210531_mesc_cas9_KLF4_rep1
RNA-seq sample KLF4_rep1


title: ATAC-seq 20201212_hek293t_cas9_ZSWIM3-L_rep3

description:
Library name: 20201212_hek293t_cas9_ZSWIM3-L_rep3
ATAC-seq sample ZSWIM3-L_rep3


title: delta afu-182 grown on Azole media, biol rep 1

description:
Library name: Azole_182_1
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: ATAC-seq 20201230_hek293t_cas9_timeseries_EMX1_editing_48h_rep1

description:
Library name: 20201230_hek293t_cas9_timeseries_EMX1_editing_48h_rep1
ATAC-seq sample EMX1_editing_48h_rep1


title: Sp CO3

description: Library name: 20


title: Sp CO2

description: Library name: 19


title: delta afu-182 grown on Azole media, biol rep 2

description:
Library name: Azole_182_2
Growth in presence of 0.15µg/ml voriconazole, grown as stationary cultures for 48 hours.


title: RNA-seq 20210119_nih3t3_cas9_ZSWIM3-L_rep3

description:
Library name: 20210119_nih3t3_cas9_ZSWIM3-L_rep3
RNA-seq sample ZSWIM3-L_rep3


title: BMDC FO5

description: Library name: 17


title: Postpartum rep3 snMultiome(RNA-seq)

city: Bronx

first: Marija

last: Kundakovic

state: NY

address: 441 E. Fordham Road

department: Biological Sciences

institute: Fordham University

description: Library name: PP3_GE

data_processing:
Raw sequencing data were processed using Cell Ranger ARC v2.0.2 (10X Genomics) for demultiplexing, alignment to the mm10 reference genome (refdata-cellranger-arc-mm10-2020-A-2.0.0), barcode processing, and UMI counting to generate feature-barcode matrices. Quality filtered outputs including the feature-barcode matrix (filtered_feature_bc_matrix.h5) and ATAC fragment files (atac_fragments.tsv.gz with corresponding index) were generated for downstream multimodal analysis. These processed data files contain both gene expression counts and chromatin accessibility information for high-quality cells passing Cell Ranger ARC's default filtering criteria.
Assembly: mm10 (GRCm38) - Cell Ranger reference genome 2020-A release
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 file containing filtered feature-barcode matrices for both RNA and ATAC modalities following 10X Genomics Multiome specifications. Includes gene expression counts, ATAC peak accessibility counts, feature annotations (gene IDs, symbols, chromosome locations), and cell barcodes. atac_fragments.tsv.gz: Compressed tab-delimited file containing ATAC-seq fragment coordinates with columns for chromosome, start position, end position, cell barcode, and duplicate count. Represents all high-quality fragments used for peak calling and accessibility analysis. atac_fragments.tsv.gz.tbi: Tabix index file for the compressed fragments file, enabling rapid genomic region queries.

molecule: nuclear RNA

source_name: ventral hippocampus

growth_protocol: Mice were housed under standard laboratory conditions with a 12:12 h light-dark cycle, ad libitum access to food and water, at 21 °C and 30-70% humidity. Animals were allowed to habituate to the facility for at least two weeks prior to tissue collection.

extract_protocol:
Frozen ventral hippocampal tissue was homogenized and nuclei were isolated using a sucrose gradient-based protocol. Briefly, tissue was lysed in ice-cold buffer, layered over a sucrose cushion, and centrifuged to pellet nuclei. Isolated nuclei were washed, resuspended in nuclei buffer supplemented with RNase inhibitor, counted, and assessed for quality prior to library preparation.
Single-nucleus multiome libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit according to the manufacturer’s instructions. Isolated nuclei were loaded onto the Chromium controller to generate gel bead-in-emulsions (GEMs), enabling parallel barcoding of RNA and chromatin accessibility from individual nuclei. Separate gene expression and ATAC libraries were constructed and sequenced independently.

treatment_protocol: Mice were housed in same-sex groups of 3-5 animals per cage and assigned to experimental groups based on biological condition, including estrous cycle stage, sex, pregnancy, or postpartum status. No additional experimental treatments were applied prior to tissue collection.

value: ventral hippocampus

tag: Sex

value: Female

tag: condition

value: Postpartum


title: BMDC FO4

description: Library name: 15


title: ATAC-seq 20201212_hek293t_cas9_ZSWIM3-L_rep2

description:
Library name: 20201212_hek293t_cas9_ZSWIM3-L_rep2
ATAC-seq sample ZSWIM3-L_rep2


title: BMDC FO3

description: Library name: 13


title: Postpartum rep2 snMultiome(RNA-seq)

description: Library name: PP2_GE


title: ATAC-seq 20201212_hek293t_cas9_ZSWIM3-L_rep1

description:
Library name: 20201212_hek293t_cas9_ZSWIM3-L_rep1
ATAC-seq sample ZSWIM3-L_rep1


title: RNA-seq 20210119_nih3t3_cas9_ZSWIM3-L_rep1

description:
Library name: 20210119_nih3t3_cas9_ZSWIM3-L_rep1
RNA-seq sample ZSWIM3-L_rep1


title: Postpartum rep3 snMultiome(ATAC)

description: Library name: PP3_ATAC

library_source: genomic single cell


title: ATAC-seq 20201212_hek293t_cas9_ZIM3-L_rep3

description:
Library name: 20201212_hek293t_cas9_ZIM3-L_rep3
ATAC-seq sample ZIM3-L_rep3


title: RNA-seq 20210119_nih3t3_cas9_ZIM-L_rep2

description:
Library name: 20210119_nih3t3_cas9_ZIM-L_rep2
RNA-seq sample ZIM-L_rep2


title: Postpartum rep2 snMultiome(ATAC)

description: Library name: PP2_ATAC


title: ATAC-seq 20201212_hek293t_cas9_ZIM3-L_rep2

description:
Library name: 20201212_hek293t_cas9_ZIM3-L_rep2
ATAC-seq sample ZIM3-L_rep2


title: Postpartum rep1 snMultiome(RNA-seq)

description: Library name: PP1_GE


title: BMDC FO1

description: Library name: 9


title: RNA-seq 20210119_nih3t3_cas9_SMPDL3B-L_rep3

description:
Library name: 20210119_nih3t3_cas9_SMPDL3B-L_rep3
RNA-seq sample SMPDL3B-L_rep3


title: ATAC-seq 20201212_hek293t_cas9_SMPDL3B-L_rep3

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-L_rep3
ATAC-seq sample SMPDL3B-L_rep3


title: BMDC CO1

description: Library name: 2


title: ATAC-seq 20201212_hek293t_cas9_ZIM3-L_rep1

description:
Library name: 20201212_hek293t_cas9_ZIM3-L_rep1
ATAC-seq sample ZIM3-L_rep1


title: RNA-seq 20210119_nih3t3_cas9_ZIM-L_rep3

description:
Library name: 20210119_nih3t3_cas9_ZIM-L_rep3
RNA-seq sample ZIM-L_rep3


title: Postpartum rep1 snMultiome(ATAC)

description: Library name: PP1_ATAC


title: P28 retina, H3K18La (CUT&Tag), replicate 3

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Library name: P28_H3K18La_rep3

data_processing:
H3K18La CUT&Tag fastq files were processed using nf-core/cutandrun v3.1 to GRCm38 assembly. MACS peaks, filtered for qValue > 6, present in at least two biological replicates were used as consensus peaks for each experimental grouping.
Annotation of consensus peaks was performed in R with ChipSeeker v1.34.1 using Ensembl v102 annotation.
Peak quantitation was performed on merged consensus peaks using CSAW v1.32.0. Normalization was performed using windowCounts function in CSAW with 10,000 base windows. Differential peak analysis was performed using gene wise negative binomial generalized linear models with quasi-likelihood tests using edgeR v3.40.2.
Assembly: GRCm38/Ensembl v102
Supplementary files format and content: bigWig of alignment data
Supplementary files format and content: xlsx files of annotated concensus peaks for each timepoint
Supplementary files format and content: bed file of peaks used for quantitation in tsv file
Supplementary files format and content: tsv of peak quantitation and differential binding results
Library strategy: CUT&Tag

source_name: retina

extract_protocol:
CUT&Tag protocol was performed using CUT&Tag-IT® Assay Kit – Tissue (Active Motif) with slight modifications. In brief, retinas were dissected at P4, P10 and P28 and cells were dissociated in a 5 ml polypropylene round-bottom tube with a papain dissociation protocol adapted from previous study (Fadl, et al., Mol Vis. 2020) . After dissociation the cells were washed using 1X wash buffer provided in the kit at 200g for 5 minutes. CUT&Tag was performed using 500,000 cells per experiment following kit protocol. Antibodies against H3K18La (Rabbit, cat.no. PTM1406), and H3K27Ac (1:00, monoclonal Antibody (2D7B3) Invitrogen) were used at a concentration of 1:100 in 100 μl and pA-MNase conjugated to protein A (generous gift of Dr. Steven Henikoff, Howard Hughes Medical Institute, Washington, USA) used at a concentration of 700 ng/ml.
CUT&Tag-IT® Assay Kit – Tissue (Active Motif)

value: retina


title: RNA-seq 20210119_nih3t3_cas9_ZIM-L_rep1

description:
Library name: 20210119_nih3t3_cas9_ZIM-L_rep1
RNA-seq sample ZIM-L_rep1


title: ATAC-seq 20201212_hek293t_cas9_SMPDL3B-H_rep3

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-H_rep3
ATAC-seq sample SMPDL3B-H_rep3


title: RNA-seq 20210119_nih3t3_cas9_RPA2-H_rep3

description:
Library name: 20210119_nih3t3_cas9_RPA2-H_rep3
RNA-seq sample RPA2-H_rep3


title: RNA-seq 20210119_nih3t3_cas9_SMPDL3B-L_rep2

description:
Library name: 20210119_nih3t3_cas9_SMPDL3B-L_rep2
RNA-seq sample SMPDL3B-L_rep2


title: RNA-seq 20210119_nih3t3_cas9_SMPDL3B-L_rep1

description:
Library name: 20210119_nih3t3_cas9_SMPDL3B-L_rep1
RNA-seq sample SMPDL3B-L_rep1


title: BMDC FO2

description: Library name: 11


title: Pregnant rep3 snMultiome(RNA-seq)

description: Library name: G3_GE

value: Pregnant


title: Pregnant rep3 snMultiome(ATAC)

description: Library name: G3_ATAC


title: BMDC CO2

description: Library name: 4


title: BMDC CO5

description: Library name: 7


title: Pregnant rep2 snMultiome(RNA-seq)

description: Library name: G2_GE


title: ATAC-seq 20201212_hek293t_cas9_SMPDL3B-L_rep1

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-L_rep1
ATAC-seq sample SMPDL3B-L_rep1


title: P28 retina, H3K18La (CUT&Tag), replicate 1

description: Library name: P28_H3K18La_rep1


title: RNA-seq 20210119_nih3t3_cas9_RPA2-H_rep2

description:
Library name: 20210119_nih3t3_cas9_RPA2-H_rep2
RNA-seq sample RPA2-H_rep2


title: P28 retina, H3K18La (CUT&Tag), replicate 2

description: Library name: P28_H3K18La_rep2


title: Pregnant rep2 snMultiome(ATAC)

description: Library name: G2_ATAC


title: Pregnant rep1 snMultiome(RNA-seq)

description: Library name: G1_GE


title: ATAC-seq 20201212_hek293t_cas9_SMPDL3B-H_rep2

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-H_rep2
ATAC-seq sample SMPDL3B-H_rep2


title: RNA-seq 20210119_nih3t3_cas9_ZSWIM3-L_rep2

description:
Library name: 20210119_nih3t3_cas9_ZSWIM3-L_rep2
RNA-seq sample ZSWIM3-L_rep2


title: ATAC-seq 20201212_hek293t_cas9_SMPDL3B-H_rep1

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-H_rep1
ATAC-seq sample SMPDL3B-H_rep1


title: ATAC-seq 20201212_hek293t_cas9_SMPDL3B-L_rep2

description:
Library name: 20201212_hek293t_cas9_SMPDL3B-L_rep2
ATAC-seq sample SMPDL3B-L_rep2


title: RNA-seq 20210119_nih3t3_cas9_RPA2-H_rep1

description:
Library name: 20210119_nih3t3_cas9_RPA2-H_rep1
RNA-seq sample RPA2-H_rep1


title: RNA-seq 20210119_nih3t3_cas9_PI4K2A-L_rep3

description:
Library name: 20210119_nih3t3_cas9_PI4K2A-L_rep3
RNA-seq sample PI4K2A-L_rep3


title: Pregnant rep1 snMultiome(ATAC)

description: Library name: G1_ATAC


title: Proestrus rep3 snMultiome(RNA-seq)

description: Library name: P3_GE

value: Proestrus


title: RNA-seq 20210119_nih3t3_cas9_PI4K2A-L_rep2

description:
Library name: 20210119_nih3t3_cas9_PI4K2A-L_rep2
RNA-seq sample PI4K2A-L_rep2


title: ATAC-seq 20201212_hek293t_cas9_NDUFS3-L_rep2

description:
Library name: 20201212_hek293t_cas9_NDUFS3-L_rep2
ATAC-seq sample NDUFS3-L_rep2


title: P10 retina, H3K18La (CUT&Tag), replicate 1

description: Library name: P10_H3K18La_rep1


title: P4 retina, H3K18La (CUT&Tag), replicate 1

description: Library name: P4_H3K18La_rep1


title: ATAC-seq 20201212_hek293t_cas9_NDUFS3-L_rep3

description:
Library name: 20201212_hek293t_cas9_NDUFS3-L_rep3
ATAC-seq sample NDUFS3-L_rep3


title: RNA-seq 20210119_nih3t3_cas9_PI4K2A-L_rep1

description:
Library name: 20210119_nih3t3_cas9_PI4K2A-L_rep1
RNA-seq sample PI4K2A-L_rep1


title: Proestrus rep2 snMultiome(ATAC)

description: Library name: P2_ATAC


title: P10 retina, H3K18La (CUT&Tag), replicate 2

description: Library name: P10_H3K18La_rep2


title: ATAC-seq 20201212_hek293t_cas9_NDUFS3-L_rep1

description:
Library name: 20201212_hek293t_cas9_NDUFS3-L_rep1
ATAC-seq sample NDUFS3-L_rep1


title: 25mM glucose, H3K18Ac (CUT&Tag), replicate 1

description: Library name: H3K27Ac_25mM_rep1

data_processing:
H3K18La CUT&Tag fastq files were processed using nf-core/cutandrun v3.1 to GRCm38 assembly. MACS peaks, filtered for qValue > 6, present in at least two biological replicates were used as consensus peaks for each experimental grouping.
Annotation of consensus peaks was performed in R with ChipSeeker v1.34.1 using Ensembl v102 annotation.
Peak quantitation was performed on merged consensus peaks using CSAW v1.32.0. Normalization was performed using windowCounts function in CSAW with 10,000 base windows. Differential peak analysis was performed using gene wise negative binomial generalized linear models with quasi-likelihood tests using edgeR v3.40.2.
Assembly: GRCm38/Ensembl v102
Supplementary files format and content: bigWig of alignment data
Supplementary files format and content: xlsx files of annotated concensus peaks for each condition
Supplementary files format and content: tsv files of CUT&Tag peak quantitation and differential binding results
Library strategy: CUT&Tag

source_name: retina explant

extract_protocol:
CUT&Tag protocol was performed using CUT&Tag-IT® Assay Kit – Tissue (Active Motif) with slight modifications. In brief, explanted retinas were dissected and cells were dissociated in a 5 ml polypropylene round-bottom tube with a papain dissociation protocol adapted from previous study {Fadl, 2020 #16} . After dissociation the cells were washed using 1X wash buffer provided in the kit at 200g for 5 minutes. CUT&Tag was performed using 500,000 cells per experiment following kit protocol. Antibodies against H3K18La (Rabbit, cat.no. PTM1406), and H3K9me3 (Rabbit, cat.no. ab6002, Abcam, Cambridge, UK) were used at a concentration of 1:100 in 100 μl and pA-MNase conjugated to protein A (generous gift of Dr. Steven Henikoff, Howard Hughes Medical Institute, Washington, USA) used at a concentration of 700 ng/ml. Total RNA from explant retinae was extracted using TRIzol® (Invitrogen, Carlsbad, CA), treated with DNase and cleaned up using the MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems, Foster City, CA) following the manufacturer’s instructions. Libraries were constructed with SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA, Mountain View, CA) with 4 ng of RNA and 13 PCR cycles library amplification. Paired-end sequencing of 101 bases were obtained using the NextSeq 2000 (Illumina, San Diego, CA).
CUT&Tag-IT® Assay Kit – Tissue (Active Motif)

treatment_protocol: Wild-type, P28 C57BL/6J mice used for retinal explant cultures were euthanized by CO2 asphyxiation and freshly dissected in 1X Hank's Balanced Salt Solution (HBSS) To avoid variability due to circadian effects, retinas were dissected 2 hours after lights are turned ON in the facility for all experiments. Extraocular tissue was trimmed off and the cornea and iris were carefully removed. Sclera along with the RPE was gently removed to get the clean retina tissue. The dissected retinas were incubated in Neurobasal-A media supplemented with 5 mM glucose/25 mM glucose or 5 mM glucose with different concentration of 2DG (10mM and 15mM), 0.2% B27 supplement, 0.1% N2 supplement, 0.1%   and penicillin/streptomycin (Thermofisher Scientific) with 5% CO2 at 37°C for 48 hours times as described in previous reports {Chinchore, 2017 #9}. At the end of incubation period, the retinas were rinsed with prewarmed Krebs’ Ringers medium and were further incubated in 0.3 mL Krebs’ Ringers medium for 1hr in 37°C incubator. The supernatant and retinas were rapidly frozen separately at the end of the experiment for lactate assay and western blot respectively. For CUT&Tag and RNAseq retinas were processed immediately.

value: retina explant

value: 25mM glucose


title: RNA-seq 20210119_nih3t3_cas9_PI4K2A-H_rep3

description:
Library name: 20210119_nih3t3_cas9_PI4K2A-H_rep3
RNA-seq sample PI4K2A-H_rep3


title: ATAC-seq 20201212_hek293t_cas9_NDUFS3-H_rep2

description:
Library name: 20201212_hek293t_cas9_NDUFS3-H_rep2
ATAC-seq sample NDUFS3-H_rep2


title: RNA-seq 20210119_nih3t3_cas9_PI4K2A-H_rep1

description:
Library name: 20210119_nih3t3_cas9_PI4K2A-H_rep1
RNA-seq sample PI4K2A-H_rep1


title: Proestrus rep3 snMultiome(ATAC)

description: Library name: P3_ATAC


title: ATAC-seq 20201212_hek293t_cas9_NDUFS3-H_rep3

description:
Library name: 20201212_hek293t_cas9_NDUFS3-H_rep3
ATAC-seq sample NDUFS3-H_rep3


title: Proestrus rep1 snMultiome(RNA-seq)

description: Library name: P1_GE


title: P4 retina, H3K18La (CUT&Tag), replicate 2

description: Library name: P4_H3K18La_rep2


title: Proestrus rep1 snMultiome(ATAC)

description: Library name: P1_ATAC


title: RNA-seq 20210119_nih3t3_cas9_PI4K2A-H_rep2

description:
Library name: 20210119_nih3t3_cas9_PI4K2A-H_rep2
RNA-seq sample PI4K2A-H_rep2


title: RNA-seq 20210119_nih3t3_cas9_NDUFS3-L_rep3

description:
Library name: 20210119_nih3t3_cas9_NDUFS3-L_rep3
RNA-seq sample NDUFS3-L_rep3


title: Proestrus rep2 snMultiome(RNA-seq)

description: Library name: P2_GE


title: ATAC-seq 20201212_hek293t_cas9_MPP4-L_rep3

description:
Library name: 20201212_hek293t_cas9_MPP4-L_rep3
ATAC-seq sample MPP4-L_rep3


title: 25mM glucose, H3K18Ac (CUT&Tag), replicate 2

description: Library name: H3K27Ac_25mM_rep2


title: Male rep3 snMultiome(RNA-seq)

description: Library name: M3_GE

value: Male


title: ATAC-seq 20201212_hek293t_cas9_NDUFS3-H_rep1

description:
Library name: 20201212_hek293t_cas9_NDUFS3-H_rep1
ATAC-seq sample NDUFS3-H_rep1


title: RNA-seq 20210119_nih3t3_cas9_NDUFS3-L_rep2

description:
Library name: 20210119_nih3t3_cas9_NDUFS3-L_rep2
RNA-seq sample NDUFS3-L_rep2


title: 5mM glucose, H3K18Ac (CUT&Tag), replicate 1

description: Library name: H3K27Ac_5mM_rep1

value: 5mM glucose


title: 5mM glucose, H3K18Ac (CUT&Tag), replicate 2

description: Library name: H3K27Ac_5mM_rep2


title: ATAC-seq 20201212_hek293t_cas9_MPP4-L_rep2

description:
Library name: 20201212_hek293t_cas9_MPP4-L_rep2
ATAC-seq sample MPP4-L_rep2


title: 25mM glucose, H3K18La (CUT&Tag), replicate 3

description: Library name: H3K18La_25mM_rep3


title: Male rep3 snMultiome(ATAC)

description: Library name: M3_ATAC


title: ATAC-seq 20201212_hek293t_cas9_IKZF5-L_rep3

description:
Library name: 20201212_hek293t_cas9_IKZF5-L_rep3
ATAC-seq sample IKZF5-L_rep3


title: RNA-seq 20210119_nih3t3_cas9_NDUFS3-H_rep3

description:
Library name: 20210119_nih3t3_cas9_NDUFS3-H_rep3
RNA-seq sample NDUFS3-H_rep3


title: ATAC-seq 20201212_hek293t_cas9_MPP4-L_rep1

description:
Library name: 20201212_hek293t_cas9_MPP4-L_rep1
ATAC-seq sample MPP4-L_rep1


title: 25mM glucose, H3K18La (CUT&Tag), replicate 2

description: Library name: H3K18La_25mM_rep2


title: 25mM glucose, H3K18La (CUT&Tag), replicate 1

description: Library name: H3K18La_25mM_rep1


title: RNA-seq 20210119_nih3t3_cas9_NDUFS3-H_rep2

description:
Library name: 20210119_nih3t3_cas9_NDUFS3-H_rep2
RNA-seq sample NDUFS3-H_rep2


title: Male rep2 snMultiome(RNA-seq)

description: Library name: M2_GE


title: 5mM glucose, H3K18La (CUT&Tag), replicate 3

description: Library name: H3K18La_5mM_rep3


title: 5mM glucose, H3K18La (CUT&Tag), replicate 2

description: Library name: H3K18La_5mM_rep2


title: ATAC-seq 20201212_hek293t_cas9_IKZF5-L_rep2

description:
Library name: 20201212_hek293t_cas9_IKZF5-L_rep2
ATAC-seq sample IKZF5-L_rep2


title: ATAC-seq 20201212_hek293t_cas9_IKZF5-L_rep1

description:
Library name: 20201212_hek293t_cas9_IKZF5-L_rep1
ATAC-seq sample IKZF5-L_rep1


title: RNA-seq 20210119_nih3t3_cas9_NDUFS3-L_rep1

description:
Library name: 20210119_nih3t3_cas9_NDUFS3-L_rep1
RNA-seq sample NDUFS3-L_rep1


title: Male rep1 snMultiome(ATAC)

description: Library name: M1_ATAC


title: RNA-seq 20210119_nih3t3_cas9_MPP4-L_rep3

description:
Library name: 20210119_nih3t3_cas9_MPP4-L_rep3
RNA-seq sample MPP4-L_rep3


title: ATAC-seq 20201212_hek293t_cas9_GALE-L_rep3

description:
Library name: 20201212_hek293t_cas9_GALE-L_rep3
ATAC-seq sample GALE-L_rep3


title: 5mM glucose, H3K18La (CUT&Tag), replicate 1

description: Library name: H3K18La_5mM_rep1


title: RNA-seq 20210119_nih3t3_cas9_MPP4-L_rep2

description:
Library name: 20210119_nih3t3_cas9_MPP4-L_rep2
RNA-seq sample MPP4-L_rep2


title: ATAC-seq 20201212_hek293t_cas9_GALE-L_rep2

description:
Library name: 20201212_hek293t_cas9_GALE-L_rep2
ATAC-seq sample GALE-L_rep2


title: Male rep1 snMultiome(RNA-seq)

description: Library name: M1_GE


title: RNA-seq 20210119_nih3t3_cas9_NDUFS3-H_rep1

description:
Library name: 20210119_nih3t3_cas9_NDUFS3-H_rep1
RNA-seq sample NDUFS3-H_rep1


title: 25mM glucose, RNA-seq, biological replicate 3, technical replicate 1

description: Library name: RNA_25mM_rep3a

data_processing:
RNA-seq analysis pipeline was employed as previously described (Brooks, Stem Cell Reports, 2019).
Assembly: GRCm38/Ensembl v102
Supplementary files format and content: tsv files of RNA-seq transcript counts, gene-level counts and normalized gene-level counts-per-million (CPM)

extract_protocol:
Total RNA from explant retinae was extracted using TRIzol® (Invitrogen, Carlsbad, CA), treated with DNase and cleaned up using the MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems, Foster City, CA) following the manufacturer’s instructions. Libraries were constructed with SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA, Mountain View, CA) with 4 ng of RNA and 13 PCR cycles library amplification. Paired-end sequencing of 101 bases were obtained using the NextSeq 2000 (Illumina, San Diego, CA).
CUT&Tag-IT® Assay Kit – Tissue (Active Motif), SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA, Mountain View, CA)


title: 25mM glucose, RNA-seq, biological replicate 3, technical replicate 2

description: Library name: RNA_25mM_rep3b


title: Diestrus rep2 snMultiome(RNA-seq)

description: Library name: D2_GE

value: Diestrus


title: ATAC-seq 20201212_hek293t_cas9_GALE-L_rep1

description:
Library name: 20201212_hek293t_cas9_GALE-L_rep1
ATAC-seq sample GALE-L_rep1


title: RNA-seq 20210119_nih3t3_cas9_MPP4-L_rep1

description:
Library name: 20210119_nih3t3_cas9_MPP4-L_rep1
RNA-seq sample MPP4-L_rep1


title: Diestrus rep3 snMultiome(ATAC)

description: Library name: D3_ATAC


title: RNA-seq 20210119_nih3t3_cas9_MPP4-H_rep3

description:
Library name: 20210119_nih3t3_cas9_MPP4-H_rep3
RNA-seq sample MPP4-H_rep3


title: 25mM glucose, RNA-seq, biological replicate 2, technical replicate 2

description: Library name: RNA_25mM_rep2b


title: RNA-seq 20210119_nih3t3_cas9_MPP4-H_rep2

description:
Library name: 20210119_nih3t3_cas9_MPP4-H_rep2
RNA-seq sample MPP4-H_rep2


title: 25mM glucose, RNA-seq, biological replicate 2, technical replicate 1

description: Library name: RNA_25mM_rep2a


title: ATAC-seq 20201212_hek293t_cas9_GALE-H_rep2

description:
Library name: 20201212_hek293t_cas9_GALE-H_rep2
ATAC-seq sample GALE-H_rep2


title: Diestrus rep2 snMultiome(ATAC)

description: Library name: D2_ATAC


title: RNA-seq 20210119_nih3t3_cas9_MPP4-H_rep1

description:
Library name: 20210119_nih3t3_cas9_MPP4-H_rep1
RNA-seq sample MPP4-H_rep1


title: Diestrus rep1 snMultiome(ATAC)

description: Library name: D1_ATAC


title: ATAC-seq 20201212_hek293t_cas9_GALE-H_rep3

description:
Library name: 20201212_hek293t_cas9_GALE-H_rep3
ATAC-seq sample GALE-H_rep3


title: ATAC-seq 20201212_hek293t_cas9_GALE-H_rep1

description:
Library name: 20201212_hek293t_cas9_GALE-H_rep1
ATAC-seq sample GALE-H_rep1


title: Diestrus rep1 snMultiome(RNA-seq)

description: Library name: D1_GE


title: Diestrus rep3 snMultiome(RNA-seq)

description: Library name: D3_GE


title: ATAC-seq 20201212_hek293t_cas9_FKBP2-L_rep2

description:
Library name: 20201212_hek293t_cas9_FKBP2-L_rep2
ATAC-seq sample FKBP2-L_rep2


title: 5mM glucose, RNA-seq, biological replicate 3, technical replicate 2

description: Library name: RNA_5mM_rep3b


title: 25mM glucose, RNA-seq, biological replicate 1, technical replicate 2

description: Library name: RNA_25mM_rep1b


title: Sample1 BCR

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Library name: Sample1_BCR

data_processing:
Data was processed with the BD Rhapsody pipeline version 2.4b3.post1
Assembly: BD_Rhapsody_Immune_Response_Panel_Mm
Supplementary files format and content: BCR_VDJ_Unfiltered_Contigs_AIRR.tsv.gz: AIRR formated text file with BCR sequence and annotation
Supplementary files format and content: BCR_Sample_Tag_Calls.csv: text file with sample tag calls per cell
Supplementary files format and content: BCR_Sample_Tag_ReadsPerCell.csv: text file with sample tag reads per cells
Supplementary files format and content: barcodes.tsv.gz: text file with cell barcodes (cell index)
Supplementary files format and content: features.tsv.gz: text file with mouse immune panel features
Supplementary files format and content: matrix.mtx.gz: UMI count matrix
Supplementary files format and content: feature_README.txt: feature reference file with sample tag and multiplexed sample information
Library strategy: BCR-Seq

source_name: spleen

extract_protocol:
Splenic single-cell suspensions were generated by mechanical dissociation into supplemented Opti-MEM. Negative enrichment of CD45.1 HkiL B cells was performed using the EasySep Mouse Streptavidin RapidSpheres Isolation Kit (STEMCELL Technologies). Cells were sample-tagged with anti-mouse MHC-H2 class I antibodies and stained for surface markers. Live CD138- B220+ CD45.1+ CD45.2- cells were purified by FACS sorting. Post-sorting, cell viability was confirmed using a Cellometer K2 Image Cytometer.
Pooled single-cell suspensions were loaded into a BD Rhapsody cartridge targeting 100,000 cells per lane. Libraries were prepared following the BD Rhapsody System Mouse TCR/BCR, Targeted mRNA, and Sample Tag Library Preparation Protocol. Library QC was performed using an Agilent 5200 Fragment Analyzer and quantified via Qubit. Sequencing was performed on an Element Biosciences Aviti System using a High Output 2x75 cycles Flowcell.

value: spleen

value: mouse B cells

value: HKIL

value: mixed sample (rLCMV, LASVLIIA, LASVLIVC)


title: RNA-seq 20210119_nih3t3_cas9_HMGC-L_rep1

description:
Library name: 20210119_nih3t3_cas9_HMGC-L_rep1
RNA-seq sample HMGC-L_rep1


title: RNA-seq 20210119_nih3t3_cas9_HMGC-L_rep3

description:
Library name: 20210119_nih3t3_cas9_HMGC-L_rep3
RNA-seq sample HMGC-L_rep3


title: 25mM glucose, RNA-seq, biological replicate 1, technical replicate 1

description: Library name: RNA_25mM_rep1a


title: ATAC-seq 20201212_hek293t_cas9_FKBP2-L_rep3

description:
Library name: 20201212_hek293t_cas9_FKBP2-L_rep3
ATAC-seq sample FKBP2-L_rep3


title: Sample1 Sample Tag

description: Library name: Sample1_SampleTag

library_source: other

data_processing:
Data was processed with the BD Rhapsody pipeline version 2.4b3.post1
Assembly: BD_Rhapsody_Immune_Response_Panel_Mm
Supplementary files format and content: BCR_VDJ_Unfiltered_Contigs_AIRR.tsv.gz: AIRR formated text file with BCR sequence and annotation
Supplementary files format and content: BCR_Sample_Tag_Calls.csv: text file with sample tag calls per cell
Supplementary files format and content: BCR_Sample_Tag_ReadsPerCell.csv: text file with sample tag reads per cells
Supplementary files format and content: barcodes.tsv.gz: text file with cell barcodes (cell index)
Supplementary files format and content: features.tsv.gz: text file with mouse immune panel features
Supplementary files format and content: matrix.mtx.gz: UMI count matrix
Supplementary files format and content: feature_README.txt: feature reference file with sample tag and multiplexed sample information
Library strategy: CITE-seq

molecule: protein


title: ATAC-seq 20201212_hek293t_cas9_FKBP2-L_rep1

description:
Library name: 20201212_hek293t_cas9_FKBP2-L_rep1
ATAC-seq sample FKBP2-L_rep1


title: 5mM glucose, RNA-seq, biological replicate 3, technical replicate 1

description: Library name: RNA_5mM_rep3a


title: ATAC-seq 20201212_hek293t_cas9_FKBP2-H_rep3

description:
Library name: 20201212_hek293t_cas9_FKBP2-H_rep3
ATAC-seq sample FKBP2-H_rep3


title: RNA-seq 20210119_nih3t3_cas9_FKBP2-L_rep3

description:
Library name: 20210119_nih3t3_cas9_FKBP2-L_rep3
RNA-seq sample FKBP2-L_rep3


title: Sample1 mRNA

description: Library name: Sample1_mRNA

data_processing:
Data was processed with the BD Rhapsody pipeline version 2.4b3.post1
Assembly: BD_Rhapsody_Immune_Response_Panel_Mm
Supplementary files format and content: BCR_VDJ_Unfiltered_Contigs_AIRR.tsv.gz: AIRR formated text file with BCR sequence and annotation
Supplementary files format and content: BCR_Sample_Tag_Calls.csv: text file with sample tag calls per cell
Supplementary files format and content: BCR_Sample_Tag_ReadsPerCell.csv: text file with sample tag reads per cells
Supplementary files format and content: barcodes.tsv.gz: text file with cell barcodes (cell index)
Supplementary files format and content: features.tsv.gz: text file with mouse immune panel features
Supplementary files format and content: matrix.mtx.gz: UMI count matrix
Supplementary files format and content: feature_README.txt: feature reference file with sample tag and multiplexed sample information


title: RNA-seq 20210119_nih3t3_cas9_FKBP2-L_rep2

description:
Library name: 20210119_nih3t3_cas9_FKBP2-L_rep2
RNA-seq sample FKBP2-L_rep2


title: RNA-seq 20210119_nih3t3_cas9_HMGC-L_rep2

description:
Library name: 20210119_nih3t3_cas9_HMGC-L_rep2
RNA-seq sample HMGC-L_rep2


title: ATAC-seq 20201212_hek293t_cas9_FKBP2-H_rep2

description:
Library name: 20201212_hek293t_cas9_FKBP2-H_rep2
ATAC-seq sample FKBP2-H_rep2


title: 5mM glucose, RNA-seq, biological replicate 2, technical replicate 2

description: Library name: RNA_5mM_rep2b


title: Control, Spherule, CellFree, RiboMarker

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

address: 2125 Delaware Ave. Suite B

institute: RealSeq Biosciences

description: Library name: Control_Spherule_CellFree_RiboMarker

data_processing:
Sequencing reads were trimmed of adapter sequence using cutadapt version 4.6 [--nextseq-trim=15 -u 1 -a TGGAATTCTCGGGTGCCAAGG -m 15] (31). Reads were then aligned to ncRNA transcripts identified using RFAM, with the addition of the high-confidence set of tRNA isodecoders containing -CCA tails identified using tRNAScan-SE (32),  and then to theC. posadasii strain Silveira (GCA_000170175.2) genome. ShortStack v4.1.0 (33) with the parameters [-pad 3 –mincov 0.5rpm] was used to identify potential novel sRNA transcripts. Reads overlapping with known annotations were summed and the corresponding read counts were used for downstream differential analysis.
Assembly: GCA_000170175.2 (Silveria 2011)
Supplementary files format and content: csv files contain raw read counts for each sample

organism: unidentified

source_name: cell-free media

growth_protocol: C. posadasii (strain Δcts2/Δard1/Δcts3, NR-166; BEI Resources) arthroconidia were harvested from 6-week-old plates as previously described (29). The spores were inoculated at 1 × 106 arthroconidia into a 250 mL baffled Erlenmeyer flask containing 100 mL of 2xGYE at 150 rpm at 30 °C for 48 hours. Conditioned medium was harvested by collecting conditioned media with cells into centrifuge tubes and spun at 12,000 × g for 8 min to pellet the cells. The supernatant was pooled and filtered with a 0.22-µm syringe filter before being stored at −80°C.  To generate samples for the time course, in which arthroconidia transition to mycelia, 1 × 106 of harvested arthroconidia were incubated in 250 mL flat-bottom Erlenmeyer flasks (Corning, Corning, NY, USA) in 100 mL of 2x GYE media at 150 rpm at 30 °C. After 48 hours, the conditioned medium with cells was placed in into centrifuge tubes and spun at 12,000 × g for 8 min to pellet the cells. Half of the filtered fungal cells were kept for RNA isolation, while the condition media was spun down and supernatant was removed for extracellular RNA isolation. The remaining cells were reinoculated in fresh 2X GYE for 48 hours at 150 rpm at 30 °C. At 72 hrs post-media change, the fungal cells were separated from the growth media by filtering with a sterile 40 µm nylon mesh cell strainer.  Half of the filtered fungal cells were kept for RNA isolation, while the condition media was filtered with a 0.22-µm syringe filter before being stored at −80°C for extracellular RNA isolation. The remaining half of the filtered fungal cells were reintroduced again into fresh 2X GYE for 24 hours at 150 rpm at 30 °C.  This sample processing was performed again at 96 hrs for a total of 3 replicates of fungal cell samples and filtered conditioned media. C. posadasii spherules were propagated and harvested from 6-week-old plates as previously described (29). For spherule samples, 50 mL of Converse medium (30) was inoculated to a final concentration of 106 arthroconidia/mL. Cultures are then incubated at 39°C in a 10% CO2 shaking incubator at 150 rpm for ~ 3 days. Spherules are harvested by filtering culture through a nested filter into a 50 mL conical tube and then centrifuged at 9000 x g for 8 mins to pellet. Pellets were washed with 1x PBS twice, pelleted, then snap frozen for storage at -80°C until use.

extract_protocol:
C. posadasii mycelium, arthroconidia, and young (no endosporulation) spherule samples were stored in RNA Shield (Zymo Research) at −80°C until processing using the Quick-RNA™ Fungal
For small RNA-seq, libraries were prepared from total RNA using the RealSeq®-Biofluids library preparation kit (RealSeq Biosciences) according to the manufacturer’s instructions. Libraries for each ecotype, as well as cell-free and exosome samples, were generated separately and then pooled for the analysis. In some cases, triplicate libraries for each sample type and condition were not met, and thus, only duplicates were used in downstream analyses to avoid batch effects in the data. Finally, prepared libraries were pooled and subjected to single-end 75 cycles of sequencing using the F3 50 cycle sequencing kit (Note: reagents for 50 additional cycles above what is represented were included to account for index sequencing needs) on the Singular G4 system according to the manufacturer’s instructions (Singular Genomics).

treatment_protocol: For treatment of RNA with the Ribomarker® platform, 10 uL of RNA sample was incubated in a 15 μl reaction mixture containing 1.5 μl Ribomarker® Buffer 1, 1.5 uL of Ribomarker® Enzyme 1, and 2 uL of RNase-Free H2O at 37 °C for 10 min, followed by 80 °C for 2 min. Then, to this mixture was added 2 uL of Ribomarker® Buffer 2 and 2 uL of Ribomarker® Enzyme 2, which was then incubated at 37 °C for 60 min. Finally, 1 uL of Buffer 3 was added to the reaction and incubated at 37 °C for 60 min. The treated RNA was then isolated using an RNA Clean and Concentrator-5 kit for downstream use in library preparation.

value: cell-free media


title: Male rep2 snMultiome(ATAC)

description: Library name: M2_ATAC


title: RNA-seq 20210119_nih3t3_cas9_FKBP2-L_rep1

description:
Library name: 20210119_nih3t3_cas9_FKBP2-L_rep1
RNA-seq sample FKBP2-L_rep1


title: RNA-seq 20210119_nih3t3_cas9_FKBP2-H_rep3

description:
Library name: 20210119_nih3t3_cas9_FKBP2-H_rep3
RNA-seq sample FKBP2-H_rep3


title: ATAC-seq 20201212_hek293t_cas9_EMX1_rep3

description:
Library name: 20201212_hek293t_cas9_EMX1_rep3
ATAC-seq sample EMX1_rep3


title: Control, Arthrocelia, CellFree, RiboMarker

description: Library name: Control_Arthrocelia_CellFree_RiboMarker


title: ATAC-seq 20201212_hek293t_cas9_FKBP2-H_rep1

description:
Library name: 20201212_hek293t_cas9_FKBP2-H_rep1
ATAC-seq sample FKBP2-H_rep1


title: Control, Mycelia, CellFree, RiboMarker

description: Library name: Control_Mycelia_CellFree_RiboMarker


title: Control, Arthroconidia, CellFree, RiboMarker

description: Library name: Control_Arthroconidia_CellFree_RiboMarker


title: 5mM glucose, RNA-seq, biological replicate 1, technical replicate 2

description: Library name: RNA_5mM_rep1b


title: 5mM glucose, RNA-seq, biological replicate 2, technical replicate 1

description: Library name: RNA_5mM_rep2a


title: Control, Spherule, CellFree

description: Library name: Control_Spherule_CellFree


title: ATAC-seq 20201212_hek293t_cas9_EMX1_rep2

description:
Library name: 20201212_hek293t_cas9_EMX1_rep2
ATAC-seq sample EMX1_rep2


title: Control, Mycelia, CellFree

description: Library name: Control_Mycelia_CellFree


title: 5mM glucose, RNA-seq, biological replicate 1, technical replicate 1

description: Library name: RNA_5mM_rep1a


title: RNA-seq 20210119_nih3t3_cas9_CIB4-L_rep3

description:
Library name: 20210119_nih3t3_cas9_CIB4-L_rep3
RNA-seq sample CIB4-L_rep3


title: RNA-seq 20210119_nih3t3_cas9_FKBP2-H_rep2

description:
Library name: 20210119_nih3t3_cas9_FKBP2-H_rep2
RNA-seq sample FKBP2-H_rep2


city: Vancouver

first: STEMCELL

last: Technologies

state: BC

address: 1618 Station st

department: RND

country: Canada

institute: STEMCELL Technologies

description: Library name: CHO3-1C-ODM

data_processing:
10X libraries: the barcoded processing, gene counting and aggregation were made using the 10X Genomics Cell Ranger software v3.1.0. Sequencing data was demultiplexed using Illumina's cellranger multi.
Downstream analysis were performed with Seurat v5.2.1. Cells with gene count between 2,000 and 10,000 genes and less than 10% mitochondrial genes were retained for analysis. RPCA integration was performed in order to incorporate all samples under a single UMAP. Gene expression of key markers was used to identify cell types.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: WLS 1C Hepatocyte Like Cell-derived differentiated hepatic organoids in STEMdiff™ Hepatic Organoid Differentiation Medium

extract_protocol:
Proliferative and differentiated hepatic organoids, cultured in STEMdiff Hepatic Organoid Growth Medium or STEMdiff Hepatic Organoid Differentiation Medium, respectively, were recovered from Matrigel domes by adding Gentle Cell Dissociation Reagent to domes, gently triturating to dislodge, and incubating at 37°C for 10 minutes. Recovered organoid suspensions were diluted further with Advanced DMEM/F-12 + 1% BSA and centrifuged at 300 x g for 5 minutes. 1mL Animal Component Free (ACF) Enzymatic Dissociation Solution was added to pellets, after which organoid suspensions were triturated ten times and then incubated at 37°C for 5 minutes. This was repeated a second time to generate a uniform single cell suspension, followed by addition of 1mL ACF Enzyme Inhibition Solution. Suspensions were centrifuged at 300 x g for 5 minutes, and cell pellets were resuspended in 1 mL Advanced DMEM/F-12 + 1% BSA, then passed through a 37μm reversible cell strainer to remove remaining aggregates. The <37μm filtrant was centrifuged at 300 x g for 5 minutes, and the pellet was resuspended in 1mL of PBS + 0.04% BSA. Cell concentration, viability, and percent aggregates were determined using a Nucleocounter NC-250. A suspension of 1600 cells/μL was then generated using PBS + 0.04% BSA, targeting a minimum sample volume of 10μL.
Library was prepared using Chromium Single Cell 3ʹ v1 protocol with GEM-X Universal Multiplex technology (10x Genomics). Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq 2000 with Paired End 59 bp × 59 bp reads.

value: Hepatic Organoid


title: experiment:alt_KOLF condition:old sample[8]

description: Library name: alt_KOLF_old_sample8

data_processing:
Quality assessment of the fastq data files was conducted using fastqc (v 0.11.5) [2], followed by polyA trimming using cutadapt (v 4.1) [3]. Subsequent read filtering, mapping, and counting were performed using the zUMIs pipeline (v 2.9.7) [4], with reads mapped to the mouse genome (mm10). Fastq files were sample-demultiplexed using deML [5].
2 Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
3 Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1), 10-12.
4 Parekh, S., Ziegenhain, C., Vieth, B., Enard, W., & Hellmann, I. (2018). zUMIs- A fast and flexible pipeline to process RNA sequencing data with UMIs. GigaScience, 7(6), giy059.
5 Gabriel Renaud, Udo Stenzel, Tomislav Maricic, Victor Wiebe, Janet Kelso (2015) deML: robust demultiplexing of Illumina sequences using a likelihood-based approach, Bioinformatics, Volume 31, Issue 5, March 2015, Pages 770–772, https://doi.org/10.1093/bioinformatics/btu719
Assembly: GRCm39
Supplementary files format and content: processed data files contain the Barcode (BC) of each sample with the associated counts (N) per feature (type), e.g. Intergenic, Intron, Exon, Ambiguity and Unmapped.

source_name: cultured iPSCs

value: cultured iPSCs

value: KOLF

value: iPSC


title: RNA-seq 20210119_nih3t3_cas9_FKBP2-H_rep1

description:
Library name: 20210119_nih3t3_cas9_FKBP2-H_rep1
RNA-seq sample FKBP2-H_rep1

data_processing:
RNA-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to the reference genome using STAR (version 2.5.3a) with parameters "--twopassMode Basic --outSAMstrandField introMotif --quantMode TranscriptomeSAM".
The STAR index was constructed using the Gencode annotation gtf file (version 32 for human or version m23 for mouse) and its corresponding genome reference (hg38 for human and mm10 for mouse).
Post alignment, RSEM (version 1.3.0) was used to extract the final read count from the aligned bam file, with parameters "--no-bam-output --paired-end".
Assembly: mm10/hg38
Supplementary files format and content: raw count matrix (RSEM)
Supplementary files format and content: tpm matrix (RSEM)


title: ATAC-seq 20201212_hek293t_cas9_EMX1-H_rep3

description:
Library name: 20201212_hek293t_cas9_EMX1-H_rep3
ATAC-seq sample EMX1-H_rep3

data_processing:
ATAC-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to hg38 (human) or mm10 (mouse) using bowtie2 (version 2.4.4) with parameters -X2000 --mm -t -q -N1 -L 25 --no-mixed --no-discordant.
Aligned reads were filtered using samtools (version 1.13) to exclude unmapped reads, unmapped mates, non-primary alignments, vendor/quality-fail reads, and duplicates (SAM flag 1804).
Standard samtools sort and fixmate operations were applied. PCR duplicates were removed using picard MarkDuplicates (version 2.20.4), followed by samtools view filtering (-F1804 -f2). ENCODE blacklist regions were removed in the final alignment set.
For uploaded processed bigWig files, bamCoverage was used with -p 8 --normalizeUsing RPKM --binSize 100.
Assembly: mm10/hg38
Supplementary files format and content: ATAC-seq coverage bigWig


title: experiment:alt_KOLF condition:old sample[7]

description: Library name: alt_KOLF_old_sample7


title: RNA-seq 20210119_nih3t3_cas9_CIB4-L_rep1

description:
Library name: 20210119_nih3t3_cas9_CIB4-L_rep1
RNA-seq sample CIB4-L_rep1


title: Control, Arthrocelia, CellFree

description: Library name: Control_Arthrocelia_CellFree


title: ATAC-seq 20201212_hek293t_cas9_EMX1_rep1

description:
Library name: 20201212_hek293t_cas9_EMX1_rep1
ATAC-seq sample EMX1_rep1


title: Control, Arthroconidia, CellFree

description: Library name: Control_Arthroconidia_CellFree


title: experiment:alt_KOLF condition:old sample[6]

description: Library name: alt_KOLF_old_sample6


description: Library name: CHO2-1C-OGM

source_name: WLS 1C Hepatocyte Like Cell-derived proliferative hepatic organoids in STEMdiff™ Hepatic Organoid Growth Medium


title: RNA-seq 20210119_nih3t3_cas9_CIB4-L_rep2

description:
Library name: 20210119_nih3t3_cas9_CIB4-L_rep2
RNA-seq sample CIB4-L_rep2


title: RNA-seq 20201013_nih3t3_cas9_wt_rep6

description:
Library name: 20201013_nih3t3_cas9_wt_rep6
RNA-seq sample wt_rep6


title: ATAC-seq 20201212_hek293t_cas9_EMX1-H_rep2

description:
Library name: 20201212_hek293t_cas9_EMX1-H_rep2
ATAC-seq sample EMX1-H_rep2


title: ATAC-seq 20201212_hek293t_cas9_CIB4-L_rep3

description:
Library name: 20201212_hek293t_cas9_CIB4-L_rep3
ATAC-seq sample CIB4-L_rep3


title: experiment:alt_KOLF condition:old sample[5]

description: Library name: alt_KOLF_old_sample5


title: ATAC-seq 20201212_hek293t_cas9_CIB4-L_rep2

description:
Library name: 20201212_hek293t_cas9_CIB4-L_rep2
ATAC-seq sample CIB4-L_rep2


title: experiment:alt_KOLF condition:old sample[4]

description: Library name: alt_KOLF_old_sample4


title: Control, Spherule, Exosome, RiboMarker

description: Library name: Control_Spherule_Exosome_RiboMarker

source_name: exosomes

value: exosomes


title: RNA-seq 20201013_nih3t3_cas9_wt_rep4

description:
Library name: 20201013_nih3t3_cas9_wt_rep4
RNA-seq sample wt_rep4


title: Control, Mycelia, Exosome, RiboMarker

description: Library name: Control_Mycelia_Exosome_RiboMarker


title: RNA-seq 20201013_nih3t3_cas9_wt_rep5

description:
Library name: 20201013_nih3t3_cas9_wt_rep5
RNA-seq sample wt_rep5


title: experiment:alt_KOLF condition:old sample[2]

description: Library name: alt_KOLF_old_sample2


title: ATAC-seq 20200928_hek293t_cas9_wt_rep3

description:
Library name: 20200928_hek293t_cas9_wt_rep3
ATAC-seq sample wt_rep3


title: Control, Arhtrocelia, Exosome, RiboMarker

description: Library name: Control_Arhtrocelia_Exosome_RiboMarker


title: ATAC-seq 20201212_hek293t_cas9_CIB4-L_rep1

description:
Library name: 20201212_hek293t_cas9_CIB4-L_rep1
ATAC-seq sample CIB4-L_rep1


title: Control, Spherule, Exosome

description: Library name: Control_Spherule_Exosome


title: RNA-seq 20201013_nih3t3_cas9_wt_rep3

description:
Library name: 20201013_nih3t3_cas9_wt_rep3
RNA-seq sample wt_rep3


title: experiment:alt_KOLF condition:old sample[1]

description: Library name: alt_KOLF_old_sample1


title: Control, Arthroconidia, Exosome, RiboMarker

description: Library name: Control_Arthroconidia_Exosome_RiboMarker


title: ATAC-seq 20200928_hek293t_cas9_wt_rep2

description:
Library name: 20200928_hek293t_cas9_wt_rep2
ATAC-seq sample wt_rep2


title: Control, Arthrocelia, Exosome

description: Library name: Control_Arthrocelia_Exosome


title: Control, Mycelia, Exosome

description: Library name: Control_Mycelia_Exosome


title: ATAC-seq 20200928_hek293t_cas9_wt_rep1

description:
Library name: 20200928_hek293t_cas9_wt_rep1
ATAC-seq sample wt_rep1


title: RNA-seq 20201013_nih3t3_cas9_wt_rep1

description:
Library name: 20201013_nih3t3_cas9_wt_rep1
RNA-seq sample wt_rep1


title: RNA-seq 20201013_nih3t3_cas9_empty_vector_rep3

description:
Library name: 20201013_nih3t3_cas9_empty_vector_rep3
RNA-seq sample empty_vector_rep3


title: experiment:alt_KOLF condition:PTO sample[7]

description: Library name: alt_KOLF_PTO_sample7


title: ATAC-seq 20200928_hek293t_cas9_empty_vector_rep3

description:
Library name: 20200928_hek293t_cas9_empty_vector_rep3
ATAC-seq sample empty_vector_rep3


title: RNA-seq 20201013_nih3t3_cas9_wt_rep2

description:
Library name: 20201013_nih3t3_cas9_wt_rep2
RNA-seq sample wt_rep2


title: experiment:alt_KOLF condition:old sample[3]

description: Library name: alt_KOLF_old_sample3


title: ATAC-seq 20200928_hek293t_cas9_empty_vector_rep2

description:
Library name: 20200928_hek293t_cas9_empty_vector_rep2
ATAC-seq sample empty_vector_rep2


title: Control, Arthroconidia, Exosome

description: Library name: Control_Arthroconidia_Exosome


title: RNA-seq 20201013_nih3t3_cas9_empty_vector_rep2

description:
Library name: 20201013_nih3t3_cas9_empty_vector_rep2
RNA-seq sample empty_vector_rep2


title: experiment:alt_KOLF condition:PTO sample[5]

description: Library name: alt_KOLF_PTO_sample5


title: RNA-seq 20201013_nih3t3_cas9_empty_vector_rep1

description:
Library name: 20201013_nih3t3_cas9_empty_vector_rep1
RNA-seq sample empty_vector_rep1


title: RNA-seq 20201013_nih3t3_cas9_cas9_only_vector_rep3

description:
Library name: 20201013_nih3t3_cas9_cas9_only_vector_rep3
RNA-seq sample cas9_only_vector_rep3


title: experiment:alt_KOLF condition:PTO sample[8]

description: Library name: alt_KOLF_PTO_sample8


title: PPARgKO 2wks, rep2

type: RNA

city: La Jolla

first: Ruth

middle: T

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description:
4903688033_H
Replicate 2.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

label: biotin

source_name: primary cardiac endothelial cells, PPARgKO, atherogenic diet

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain/background

value: PPARgfl/fl-Tie2-Cre KO in LDLr-/-

value: 15 wks

value: heart

value: primary cardiac endothelial cells

value: atherogenic diet

tag: treatment duration

value: 2 wks


title: experiment:alt_KOLF condition:PTO sample[6]

description: Library name: alt_KOLF_PTO_sample6


title: experiment:alt_KOLF condition:PTO sample[3]

description: Library name: alt_KOLF_PTO_sample3


title: ATAC-seq 20200928_hek293t_cas9_cas9_only_vector_rep2

description:
Library name: 20200928_hek293t_cas9_cas9_only_vector_rep2
ATAC-seq sample cas9_only_vector_rep2


title: RNA-seq 20201013_nih3t3_cas9_cas9_only_vector_rep1

description:
Library name: 20201013_nih3t3_cas9_cas9_only_vector_rep1
RNA-seq sample cas9_only_vector_rep1


title: experiment:alt_KOLF condition:PTO sample[4]

description: Library name: alt_KOLF_PTO_sample4


title: RNA-seq 20201013_nih3t3_cas9_cas9_only_vector_rep2

description:
Library name: 20201013_nih3t3_cas9_cas9_only_vector_rep2
RNA-seq sample cas9_only_vector_rep2


title: ATAC-seq 20200928_hek293t_cas9_cas9_only_vector_rep1

description:
Library name: 20200928_hek293t_cas9_cas9_only_vector_rep1
ATAC-seq sample cas9_only_vector_rep1


title: ATAC-seq 20200928_hek293t_cas9_cas9_only_vector_rep3

description:
Library name: 20200928_hek293t_cas9_cas9_only_vector_rep3
ATAC-seq sample cas9_only_vector_rep3


title: ATAC-seq 20201212_hek293t_cas9_EMX1-H_rep1

description:
Library name: 20201212_hek293t_cas9_EMX1-H_rep1
ATAC-seq sample EMX1-H_rep1


title: experiment:alt_KOLF condition:PTO sample[2]

description: Library name: alt_KOLF_PTO_sample2


title: Cont 2wks, rep2

description:
4903688033_F
Replicate 2.

source_name: primary cardiac endothelial cells, control, atherogenic diet

value: LDLr-/- mice in C57BL/6 bkg


title: Cont 2wks, rep1

description:
4903688033_E
Replicate 1.


title: experiment:alt_KOLF condition:PTO sample[1]

description: Library name: alt_KOLF_PTO_sample1


title: PPARgKO 0wks, rep2

description:
4903688033_D
Replicate 2.

source_name: primary cardiac endothelial cells, PPARgKO, chow diet

value: 13 wks

value: chow diet


title: ATAC-seq 20200928_hek293t_cas9_ZSWIM3_rep2

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_rep2
ATAC-seq sample ZSWIM3_rep2


title: PPARgKO 0wks, rep1

description:
4903688033_C
Replicate 1.


title: RNA-seq 20201013_nih3t3_cas9_ZSWIM3_rep1

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_rep1
RNA-seq sample ZSWIM3_rep1


title: ATAC-seq 20200928_hek293t_cas9_ZSWIM3_rep1

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_rep1
ATAC-seq sample ZSWIM3_rep1


title: RNA-seq 20201013_nih3t3_cas9_ZSWIM3_rep3

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_rep3
RNA-seq sample ZSWIM3_rep3


title: RNA-seq 20201013_nih3t3_cas9_ZSWIM3_rep2

description:
Library name: 20201013_nih3t3_cas9_ZSWIM3_rep2
RNA-seq sample ZSWIM3_rep2


title: PPARgKO 2wks, rep1

description:
4903688033_G
Replicate 1.


title: ATAC-seq 20200928_hek293t_cas9_ZSWIM3_rep3

description:
Library name: 20200928_hek293t_cas9_ZSWIM3_rep3
ATAC-seq sample ZSWIM3_rep3