title: 439_Wang_WGS_AtWX278_ATGN

data_processing:
Library strategy: WGS
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the A. tumefaciens C58 genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of A. tumefaciens C58 was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: GCA_000092025.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices; column information (10kb bins of A. tumefaciens genome); matrix value (normalized Hi-C interaction scores).
Supplementary_files_format_and_content: Files inside the .zip files containing multiple  .csv files which are comma-separated values files of ChIP-seq results; column information (genome position; reads), matrix value (number of reads at each genome position).


title: 437_Wang_input_AtWX372_ATGN_250uMIPTG4h

status: Public on Jan 30 2022

type: SRA

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University at Bloomington

library_source: genomic

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq, we mapped reads in each FASTQ file back to the genome of A. tumefaciens C58 (NCBI Reference Sequence GCA_000092025.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the A. tumefaciens C58 genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of A. tumefaciens C58 was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: GCA_000092025.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices; column information (10kb bins of A. tumefaciens genome); matrix value (normalized Hi-C interaction scores).
Supplementary_files_format_and_content: Files inside the .zip files containing multiple  .csv files which are comma-separated values files of ChIP-seq results; column information (genome position; reads), matrix value (number of reads at each genome position).

molecule: genomic DNA

organism: Agrobacterium tumefaciens

source_name: Agrobacterium tumefaciens C58

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-GFP, anti-ParB1 and anti-RepBCh2 antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq550 sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in ATGN at 30˚C, IPTG was added to 0.25mM final concentration for 4h, fixed by 3% formaldehyde for 30min at room temperature
None

tag: strain

tag: treatment

value: ATGN, 30˚C, 0.25mM IPTG for 4h

tag: chip antibody


title: PRO_dTAG-3h_FP-1h_PAF1-fkbp_DLD1_Batch9

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

country: China

institute: Fudan University

library_source: transcriptomic

data_processing:
Library strategy: PRO-seq
ChIP-Rx: paired raw reads were quality checked with FastQC v0.11.9 (Babraham-Institute) and trimmed by Trim Galore v0.6.6 (Babraham-Institute) with the parameter “-q 25” to remove adaptors and low-quality reads. Then the remaining reads were aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 (Langmead and Salzberg, 2012). Duplicates and low mapping quality reads were removed using Picard v2.23.3 (Broad-Institute) and SAMtools v1.9 (Li et al., 2009). The number of spike-in mm10 reads was counted with SAMtools v1.9 and used to generate normalization factor alpha = 1e6/mm10_count for coverage profiles (Li et al., 2009). Normalized bigwig files were generated with deepTools v3.5.0 (Ramirez et al., 2016) and peaks were called using MACS 2.1.0 (Zhang et al., 2008). The called peaks overlapped with ENCODE Blacklist regions (Amemiya et al., 2019) were further removed by BEDTools v2.29.2 (Quinlan and Hall, 2010).
PRO-seq: The PRO-seq raw reads were processed with Trim Galore v0.6.6 (Babraham-Institute) and reads shorter than 15 bp after clipping were discarded. Ribosomal RNA reads were removed by Bowtie v2.3.5.1 with “--un-conc-gz” (Langmead and Salzberg, 2012). Then the remaining reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with the parameter “--very-sensitive-local” (Langmead and Salzberg, 2012). PCR duplicate and low-quality reads were removed. The normalization factor was calculated the same as described in ChIP-Rx. Strand-specific normalized bigwig files were generated with deepTools v3.5.0 (Ramirez et al., 2016).
TT-seq: The TT-seq raw reads were trimmed with Trim Galore v0.6.6 (Babraham-Institute)  and then aligned to hg19 or mm10 genome using STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate” (Langmead and Salzberg, 2012). We removed duplicates and low-quality reads and kept only properly paired reads for the downstream analyses. The number of spike-in mm10 reads was counted to generate the normalization factor. Strand-specific normalized bigwigs were generated with deepTools v3.5.0 (Ramirez et al., 2016).
RNA-seq: Raw reads were first trimmed by Trim Galore v0.6.6 (Babraham-Institute), followed by mapping to hg19 or mm10 genome using STAR v2.7.5c with parameters “--outSAMtype BAM SortedByCoordinate –twopassMode Basic --outFilterMismatchNmax 2” (Langmead and Salzberg, 2012). Duplicates and low-quality reads were removed, and reads mapped in proper pairs were isolated using SAMtools v1.9 with parameter “-f 2” (Li et al., 2009). The normalization factor was calculated the same as described in ChIP-Rx. Strand-specific Normalized bigwigs were generated.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

molecule: total RNA

organism: Homo sapiens

source_name: PAF1-dTAG DLD1

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
ChIP-seq: Lysates were clarified from sonicated cells and protein was isolated with antibody.  TT-seq/PRO-seq/RNA-seq: RNA was isolated with TRIzol.
ChIP-seq: Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.  TT-seq/PRO-seq/RNA-seq:  Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: The cell was  treated with dTAG13

tag: cell type

value: colorectal adenocarcinoma cell lines

value: treated with dTAG-13


title: T1Mut3d_DP_R1

city: Dresden

first: Maximina

last: Yun

state: Saxony

address: Fetscherstrasse 105

department: CRTD

country: Germany

institute: TUD

data_processing:
Basecalls were done with Illumina bcl2fastq version 2.19.1.
Sequence and gene annotation of the axolotl nuclear genome assembly AmexG_v6.0-DD were downloaded from https://www.axolotl-omics.org. The gene models for the HoxA and HoxD genes were replaced with manual curated gene models (personal communication with Sergej Nowoshilow, axolotl-omics.org). Sequence and gene annotation of the mitochondrial genome assembly (NCBI GenBank, AY659991.1) and RNA spike-in control sequences (ERCC, Ambion; for quality control) were included as well.
Reads were aligned to the axolotl reference genome  AmexG_v6.0-DD using the aligner STAR (v2.7.6a) with AmexG_v6.0-DD splice sites as support (parameters:--outSAMmultNmax 1).
Uniquely mapped fragments were compared based on their overlap to AmexG_v6.0-DD gene annotations using featureCounts (v2.0.1) to create a table of counts per gene and cell (parameters:  -a AmexG_v6_DD/AmexG_v6_DD.gtf -s 0 -o genecount/bfx1392.AmexG_v6_DD.eAmexG_v6_DD.txt -Q 1).
Genome_build: AmexG_v6.0-DD
Supplementary_files_format_and_content: bfx1392.AmexG_v6_DD.eAmexG_v6_DD.txt.gz is a tab separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the samples.

organism: Ambystoma mexicanum

source_name: Blastema cells

extract_protocol:
Samples were collecte, dissociated with LiberaseTM and immediated isolated by FACs sorting based on double positive (Ch+GFP+) or single channel fluorescence (CH+). cDNA library preparation was performed using 300 cells per sample.
RNAseq was based on Smart-seq2 sensitive full-length transcriptome profiling and modified from Picelli et. al., 2013 (Picelli et al., 2013).

treatment_protocol: Forelimb were amputated and electroporated with Tig1-t2A-GFP  or Tig1P155Amut-t2A-GFP constructs-containing plasmids when the hoxa13:Cherry+ domain was visible; Blastema tissue was collected at 3 or 8 days post-electroporation.

tag: animal line

value: Hoxa13:Cherry  transgenic line

value: Cells transfected with Tig1P155Amut construct

tag: isolation

value: Dissociation and FACS isolation at 3 days post- transfection


title: PRO_dTAG-24h_PAF1-fkbp_DLD1_Batch9


title: 2_T-N1G_Vehicle

city: Aoba-ku, Sendai

first: Fumiki

last: Katsuoka

state: Miyagi

address: 2-1 Seiryo-cho

country: Japan

institute: Tohoku University

data_processing:
Illumina bcl2fastq v2.16.0.10 was used for basecalling.
Reads were mapped against mouse (mm9) genome using the TopHat v2.0.8b.
Differential gene analaysis was performed using Cuffdiff v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genotype were generated using Cuffdiff.

organism: Mus musculus

source_name: embryonic fibroblast

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was prepared by using RNeasy Mini Kit (QIAGEN).
Isolation of poly(A)-tailed RNA and library construction were performed using SureSelect Strand Specific RNA Sample Prep Kit (Agilent Technologies).

treatment_protocol: Cells were treated with Vehcle, 0.3 µM or 1.0 µM  Proteasome Inhibitor (MG132)  for 12hr.

value: embryonic fibroblast

tag: genotype

value: Vehicle


title: 436_Wang_ChIP_anti_GFP_AtWX372_ATGN_250uMIPTG4h

description: ChIP using anti-GFP antibodies

value: anti-GFP


title: 2_Mock_1.0µM_MG132

value: 1.0 microM_MG132


title: 3_T-N1G_Vehicle


title: 2_Mock_Vehicle


title: PRO_DMSO-3h_PAF1-fkbp_DLD1_Batch9

value: untreated


title: PRO_DMSO-3h_FP-1h_PAF1-fkbp_DLD1_Batch9


title: 434_Wang_ChIP_anti_GFP_AtWX179_ATGN_250uMIPTG4h

description: ChIP using anti-GFP antibodies


title: 433_Wang_input_AtWX228_ATGN_250uMIPTG4h


title: PRO_dTAG-3h_PAF1-fkbp-DLD1_rep2_Batch9


title: 440_Wang_WGS_AtWX295_ATGN

treatment_protocol:
Cells were growing in ATGN at 30˚C, fixed by 3% formaldehyde for 30min at room temperature
None

value: ATGN, 30˚C


title: 1_T-N1G_Vehicle


title: PRO_DMSO-3h_PAF1-fkbp-DLD1_rep2_Batch9


title: 1_T-N1G_0.3µM_MG132

value: 0.3 microM_MG132


title: 1_T-N1G_1.0µM_MG132


title: PRO_dTAG-3h_PAF1-fkbp_DLD1_rep1_Batch8


title: 432_Wang_ChIP_anti_GFP_AtWX228_ATGN_250uMIPTG4h

description: ChIP using anti-GFP antibodies


title: 438_Wang_WGS_AtWX063_ATGN_rep2


title: 1_Mock_1.0µM_MG132


title: PRO_DMSO-3h_PAF1-fkbp_DLD1_rep1_Batch8


title: 429_Wang_HiC_AtWX192_LB_12h

treatment_protocol:
Cells were growing in LB at 30˚C for 12h, fixed by 3% formaldehyde for 30min at room temperature
None

value: LB, 30˚C

tag: restriction enzyme

value: HindIII


title: 430_Wang_ChIP_anti_GFP_AtWX226_ATGN_250uMIPTG4h

description: ChIP using anti-GFP antibodies


title: 431_Wang_input_AtWX226_ATGN_250uMIPTG4h


title: ChIP-H3K4Me3_dTAG-24h_PAF1-fkbp-DLD1_Batch7

data_processing:
ChIP-Rx: paired raw reads were quality checked with FastQC v0.11.9 (Babraham-Institute) and trimmed by Trim Galore v0.6.6 (Babraham-Institute) with the parameter “-q 25” to remove adaptors and low-quality reads. Then the remaining reads were aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 (Langmead and Salzberg, 2012). Duplicates and low mapping quality reads were removed using Picard v2.23.3 (Broad-Institute) and SAMtools v1.9 (Li et al., 2009). The number of spike-in mm10 reads was counted with SAMtools v1.9 and used to generate normalization factor alpha = 1e6/mm10_count for coverage profiles (Li et al., 2009). Normalized bigwig files were generated with deepTools v3.5.0 (Ramirez et al., 2016) and peaks were called using MACS 2.1.0 (Zhang et al., 2008). The called peaks overlapped with ENCODE Blacklist regions (Amemiya et al., 2019) were further removed by BEDTools v2.29.2 (Quinlan and Hall, 2010).
PRO-seq: The PRO-seq raw reads were processed with Trim Galore v0.6.6 (Babraham-Institute) and reads shorter than 15 bp after clipping were discarded. Ribosomal RNA reads were removed by Bowtie v2.3.5.1 with “--un-conc-gz” (Langmead and Salzberg, 2012). Then the remaining reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with the parameter “--very-sensitive-local” (Langmead and Salzberg, 2012). PCR duplicate and low-quality reads were removed. The normalization factor was calculated the same as described in ChIP-Rx. Strand-specific normalized bigwig files were generated with deepTools v3.5.0 (Ramirez et al., 2016).
TT-seq: The TT-seq raw reads were trimmed with Trim Galore v0.6.6 (Babraham-Institute)  and then aligned to hg19 or mm10 genome using STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate” (Langmead and Salzberg, 2012). We removed duplicates and low-quality reads and kept only properly paired reads for the downstream analyses. The number of spike-in mm10 reads was counted to generate the normalization factor. Strand-specific normalized bigwigs were generated with deepTools v3.5.0 (Ramirez et al., 2016).
RNA-seq: Raw reads were first trimmed by Trim Galore v0.6.6 (Babraham-Institute), followed by mapping to hg19 or mm10 genome using STAR v2.7.5c with parameters “--outSAMtype BAM SortedByCoordinate –twopassMode Basic --outFilterMismatchNmax 2” (Langmead and Salzberg, 2012). Duplicates and low-quality reads were removed, and reads mapped in proper pairs were isolated using SAMtools v1.9 with parameter “-f 2” (Li et al., 2009). The normalization factor was calculated the same as described in ChIP-Rx. Strand-specific Normalized bigwigs were generated.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig


title: ChIP-H3K4Me3_dTAG-3h_PAF1-fkbp-DLD1_Batch7


title: 1_Mock_0.3µM_MG132


title: 435_Wang_input_AtWX179_ATGN_250uMIPTG4h


title: 1_Mock_Vehicle


title: ChIP-H3K4Me3_DMSO_PAF1-fkbp-DLD1_Batch7


title: 23_Total

city: Urbana

first: Liqing

last: Chen

state: IL

address: 1201 W Gregory Dr

department: Plant Biology

institute: University of Illinois at Urbana Champaign

description:
Removed
None
None

data_processing:
FastQC/.11.8-Java-1.8.0_152 was used to filter FastQ files, which were subsequently trimmed using Trimmomatic/.038-Java-1.8.0_152 to a minimum length of 60bp.
Reads were aligned to the exon set of the Araport11 genome with STAR/2.7.6a-IGB-gcc-8.2.0 with a minimum match length of 35.
Counts were produced from the BAM files by using featCounts from the package Subread/2.0.0-IGB-gcc-8.2.0
TPM values were calculated manually with R.
Genome_build: Araport11
Supplementary_files_format_and_content: TPM text files in tab-delimited format.

organism: Arabidopsis thaliana

source_name: Arabidopsis

growth_protocol: p35s: HF-RPL18 transgenic plants were grown under normal condition (10h light/14 h dark, 22-23 ℃, 100-110 μmol photon m −2 ⋅s −1) for 6-week (before bolting) in the hydroponic culture system according to Zeng et al. (2018).

extract_protocol:
The ribosome-associated RNA was conducted according to Reynoso et al. (2015). Total RNA was extracted using TRIzol (Fisher Scientific, 15596018).
Libraries of total mRNA and ribosome-associated mRNA were prepared using KAPA mRNA HyperPrep Kit (KR1352) according to manufacturer’s protocol.

treatment_protocol: Plants were then transferred to Mg deficiency condition (MgD) or normal nutrition condition to treat for 1 day. For MgD medium, MgSO4·7H2O was replaced with Na2SO4·10H2O.

tag: age

value: 6-week plants

tag: tissue

value: root

value: Mg deficiency treatment for 24h


title: 14_Total

description:
Removed
None
None

value: normal growth


title: 2_T-N1G_Input

data_processing:
Illumina bcl2fastq v2.16.0.10 was used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 v2.2.9.
Peaks were called using MACS2 version2.1.4
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS2.

extract_protocol:
The cells were fixed with 1% formaldehyde for 10 min at room temperature and subsequently quenched with 0.125 M glycine. ChIP was performed with anti-MafG antibody ().The antibody incubation were pereformed overnight at 4℃.
Purified ChIPed DNA and input DNA were used for preparing the sequencing libraries by a NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Cells were treated with Vehcle or 1.0 µM  Proteasome Inhibitor (MG132)  for 4hr.

value: Input

value: none (input)


title: 2_Mock_0.3µM_MG132


title: 11_Total

description:
Removed
None
None

value: rosette leaf


title: ChIP-input_DMSO_PAF1-fkbp-DLD1_Batch7

value: colorectal adenocarcinoma cell lines

value: input


title: 1_Total

description:
Removed
None
None


title: 2_T-N1G_MG132_ChIPed

value: embryonic fibroblast

value: 1.0 microM MG132

value: anti-MafG antibody


title: 2_T-N1G_Veh_ChIPed

value: Vehicle


title: ChIP-H3K36Me3_dTAG-3h_PAF1-fkbp-DLD1_Batch6

value: treated with dTAG-13


title: 9_ribosome-associated RNA

description:
ribosome-associated RNA
Removed
None
None


title: 3_ribosome-associated RNA


title: 12_ribosome-associated RNA


title: ChIP-input_dTAG-3h_PAF1-fkbp-DLD1_Batch6


title: ChIP-H3K36Me3_dTAG-24h_PAF1-fkbp-DLD1_Batch6


title: 4_ribosome-associated RNA


title: ChIP-H2BUb_dTAG-24h_PAF1-fkbp-DLD1_Batch6


title: 1_T-N1G_MG132_ChIPed


title: 1_T-N1G_Veh_ChIPed


title: 1_T-N1G_Input


title: Shoot TRAP MgD_rep3

description:
ribosome-associated RNA
TPM_data.txt
Count_data.txt


title: ChIP-input_dTAG-24h_PAF1-fkbp-DLD1_Batch6


title: Shoot TRAP MgD_rep2


title: ChIP-H3K36Me3_DMSO_PAF1-fkbp-DLD1_Batch6

value: untreated


title: MM.1S_Ikaros_ChIP

city: Yakushiji

first: NAOKI

last: OSADA

address: Tochigi

department: Center for Molecular Medicine

institute: Jichi Medical University

data_processing:
Basecalls performed using bcl2Fastq version 2.20
ChIP-seq reads were aligned to the hg38 genome assembly using bwa version 0.7.12
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is implemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
The two main peak callers used at Active Motif are MACS(v2.1.0) and SICER(v1.1) .MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II).
Genome_build: hg38

source_name: Multiple Myeloma

growth_protocol: We cultured MM.1S cells in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and isolated with anti-IKZF1 antibody.
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.

treatment_protocol: No treatment

value: Multiple Myeloma_MM.1S

value: Hematopoietic cells


title: MM.1S_Ikaros_input


title: MM.1S_c-Fos_input

data_processing:
Basecalls performed using bcl2Fastq version 2.20
ChIP-seq reads were aligned to the hg38 genome assembly using bwa version 0.7.12
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is implemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
The two main peak callers used at Active Motif are MACS2(v2.1.0) and SICER(v1.1) .MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II).
Genome_build: hg38

growth_protocol: We cultured MM.1S cells  in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and isolated with anti-c-fos antibody.
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.

treatment_protocol: Untreatment


title: Shoot TRAP MgD_rep1

value: 6-week plants


title: ChIP-H2BUb_DMSO_PAF1-fkbp-DLD1_Batch6


title: Shoot TRAP CK_rep3


title: ChIP-input_DMSO_PAF1-fkbp-DLD1_Batch6


title: ChIP-TOTAL-SPT5_dTAG-3h_PAF1-fkbp-DLD1_Batch5


title: IgG_C42B_JQ1

city: gainesville

first: jiqiang

last: yao

state: United States

address: 9453 nw 24th rd

institute: moffitt cancer center

data_processing:
Illumina HiSeq pair-end reads from RNA-Seq libraries were alignmed with human reference genome build hg19 using bwa
then peak call was made using macs2 with controls; pvalue was set at 0.01
Genome_build: hg19
Supplementary_files_format_and_content: bdg format; fragment coverage profile

source_name: prostate cancer cell line

growth_protocol: C4-2B were grown as described in Mahajan K et al (Cancer Cell, 2017)

extract_protocol:
Chromatin was prepared as described in Nerlakanti et al (MCT, 2018). Chromatin was cross-linked with formaldehyde prepared according to the Active Motif protocol. Genomic DNA was purified using the Qiagen PCR purification kit. Samples were quantitated using Nanodrop.
Chromatin immunoprecipitation sequencing (ChIP-seq) was performed by the Molecular Genomics Core Facility at the Moffitt Cancer Center.  One to ten nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA). The size and quality of the library was evaluated using the Agilent BioAnalyzer, and the library was quantitated with the Kapa Library Quantification Kit.  Each enriched DNA library was then sequenced on an Illumina NextSeq 500 sequencer to generate 40-50 million 75-base paired-end reads.  The raw sequence data were aligned using BowTie 2, and the binding sites were identified using the MACS peak-finding software.

treatment_protocol: C4-2B were treated with DMSO (Vehicle), Enzalutamide (10 uM), JQ1 (2.5 uM) for 24h and harvested for chromatin immunoprecipitation.

value: cell line of tumor origin

tag: type

value: androgen-independent, metastatic


title: IgG_C42B_ENZ

value: Enzalutamide (10 micromolar)


title: Shoot TRAP CK_rep1

value: normal growth


title: ChIP-RTF1_dTAG-3h_PAF1-fkbp-DLD1_Batch5


title: Shoot Total MgD_rep2

description:
TPM_data.txt
Count_data.txt

value: Mg deficiency treatment for 24h


title: MM.1S_c-Fos_ChIP


title: ChIP-TOTAL-SPT5_DMSO_PAF1-fkbp-DLD1_Batch5


title: HBA_C42B_ENZ


title: HBA_C42B_JQ1


title: Shoot Total MgD_rep3

description:
TPM_data.txt
Count_data.txt

value: rosette leaf


title: IgG_C42B_DMSO

value: DMSO


title: ChIP-RTF1_DMSO_PAF1-fkbp-DLD1_Batch5

value: colorectal adenocarcinoma cell lines


title: Shoot Total MgD_rep1

description:
TPM_data.txt
Count_data.txt


title: HBA_C42B_DMSO


title: ChIP-input_dTAG-3h_PAF1-fkbp-DLD1_Batch5

value: input


title: ChIP-H2BUb_dTAG-3h_PAF1-fkbp-DLD1_Batch6


title: Shoot Total CK_rep3

description:
TPM_data.txt
Count_data.txt


title: ChIP-input_DMSO_PAF1-fkbp-DLD1_Batch5


title: Root TRAP MgD_rep3

value: root


title: ChIP-INT11_dTAG-3h_PAF1-fkbp-DLD1_rep2_Batch4


title: ChIP-input_dTAG-3h_PAF1-fkbp-DLD1_rep2_Batch4


title: Shoot Total CK_rep2

description:
TPM_data.txt
Count_data.txt


title: ChIP-INT11_DMSO_PAF1-fkbp-DLD1_rep2_Batch4


title: Root TRAP MgD_rep2


title: Shoot Total CK_rep1

description:
TPM_data.txt
Count_data.txt


title: ChIP-input_DMSO_PAF1-fkbp-DLD1_rep2_Batch4


title: Root TRAP MgD_rep1


title: Root TRAP CK_rep3


title: ChIP-INT11_dTAG-3h_PAF1-fkbp-DLD1_rep1_Batch3


title: Shoot TRAP CK_rep2


title: ChIP-input_dTAG-3h_PAF1-fkbp-DLD1_rep1_Batch3


title: Root TRAP CK_rep2


title: ChIP-INT11_DMSO-3h_PAF1-fkbp-DLD1_rep1_Batch3


title: Root TRAP CK_rep1


title: ChIP-input_DMSO-3h_PAF1-fkbp-DLD1_rep1_Batch3


title: Root Total MgD_rep3

description:
TPM_data.txt
Count_data.txt


title: Root Total MgD_rep2

description:
TPM_data.txt
Count_data.txt


title: ChIP-P-SPT5_dTAG-3h_PAF1-fkbp-DLD1_Batch2


title: Root Total MgD_rep1

description:
TPM_data.txt
Count_data.txt


title: ChIP-PAF1_dTAG-3h_PAF1-fkbp-DLD1_rep2_Batch2


title: Root Total CK_rep3

description:
TPM_data.txt
Count_data.txt


title: ChIP-input_dTAG-3h_PAF1-fkbp-DLD1_rep2_Batch2


title: Root Total CK_rep2

description:
TPM_data.txt
Count_data.txt


title: ChIP-PAF1_DMSO-3h_PAF1-fkbp-DLD1_rep2_Batch2


title: NKO mice_snRNA-seq_NKO_female rep2

city: Beijing

first: Qing-Feng

last: Wu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

description: C_NKO mice snRNA-seq_neurons_50872.rds

data_processing:
CellRanger Mkfatsq/Count Analysis
For scRNA-seq or snRNA-seq, the matrix files arising from different batches of experiments were subsequently integrated and analyzed using Seurat v3 software. For quality control, cells or nuclei with more than 10% mitochondrial gene counts were removed. In addition, cells with less than 600 genes or 500 UMIs were filtered out from the analysis, while nuclei were filtered on the basis of gene detection between 800 and 8,000.
CUT&Tag data were mapped to mouse (mm9) reference genome using Bowtie2 software. Only paired-end reads with both ends mapped correctly were kept for further analysis. All multimapped reads were removed using SAMtools for further analysis and duplicate reads were removed using Sambamba software. Peak calling was performed using peak calling algorithm MACS2.
Genome_build: mm10 for RNA-seq, mm9 for CUT&Tag
Supplementary_files_format_and_content: Lineage tracing experiment: A_TA lineage tracing_total cells_9224.rds; Tbx3 knockout experiment: B_NKO mice scRNA-seq_total cells_45406.rds, C_NKO mice snRNA-seq_neurons_50872.rds. RDS files are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with `readRDS(“A_TA lineage tracing_total cells_9224.rds”)`. It contains the gene counts, sample metadata, and feature metadata for single cell / nucleus that passed quality control.
Supplementary_files_format_and_content: CUT&Tag experiment: D_02_89-Ab-WT_peak_summits.motif.bed, D_03_89-Ab-WT_peak_summits.motif.bed. BED is used to save genomic data and linked annotations in a text format. BED files can be read and modified using bedtools, Integrative Genomics Viewer (IGV) and UCSC genome browser.

source_name: Hypothalamus (Tuberal and Mammillary zones)

extract_protocol:
Lineage tracing experiment: Hypothalamus were dissected from Tbx3-CreER::Ai14 mice (E9 > P12). Then Tbx3-derived cells were isolated by FACS and sequenced by scRNA-seq. Tbx3 knockout experiment: Tuberal and mammillary zones of hypothalamus were dissected from NKO mice and its littermate control. Then tissue were dissociated into single cell for scRNA-seq, or were ground to power to extract the nuclei for snRNA-seq. CUT&Tag experiment: Hypothalamus were dissected from NKO mice and its littermate control and ground to power to extract the nuclei for CUT&Tag.
We took advantage of DNBSEQTM technology platforms (BGI Genomics, China) and DNBelab C4 Single-Cell Library Prep Set (MGI, #1000021082) for single-nucleus RNA library preparation. And we followed the manufacturer’s recommendations for the 10x Genomics 3’ Gene Expression v3 chemistry to prepare single-cell RNA library. For CUT&Tag library, DNA samples were processed with TruePrep DNA Library Prep kit (Vazyme; #TD501-01) according to manufacturer’s instructions.

tag: strain background

value: Brain

value: Postnatal day 14

value: NKO


title: Root Total CK_rep1

description:
TPM_data.txt
Count_data.txt


title: ChIP-P-SPT5_DMSO-3h_PAF1-fkbp-DLD1_Batch2

value: untreated


title: ChIP-input_DMSO-3h_PAF1-fkbp-DLD1_rep2_Batch2


title: ChIP-LEO1_DMSO-3h_PAF1-fkbp-DLD1_rep2_Batch2


title: NKO mice_snRNA-seq_NKO_female rep1

description: C_NKO mice snRNA-seq_neurons_50872.rds

value: Hypothalamus (Tuberal and Mammillary zones)


title: ChIP-PAF1_dTAG-3h_PAF1-fkbp-DLD1_rep1_Batch1

value: treated with dTAG-13


title: NKO mice_snRNA-seq_NKO_male rep3

description: C_NKO mice snRNA-seq_neurons_50872.rds


title: NKO mice_snRNA-seq_NKO_male rep1

description: C_NKO mice snRNA-seq_neurons_50872.rds


title: NKO mice_snRNA-seq_NKO_male rep2

description: C_NKO mice snRNA-seq_neurons_50872.rds


title: ChIP-LEO1_dTAG-3h_PAF1-fkbp-DLD1_rep1_Batch1


title: ChIP-input_dTAG-3h_PAF1-fkbp-DLD1_rep1_Batch1


title: ChIP-PAF1_DMSO-3h_PAF1-fkbp-DLD1_rep1_Batch1


title: NKO mice_snRNA-seq_WT_female rep2

description: C_NKO mice snRNA-seq_neurons_50872.rds

value: Wildtype


title: NKO mice_snRNA-seq_WT_female rep1

description: C_NKO mice snRNA-seq_neurons_50872.rds


title: NKO mice_snRNA-seq_WT_male rep3

description: C_NKO mice snRNA-seq_neurons_50872.rds


title: NKO mice_snRNA-seq_WT_male rep1

description: C_NKO mice snRNA-seq_neurons_50872.rds


title: NKO mice_snRNA-seq_WT_male rep2

description: C_NKO mice snRNA-seq_neurons_50872.rds


title: ChIP-input_DMSO-3h_PAF1-fkbp-DLD1_rep1_Batch1


title: 2wSD_RNAi_rep3

city: Madrid

first: Rafael

last: Torres

state: Madrid

address: Darwin 3

department: Bioinformatics for Genomics and Proteomics (BioinfoGP)

country: Spain

institute: CNB

description:
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt
2wSD_WT-vs-2wSD_RNAi.diffexp.txt
LD_RNAi-vs-2wSD_RNAi.diffexp.txt
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2wSD_WT-vs-2wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
sequencing sample name: 2W-A5-3

data_processing:
24 samples of Solanum tuberosum (spp. andigena) were sequenced by BGI on BGISEQ-500 Platform, generating about 7.01 Gb per sample. Pair-end reads of 100 bp were generated.
RNA-Seq paired-ends reads were filtered using SOPAnuke v1.5.2 to remove reads with adaptors, having more than 5% unknown bases or with poor base quality (more than 20% bases having quality <15)
The cleaned reads were then aligned to the PGSC_DM_v4.03_pseudomolecules reference genome (Sharma et al., 2013, available at http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml) using HISAT v2.0.4 with the sensitive mode, options no-discordant and no-mixed, minimum fragment size 1 and maximum fragment size to 1000
Reads per gene quantification for each sample was performed using the function featureCounts implemented in the R package Rsubread v2.0.0 with the http://solanaceae.plantbiology.msu.edu/data/PGSC_DM_V403_genes.gff.zip file (downloadable in http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml) as genome annotation and parameter isPairedEnd=TRUE
Differentially Expressed Genes were calculated for 16 comparisons between conditions using the R package DESeq2 v1.26.0 with default values
Genome_build: http://solanaceae.plantbiology.msu.edu/data/PGSC_DM_v4.03_pseudomolecules.fasta.zip (accessible from Spud DB Potato Genomics Resource: http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml )
Supplementary_files_format_and_content: 16 tab-delimited text files with the DESeq2 as-is result for 16 comparisons (DESeq2 output format)
Supplementary_files_format_and_content: 16 tab-delimited text files with the raw & normalized counts, log2 fold change, p-value, adjusted p-value and other info for the DESeq2-computed differential expression in 16 comparisons

organism: Solanum tuberosum subsp. andigenum

source_name: Axillary buds

growth_protocol: Plants were grown in the greenhouse for 6 weeks

extract_protocol:
Stem were flash-frozen in N2(l) one hour after dawn and the axillary buds were dissected in the cold room. The four axillary buds below the third visible node counting from the apex were collected. RNA was extracted with FavorPrep™ Plant Total RNA Mini Kit from FAVORGEN. DNA was degraded in the column with RNase-free DNase I (Roche). Each replicate is a pool of axillary buds from 4 plants.
Library construction was performed by BGI  Genomics following standard Ilumina protocol

treatment_protocol: Afterwards plants were placed in a LD growth chamber for 1 week. After one week, samples corresponding to the long-day time point were collected. Growth chamber photoperiod was then set to SD. The following day corresponds to the first day in SD.

value: Axillary buds

value: BRC1b RNAi

value: 2 week in Short Days


title: IBD GSDMB 2

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

description: Stably transfected with mutant GSDMB; glycine to arginine at position 299 and proline to serine at position 306

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM.
Differential expression analysis was done using Cuffdiff.
Genome_build: GRCh38
Supplementary_files_format_and_content: genematrix.tsv: Tab-delimited text file containing FPKM for all samples and genes.

source_name: HT-29 cells

growth_protocol: All cell lines were grown at 37°C under 5% CO2 McCoy’s 5A medium modified with L-glutamine and sodium bicarbonate, supplemented with 10% FBS and 2% penicillin/streptomycin.

extract_protocol:
Total RNA was harvested from HT-29 cells and colonoids using High Pure RNA Isolation Kits (Roche Life Science, 11828665001).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: Colonic epithelial cell line

value: CRISPR cas9 GSDMB-KO

tag: stable transfection


title: TT-seq_dTAG-3h_PAF1-fkbp-DLD1_Batch10

data_processing:
Raw reads were trimmed by Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality sequences (-q 25)
The remaining reads were mapped to hg19 or mm10 genome with STAR v2.7.5c with parameters “--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 -outSAMtype BAM SortedByCoordinate”
Duplicates and low-quality reads were removed, and only properly paired reads were kept.
The counts of reads mapping to spike-in mm10 reads were used to generate the normalization factor.
Strand-specific normalized bigwigs were generated by deeptools v3.5.0 (Ramirez et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.


title: TT-seq_DMSO-3h_PAF1-fkbp-DLD1_Batch10


title: 2wSD_RNAi_rep2

description:
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt
2wSD_WT-vs-2wSD_RNAi.diffexp.txt
LD_RNAi-vs-2wSD_RNAi.diffexp.txt
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2wSD_WT-vs-2wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
sequencing sample name: 2W-A5-2


title: ChIP-LEO1_dTAG-3h_PAF1-fkbp-DLD1_rep2_Batch2


title: IBD GSDMB 1

value: mutant GSDMB; glycine to arginine at position 299 and proline to serine at position 306


title: vehicle control treated CD16+ monocytes - replicate 6

city: Philadelphia

first: Steven

middle: D

last: Douglas

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: The Children's Hospital of Philadelphia

data_processing:
Illumina NovaSeq software was used to create sequencing files
STAR software was used to align sequencing data to the  Ensembl hg38 genome with parameters  --runMode alignReads --runThreadN 20 --readFilesCommand zcat --twopassMode Basic
HTSeq was used to count reads with the htseq-count command using the folowing parameters   -f sam -r name -s no -a 10 -i gene_id -m intersection-strict sorted.sam
Genome_build: hg38
Supplementary_files_format_and_content: .out count files for each sample

source_name: primary monocytes

extract_protocol:
RNA was purified from sorted monocytes with the Qiagen RNeasy Mini Kit. For each sample 200 ng of RNA was used to construct libraries with he Illumina TruSeq stranded total RNA library Prep kit
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For SP treatment, monocytes were incubated for 3 hours at 37°C with 10 µM SP. For vehicle control treatment, monocytes were incubated for 3 hours at 37°C with or 50 µM acetic acid.

value: blood

tag: cell subset

value: CD16+ monocytes

tag: donor sex

value: male

tag: donor age

tag: cell treatment

value: vehicle control treatment


title: 2wSD_WT_rep3

description:
2wSD_WT-vs-2wSD_RNAi.diffexp.txt
1wSD_WT-vs-2wSD_WT.diffexp.txt
2SD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-2wSD_WT.diffexp.txt
2wSD_WT-vs-2wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-2wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2wSD_WT.diffexp.txt.deseq2
sequencing sample name: 2W-WT3

value: wild type

tag: treatment


title: Substance P treated CD16- monocytes - replicate 6

value: CD16- monocytes

value: Substance P treatment


title: 2wSD_RNAi_rep1

description:
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt
2wSD_WT-vs-2wSD_RNAi.diffexp.txt
LD_RNAi-vs-2wSD_RNAi.diffexp.txt
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2wSD_WT-vs-2wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
sequencing sample name: 2W-A5-1


title: vehicle control treated CD16- monocytes - replicate 6


title: WT GSDMB 1

description: Stably transfected with canonical GSDMB

value: canonical GSDMB


title: 2wSD_WT_rep1

description:
2wSD_WT-vs-2wSD_RNAi.diffexp.txt
1wSD_WT-vs-2wSD_WT.diffexp.txt
2SD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-2wSD_WT.diffexp.txt
2wSD_WT-vs-2wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-2wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2wSD_WT.diffexp.txt.deseq2
sequencing sample name: 2W-WT1


title: Substance P treated CD16+ monocytes - replicate 5

value: female


title: WT GSDMB 2

description: Stably transfected with canonical GSDMB


title: GSDMB-KO 3


title: vehicle control treated CD16+ monocytes - replicate 5


title: 1wSD_RNAi_rep3

description:
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt
1wSD_WT-vs-1wSD_RNAi.diffexp.txt
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt
LD_RNAi-vs-1wSD_RNAi.diffexp.txt
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-1wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
sequencing sample name: 1W-A5-3

value: 1 week in Short Days


title: GSDMB-KO 2


title: ChIP-LEO1_DMSO-3h_PAF1-fkbp-DLD1_rep1_Batch1

value: colorectal adenocarcinoma cell lines

tag: chip antibody

value: untreated


title: 1wSD_RNAi_rep2

description:
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt
1wSD_WT-vs-1wSD_RNAi.diffexp.txt
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt
LD_RNAi-vs-1wSD_RNAi.diffexp.txt
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-1wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
sequencing sample name: 1W-A5-2

value: Axillary buds

value: BRC1b RNAi


title: vehicle control treated CD16- monocytes - replicate 5


title: GSDMB-KO 1

tag: cell type

value: Colonic epithelial cell line


title: 1wSD_RNAi_rep1

description:
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt
1wSD_WT-vs-1wSD_RNAi.diffexp.txt
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt
LD_RNAi-vs-1wSD_RNAi.diffexp.txt
1wSD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-1wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
sequencing sample name: 1W-A5-1


title: IBD GSDMB 3

value: CRISPR cas9 GSDMB-KO


title: Substance P treated CD16+ monocytes - replicate 6


title: HT-29 2

value: WT


title: HT-29 3


title: 1wSD_WT_rep3

description:
1wSD_WT-vs-1wSD_RNAi.diffexp.txt
1wSD_WT-vs-2wSD_WT.diffexp.txt
2SD_WT-vs-1wSD_WT.diffexp.txt
LD_WT-vs-1wSD_WT.diffexp.txt
1wSD_WT-vs-1wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-2wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-1wSD_WT.diffexp.txt.deseq2
LD_WT-vs-1wSD_WT.diffexp.txt.deseq2
sequencing sample name: 1W-WT3


title: Substance P treated CD16- monocytes - replicate 4

value: blood


title: HT-29 1


title: vehicle control treated CD16- monocytes - replicate 4


title: vehicle control treated CD16+ monocytes - replicate 4

value: CD16+ monocytes


title: 2SD_RNAi_rep3

description:
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt
2SD_WT-vs-2SD_RNAi.diffexp.txt
LD_RNAi-vs-2SD_RNAi.diffexp.txt
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2SD_WT-vs-2SD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2SD_RNAi.diffexp.txt.deseq2
sequencing sample name: SD2-A5-3

value: 2 days in Short Days


title: 2SD_RNAi_rep2

description:
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt
2SD_WT-vs-2SD_RNAi.diffexp.txt
LD_RNAi-vs-2SD_RNAi.diffexp.txt
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2SD_WT-vs-2SD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2SD_RNAi.diffexp.txt.deseq2
sequencing sample name: SD2-A5-2


title: Substance P treated CD16+ monocytes - replicate 4

value: male


title: Day 30 cardiac fibroblast cells

city: Palo Alto

first: Laksshman

last: Sundaram

state: California

address: stanford

department: Computer science

institute: Stanford University

description: Day 30 cardiac fibroblast aligned tn5 insertion fragments

data_processing:
fastqs generated using bcl2fastq utility
scATAC reads aligned to hg38 using cellranger-atac v1 software
Genome_build: hg38
Supplementary_files_format_and_content: fragment files indicating tn5 insertions along with the single cell barcode

source_name: iPS derived cardiac fibroblast

growth_protocol: To generate cardiac-specific fibroblasts, iPSC-derived epicardial cells were dissociated with accutase into singlets and a density of 104 cells/cm2 were seeded in fibroblast growth medium supplemented with 20 ng/ml FGF2 and 10 μM SB431542. The cells were refreshed with the same medium every other day for 6 days before being re-plated in a 1:3 ratio in fibroblast growth medium supplemented with 10 μM SB431542 only for long-term maintenance. The generated fibroblasts exhibit a quiescent phenotype with negligible (< 5%) α-SMA expression for at least five passages

extract_protocol:
Samples were dissociated in digestion buffer(Liberase TM, 0.5 mg/ml; DNase I, 20 mg/ml; HEPEs, 10mM) and resuspended in ice-cold PBS + 0.02% BSA. For ATAC-seq, resuspension buffer (RSB) and lysis buffer (ALB) were prepared ice-cold. RSB: 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2. ALB: RSB + 0.1 % Tween-20 + 0.1% NP-40. Dissociated cells were counted and 100,000 cells were incubated for 5 minutes on ice in 100 uL ALB. ALB was diluted by adding 900 uL RSB, then samples were centrifuged at 500 x g for 5 minutes at 0 C. Nuclei were resuspended in 1X Nuclei Dilution Buffer (10X), checked for complete lysis, and counted. 4,000 cells per channel were loaded onto the Chromium 10X controller for ATAC, and 10,000 cells were loaded for RNA.
Libraries were constructed using the 10X Genomics scATAC-seq kits

tag: differentiation day

value: Day 30


title: Day 30 epicardial cells

description: Day 30 epicardial cells aligned tn5 insertion fragments

source_name: iPS derived epicardial cells

growth_protocol: The iPSC-derived epicardial cells were differentiated in a chemically defined medium (CDM), which is made of 50% IMDM, 50% Ham’s F-12 Nutrient Mix, 1% chemically defined lipid concentrate, 2 mM Glutamax, 1 mg/ml PVA, 15 μg/ml transferrin, and 450 μM monothioglycerol. Briefly, when iPSCs reached ~80% confluency, 1 ml of Accutase was added to each well for 3-5 min. When iPSCs became granular, 1 ml of Brew medium + 10 μM Y27632 was perpendicular added to each well and iPSCs were triturated to singlets. A low density of 1.5´ 104 cells/cm2 iPSCs were evenly distributed to each well to allow attachment in Brew + 10 μM Y27632 medim. Each well was washed with DPBS in the next day, and epicardial cells differentiation (day 1) was initiated by adding the mid-primitive streak induction medium (consisting of 10 ng/ml Activin A, 6 μM CHIR99021, 50 ng/ml BMP4, 20 ng/ml FGF2, and 2 μM LY294002 in CDM). At day 2, each well was refreshed with the lateral plate mesoderm induction medium (consisting of 1 μM A83-01, 30 ng/ml BMP4, and 1 μM C59 in CDM). At days 3-4, each well was refreshed with the splanchnic mesoderm induction medium (consisting of 1 μM A83-01, 30 ng/ml BMP4, 1 μM C59, 20 ng/ml FGF2, and 2 μM retinoic acid in CDM). At days 5-8, each was refreshed with the septum transversum induction medium (consisting of 2 μM retinoic acid and 40 ng/ml BMP4 in CDM). At day 9, cells were dissociated into singlets using accutase, and sparsely seeded (1´ 104 cells/cm2) on gelatin-coated 6-well plates in the proepicardium induction medium (consisting of 100 μg/ml ascorbic acid, 2 μM of retinoic acid, and 0.7 μg/ml insulin in CDM) for 2 days without medium change. Starting at day 11, each well was refreshed every other day with the epicardial cell induction/maintenance medium (consisting of 100 μg/ml ascorbic acid, 10 μM SB431542, and 0.7 μg/ml insulin in CDM). The iPSC-derived epicardial cells can preserve their cell type-specific markers (e.g., TBX18, WT1, and TCF21) for at least 18 passages in the epicardial cell induction/maintenance medium in our hands.


title: Substance P treated CD16+ monocytes - replicate 3


title: 2wSD_WT_rep2

description:
2wSD_WT-vs-2wSD_RNAi.diffexp.txt
1wSD_WT-vs-2wSD_WT.diffexp.txt
2SD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-2wSD_WT.diffexp.txt
2wSD_WT-vs-2wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-2wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2wSD_WT.diffexp.txt.deseq2
sequencing sample name: 2W-WT2

value: wild type

value: 2 week in Short Days


title: 1wSD_WT_rep1

description:
1wSD_WT-vs-1wSD_RNAi.diffexp.txt
1wSD_WT-vs-2wSD_WT.diffexp.txt
2SD_WT-vs-1wSD_WT.diffexp.txt
LD_WT-vs-1wSD_WT.diffexp.txt
1wSD_WT-vs-1wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-2wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-1wSD_WT.diffexp.txt.deseq2
LD_WT-vs-1wSD_WT.diffexp.txt.deseq2
sequencing sample name: 1W-WT1


title: 2SD_RNAi_rep1

description:
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt
2SD_WT-vs-2SD_RNAi.diffexp.txt
LD_RNAi-vs-2SD_RNAi.diffexp.txt
2SD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
2SD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
2SD_WT-vs-2SD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2SD_RNAi.diffexp.txt.deseq2
sequencing sample name: SD2-A5-1


title: Day 30 smooth muscle cells

description: Day 30 smooth muscle cells aligned tn5 insertion fragments

source_name: iPS derived smooth muscle cells

growth_protocol: To generate cardiac-specific smooth muscle cells (SMCs), iPSC-derived epicardial cells were dissociated with accutase into singlets and a density of 3×104 cells/cm2 were seeded in the nascent SMC induction medium (consisting of 100 μg/ml ascorbic acid, 0.7 μg/ml insulin, 10 ng/ml Activin A, and 10 ng/ml PDGF-BB in CDM) for 2 days. Then cells were refreshed every other day with the SMC full growth medium (Medium 231 supplemented with SMGS) for at least 14 days to allow the expression of SMC-specific markers (e.g, TAGLN, CNN1, SMTNB, and MYH11).


title: Substance P treated CD16- monocytes - replicate 5

value: CD16- monocytes

value: Substance P treatment


title: WT GSDMB 3

description: Stably transfected with canonical GSDMB

value: canonical GSDMB


title: vehicle control treated CD16+ monocytes - replicate 3

value: female

value: vehicle control treatment


title: 2SD_WT_rep3

description:
2SD_WT-vs-1wSD_WT.diffexp.txt
2SD_WT-vs-2SD_RNAi.diffexp.txt
2SD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-2SD_WT.diffexp.txt
2SD_WT-vs-1wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-2SD_RNAi.diffexp.txt.deseq2
2SD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2SD_WT.diffexp.txt.deseq2
sequencing sample name: SD2-WT4

value: Axillary buds


title: Day 30 endothelial cells

description: Day 30 endothelial cells aligned tn5 insertion fragments

source_name: iPS derived endothelial cells

growth_protocol: The iPSCs used for this study were at passages 22 to 25. iPSCs were cultured as described above until reaching 80% confluence. The medium was switched to RPMI-B27 without insulin (Life Technologies) with 6 uM CHIR99021 for 2 days and then changed to 2 uM CHIR99021 for another 2 days. During the differentiation process, from days 4 to 12, the medium was changed to EGM2 (Lonza) supplemented with vascular endo- thelial growth factor (VEGF) (50 ng/ml) (PeproTech), bone mor- phogenetic protein 4 (BMP4) (20 ng/ml), and fibroblast growth factor 2 (FGF2) (20 ng/ml) (PeproTech). By day 12, cells were dis- sociated using TrypLE for 5 min and sorted using CD144-conjugated magnetic microbeads (Miltenyi Biotec) according to the manufac- turer’s instructions. CD144-positive cells were seeded on 0.2% gelatin- coated plates and maintained in EGM2 medium supplemented with 10 M transforming growth factor  (TGF) inhibitor (SB431542). (Selleckchem). After passage 2, iPSC-ECs were cultured in normal EGM2, without SB431542. The iPSC-ECs used for this study were all at passage 3.


title: vehicle control treated CD16- monocytes - replicate 3


title: 2SD_WT_rep2

description:
2SD_WT-vs-1wSD_WT.diffexp.txt
2SD_WT-vs-2SD_RNAi.diffexp.txt
2SD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-2SD_WT.diffexp.txt
2SD_WT-vs-1wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-2SD_RNAi.diffexp.txt.deseq2
2SD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2SD_WT.diffexp.txt.deseq2
sequencing sample name: SD2-WT2


title: Day 30 mature cardiomyocyte cells

description: Day 30 mature cardiomyocytes aligned tn5 insertion fragments

source_name: iPS derived mature cardiomyocytes

growth_protocol: Cardiomyocytes were differentiated using a monolayer method as previously described(refs)with minor modification. hiPSCs (passage 25-30) were seeded at 1.2 × 105 per well in Matrigel™-coated 6 cm culture wells and grown for four days prior to starting hiPSC-CM differentiation. To initiate differentiation, B27 without insulin (A1895601, Life Technologies) in RPMI supplemented with 6 µM CHIR-99021 (CT99021, Selleckchem) was added to the hiPSCs for two days. CHIR was removed from the cultures and cells were incu- bated for one day in RPMI supplemented with B27 without insulin. Cultures were then treated with 5 µM IWR-1 (I0161, Sigma) in RPMI supplemented with B27 without insulin for two days and incubated for two days with RPMI containing B27 without insulin. For two days, cultures were maintained in RPMI with B27 with insulin (17504-044, Life Technologies) and glucose starved for three days (using RPMI minus glucose). After glucose starvation, hiPSC-CMs were maintained in RPMI with B27. Cardiomyocyte differentiation was repeated three additional times and the cells were then processed for scATAC. Specific day time point of selected four different stages are day 0 (hiPSC), day 2 (MES), day 5 (CP), day 15 (PCM), and day 30 (CM).


title: Substance P treated CD16+ monocytes - replicate 2


title: Substance P treated CD16- monocytes - replicate 2


title: 2SD_WT_rep1

description:
2SD_WT-vs-1wSD_WT.diffexp.txt
2SD_WT-vs-2SD_RNAi.diffexp.txt
2SD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-2SD_WT.diffexp.txt
2SD_WT-vs-1wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-2SD_RNAi.diffexp.txt.deseq2
2SD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2SD_WT.diffexp.txt.deseq2
sequencing sample name: SD2-WT1


title: LD_RNAi_rep3

description:
LD_RNAi-vs-1wSD_RNAi.diffexp.txt
LD_RNAi-vs-2SD_RNAi.diffexp.txt
LD_RNAi-vs-2wSD_RNAi.diffexp.txt
LD_WT-vs-LD_RNAi.diffexp.txt
LD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2SD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
LD_WT-vs-LD_RNAi.diffexp.txt.deseq2
sequencing sample name: LD-A5-3

value: BRC1b RNAi

value: Long Days


title: Day 15 primitive cardiomyocyte cells

description: Day 15 primitive cardiomyocytes aligned tn5 insertion fragments

source_name: iPS derived primitive cardiomyocytes

value: Day 15


title: vehicle control treated CD16+ monocytes - replicate 2 [ND517]


title: Day 5 cardiac progenitor cells

description: Day 5 aligned tn5 insertion fragments

source_name: iPS derived cardiac progenitors

value: Day 5


title: LD_RNAi_rep2

description:
LD_RNAi-vs-1wSD_RNAi.diffexp.txt
LD_RNAi-vs-2SD_RNAi.diffexp.txt
LD_RNAi-vs-2wSD_RNAi.diffexp.txt
LD_WT-vs-LD_RNAi.diffexp.txt
LD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2SD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
LD_WT-vs-LD_RNAi.diffexp.txt.deseq2
sequencing sample name: LD-A5-2


title: Day 2 cardiac mesoderm cells

description: Day 2 aligned tn5 insertion fragments

source_name: iPS derived cardiac mesoderm

value: Day 2


title: 1wSD_WT_rep2

description:
1wSD_WT-vs-1wSD_RNAi.diffexp.txt
1wSD_WT-vs-2wSD_WT.diffexp.txt
2SD_WT-vs-1wSD_WT.diffexp.txt
LD_WT-vs-1wSD_WT.diffexp.txt
1wSD_WT-vs-1wSD_RNAi.diffexp.txt.deseq2
1wSD_WT-vs-2wSD_WT.diffexp.txt.deseq2
2SD_WT-vs-1wSD_WT.diffexp.txt.deseq2
LD_WT-vs-1wSD_WT.diffexp.txt.deseq2
sequencing sample name: 1W-WT2

value: 1 week in Short Days


title: LD_RNAi_rep1

description:
LD_RNAi-vs-1wSD_RNAi.diffexp.txt
LD_RNAi-vs-2SD_RNAi.diffexp.txt
LD_RNAi-vs-2wSD_RNAi.diffexp.txt
LD_WT-vs-LD_RNAi.diffexp.txt
LD_RNAi-vs-1wSD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2SD_RNAi.diffexp.txt.deseq2
LD_RNAi-vs-2wSD_RNAi.diffexp.txt.deseq2
LD_WT-vs-LD_RNAi.diffexp.txt.deseq2
sequencing sample name: LD-A5-1


title: Day 0 iPS cells

description: Day 0 aligned tn5 insertion fragments

source_name: iPS cell derived from human donor

growth_protocol: Peripheral blood mononuclear cells were collected, and non-integrative Sendai virus (CytoTune™-iPS 2.0 Sendai Reprogramming Kit, Thermo Fisher Scientific) reprogramming was used to generate iPSCs. hiPSC colonies were picked and expanded until passage 10 before being used in experiments outlined below. hiPSCs were tested to be mycoplasma negative using the Mycoalert Mycoplasma testing kits (LT07-318, Lonza). hiPSC clone karyotype was assessed through a single nucleotide polymorphism assay, and one single clone was used for the next experiments. All iPSCs used for the subsequent studies were within passages 25 to 30. Daily iPSC maintenance was performed with defined E8 medium (Life Technologies) on cell culture plates coated with human ESC-qualified Matrigel (BD Biosciences) under controlled environment (8% O2, 5% CO2) at 37 oC. For passaging, iPSCs were dissociated with Gentle Cell Dissociation Reagent (StemCell Technologies) and cultured on Matrigel plates with E8 medium supplemented with 5 μM Y-27632 (SelleckChem).

value: Day 0


title: LD_WT_rep3

description:
LD_WT-vs-1wSD_WT.diffexp.txt
LD_WT-vs-2SD_WT.diffexp.txt
LD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-LD_RNAi.diffexp.txt
LD_WT-vs-1wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2SD_WT.diffexp.txt.deseq2
LD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-LD_RNAi.diffexp.txt.deseq2
sequencing sample name: LD-WT3


title: Substance P treated CD16+ monocytes - replicate 1

value: blood

value: CD16+ monocytes

value: male


title: vehicle control treated CD16+ monocytes - replicate 1 [ND429]


title: Post conception week 6 human heart

description: PCW 6 aligned tn5 insertion fragments

source_name: Human tissue

value: Heart

tag: developmental stage

value: Post conception week (PCW) 6


title: LD_WT_rep1

description:
LD_WT-vs-1wSD_WT.diffexp.txt
LD_WT-vs-2SD_WT.diffexp.txt
LD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-LD_RNAi.diffexp.txt
LD_WT-vs-1wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2SD_WT.diffexp.txt.deseq2
LD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-LD_RNAi.diffexp.txt.deseq2
sequencing sample name: LD-WT1

tag: genotype

value: wild type


title: Post conception week 19 human heart

description: PCW 19 aligned tn5 insertion fragments

value: Post conception week (PCW) 30


title: LD_WT_rep2

description:
LD_WT-vs-1wSD_WT.diffexp.txt
LD_WT-vs-2SD_WT.diffexp.txt
LD_WT-vs-2wSD_WT.diffexp.txt
LD_WT-vs-LD_RNAi.diffexp.txt
LD_WT-vs-1wSD_WT.diffexp.txt.deseq2
LD_WT-vs-2SD_WT.diffexp.txt.deseq2
LD_WT-vs-2wSD_WT.diffexp.txt.deseq2
LD_WT-vs-LD_RNAi.diffexp.txt.deseq2
sequencing sample name: LD-WT2


title: Substance P treated CD16- monocytes - replicate 1

value: CD16- monocytes

value: Substance P treatment


title: Lean chow 3

status: Public on Jan 29 2022

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

data_processing:
Reads were mapped to the GRCm38.p89 Ensembl mouse genome using STAR v.2.5.2a with default parameters.
Counts in protein coding genes was quantified using STAR and can be found in supplementary.
Genome_build: GRCm38
Supplementary_files_format_and_content: .txt file of raw gene counts

source_name: Liver

extract_protocol: Illumina TruSeq Stranded mRNA Library Prep kit (#20020594, Illumina, San Diego, CA, USA)

value: Lean chow

tag: diet

value: Rodent chow

tag: time on diet

value: 36 weeks

value: Liver


title: DIO-NASH 3

value: DIO-NASH

value: AMLN diet

tag: tissue


title: DIO-NASH 4


title: Lean chow 4


title: Lean chow 5


title: DIO-NASH 2


title: DIO-NASH 1


title: Lean chow 2


title: Lean chow 1


title: Lesion

city: Seoul

first: Kyung Bae

last: Chung

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

country: South Korea

institute: Yonsei University College of Medicine

description: (barcode -1_2)

data_processing:
Illumina Casava1.9 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38 whole genome using Cell ranger v3.1.0
Read count extraction and normalization were performed using Seurat v4.0.5.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

extract_protocol:
Skin fresh tissue was achieved, and dispase was applied to achieve only dermal tissue. After enzymatic dissociation using 50 μg/mL of Liberase TL and 24 U/mL of DNase(Roche, Mannheim, Germany), viable cells were enriched using flow cytometry then were captured using Chromium GEM Single Cell 5' Kit v3 (10x Genomics, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nodular lesion


title: Nonlesion

description: (barcode -1_1)

value: non-lesional


title: KO2

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

institute: Michigan State University

data_processing:
After investigating the quality of the raw data (the quality was judged based on Illumina’s Q score, which represents the error rate at
each base, built on a log10 score), sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor
quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference mouse genome available on ENSEMBL (Mus musculus GRCm38) using the STAR aligner v.2.5.2b.
The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: WT vs KO with raw values in txt file

source_name: Ovary

extract_protocol:
Total RNA was extracted from freshly isolated granulosa cells from the WT and KO ovary samples using Qiagen RNeasy Plus Universal mini kit. The samples were sequenced using a 2x150bp Paired End (PE) configuration. The total number of reads/sample were 45-50 million. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq wereas converted into fastq files and de-multiplexed using Illumina'’s bcl2fastq 2.17 software. configuration. The total number of reads/sample were 45-50 million. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq wereas converted into fastq files and de-multiplexed using Illumina'’s bcl2fastq 2.17 software.
RNA sequencing libraries were prepared using 500 ng RNA, and the NEB Next Ultra RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: Granulosa cells were isolated from Wild type (WT) and Jmjd3 knock out (KO) mice

tag: strain

value: Granulosa cells

tag: age

value: 8-9 weeks

value: Jmjd3 knock out


title: KO3


title: KO1


title: CISPT_4

city: Bellinzona

first: Federico

last: Costanzo

address: Via Vela 6

country: Switzerland

institute: Institute of Oncology Research IOR

data_processing:
Processed using nf-core ChipSeq pipeline v1.0.0
Alingment with  BWA v0.7.17-r1188
peaks called with MACS2 v2.1.2 narrowpeak default
BigWig generated with bedtools bedgraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: SCLC cell lines

growth_protocol: All cell lines were cultured in the medium and conditions recommended by the supplier and supplemented with 10%FBS, 2nmol/L L-glutamine, and penicillin-streptomycin mix (Sigma).

extract_protocol: P2644 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: DMS53 cells were seeded in 15 cm dishes and grown to subconfluency before treatment with 50nM Lurbinectedin.

tag: ip antibody

value: Biotin antibody

value: treated with Cis-platin


title: WT2

value: wild type


title: WT3


title: WT1


title: LURBI_4

value: treated with PM01183


title: INPUT_4


title: INPUT_4_PT


title: vehicle control treated CD16- monocytes - replicate 2 [ND517]

value: blood

value: CD16- monocytes

value: female

value: vehicle control treatment


title: Post conception week 8 human heart

description: PCW 8 aligned tn5 insertion fragments

value: Heart

value: Post conception week (PCW) 8


title: vehicle control treated CD16- monocytes - replicate 1 [ND429]

value: male


title: KR4M0

first: Wei

last: Zhou

address: N0.280 South Chongqing Road

institute: Shanghai Jiao Tong University

data_processing:
Raw sequencing data generated from Illumina HiSeq 4000 that pass the Illumina chastity filter are used for  following analysis.
Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on  alignment statistical analysis (mapping ratio, rRNA/mtRNA content, fragment sequence bias), we determine  whether the results can be used for subsequent data analysis.
The expression profiling, differentially expressed genes and differentially expressed transcripts are calculated. The novel genes and transcripts are also  predicted. Principal Component Analysis (PCA), Correlation Analysis, Hierarchical Clustering, Gene Ontology  (GO), Pathway Analysis, scatter plots and volcano plots are performed for the differentially expressed genes in  R or Python environment for statistical computing and graphics.
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values for each Sample

source_name: Macrophage

growth_protocol: Macrophages(BMDMs) isolated from mice were differentiated for 7 d in the presence of recombinant mouse macrophage colony-stimulating factor (M-CSF; 20 ng/ml) in complete medium RPMI-1640 medium containing 10 mM glucose, 2 mM L-glutamine, 100 units/ml of penicillin-streptomycin and 10% FBS).

extract_protocol:
Macrophages were removed from dish, flash frozen on dry ice, and RNA was harvested using Trizol reagent.Samples were quantified on a NanoDrop ND-1000 instrument. Agarose electrophoresis was used to check the integrality of total RNA samples. 1 _x0018_ 2 _x0016_g total RNA of each sample was taken for RNA-seq library preparation.  Briefly, mRNA was isolated from total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module.  Alternatively, rRNA is removed from the total RNA with a RiboZero Magnetic Gold Kit; The enriched mRNA  or rRNA depleted RNA was used for RNA-seq library preparation using KAPA Stranded RNA-Seq Library  Prep Kit (Illumina).
RNA-seq library preparation using KAPA Stranded RNA-Seq Library  Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library  strand-specific.
The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded  libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified  in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument

treatment_protocol: Macrophages were cultured for 7 days, and then washed and stimulated with IL-4 (20 ng/ml; PeproTech) for 24hrs for M2 polarization (Murray et al., 2014).

value: Macrophage

value: post natal 8 weeks

value: untreated


title: KR4M2


title: scRNAseq_Islets_Untreated

city: Chicago

first: Weiguo

last: Cui

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: Untreated

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: Islets

extract_protocol:
10x Genomics
Single-cell RNA sequencing

treatment_protocol: Pancreatic islets were harvested from mice, exposed to cytokines ex vivo, dissociated, and loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles).

value: C57BL/6 mice

value: Pancreas


title: KR3M0


title: KR3M2


title: INPUT_0


title: Idiopathic Intermediate Uveitis [SystUviIU016]

city: Utrecht

first: Jonas

last: Kuiper

address: Heidelberglaan 100

department: Ophthalmology

country: Netherlands

institute: Universitair Medisch Centrum Utrecht

description: RNA sequencing

data_processing:
FastQC for quality check
STAR aligner for genome indexing and alignment of reads
Htseq to generate count data
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: .count data in processed folder present in Uveitis_Replication directory. Contains the read counts generated using Htseq count (python) module.

source_name: Idiopathic Intermediate Uveitis

extract_protocol: Nitrogen-stored PBMCs were thawed and subjected to cDC2 purification by flow cytometry and subjected to RNA-sequencing by NextSeq.

tag: disease status

value: Active uveitis, without systemic inflammatory disease, systemic treatment free

tag: Sex

value: M

value: PBMC

tag: cell population

value: HLA-DR+ Lin-(CD19-CD3-CD14-) CD1c+ cDC2s


title: Idiopathic Intermediate Uveitis [SystUviIU015]

description: RNA sequencing


title: Idiopathic Intermediate Uveitis [SystUviIU005]

description: RNA sequencing

value: F


title: Idiopathic Intermediate Uveitis [SystUviIU014]

description: RNA sequencing


title: KR2M0

city: Shanghai


title: Idiopathic Intermediate Uveitis [SystUviIU004]

description: RNA sequencing


title: KR1M0


title: WT4M2

value: wild type


title: Healthy blood donor [SystUviHC31-FACS]

description: RNA sequencing

source_name: Healthy blood donor

value: No History of inflammatory eye disease, no  systemic inflammatory condition


title: Healthy blood donor [SystUviHC33-FACS]

description: RNA sequencing


title: Healthy blood donor [SystUviHC32-FACS]

description: RNA sequencing


title: WT3M2


title: CTL_0

value: Biotin antibody


title: WT3M0


title: HCM ctrl 13

city: Moscow

first: Maria

last: Pisklova

address: 3rd Cherepkovskaya, 15a

country: Russia

institute: NATIONAL MEDICAL RESEARCH CENTER OF CARDIOLOGY

data_processing:
Each library was indexed in order to multiplex four samples per sequencing run on the Illumina MiSeq platform using MiSeq 50 cycle Reagent Kits v2. A minimum of 15 million 50bp sequencing reads were collected from each sample
Illumina Casava1.7 software used for basecalling
The Illumina adapter sequences as well as low quality nucleotides were trimmed from the raw fastq files using Trimmomatic
The trimmed reads were aligned and annotated to miRBase version 21 using Bowtie2
Differential expression analysis was conducted using the limma package
Genome_build: miRBase version 21
Supplementary_files_format_and_content: CPM

source_name: plasma from peripheral blood

extract_protocol:
Platelet-free plasma was obtained by centrifugation. Plasma miRNAs were isolated using a miRNeasy Serum/Plasma Kit.
Small RNA libraries were constructed using TruSeq® Small RNA Library Prep Kit, according to manufacturer instructions. Individual libraries were constructed using 1µg of total RNA isolated from each sample. Samples were individually barcoded and sequenced on Illumina MiSeq platform in multiplexed pools (3 samples per sequencing run) following the 36 bp fragment protocol.

tag: disease

value: healthy control

tag: gender

value: female


title: Healthy blood donor [SystUviHC029]

description: RNA sequencing


title: endometrium, soybean oil (0.2ml), replicate 3

type: RNA

city: Soochow

first: Zi

middle: wei

last: Zhao

state: Jiangsu

address: Pinghai Road

department: Reproductive Medicine Center

institute: the First Affiliated Hospital of Soochow University

hyb_protocol: The concentration and  specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1  μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 ×  Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization  buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the  gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for  17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.  Quantile normalization and subsequent data processing were performed using the R software limma  package.

source_name: endometrium, soybean oil (0.2ml)

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit,   Arraystar;pmol Cy3/μg cRNA ).

growth_protocol: Gene expression in endometrial tissues of PCOS mice during implantation window

extract_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: All mice were killed by the cervical dislocation to remove the embryo and collect endometrial samples by squeezing.One sample set is mixed by the same endometrial samples of 3 mice.These samples were immediately cryopreserved in liquid nitrogen overnight and then stored in -80℃ refrigerator for gene chip sequencing and RT-PCR verification.

value: endometrium

tag: treatment

value: control

tag: disease state

value: NC group (N)


title: Healthy blood donor [SystUviHC028]

description: RNA sequencing

tag: cell type


title: HCM ctrl 12


title: HCM ctrl 3


title: WT2M0

value: Macrophage

value: post natal 8 weeks


title: KR2M2


title: endometrium, soybean oil (0.2ml), replicate 2


title: HCM ctrl 8

value: male


title: endometrium, soybean oil (0.2ml), replicate 1


title: Healthy blood donor [SystUviHC026]

description: RNA sequencing


title: Healthy blood donor [SystUviHC027]

description: RNA sequencing


title: WT4M0

value: untreated


title: WT1M2


title: Healthy blood donor [SystUviHC025]

description: RNA sequencing


title: HCM ctrl 16


title: HCM ctrl 15


title: Healthy blood donor [SystUviHC024]

description: RNA sequencing


title: endometrium, DHEA (6mg·100g-1)+soybean oil (0.2ml), replicate 3

value: DHEA

value: PCOS group (P)


title: HCM22

value: hypertrophic cardiomyopathy


title: Healthy blood donor [SystUviHC022]

description: RNA sequencing

value: PBMC

value: HLA-DR+ Lin-(CD19-CD3-CD14-) CD1c+ cDC2s


title: endometrium, DHEA (6mg·100g-1)+soybean oil (0.2ml), replicate 2


title: HCM13


title: Healthy blood donor [SystUviHC021]

description: RNA sequencing

value: F


title: Substance P treated CD16- monocytes - replicate 3

source_name: primary monocytes

value: blood

tag: cell subset

value: CD16- monocytes

tag: donor sex

tag: donor age

tag: cell treatment

value: Substance P treatment


title: Gamma-H2AX 4h, DMS-53

source_name: Inmunoprecipitated material from SCLC samples treated  4h with Lurbinectidin

tag: cell line

value: treated with PM01183


title: HCM20

value: female


title: Healthy blood donor [SystUviHC020]

description: RNA sequencing

value: No History of inflammatory eye disease, no  systemic inflammatory condition

value: M


title: HCM11


title: HCM29


title: HLA-A29-positive Birdshot Uveitis [SystUviBS021]

description: RNA sequencing

source_name: HLA-A29-positive Birdshot Uveitis

value: Active uveitis, without systemic inflammatory disease, systemic treatment free


title: RNAPol II 4h

value: 7c2 (IGBMC facility)


title: SP treated CD16+ monocytes - replicate 2

data_processing:
Illumina HiSeq software was used to create sequencing files
STAR software was used to align sequencing data to the  Ensembl hg38 genome with parameters  --runMode alignReads --runThreadN 20 --readFilesCommand zcat --twopassMode Basic
HTSeq was used to count reads with the htseq-count command using the folowing parameters   -f sam -r name -s no -a 10 -i gene_id -m intersection-strict sorted.sam
Genome_build: hg38
Supplementary_files_format_and_content: .out.txt count files for each sample

tag: tissue

value: CD16+ monocytes

value: Female

value: SP treatment


title: HCM12

value: male


title: Gamma-H2AX 0h

source_name: Inmunoprecipitated material from SCLC samples untreated

value: untreated


title: HLA-A29-positive Birdshot Uveitis [SystUviBS020]

description: RNA sequencing

value: PBMC


title: HLA-A29-positive Birdshot Uveitis [SystUviBS019]

description: RNA sequencing

value: HLA-DR+ Lin-(CD19-CD3-CD14-) CD1c+ cDC2s


title: HLA-A29-positive Birdshot Uveitis [SystUviBS018]

description: RNA sequencing


title: HCM6

value: hypertrophic cardiomyopathy


title: RNAPol II Ser2 Phosphorilation 0h

value: Phospho-Serine 2 RNAPII (Abcam ab5095)


title: Input 4h, DMS-53


title: Healthy blood donor [SystUviHC023]

description: RNA sequencing


title: HCM3


title: RNAPol II 0h


title: HLA-A29-positive Birdshot Uveitis [SystUviBS015]

description: RNA sequencing


title: HLA-A29-positive Birdshot Uveitis [SystUviBS014]

description: RNA sequencing


title: RPF-Seq, AAV9-treated

city: Salt Lake City

first: Robert

middle: B

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

description:
dystrophin mutation (HGVS_Genomic_GRCh37 of cDNA) :
Dmd Dup2 mouse model

data_processing:
Library strategy: ribosome footprinting
Single-end FASTQ reads were preprocessed using Trimmomatic for adaptor removal and with the quality filtering/clipping MAXINFO parameter set to 50:0.2 (Bolger, Lohse, & Usadel, 2014; DOI: 10.1093/bioinformatics/btu170) .
Trimmed and filtered RPF- and RNA-Seq reads were mapped to reference genomes using the STAR aligner or to RefSeq transcript sequences using cross_match.
Perl scripts were used to generate read count tables from mapped RPF and RNA-Seq reads, and edgeR (Bioconductor) was used for model-based read count normalization.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab-delimited text file includes raw and normalized counts for each sample mapped to RefSeq coding sequence for the top 1000 most abundant transcripts by read count.

source_name: Frozen TA muscle from Dmd Dup2 mice

extract_protocol:
Frozen muscle biopsies (~ 4 milligrams) were cut on a cryostat (20 microns) and homogenized with a 26-gauge needle in 400 microliters of 20 mM Tris*Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide and 1% Triton X-100.  Ribosome protected fragments were isolated from one half of the homogenate as previously described (N. Wein et al.,(2014). Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. Nature medicine 20: 992-1000). RNA was extracted using TRIzol® and precipitated with isopropanol according to the manufacturer’s instruction (Life Technologies).
Illumina TruSeq Stranded Total RNA library kits were used to prepare RNA-Seq indexed libraries and 50 bp reads were generated on an Illumina HiSeq instrument using v4 chemistry.  RPF-Seq libraries were prepared using the Illumina TruSeq Small RNA Sample Kit according to the manufacturer’s specifications and 50 bp reads were generated on an Illumina HiSeq instrument.

value: skeletal muscle

tag: genotype

value: Dmd Dup2

value: scAAV9.U7-ACCA treated


title: RPF-Seq, untreated

value: untreated control


title: HLA-A29-positive Birdshot Uveitis [SystUviBS004]

description: RNA sequencing


title: RNAPol II Ser2 Phosphorilation 4h

value: treated with PM01183


title: RNA-Seq, AAV9-treated

data_processing:
Single-end FASTQ reads were preprocessed using Trimmomatic for adaptor removal and with the quality filtering/clipping MAXINFO parameter set to 50:0.2 (Bolger, Lohse, & Usadel, 2014; DOI: 10.1093/bioinformatics/btu170) .
Trimmed and filtered RPF- and RNA-Seq reads were mapped to reference genomes using the STAR aligner or to RefSeq transcript sequences using cross_match.
Perl scripts were used to generate read count tables from mapped RPF and RNA-Seq reads, and edgeR (Bioconductor) was used for model-based read count normalization.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab-delimited text file includes raw and normalized counts for each sample mapped to RefSeq coding sequence for the top 1000 most abundant transcripts by read count.


title: endometrium, DHEA (6mg·100g-1)+soybean oil (0.2ml), replicate 1

value: female

tag: age

value: endometrium

value: DHEA

value: PCOS group (P)


title: BrdU 0h Input

tag: ip antibody


title: BrdU 4h Input


title: RNA_seq_SingleCell_Chimera_8_8_ex2

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
The 10X Genomics Cell Ranger pipeline (version 3.1.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome and the reporter sequences (mCherry), barcode/UMI processing, and gene counting for each cell.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

source_name: pancreatic islet cells

extract_protocol:
Mouse isolated islets were dissociated into single cell suspensions for 3 min at 37°C in TrypLE solution. The cells were loaded into the 10x Genomics Chromium system.
ScRNA-seq libraries were prepared using the Single Cell 3’ Reagent Kits (version 3.1; 10X Genomics). Libraries were then sequenced on a NovaSeq 6000 (Illumina) with paired-end sequencing.

tag: strain

value: R26-M2-rtTA; Col-TetOP-Mycl-ires-mCherry; Gcg-CreERT2; R26-mTmG

tag: perinatal date

value: Dox on 8wks in 8-week-old mice

value: pancreatic islet cells


title: RNA-Seq, untreated


title: BrdU 4h

value: BrdU-biotin antibody


title: Seq_09_11: CD0000009_CD0000011_scRNA_seq

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description: Transcroptomic single cell mRNA library

data_processing:
10× Genomics Cell Ranger v4 was used to process raw sequencing data. Briefly, sequencing data were aligned to the human GRCh38/hg38 genome with spike-in gRNA sequences as artificial chromosomes (20 bp gRNA sequence and 250 bp downstream plasmid backbone per each gRNA, together with one additional full sequence of CROP-Seq-Guide-Puro construct also included as a decoy to capture vector-borne sequences). The alignment was performed using STAR 2.7.0 included in Cell Ranger v4 and a customized spiked-in version of GENCODE v28 GTF file containing the aforementioned gRNA sequences and vector backbone as annotations. The filtered gene count matrix output from Cell Ranger was used in subsequent R analysis. In all, we achieved a total mapping rate of 88.7%, with 58.1% mapping rate to the human transcriptome.
The R package Seurat v 3.2 was used to extract information and assemble data tables from the output files to generate the digital gene expression matrix, which was constructed based on per-gene UMI count. Since the Cell Ranger package had already performed preliminary QC filtering and removed low-counting barcodes (i.e., cells) from its filtered output data set (filtered_bc_matrix), we directly imported the output of these processed barcode matrices as raw data. Outputs from one capture (using a mix of CD000009 + CD000011) were imported, which resulted in a total of 10,247 cells used in the initial analysis. The Seurat matrix was subsequently re-normalized using SCTransform() and analyzed on the generated SCT object. Cells with > 20% mitochondria content were removed from analysis after SCTransform. A cell assigned with a unique RNA was defined as the UMI count of its dominant gRNA in the cell being at least three times more than the sum of UMI counts from all other gRNAs. Only MAP2+ cells that express glutamatergic neuron marker genes (SLC17A6 or SLC17A7) falling within clusters 2, 3, 4, 5, 6, and 7 were used (Fig. 2b). Eventually, 4,057 cells survived the filter and were designated as cells with uniquely assigned gRNA for subsequent study. Dimension reduction, UMAP, clustering, and pseudo-bulk DE analysis were performed using package Seurat and EdgeR. Graphs were made in Seurat and ggplot2.

growth_protocol: hiPSC lines (Line CD000009 and CD000011) that stably express dCas9-KRAB-BSD were established as previously described (Zhang et al., 2020). Briefly, on day 0, hiPSCs were replated as small clumps using ReLeSR (STEMCELL) at 10-20% confluence. On Day 1, refresh media with mTeSR Plus containing dCas9-KRAB-BSD virus. 24 hrs post transduction, media was refreshed with mTeSR Plus containing 5 µg/ml Blasticidin. Antibiotics selection was refreshed daily and maintained for 10 days. NGN2-Glut were prepared from hiPSCs stably expressing dCas9-KRAB-BSD using NGN2-hygro virus as described in a previous section (Generation of NGN2-Glut neurons). From Days 2-4, cells were selected using 150 µg/ml hygromycin (Sigma).

extract_protocol: On Day 20, iNs were dissociated using Accutase and replated in Neurobasal Medium supplemented with 1× Glutamax/B27, 10 ng/ml BDNF/GDNF/NT-3, 5 µM ROCK inhibitor, and CROPseq-Guide-Puro virus (vector carrying gRNA targeting genes of interest, MOI=0.2) as described in the original CROP-seq article (Datlinger et al., 2017). 48 hrs post transduction, cells were selected using 2 µg/ml puromycin. 7 days after selection, cells were harvested using Accutase for single cell RNA-seq preparation using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10× Genomics).

value: Glutamatergic, NGN2-induced, day-20 neuron


title: BrdU 0h

value: untreated


title: RNA_seq_SingleCell_WT

data_processing:
The 10X Genomics Cell Ranger pipeline (version 3.1.0) was used to perform sample demultiplexing, alignment to the mm10 mouse reference genome or hg38 human reference genome and the reporter sequences (mCherry or mCherry and zsGreenDR), barcode/UMI processing, and gene counting for each cell.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

extract_protocol:
Mouse isolated islets and human cadaveric islets were dissociated by agitation for 5 min at 37°C in dispersion solution. Dead cells with positive DAPI staining were removed by FACS, and cells were loaded into the 10x Genomics Chromium system.
ScRNA-seq libraries were prepared using the Single Cell 3’ Reagent Kits (version 3.1; 10X Genomics). Libraries were then sequenced on a NovaSeq 6000 (Illumina) with paired-end sequencing.

value: Dox on 8wks and Dox off 4wks in 8-week-old mice


title: HLA-B27-positive acute anterior uveitis [SystUviAU019]

description: RNA sequencing

source_name: HLA-B27-positive acute anterior uveitis

tag: disease status

value: Active uveitis, without systemic inflammatory disease, systemic treatment free

tag: Sex

value: F

value: PBMC

tag: cell population

value: HLA-DR+ Lin-(CD19-CD3-CD14-) CD1c+ cDC2s


title: HLA-B27-positive acute anterior uveitis [SystUviAU018]

description: RNA sequencing


title: HCM4

tag: disease

value: hypertrophic cardiomyopathy

tag: gender

value: male


title: HLA-A29-positive Birdshot Uveitis [SystUviBS016]

description: RNA sequencing

tag: cell type


title: RNA_seq_SingleCell_Mycl_8_8_4


title: HLA-B27-positive acute anterior uveitis [SystUviAU016]

description: RNA sequencing


title: H3K27Ac 4h

data_processing:
Processed using nf-core ChipSeq pipeline v1.0.0
Alingment with  BWA v0.7.17-r1188
peaks called with MACS2 v2.1.2 narrowpeak default
bigWig  generated with bedtools bedgraphTobigWig
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: ChIP material from SCLC samples treated 0 or 4h with a dna binding drug

extract_protocol: none provided by the submitter

tag: chip antibody

tag: treatment

value: treated with biotinilated PM01183 50nM for 4 hours


title: Input 0h, DMS-53


title: STK25KO cardiomyocyte rep 2

city: NEW YORK

first: Barry

last: Fine

state: NY

address: 622 West 168th Street, PH8-406

department: Medicine

institute: Columbia University

data_processing:
Illumina RTA software was used for base calling and bcl2fastq2 (v2.19) was used for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment to a kallisto index created from transcriptomes was done using kallisto (v0.44.0).
Differential expression analysis was performed using the R package DESeq2(v1.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized abundance measurements from DESeq2

source_name: Cell Culture

growth_protocol: iPS cells were maintained in MTESR1 medium. iPS-CM were maintained in RPMI 1640 with B27 supplment (Thermo)

extract_protocol:
Qiagen RNeasy kit was used to isolate RNA following manufacturer's guidelines. DNAse digestion on column was performed.
Clontech Ultra Low v4 kit was used for cDNA synthesis followed by NexteraXT.

value: STK25KO (WTC11 background)

value: STK25 homozygous knockout


title: STK25KO cardiomyocyte rep 3


title: H3K27Ac 0h


title: SM_STG2_T24_4

city: Madison

first: Vania

last: Pankievicz

state: WI

address: 1550 Linder Dr.

department: Bacteriology

institute: University of Wiscosin - Madison

data_processing:
Pseudo sequence alignment, Kallisto (Kallisto-0.42.3).
100 bootstraps with four threads.
RStudio was used to run R-package sleuth and perform subsequent differential gene expression analysis.
Transcript abundance - Sleuth (version 0.30.0).
Differentially expressed genes (DEGs) between two groups accessed using a Wald test.
Differentially expressed genes FDR < 0.05.
Cut-off was set to a TPM (transcripts per million) expression value of 1.
Genome_build: Zea_mays.B73_RefGen_v4.cdna
Supplementary_files_format_and_content: Tar archives include abundance.h5 and abundance.tsv files; estimated counts and TPM values for each target transcript.

molecule: polyA RNA

organism: Zea mays

source_name: aerial root

growth_protocol: Sierra Mixe and B73 maize growing in a high ceiling room (14/10h light/dark cycles and 25/17º C and 85%/90% relative humidity).

extract_protocol:
The total RNA present in secreted mucilage was extracted using PureLink® RNA Mini Kit (Ambion) and treated with DNase (Ambion®) following the manufacturer’s instructions. A nanodrop spectrophotometer and Agilent Bioanalyzer’s electrophoresis on-chip were used to check RNA quantity and purity.
Libraries for sequencing were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina®) and sequenced in next-generation sequencing platform HiSeq 2500 system (Illumina®) using the TruSeq SBS Kit v3-HS (pair-end 100).

treatment_protocol: Rain events twice a week to trigger mucilage production. Stage 1 Sierra Mixe aerial roots, stage 2 Sierra Mixe aerial roots, and stage 1 B73 aerial roots were collected before a rain event and then 2 and 24 hours after a rain event. After excision, the roots were individually snap-frozen in liquid nitrogen and then stored.

tag: cultivar

value: Sierra Mixe

value: aerial root

tag: Stage

value: stage 2

value: 24 hours after rain event


title: HLA-B27-positive acute anterior uveitis [SystUviAU015]

description: RNA sequencing


title: STK25KO cardiomyocyte rep 1

tag: cell line


title: input 4h


title: HLA-B27-positive acute anterior uveitis [SystUviAU014]

description: RNA sequencing

value: M


title: WT cardiomyocyte rep 3

value: Wildtype


title: KR1M2

tag: tissue

value: Macrophage

value: post natal 8 weeks


title: SM_STG2_T24_2


title: RNA_seq_SingleCell_Chimera_8_8_ex1

tag: genotype

value: R26-M2-rtTA; Col-TetOP-Mycl-ires-mCherry; Gcg-CreERT2; R26-mTmG

value: Dox on 8wks in 8-week-old mice

value: pancreatic islet cells


title: WT cardiomyocyte rep 2


title: POl II 4h

value: RNAPOL II


title: SM_STG2_T24_1


title: WT cardiomyocyte rep 1


title: HLA-B27-positive acute anterior uveitis [SystUviAU012]

description: RNA sequencing

value: Active uveitis, without systemic inflammatory disease, systemic treatment free

value: F

value: PBMC

value: HLA-DR+ Lin-(CD19-CD3-CD14-) CD1c+ cDC2s


title: HLA-B27-positive acute anterior uveitis [SystUviAU013]

description: RNA sequencing


title: RNA_seq_SingleCell_Mycl_8_8


title: Biotin 4h

value: Biotin

value: treated with biotinilated PM01183 50nM for 4 hours


title: WT1M0

tag: age

value: wild type

value: untreated