title: Iso-seq_male_gonad2_B01

status: Public on Feb 18 2022

first: Zhen-Xia

last: Chen

department: College of Life Science and Technology

data_processing:
Library strategy: Iso-seq
RNA-Seq: High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis.
RNA-Seq: We used FastqC (0.11.8) to evaluate the raw reads quality. Sequencing report tool was MultiQC (0.9).
Iso-seq: The Raw data was subjected to SmrtLink Pipeline ccs to self-correct and obtain full-length circular consensus sequencing (CCS) reads based on PacBio recommended pipeline. We used the SmrtLink Pipeline classify subprogram to distinguish full-length non-chimeric sequences with the limitation of the transcript length longer than 300bp and applied the SmrtLink Pipeline cluster subprogram to cluster the full-length non-chimeric sequences into full-length transcripts, and retained the full-length transcript supported by at least one full-length non-chimeric sequences. The LoRDEC program was used to correct the full-length transcripts based on the results of Illumina RNA-seq to improve the accuracy of the third-generation transcripts.
RNA-Seq: Reads were mapped to the corresponding reference genomes (mm10, ENSEMBL98) by Hisat2 (2.0.5) with parameters “-x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation that conbined reference annotation and Iso-seq full-length transcript.
RNA-Seq: The output of Hisat2 were converted to BAM format, sorted and only uniqe mapped reads were retained.
RNAseq: featurecounts (1.6.3) was used for counting reads with parameters "-s 2 -t exon -g gene_id".
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts of all the genes for each RN-Aseq sample, as well as Iso-seq full transcript gtf files.
Supplementary_files_format_and_content: mouse_reference_iso.txt: conversion from PacBioID to geneID
Supplementary_files_format_and_content: mouse_final.gtf: full length transcripts
Supplementary_files_format_and_content: Count.matrix.txt: count matrix table

extract_protocol: Total RNAs from mouse (C57BL/6J) adult brain, cerebellum, heart, colon, and gonad in both sexes were extracted. The RNAs were classified into two parts, one part was subsequently treated with Ribo-off rRNA Depletion Kit to remove ribosome RNA (rRNA). Then the VAHTS TM Stranded mRNA-seq Library Prep Kit for Illumina was used for strand-specific library preparation. After finished, the library was suquenced on the Illumina Nova platform. The another part was used to constructe for cDNA using P Clontech SMARTer PCR cDNA Synthesis Kit and PrimeSTAR GXL DNA Polymerase, followed by library preparation by using SMRTbellTM Template prep and sequencing on the Pacific Biosciences Sequel I platform.

value: gonad

tag: development stage

value: Adult

tag: gender

value: male

tag: library type

value: Iso-seq


title: Iso-seq_female_stem_plus2_B01

type: SRA

city: Wuhan

state: Hubei

address: No.1 Shizishan Street

country: China

institute: Huazhong Agricultural University

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

value: somatic (pooled:brain, cerebellum, heart, colon)

value: female

tag: strain


title: BT474_pROR2_3

status: Public on Feb 21 2022

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

description: RNA_Seq_featureCount_counts_BT474_SKBR3.csv

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.  RNA sequencing data were first quality checked via FastQC (Babraham Bioinformatics). For MCF-7 the reads were then mapped against the reference genome GRCh38 with the STAR RNA-Seq alignment tool and gene-level abundances were estimated using the RSEM algorithm. For SK-BR-3 and BT-474 cells sequence reads were aligned with the reference genome GRCh38 using the HISAT2 (v2.1.0) alignment tool, while incorporating database information from Ensembl (v38.87) during the reference indexing step.   Gene-level abundances were estimated using featureCounts (v1.6.3).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene-level counts for every sample

organism: Homo sapiens

source_name: BT-474 cells

growth_protocol: MCF-7 and SK-BR-3 cells were cultured in RPMI-1640, BT-474 cells in DMEM/F12, all supplemented with 10% heat-inactivated (56°C, 30 min) fetal calf serum (FCS).

extract_protocol:
Total RNA was isolated with the Trizol reagent for MCF-7 cells and with the High Pure RNA isolation kit (Roche) for BT-474 and SK-BR-3 cells. RNA concentration was measured at the Nanodrop ND-1000 and RNA integrity was checked with the Bioanalyzer 2100 (Agilent).
For MCF-7 cells, library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) starting from 1,000 ng of total RNA. For SK-BR-3 and BT-474 cells libraries for RNA-Seq were prepared with the NEBNext Ultra RNA II directional kit including NEBNext mRNA enrichment. RNA and library quality control was checked by TapeStation (Agilent).

treatment_protocol: To achieve gene overexpression, cells were transfected with Fugene HD transfection reagent (Promega) and stable clones generated by geneticin or zeocin selection (750 µg/ml or 100 µg/ml, respectively).  For siRNA-mediated gene knockdown, cells were transfected with 10 nM siRNA (santa cruz) using the RNAimax transfection reagent (Invitrogen). Cells were used 72h post transfection for expression analysis.

tag: cell type

value: mammary gland, ductal carcinoma

value: epithelial

tag: treatment

value: BT-474 human breast cancer cells were transfected with a hROR2 overexpression plasmid (pROR2).


title: BT474_pROR2_2


title: Iso-seq_male_stem3_C01


title: SKBR3_pROR2_2

source_name: SK-BR-3 cells

value: SK-BR-3 (DSMZ, ACC 736)

value: mammary gland, breast adenocarcinoma; derived from a pleural effusion

value: SK-BR-3 human breast cancer cells were transfected with a hROR2 overexpression plasmid (pROR2).


title: female heart replicate3

data_processing:
RNA-Seq: High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis.
RNA-Seq: We used FastqC (0.11.8) to evaluate the raw reads quality. Sequencing report tool was MultiQC (0.9).
Iso-seq: The Raw data was subjected to SmrtLink Pipeline ccs to self-correct and obtain full-length circular consensus sequencing (CCS) reads based on PacBio recommended pipeline. We used the SmrtLink Pipeline classify subprogram to distinguish full-length non-chimeric sequences with the limitation of the transcript length longer than 300bp and applied the SmrtLink Pipeline cluster subprogram to cluster the full-length non-chimeric sequences into full-length transcripts, and retained the full-length transcript supported by at least one full-length non-chimeric sequences. The LoRDEC program was used to correct the full-length transcripts based on the results of Illumina RNA-seq to improve the accuracy of the third-generation transcripts.
RNA-Seq: Reads were mapped to the corresponding reference genomes (mm10, ENSEMBL98) by Hisat2 (2.0.5) with parameters “-x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation that conbined reference annotation and Iso-seq full-length transcript.
RNA-Seq: The output of Hisat2 were converted to BAM format, sorted and only uniqe mapped reads were retained.
RNAseq: featurecounts (1.6.3) was used for counting reads with parameters "-s 2 -t exon -g gene_id".
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts of all the genes for each RN-Aseq sample, as well as Iso-seq full transcript gtf files.
Supplementary_files_format_and_content: mouse_reference_iso.txt: conversion from PacBioID to geneID
Supplementary_files_format_and_content: mouse_final.gtf: full length transcripts
Supplementary_files_format_and_content: Count.matrix.txt: count matrix table

source_name: female heart replicate3

value: heart

value: fr-firststrand (dUTP)


title: Iso-seq_male_gonad_plus1_A01


title: Iso-seq_female_stem5_E01


title: male cerebellum replicate3

source_name: male cerebellum replicate3

value: cerebellum


title: male gonad replicate3

source_name: male gonad replicate3


title: male brain replicate3

source_name: male brain replicate3

value: brain


title: male colon replicate1

source_name: male colon replicate1

value: colon


title: male gonad replicate2

source_name: male gonad replicate2

value: gonad


title: MAC-T cells, C1.Input

status: Public on Feb 23 2022

first: Changmin

last: Hu

description: CircRNA Expression Profiling.xlsx

data_processing:
After paired-end sequencing, raw circRNA data were obtained. According to Q30 for quality control, cutadapt software (v1.9.3) was used to obtain high-quality reads.
STAR software (v2.5.1b) was used to compare high-quality reads to the reference genome/transcriptome (bosTau9)
DCC software (v0.4.4) was used for circRNA detection and identification.
The circBase database and Circ2Traits were used to annotate the identified circRNA.
edgeR software (v3.16.5) was used for data standardization and differential expression circRNA screening (fold change>=1.5, P value <= 0.05).
Genome_build: bosTau9
Supplementary_files_format_and_content: Excel format (Number of raw junction reads)

organism: Bos taurus

source_name: MAC-T cells

growth_protocol: MAC-T were cultured in DME/F12 medium (Hyclone, China) with 10% fetal bovine serum (Gibco, United States), which incubated at 37℃ in 5% CO2. The cells were digested and passed by 0.25% trypsin - 0.02% EDTA solution.

extract_protocol:
Total RNA of the above 9 samples was extracted according to the instructions of the commercial reagent manufacturer and the RNA isolation steps. A NanoDrop ND-1000 instrument (Agilent Inc. USA) was used to measure RNA concentration and purity, and the quality control index of RNA purity was based on the OD260/OD280 value between 1.8-2.0. Denaturing agarose gel electrophoresis was used to measure RNA integrity and gDNA contamination. The sample was stored at -80 °C for later use.
Nine samples under different treatments were sent to Cloud-Seq Biotech (Shanghai, China) for MeRIP-CircRNA sequencing. The operation was briefly described as follows: 1) To enrich circRNA, a circRNA Enrichment Kit (Cloud-seq, USA) was used according to the supplier's instructions. 2) An NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) was used to pretreat RNA, and a sequencing library was constructed by immunoprecipitation. 3) Quality control and quantification of the library were performed with the BioAnalyzer 2100 system (Agilent Technologies, USA), and the Illumina HiSeq instrument was used to perform 150 bp paired-end sequencing.

treatment_protocol: MAC-T cells were seeded in 6-well plates (Corning, US) at a density of 2×10^5 cells/well. After 12 h of culture, inactivated bacteria were added at an MOI of 10:1. Inactivated bacteria and cells were cocultured for 24 hours.

value: bovine mammary epithelial cells (MAC-T cells)

value: untreated

tag: ip fraction

value: Input

tag: rna fraction

value: total RNA


title: MAC-T cells, E1.Input

description: CircRNA Expression Profiling.xlsx

value: E. coli


title: male cerebellum replicate2

source_name: male cerebellum replicate2

value: Adult

value: male


title: Iso-seq_female_gonad4_D01

value: gonad (ovary)

value: female

value: Iso-seq


title: male heart replicate1

source_name: male heart replicate1


title: female gonad replicate3

source_name: female gonad replicate3


title: male brain replicate2

source_name: male brain replicate2


title: male colon replicate2

source_name: male colon replicate2


title: male colon replicate3

source_name: male colon replicate3


title: male brain replicate1

source_name: male brain replicate1


title: female colon replicate1

source_name: female colon replicate1


title: male cerebellum replicate1

source_name: male cerebellum replicate1


title: female heart replicate2

source_name: female heart replicate2


title: female brain replicate3

source_name: female brain replicate3


title: female gonad replicate2

source_name: female gonad replicate2


title: female colon replicate2

source_name: female colon replicate2


title: male heart replicate2

source_name: male heart replicate2


title: female cerebellum replicate1

source_name: female cerebellum replicate1


title: female cerebellum replicate3

source_name: female cerebellum replicate3


title: female gonad replicate1

source_name: female gonad replicate1


title: female colon replicate3

source_name: female colon replicate3


title: female brain replicate1

source_name: female brain replicate1


title: female cerebellum replicate2

source_name: female cerebellum replicate2


title: female heart replicate1

source_name: female heart replicate1


title: male gonad replicate1

source_name: male gonad replicate1


title: female brain replicate2

source_name: female brain replicate2


title: Cisplatin 1d 03

status: Public on Feb 16 2022

city: Kunming

first: Junjun

last: Hao

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

data_processing:
All the libraries were sequenced on the MGISEQ2000 platform (BGI-Shenzhen, China) in a paired-end form with 150 bp. The low-quality reads were filtered out using the program of the fastq-quality-filter with the parameters of -Q 33 -q 20 -p 80.  A total of ~202.3 Gb clean data was obtained and averaged 7.49 Gb high-quality clean reads for 27 samples .  The clean reads were mapped onto the mouse genome (version GRCm38) using Tophat 2.1.0 with the parameter of --read-mismatches 2.  And then, the expected fragments per kilobase of transcript per million fragments (FPKM) of each gene was calculated using cufflinks 2.02  with the parameter --max-multiread-fraction 0.75 as its expression level.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: cochlear

extract_protocol:
Total RNA was qualified and quantified using a NanoDrop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cochlear

tag: age

value: 2 month


title: Cisplatin 3d 02


title: Noise 24h 03


title: Cisplatin 3d 01


title: Cisplatin 1d 01


title: Noise 24h 02


title: Cisplatin 1d 02


title: Cisplatin 1d 04


title: Noise 24h 01


title: Noise 1h 04


title: Noise 1h 03


title: Noise 1h 01


title: Age 12m 03

value: 12 month


title: Age 12m 02


title: Age 12m 01


title: Noise 1h 02


title: Age 8m 04

value: 8 month


title: Age 8m 03


title: Cisplatin 3d 03


title: Noise 24h 04


title: Control 2m 03


title: Age 8m 01


title: Age 8m 02


title: Control 2m 04


title: Control 2m 01


title: BM1-2_10x_scRNAseq

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

country: USA

institute: Cincinnati Children's Hospital

description:
BM3_10x_scRNAseq_Expression.txt
BM3_10x_scRNAseq_MetaData.txt

data_processing:
Demultiplexing  and FASTQ generation using CellRanger version 5.0.0
Generate single-cell expression matrix using CellRanger version 5.0.0
Ambient RNA removal using SoupX version 1.5.2
Quality control and filtering using R 4.1.0
Normalization using Seurat 4.0.2
Control samples: Clustering and Integration using Seurat 4.0.2
BPDCN samples: Classification using cellHarmony in AltAnalyze 2.0
TREK-seq: Demultiplexing with bcl2fastq version 2.20.0
TREK-seq: TCR sequence extraction and scRNAseq pairing using WARPT
R1 — UMI and barcode
I1 — T-cell receptor sequence
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrices (scRNAseq), metadata (scRNAseq), WARPT output (TREK-seq)

molecule: polyA RNA

source_name: Bone marrow hematopoietic cells

extract_protocol:
mRNA was extracted by 10x 3' sequencing technology
10x 3' v3 or v3.1 single-cell RNA-sequencing library construction methods were utilized for mRNA libraries. TREK-seq was used to enrich and sequence T-cell receptors.

tag: technology

value: 10x 3' v3 scRNA-seq

tag: disease state

value: control


title: BM3-1_10x_scRNAseq

description:
BM2_10x_scRNAseq_Expression.txt
BM2_10x_scRNAseq_MetaData.txt


title: BM3-3_10x_scRNAseq


title: BM2-3_10x_scRNAseq

description:
BM1_10x_scRNAseq_Expression.txt
BM1_10x_scRNAseq_MetaData.txt

value: 10x 3' v3.1 scRNA-seq


title: BM3-2_10x_scRNAseq


title: BM2-1_10x_scRNAseq


title: Age 12m 04


title: VU_COPD_40

status: Public on Feb 11 2022

city: Nashville

first: Bradley

middle: Winston

last: Richmond

state: Tennessee

address: 1161 21st Avenue South

department: Medicine

institute: Vanderbilt University Medical Center

description: scRNA-seq

data_processing:
Reads with Phred scores <30 were filtered out.
10X Genomics CellRanger v3 (for VU_COPD_29 and VU_COPD_34) or v5.0.0 (all other samples) was used to align reads to the GRCh38 reference genome.
CellRanger was also used to generate h5 matrix files.
Post-alignment analysis was performed using the Seurat v4.0.1 package in R.  Quality control filtering was performed using detected genes (minimum 750) and mitochondrial reads percent (minimum 0%, maximum 15%).  All data (COPD and control samples) were jointly normalized and scaled using the SCTransform function in Seurat. Epithelial (EPCAM+), stromal (EPCAM-/PTPRC-) and immune (PTPRC+) cells were then extracted into independent objects which underwent SCT-Integration followed by principal component analysis, recursive clustering, UMAP embedding, and cell-type annotation.  Clusters comprised of non-physiologic marker combinations (i.e., PTPRC+/EPCAM+ cells) were presumed doublets and excluded from further downstream analysis.  Cell-type specific differentiation expression analysis was performed as previously described.  For this dataset, only EPCAM+ epithelial populations were examined, but raw files contain data from all cell populations.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered h5 matrix files

source_name: explanted lungs

extract_protocol:
Biopsies from each lung sample were digested in an enzymatic cocktail (Miltenyi Multi-Tissue Dissociation Kit or collagenase I/dispase II 1 mg/ml tissue) using a gentleMACS Octo Dissociator (Miltenyi, Inc).  Tissue lysates were serially filtered through sterile gauze, 100 mm, and 40 mm sterile filters (Fisher).  Single cell suspensions then underwent cell sorting using serial columns (Miltenyi Microbeads, CD235a, CD45) or FACS.  At VUMC, CD45- and CD45+ populations mixed 2-3:1 were used as input for generation of scRNA-seq libraries. At TGen, Calcien-AM was used to stain live cells and 10,000-15,000 total live cells were sorted directly into the 10X reaction buffer and transferred immediately to the 10X 5’ chip A (10X Genomics).
scRNA-seq libraries were generated using the 10X Chromium platform 5’ library preparation kits (10X Genomics) targeting 10,000 cells per sample.  Next generation sequencing was performed on an Illumina Novaseq 6000 using Illumina S1 flow cell with paired end reads.

value: explanted lungs

value: COPD

tag: source location

value: Vanderbilt

tag: cellranger version


title: VU_COPD_42

description: scRNA-seq


title: VU_COPD_45

description: scRNA-seq


title: VU_COPD_41

description: scRNA-seq


title: Control 2m 02


title: VU_COPD_38

description: scRNA-seq


title: VU_COPD_44

description: scRNA-seq


title: VU_COPD_34

description: scRNA-seq


title: VU_COPD_29

description:
scRNA-seq
read 2 file not provided due to corruption


title: VU_COPD_30

description: scRNA-seq


title: Tgen_COPD_50

description: scRNA-seq

value: Tgen


title: Tgen_COPD_63

description: scRNA-seq


title: H4_V0_NA

status: Public on Feb 10 2022

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

description: Sample title format:  Donor #, visit, additional treatment

data_processing:
Reads were aligned to the human genome (hg38) reference sequence using a short-read aligner based on Burrows-Wheeler Transform with default settings. Binary alignment map (BAM) files were sorted on coordinates and indexed with the samtools v1.3 package. Additionally, normalized read count values were calculated. Differential expression was assessed using the DESeq2 Bioconductor package in an R V.3.6.3 programming environment with gene expression called differential with a false discovery rate (FDR) < 0.05 and a median read count > 1 in at least one group.
Genome_build: hg38
Supplementary_files_format_and_content: normalized_counts.txt, RawReadCount.txt

source_name: Monocytes

extract_protocol:
For RNA isolation, 0.2 mL chloroform was added per mL of TriPure. Next, samples were centrifuged at 12000 g for 15’ at 4°C. Subsequently, the aqueous phase was added to 450 μl isopropanol containing GlycoBlue. Next, tubes were shaken vigorously, chilled for 30 min at -20°C and centrifuged at 12000 g for 10’ at 4°C. RNA pellets were washed twice with 75% ethanol and pellets were air-dried at RT and resuspended in nuclease-free water.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, rRNA was depleted from total RNA using the rRNA depletion kit (NEB#E6310). After fragmentation of the rRNA reduced RNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

value: Monocytes

tag: donor #

tag: visit

tag: additional treatment

tag: group

value: Healthy donor


title: H5_V0_NA


title: H3_V0_NA


title: BM2-2_10x_scRNAseq


title: H9_V0_NA


title: BM1-1_10x_scRNAseq


title: H1_V0_NA


title: MAC-T cells, E3.IP

source_name: MAC-T cells

value: bovine mammary epithelial cells (MAC-T cells)

value: E. coli

value: Me-RIP

value: m6A RNA


title: X10_V2_PCSK9Eze

value: FH treated

value: Familial hypercholesterolemia


title: H7_V0_NA


title: X11_V1_NA

value: FH untreated


title: X11_V2_PCSK9Eze


title: H2_V0_NA


title: X9_V2_StatinEze

value: StatinEze


title: H8_V0_NA


title: H6_V0_NA


title: Tgen_COPD_13

description: scRNA-seq


title: X8_V1_NA


title: X9_V1_NA


title: X6_V1_NA


title: X8_V2_StatinEze


title: X5_V1_NA


title: X4_V2_PCSK9Eze


title: X5_V2_PCSK9EzeStatin


title: X6_V2_StatinEze


title: X3_V1_NA


title: X2_V2_Statin

value: Statin


title: X4_V1_NA


title: X2_V1_NA


title: X1_V1_NA


title: X1_V2_PCSK9Eze


title: X3_V2_PCSK9Eze


title: X10_V1_NA


title: 786O_1%_serum_sh2_3

status: Public on Feb 07 2022

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

institute: Yale Cancer Center

description: 786O cells with PBRM1 shRNA #2 grown in RPMI with 1% RPMI

data_processing:
cutadapt
Salmon
Deseq2
Genome_build: hg38
Supplementary_files_format_and_content: Deseq2 output, normalized gene expression in TPM

extract_protocol:
Poly A
Illumina TruSeq V2

treatment_protocol: RPMI 10% or 1% FBS

value: 1% FBS

tag: transfection

value: PBRM1 shRNA #2


title: 786O_1%_serum_sh2_2


title: 786O_1%_serum_sh1_3

description: 786O cells with PBRM1 shRNA #1 grown in RPMI with 1% RPMI

value: PBRM1 shRNA #1


title: 786O_1%_serum_sh1_2


title: 786O_1%_serum_sh2_1


title: 786O_1%_serum_off_3

description: 786O cells with off target shRNA grown in RPMI with 1% RPMI

value: off target shRNA


title: 786O_1%_serum_sh1_1


title: 786O_1%_serum_off_1


title: 786O_10%_serum_sh2_2

description: 786O cells with PBRM1 shRNA #2 grown in RPMI with 10% RPMI

value: 10% FBS


title: 786O_10%_serum_sh2_3


title: 786O_10%_serum_sh2_1


title: 786O_10%_serum_sh1_3

description: 786O cells with PBRM1 shRNA #1 grown in RPMI with 10% RPMI


title: 786O_10%_serum_sh1_1


title: 786O_10%_serum_sh1_2


title: 786O_10%_serum_off_2

description: 786O cells with off target shRNA grown in RPMI with 10% RPMI


title: 786O_10%_serum_off_1


title: plate1-Raji-H12_S192

city: Chicago

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

description: Prox-seq analysis of Jurkat and Raji cells using plate-based Smart-seq2 pipeline

library_source: other

data_processing:
Library strategy: Prox-seq
Sequencing data was aligned using a custom Java program (https://github.com/tay-lab/Prox-seq) to produce a count matrix of PLA products. Sequencing reads with more than 1 bases with quality score below 20 are discarded. The list of probe barcodes used in alignment is in antibody_barcodes.csv. The list of single-cell barcodes are in R1List.csv
Count data was analyzed in Python (https://github.com/tay-lab/Prox-seq_computation). Cells with fewer than 10 UMIs or more than 30,000 UMIs are discarded. Cells with fewer than 20 detected PLA products are also discarded.
Protein complex abundances are predicted using the Python code.
Supplementary_files_format_and_content: count matrix of PLA products

molecule: protein

source_name: Raji cells

growth_protocol: Jurkat and Raji cells are kept in RPMI media with 10% FBS

extract_protocol:
PLA products were extracted from single cells following plate-based Prox-seq pipeline
Sequencing library was constructed from PLA products using PCR

value: Human-derived B cells


title: plate1-Raji-H05_S185


title: plate1-Raji-H11_S191


title: plate1-Raji-H06_S186


title: plate1-Raji-H07_S187


title: plate1-Raji-H10_S190


title: plate1-Raji-H04_S184


title: plate1-Raji-H02_S182


title: plate1-Raji-H09_S189


title: plate1-Raji-H03_S183


title: plate1-Raji-G11_S179


title: plate1-Raji-G08_S176


title: plate1-Raji-G10_S178


title: plate1-Raji-G12_S180


title: plate1-Raji-G09_S177


title: 786O_1%_serum_off_2


title: plate1-Raji-G05_S173


title: plate1-Raji-G02_S170


title: plate1-Raji-G03_S171


title: plate1-Raji-G04_S172


title: plate1-Raji-H01_S181


title: plate1-Raji-G07_S175


title: 786O_10%_serum_off_3


title: plate1-Raji-H08_S188


title: plate1-Raji-F11_S167


title: plate1-Raji-F12_S168


title: plate1-Raji-F10_S166


title: plate1-Raji-F09_S165


title: plate1-Raji-F08_S164


title: plate1-Raji-F02_S158


title: plate1-Raji-F06_S162


title: plate1-Raji-E11_S155


title: plate1-Raji-E12_S156


title: plate1-Raji-F01_S157


title: plate1-Raji-E10_S154


title: plate1-Raji-E08_S152


title: plate1-Raji-E09_S153


title: plate1-Raji-E07_S151


title: plate1-Raji-F03_S159


title: plate1-Raji-G06_S174


title: plate1-Raji-G01_S169


title: plate1-Raji-E04_S148


title: plate1-Raji-E05_S149


title: plate1-Raji-E03_S147


title: plate1-Raji-E02_S146


title: plate1-Raji-D11_S143


title: plate1-Raji-E01_S145


title: plate1-Raji-D12_S144


title: plate1-Raji-D09_S141


title: plate1-Raji-D08_S140


title: plate1-Raji-D10_S142


title: plate1-Raji-D06_S138


title: plate1-Raji-F07_S163


title: plate1-Raji-F05_S161


title: plate1-Raji-D07_S139


title: plate1-Raji-F04_S160


title: plate1-Raji-D04_S136


title: plate1-Raji-D03_S135


title: plate1-Raji-D05_S137


title: plate1-Raji-C11_S131


title: plate1-Raji-C10_S130


title: plate1-Raji-E06_S150


title: plate1-Raji-C12_S132


title: plate1-Raji-C08_S128


title: plate1-Raji-D01_S133


title: plate1-Raji-C07_S127


title: plate1-Raji-D02_S134


title: plate1-Raji-C06_S126


title: plate1-Raji-C09_S129


title: plate1-Raji-C04_S124


title: plate1-Raji-C05_S125


title: plate1-Raji-C02_S122


title: plate1-Raji-C03_S123


title: plate1-Raji-C01_S121


title: plate1-Raji-B12_S120


title: plate1-Raji-B10_S118


title: plate1-Raji-B11_S119


title: plate1-Raji-B09_S117


title: plate1-Raji-B07_S115


title: plate1-Raji-B08_S116


title: plate1-Raji-B06_S114


title: plate1-Raji-B03_S111


title: plate1-Raji-B05_S113


title: plate1-Raji-B04_S112


title: plate1-Raji-A12_S108


title: plate1-Raji-A11_S107


title: plate1-Raji-A10_S106


title: plate1-Raji-A09_S105


title: plate1-Raji-A08_S104


title: plate1-Raji-B01_S109


title: plate1-Raji-A07_S103


title: plate1-Raji-A05_S101


title: plate1-Raji-A01_S97


title: plate1-Raji-A03_S99


title: plate1-Raji-A02_S98


title: plate1-Jurkat-H12_S96

source_name: Jurkat cells

value: Human-derived T cells


title: plate1-Jurkat-H11_S95


title: plate1-Raji-A06_S102


title: plate1-Jurkat-H10_S94


title: plate1-Jurkat-H09_S93


title: plate1-Jurkat-H07_S91


title: plate1-Jurkat-H08_S92


title: plate1-Jurkat-H06_S90


title: plate1-Jurkat-H05_S89


title: plate1-Jurkat-H03_S87


title: plate1-Jurkat-H02_S86


title: plate1-Jurkat-G12_S84


title: plate1-Jurkat-H01_S85


title: plate1-Jurkat-G11_S83


title: plate1-Raji-B02_S110


title: plate1-Jurkat-G10_S82


title: plate1-Jurkat-G09_S81


title: plate1-Jurkat-G08_S80


title: plate1-Jurkat-G03_S75


title: plate1-Jurkat-G07_S79


title: plate1-Jurkat-G05_S77


title: plate1-Raji-A04_S100


title: plate1-Jurkat-G06_S78


title: plate1-Jurkat-G04_S76


title: plate1-Jurkat-G01_S73


title: plate1-Jurkat-G02_S74


title: plate1-Jurkat-F12_S72


title: plate1-Jurkat-F11_S71


title: plate1-Jurkat-F08_S68


title: plate1-Jurkat-F09_S69


title: plate1-Jurkat-F04_S64


title: plate1-Jurkat-F06_S66


title: plate1-Jurkat-F03_S63


title: plate1-Jurkat-F05_S65


title: plate1-Jurkat-H04_S88


title: plate1-Jurkat-F01_S61


title: plate1-Jurkat-F02_S62


title: plate1-Jurkat-E12_S60


title: plate1-Jurkat-E11_S59


title: plate1-Jurkat-E10_S58


title: plate1-Jurkat-E06_S54


title: plate1-Jurkat-E07_S55


title: plate1-Jurkat-E09_S57


title: plate1-Jurkat-E05_S53


title: plate1-Jurkat-E08_S56


title: plate1-Jurkat-E04_S52


title: plate1-Jurkat-F10_S70


title: plate1-Jurkat-D11_S47


title: plate1-Jurkat-D08_S44


title: plate1-Jurkat-E03_S51


title: plate1-Jurkat-D09_S45


title: plate1-Jurkat-D12_S48


title: plate1-Jurkat-D10_S46


title: plate1-Jurkat-F07_S67


title: plate1-Jurkat-D06_S42


title: plate1-Jurkat-D05_S41


title: plate1-Jurkat-D02_S38


title: plate1-Jurkat-D03_S39


title: plate1-Jurkat-D01_S37


title: plate1-Jurkat-C12_S36


title: plate1-Jurkat-C10_S34


title: plate1-Jurkat-C09_S33


title: plate1-Jurkat-C11_S35


title: plate1-Jurkat-C07_S31


title: plate1-Jurkat-C06_S30


title: plate1-Jurkat-E02_S50


title: plate1-Jurkat-C02_S26


title: plate1-Jurkat-C04_S28


title: plate1-Jurkat-C05_S29


title: plate1-Jurkat-C08_S32


title: plate1-Jurkat-C03_S27


title: plate1-Jurkat-C01_S25


title: plate1-Jurkat-D07_S43


title: plate1-Jurkat-B12_S24


title: plate1-Jurkat-E01_S49


title: plate1-Jurkat-B07_S19


title: plate1-Jurkat-D04_S40


title: plate1-Jurkat-B08_S20


title: plate1-Jurkat-B11_S23


title: plate1-Jurkat-B06_S18


title: plate1-Jurkat-B09_S21


title: plate1-Jurkat-B03_S15


title: plate1-Jurkat-B05_S17


title: plate1-Jurkat-B04_S16


title: plate1-Jurkat-B02_S14


title: plate1-Jurkat-A10_S10


title: plate1-Jurkat-A12_S12


title: plate1-Jurkat-A08_S8


title: plate1-Jurkat-A07_S7


title: plate1-Jurkat-B01_S13


title: plate1-Jurkat-A09_S9


title: plate1-Jurkat-A01_S1


title: plate1-Jurkat-A06_S6


title: plate1-Jurkat-A04_S4


title: ∆rpoN_90min_afterInd_37C_rep3

status: Public on Feb 04 2022

city: Umea

first: Maria

last: Fallman

address: Petrus Laestadius väg

department: Molecular Biology

country: Sweden

institute: Umea university

data_processing:
Reads were trimmed from 5' and 3' ends until all the adapter and low-quality bases were removed and the sequences passed QC checking by FastQC
Reads were aligned to a reference genome of Y. pseudotuberculosis (accession number NC_010465) using bowtie2 with the unique-mapping option.
Post-mapped read quality checking was done using RseQC, and the numbers of reads for each gene were counted using feaatureCount
Aligned reads were converted to BAM and wig by SAMtool and custom script
Differential gene expression was determined using DEseq2, using the shrinkage estimation of dispersion option (lfcSrink =True) to generate more accurate estimates of differential expression in fold changes
Genome_build: NC_010465
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized counts and differential expression statistics for every gene and every sample

organism: Yersinia pseudotuberculosis

source_name: bacteria grown in Lauria broth

growth_protocol: All strains were routinely grown at 26ºC in LB medium containing kanamycin (50 µg/ml) to the desired OD600.

extract_protocol:
For isolation and purification of RNA, the Trizol method (Ambion Life Technologies, Carlsbad, CA) and the Direct-zol RNA kit (Zymo Research, USA) were used. To remove unwanted DNA, purified RNA was treated with DNAse for 30 min at room temperature according to the manufacturer’s instructions. RNA quantity was measured by Qubit
RNA libraries were prepared for sequencing using RNA-tag seq protocol

treatment_protocol: To reach the virulence induction condition, overnight bacterial cultures were diluted to OD600 0.05 in LB and grown at 26ºC. After 1 h, calcium was depleted by adding EGTA to 5 mM and MgCl2 to 20 mM , and cultures were shifted to 37ºC

value: YPIII

tag: genotype

value: mutant

tag: time (minutes)


title: plate1-Jurkat-A03_S3


title: plate1-Jurkat-A05_S5


title: ∆rpoN_15min_afterInd_37C_rep3

tag: strain


title: plate1-Jurkat-A02_S2

tag: cell type


title: ∆rpoN_90min_afterInd_37C_rep2


title: WT_90min_afterInd_37C_rep2

value: wild type


title: ∆rpoN_15min_afterInd_37C_rep1


title: WT_90min_afterInd_37C_rep1


title: WT_30min_afterInd_37C_rep3


title: WT_30min_afterInd_37C_rep2


title: plate1-Jurkat-B10_S22


title: ∆rpoN_90min_afterInd_37C_rep1


title: WT_15min_afterInd_37C_rep1


title: ∆rpoN_15min_afterInd_37C_rep2


title: WT_90min_afterInd_37C_rep3


title: ∆rpoN_30min_afterInd_37C_rep3


title: ∆rpoN_30min_afterInd_37C_rep1


title: plate1-Jurkat-A11_S11


title: MapR RNA-seq CUTLL1 shSF3B1 replicate 1

status: Public on Jan 31 2022

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Bowtie2
Duplicate reads were removed using Picard tools
The read per million (RPM) normalized BigWig files were generated using BEDTools and the bedGraphToBigWig tool
Peak calling was performed using MACS
Peak count tables were created using BEDTools
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed using edgeR.
ChIPseeker R package was used for peak annotations
ngs.plot and ChIPseeker were used for TSS site visualizations and quality controls
Genome_build: hg 19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values.

growth_protocol: cells in suspension, growing in RPMI

extract_protocol:
Aurum Total RNA Mini Kit (Bio-Rad)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina NextSeq 500 using 50bp single-read method.

treatment_protocol: cells treated with short hairpin against SF3B1.

value: human T cell leukemia

tag: cell line


title: MapR RNA-seq CUTLL1 shCtrl replicate 3


title: MapR RNA-seq CUTLL1 shSF3B1 replicate 2


title: WT_15min_afterInd_37C_rep2


title: RNA-seq CUTLL1 E7107 3nM NMDi 5uM 24hr replicate 3

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed using edgeR.
Diferential alternative splicing analysis was performed using rMATS.
Genome_build: hg 19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values.

treatment_protocol: cells treated with the splicing inhibitor E7107 and NMDi with DMSO as the control.

value: human T cell leukemia cells


title: WT_30min_afterInd_37C_rep1


title: RNA-seq CUTLL1 NMDi 5uM 24hr replicate 3


title: RNA-seq CUTLL1 NMDi 5uM 24hr replicate 2


title: RNA-seq CUTLL1 E7107 3nM NMDi 5uM 24hr replicate 1


title: RNA-seq CUTLL1 E7107 3nM 24hr replicate 2


title: MapR RNA-seq CUTLL1 shCtrl replicate 2


title: MapR RNA-seq CUTLL1 shCtrl replicate 1


title: RNA-seq CUTLL1 E7107 3nM NMDi 5uM 24hr replicate 2


title: WT_15min_afterInd_37C_rep3


title: RNA-seq CUTLL1 E7107 3nM 1hr replicate 3

treatment_protocol: cells treated with the splicing inhibitor E7107 with DMSO as the control.


title: RNA-seq CUTLL1 E7107 3nM 1hr replicate 2


title: ∆rpoN_30min_afterInd_37C_rep2


title: RNA-seq CUTLL1 E7107 3nM 30min replicate 2


title: RNA-seq CUTLL1 NMDi 5uM 24hr replicate 1


title: RNA-seq CUTLL1 E7107 3nM 15min replicate 3


title: RNA-seq CUTLL1 DMSO 1hr replicate 1


title: RNA-seq CUTLL1 E7107 3nM 24hr  replicate 3


title: RNA-seq CUTLL1 DMSO 24hr replicate 3


title: RNA-seq CUTLL1 3nM  E7107 24hr replicate 2


title: RNA-seq CUTLL1 3nM  E7107 24hr replicate 1


title: RNA-seq CUTLL1 1.5nM  E7107 24hr replicate 2


title: MapR RNA-seq CUTLL1 shSF3B1 replicate 3


title: RNA-seq CUTLL1 DMSO 24hr replicate 2


title: RNA-seq CUTLL1 E7107 3nM 24hr replicate 1


title: RNA-seq CUTLL1 E7107 3nM 30min replicate 1


title: RNA-seq CUTLL1 DMSO 24hr replicate 1


title: RNA-seq CUTLL1 E7107 3nM 30min replicate 3


title: RNA-seq CUTLL1 shSF3B1.2 replicate 1


title: RNA-seq CUTLL1 DMSO 1hr replicate 2


title: RNA-seq CUTLL1 shSF3B1.2 replicate 3


title: RNA-seq CUTLL1 E7107 3nM 15min replicate 2


title: RNA-seq CUTLL1 DMSO 24hr replicate 2


title: RNA-seq CUTLL1 shSF3B1.2 replicate 2


title: RNA-seq CUTLL1 1.5nM  E7107 24hr replicate 1


title: RNA-seq CUTLL1 shSF3B1.1 replicate 3


title: RNA-seq CUTLL1 DMSO 24hr replicate 1


title: RNA-seq CUTLL1 shSF3B1.1 replicate 2


title: RNA-seq CUTLL1 E7107 3nM 15min replicate 1


title: TTseq RNA-seq CUTLL1 3nM E7107 15min replicate 3

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using STAR
The mean read insert sizes and their standard deviations were calculated using Picard tools
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed using edgeR.
The read per million (RPM) normalized BigWig files were generated using BEDTools and the bedGraphToBigWig tool
ngs.plot was use to visualize the gene body profile plots for both strands and each strand separately.
Genome_build: hg 19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values.


title: RNA-seq CUTLL1 shCtrl replicate 3


title: TTseq RNA-seq CUTLL1 DMSO 15min replicate 3


title: RNA-seq CUTLL1 3nM  E7107 24hr replicate 3


title: RNA-seq CUTLL1 E7107 3nM 1hr replicate 1


title: RNA-seq CUTLL1 shCtrl replicate 2


title: RNA-seq CUTLL1 DMSO 24hr replicate 3


title: TTseq RNA-seq CUTLL1 DMSO 15min replicate 1


title: RNA-seq CUTLL1 shCtrl replicate 1


title: TTseq RNA-seq CUTLL1 3nM E7107 24hr replicate 1


title: TTseq RNA-seq CUTLL1 DMSO 24hr replicate 2


title: RNA-seq CUTLL1 DMSO 1hr replicate 3


title: TTseq RNA-seq CUTLL1 3nM E7107 24hr replicate 2


title: RNA-seq CUTLL1 shSF3B1.1 replicate 1


title: TTseq RNA-seq CUTLL1 3nM E7107 15min replicate 2


title: RNA-seq CUTLL1 1.5nM  E7107 24hr replicate 3


title: TTseq RNA-seq CUTLL1 3nM E7107 15min replicate 1


title: TTseq RNA-seq CUTLL1 DMSO 15min replicate 2


title: TTseq RNA-seq CUTLL1 3nM E7107 24hr replicate 3


title: TTseq RNA-seq CUTLL1 DMSO 24hr replicate 3


title: Empty vector transformed leaves pool 2, 48h after transformation

status: Public on Jan 29 2022

type: RNA

city: Paterna

first: José Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

institute: Institute for Integrative Systems Biology

description: Expression profiling by array

hyb_protocol: Purified and fragmented cRNAs were hybridized with the Affymetrix GeneChip V.vinifera Genome Array ver. 1.0 cartridge

scan_protocol: Microarrays were scanned using a Hewlett-Packard GeneArray Scanner and image data were collected and processed on a GeneChip workstation using Affymetrix GCOS software.

data_processing: Raw intensity values of the probesets were processed by Robust Multi-Array Average (RMA) using the R package affy

label: biotin

organism: Vitis vinifera

label_protocol: Biotinylated complementary RNAs (cRNAs) were synthesized in vitro using T7 RNA polymerase in the presence of biotin-labeled UTP/CTP.

growth_protocol: V. vinifera cv.  'Shiraz' greenhouse grown plants on average ten weeks with stem length of 30-38 cm and leaf diameters of leaf one (counted from apex) 2-3 cm and leaf two 5-6 cm. Plants generated from wood cuttings from vineyards around Mussbach, (Neustadt/W, Germany, 49° 22′ 9′′ south, 8° 10′ 28′′ east). Cuttings of single buds were put into water for 24 h and afterward surface was sterilized by incubation for 8 h in Chinoplant (3 % (w/v)). Cuttings were afterwards stored in sealed plastic bags at 6 °C for up to 12 months.

extract_protocol:
Extracted leaf RNA from three of the time points described for both control and MYB15 infiltrated samples.
Total grapevine RNA was isolated from the various plant tissues as described in Downey et al. (2003). RNA was isolated from leaves with RNeasy kit (Qiagen) following the suppliers protocol.

treatment_protocol: Agrobacteria (strain C58C1 or ATHV), which contain a plasmid with the gene of interest, were cultured over night at 28 °C with 180 rpm in 5 ml of LB. The ten weeks old cv. 'Shiraz' greenhouse plants were put upside down into 750 ml WECK -glasses, which include 400 ml of agrobacterial suspension. To disrupt the surface tension 0.01 % (v/v) Break-Thru S240 (AlzChem AG, Germany) added to the Agrobacteria culture. Glasses were transferred to a desiccator placed on a magnetic stirrer and vacuum (20-40 mmHg) was applied for 5 min using a vacuum-pump (Type SC810, KNF Neuberger GmbH). The release of the vacuum enabled an entering of the Agrobacteria into the leaves via stomata. Successful infiltrated areas became translucent, in consequence the first transformation efficiency test was performed by a visual analysis. Afterwards plants were washed in distilled water, placed back to greenhouse and were harvested at different time points. The samples were harvested at eight hours, 16 h, 24 h, 48 h, 72 h, 96 h after transformation from leaf one, two, three (counted from the apex) from six different plants per combination, which were separated in two p.ools medium supplemented with the appropriate antibiotics (Table 6.2). The pre-culture was transferred into 500 mL of YEB medium (with appropriate antibiotics) and again grown over night at 28 °C and 180 rpm. After the inoculation the cells were harvested by centrifugation at 5000 rpm for 10 min, resuspended in MES buffer (10 mM MES pH 5.5) to an OD 600 ~ 0.3. Prior the next incubation step for 3 h at 22 °C in the dark with low agitation (50 rpm), 100 μM Acetosyringone (4'-Hydroxy-3',5'-dimethoxyacetophenone) have been applied.

tag: cultivar

value: Shiraz

tag: tissue

value: leaves

value: 10-weeks old plants

value: empty vector transformed

tag: time (hours after transformation)


title: Empty vector transformed leaves pool 1, 96h after transformation

description: Expression profiling by array

tag: age


title: Empty vector transformed leaves pool 2, 24h after transformation

description: Expression profiling by array


title: TTseq RNA-seq CUTLL1 DMSO 24hr replicate 1


title: INPUT_RIP_HMEC2

status: Public on Jan 19 2022

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
diff.Down_input_hmec_vs_ctcf_hmec.txt
diff.Up_sc35_hmec_vs_input_hmec.txt

data_processing:
Sequenced reads were quality-tested using FASTQC [85]
The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection and sjdbOverhang value of 100.
Reads were aligned to the hg19human genome using the STAR [86] version 2.5.1b. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
Raw gene expression was quantified across all gene bodies, using the top-expressed isoform as proxy for gene expression using HOMER.
Differential gene expression was carried out using the DESeq2 [87] package version 1.14 using replicates to compute within-group dispersion. Differentially bound transcripts were defined as having a false discovery rate (FDR) <0.05 and a log2 fold change >1 when comparing two experimental conditions. Transcripts showing sc35-specific binding and CTCF-specific binding were defined as those significantly upregulated in the sc35 RIP or CTCF RIP compared to the control RNA-Seq, respectively.
Transcripts showing both significant binding of CTCF and SC-35 in HMECs but no significant binding in the vHMECs were annotated with HOMER [88] and tested for term overrepresentation using WebGestalt [89].
Genome_build: hg19
Supplementary_files_format_and_content: text files listing genes enriched for binding at day 1 and day 10

source_name: human mammary epithelial cells

extract_protocol: Briefly, normal HMECs and stressed HMECs were crosslinked for 15 minutes by addition of 0.1% formaldehyde. Crosslinking was stopped upon addition of Glycine to a final concentration of 125 mM for 5 minutes. After washing with 1X PBS, cells were scraped and collected in RIPA (150 mM NaCl, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS, 50 mM Tris-HCl pH 8.0, 5 mM EDTA) containing protease inhibitors. Lysates were subsequently sonicated and 500 mg of lysate was pre-cleared for 1 hour using 40 ml of a 50% slurry of 1:1 protein A- and protein G-Sepharose beads (GE Healthcare). For immunoprecipitation, anti-CTCF (Active Motif), or mouse anti-SC-35 (Novus) was added to precleared lysates together with 40 ml of a 50% slurry of 1:1 protein A/G beads and incubated at 4°C overnight. Immuno-complexes were washed with RIPA, and with IP wash buffer (100 mM Tris-HCl pH 8.5, 500 mM LiCl, 1% NP-40, 1% Sodium Deoxycholate). After immunoprecipitation, CTCF, or SC-35-associated RNAs were isolated from the immunoprecipitate according to the manufacture's protocol (Wako). After the elution from the beads, the RNA was prepared using a miRNeasy Mini Kit (Qiagen). To remove possible genomic DNA contamination, RNase-free DNase was used during the RNA purification steps. RNA concentration was determined using a Nanodrop spectrophotometer (NanoDrop Technologies Inc.) and its integrity was ascertained by migration on 2% agarose gel and analyzed by displaying 28S and 18S rRNA. The RNAs were analyzed using small RNA deep sequencing.

tag: day

tag: replicate

tag: antibody


title: INPUT_RIP_HMEC1


title: INPUT_RIP_vHMEC2

description:
diff.Down_input_vhmec_vs_ctcf_vhmec.txt
diff.Up_sc35_vhmec_vs_input_vhmec.txt


title: INPUT_RIP_vHMEC1


title: SC35_RIP_vHMEC1

value: mouse anti-SC-35 (Novus)


title: CTCF_RIP_vHMEC2

value: anti-CTCF (Active Motif)


title: MYB15 transformed leaves pool 1, 24h after transformation

description: Expression profiling by array

value: MYB15 transformed


title: Empty vector transformed leaves pool 1, 48h after transformation

description: Expression profiling by array


title: MYB15 transformed leaves pool 1, 48h after transformation

description: Expression profiling by array


title: MYB15 transformed leaves pool 2, 24h after transformation

description: Expression profiling by array


title: Empty vector transformed leaves pool 2, 96h after transformation

description: Expression profiling by array


title: MYB15 transformed leaves pool 2, 48h after transformation

description: Expression profiling by array


title: MYB15 transformed leaves pool 2, 96h after transformation

description: Expression profiling by array


title: MYB15 transformed leaves pool 1, 96h after transformation

description: Expression profiling by array


title: Empty vector transformed leaves pool 1, 24h after transformation

description: Expression profiling by array


title: SC35_RIP_vHMEC2


title: SC35_RIP_HMEC1


title: Testis Wildtype rep1

status: Public on Jan 28 2022

city: Clayton

first: Vincent

last: Harley

state: VIC

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

description: Control testis 1

hyb_protocol: The chip was hybridised at 58C for 16 hours in an oven with a rocking platform. After hybridisation, the chip was washed using the appropriate protocols as outlined in the Illumina manual.

scan_protocol: The chips were coupled with Cy3 and scanned in the Illumina iScan Reader. The scanner operating software GenomeStudio was used to convert the signal on the array into a TXT file for analysis.

data_processing:
The GenomeStudio software was used for initial quality control (QC), background subtraction and averaging probes to gene-level estimates, before then loading the data into R with the Bioconductor package “lumi”. This data was variance stabilized and quantile normalization was performed.
Supplementary_Table_1.xlsx: Differentially expressed gene list derived from microarray of P12 ScAtrxKO mouse testes compared to wild-type mouse testes. Fold change cut-off is set at ±1.5 (adjusted p<0.05).
Supplementary_Table_2.xlsx: GO analysis of the differentially expressed genes. Data are categorized by Biological Process (BP), Molecular Function (MF) and Cellular Compartment (CC).
Supplementary_Figure_1.pdf: Kernel density estimates of the log2 signal intensity distributions are shown for the three wild-type (WT1, WT2, and WT3) and three ScAtrxKO (M1, M2, and M3) samples that were used for the microarray analysis. Left: Data prior to normalization; Right: Normalized data.

source_name: Mouse postnatal testis

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit. 500ng of total RNA was used for hybridisation to the Ilumina MouseWG6V2 Expression Beadchip.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: male

value: 12 days

value: testis

value: Wildtype


title: Testis ScAtrxKO rep1

description: ScAtrxKO testis 1

value: ScAtrxKO


title: Testis ScAtrxKO rep3

description: ScAtrxKO testis 3


title: CTCF_RIP_HMEC1


title: Testis ScAtrxKO rep2

description: ScAtrxKO testis 2


title: Testis Wildtype rep2

description: Control testis 2


title: Testis Wildtype rep3

description: Control testis 3


title: Day10 hMEC #3

description: updatedCTCDiff.txt

library_source: genomic

data_processing:
Sequenced reads were quality-tested using FASTQC [85]
The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection and sjdbOverhang value of 100.
Reads were aligned to the hg19human genome using the STAR [86] version 2.5.1b. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
ChIP-Seq analysis was carried out using HOMER findPeaks and mergePeaks subroutines using default parameters (four-fold enrichment over local tag count, Poisson p-value < 0.001, and style factor).
Peaks common to replicate 1 and replicate 2 at day 1 or day 10 were kept, and merged into a common peak file. Raw read counts were then assigned to peaks using HOMER annotatePeaks using all replicates from both days.
Differential CTCF peaks were found using raw counts of merged peaks from both day 1 and day 10 HMECs with DESeq2 using parameters of FDR < 0.05 and log2fold > 1.
Normalized read densities were visualized using the UCSC genome browser [90].
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing differential peak quantification and testing with HOMER

molecule: genomic DNA

extract_protocol: ChIPs were performed essentially as described [82] with minor modifications. Unless stated otherwise, all chemicals were purchased from Sigma. Briefly, normal HMECs and stressed HMECs were crosslinked for 15 minutes by addition of formaldehyde (Invitrogen) to a 1% final concentration. Crosslinking was stopped upon addition of glycine to a final concentration of 125 mM for 5 minutes. After washing with 1X PBS, cells were scraped and collected in RIPA (150 mM NaCl, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS, 50 mM Tris-HCl pH 8.0, 5 mM EDTA) containing protease inhibitors. Lysates were subsequently sonicated and 500 mg of lysate was pre-cleared for 1 hour using 40 ml of a 50% slurry of 1:1 protein A- and protein G-Sepharose beads (GE Healthcare). For immunoprecipitation, anti-CTCF (Millipore) was added to precleared lysates along with 40 ml of a 50% slurry of 1:1 protein A/G beads and incubated at 4°C overnight. Immuno-complexes were washed with: RIPA; IP wash buffer (100 mM Tris-HCl pH 8.5, 500 mM LiCl, 1% NP-40, 1% Sodium Deoxycholate); followed by 1X TE buffer before eluting in 200 ml of buffer containing 70 mM Tris-HCl pH 8.0, 1 mM EDTA and 1.5% SDS after incubation at 65°C for 10 or 30 minutes. Crosslinks were reversed from immuno-complexes by addition of 200 mM NaCl and incubation at 65°C for 6 hours or overnight. DNA was purified by incubation with proteinase K and phenol-chloroform extraction. Input samples were treated identically and IP DNA was quantified by real time PCR (RT-PCR).

value: anti-CTCF (Millipore)


title: SC35_RIP_HMEC2


title: CTCF_RIP_HMEC2


title: CTCF_RIP_vHMEC1


title: Day 1 hMEC #1

description: updatedCTCDiff.txt


title: Day10 hMEC #1

description: updatedCTCDiff.txt


title: H1_hESC_YAP_KO_UNT_3

status: Public on Jan 14 2022

data_processing:
RNA-Seq: reads were aligned by STAR v2.5.3a to hg19 reference using default parameters; expression was quantified using HOMER v4.9.1 by summing reads uniquely mapped to RefSeq exons; Differential expression was performed by DESeq2 v1.18.1 (adjusted p-val < 0.01 and absolute log2FC > 1).
snATAC-Seq: reads were aligned by bwa mem v0.7.12 to hg19 reference using default parameters and sorted by samtools v1.9. Then reads were preprocessed by SnapTools v1.4.7 into chromosomal bins of 5000 bp. MACS2 v2.1.2 was used for peak calling on pooled reads (-g hs --nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits). SnapATAC v1.0.0 was used for detailed analysis. In brief, cells with < 500 UMI, promoter ratio < 0.1 or > 0.6 were removed from analysis. Chromosomal bins overlapped with ENCODE blacklist or ranked top 5% by expression were also removed. Dimension reduction was performed by LSA and visualized in tSNE. Differential accessbile regions were identified by function "findDAR" (bcv=0.1, fdr=0.05, pvalue=0.01, test.method=exactTest, seed.use=10, cutoff: FDR < 0.05 and log2FC > 1).
Genome_build: hg19
Supplementary_files_format_and_content: YAP_trilineage_exons_raw.xlsx is the spread sheet that contain the gene expression count for RNA-Seq

source_name: hESC undifferentiated YAP KO

growth_protocol: hESCs were cultured in mTeSR1 medium on Matrigel-coated tissue culture plates. For expansion, hESC colonies were fragmented and split in a 1:20 ratio following ReLeSR treatment (StemCell Technologies). For directed differentiation experiments, colonies were disaggregated into single cells using Accutase and plated in presence of Rock Inhibitor (StemCell Technologies Y-27632) on matrigel-coated plates

extract_protocol:
RNA was extracted using Zymo columns and sent for library preparation and quality control. snATAC-Seq was carried out at the Center for Epigenomics at UCSD. The procedure followed the protocol described in Cusanovich et al. Briefly, DMSO-frozen hESCs were thawed in 37°C water bath until liquid (~2-3 minutes) and immediately placed on ice. Nuclei were isolated and permeabilized using OMNI buffer (0.1% NP40, 0.1% Tween-20, 0.01% Digitonin) as described40.  Nuclei were counted and 2k nuclei were dispensed per well; 96 wells per sample for tagmentation. After tagmentation (and addition of the first barcode), nuclei from individual samples were pooled. 20 nuclei from each sample were sorted per well (768 wells total). Following nuclear lysis the second barcode was added, and DNA molecules were pooled and purified. Before sequencing, the quality of the library was certified by analyzing fragment size distribution and DNA concentration
Illumina TruSeq stranded library for RNA-Seq; combinatory barcoding protocol of Cusanovich et al. was used for snATAC-Seq (details see above extract protocol).

treatment_protocol: hESCs were single-cell seeded onto 6-well matrigel-coated plates at 2*106 cells/well for ectoderm and endoderm conditions and 5*105 cells/well for mesoderm condition and treated with the appropriate differentiation medium using the STEMdiff Trilineage Differentiation Kit (StemCell Technologies #05230) according to manufacturer instructions

value: hESC H1

tag: differentiation status

value: undifferentiated

value: YAP KO


title: H1_hESC_YAP_KO_UNT_2


title: H1_hESC_YAP-KO_Meso_1

data_processing:
RNA-Seq: reads were aligned by STAR v2.5.3a to hg19 reference using default parameters; expression was quantified using HOMER v4.9.1 by summing reads uniquely mapped to RefSeq exons; Differential expression was performed by DESeq2 v1.18.1 (adjusted p-val < 0.01 and absolute log2FC > 1).
snATAC-Seq: reads were aligned by bwa mem v0.7.12 to hg19 reference using default parameters and sorted by samtools v1.9. Then reads were preprocessed by SnapTools v1.4.7 into chromosomal bins of 5000 bp. MACS2 v2.1.2 was used for peak calling on pooled reads (-g hs --nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits). SnapATAC v1.0.0 was used for detailed analysis. In brief, cells with < 500 UMI, promoter ratio < 0.1 or > 0.6 were removed from analysis. Chromosomal bins overlapped with ENCODE blacklist or ranked top 5% by expression were also removed. Dimension reduction was performed by LSA and visualized in tSNE. Differential accessbile regions were identified by function "findDAR" (bcv=0.1, fdr=0.05, pvalue=0.01, test.method=exactTest, seed.use=10, cutoff: FDR < 0.05 and log2FC > 1).
Genome_build: hg19
Supplementary_files_format_and_content: D0_totalPeaks_annotated_pval.txt.gz is the gzipped text table of called peaks and their statistics for snATAC-Seq
Supplementary_files_format_and_content: YAP_trilineage_exons_raw.xlsx is the spread sheet that contain the gene expression count for RNA-Seq

source_name: hESC induced mesoderm YAP KO

value: induced mesoderm


title: H1_hESC_H1_UNT_2

source_name: hESC undifferentiated WT

value: WT


title: H1_hESC_H1_Meso_3

source_name: hESC induced mesoderm WT


title: H1_hESC_H1_UNT_1


title: H1_hESC_H1_Meso_2


title: H1_hESC_YAP-KO_Ecto_2

source_name: hESC induced ectoderm YAP KO

value: induced ectoderm


title: H1_hESC_YAP-KO_Endo_3

source_name: hESC induced endoderm YAP KO

value: induced endoderm


title: Day 1 hMEC #2

description: updatedCTCDiff.txt


title: H1_hESC_YAP-KO_Ecto_3


title: H1_hESC_YAP-KO_Meso_2


title: H1_hESC_YAP-KO_Ecto_1


title: H1_hESC_H1_Endo_2

source_name: hESC induced endoderm WT


title: H1_hESC_YAP-KO_Endo_1


title: H1_hESC_YAP-KO_Endo_2


title: Day10 hMEC #2

description: updatedCTCDiff.txt


title: H1_hESC_H1_Endo_3


title: H1_hESC_H1_Ecto_2

source_name: hESC induced ectoderm WT


title: H1_hESC_H1_Endo_1


title: H1_hESC_H1_Ecto_1


title: H1_hESC_H1_Ecto_3


title: YAP_hESC_snATAC

source_name: undifferentiated YAP KO hESC


title: H1_hESC_YAP_KO_UNT_1


title: H1_hESC_H1_Meso_1


title: H1_hESC_YAP-KO_Meso_3


title: WT_hESC_snATAC

source_name: undifferentiated WT hESC


title: RNA_mOocy_b151

status: Public on Dec 09 2021

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
mouse_ovary_exprs_UMI_counts.csv
cell_annotation.csv
cell_barcode_sequence.csv

data_processing:
Raw reads were separated by cell barcodes, trimmed, aligned to the mm9 mouse transcriptome and de-duplicated by UMIs information.
The transcript copy numbers of each gene were counted and used for the subsequent analysis.
Single cells with high ratio of mitochondrial genes or ERCC spike-ins (TPM value higher than 5 median absolute deviations plus the median TPM) were excluded.
Somatic cells with less than 1,000 detected genes or 10,000 transcripts were excluded. Oocytes with less than 2,000 detected genes or 20,000 transcripts were excluded.
Genes that didn’t detected in any cells were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: [mouse_ovary_exprs_UMI_counts.csv]  Comma-separated values files include expression values (UMI counts).  Cells are named as RNA_mOocy_bxx_scxx.  The "bxx" means sequencing batch.  The "scxx" means different cell barcodes.
[cell_barcode_sequence.csv]  contains cell barcode sequences
[cell_annotation.xlsx]  contains annotations of each cell in  mouse_ovary_exprs_UMI_counts.csv including cell name, cell barcode, cell type and genotype.

source_name: Mouse Ovary Cells

extract_protocol:
The ovary tissues were cut into pieces and then treated with 1ml M2 medium (Sigma-Aldrich) with 50 μL collagenase IV at 37oC for 20 minutes to remove interstitial tissues, rocked samples for 30 minutes. The tissues were resuspended in 1ml M2 medium. Next, needles were used to isolate single oocyte or somatic cells under stereomicroscope.
First, hand-picked single cells from mice ovaries were placed in single-cell lysis buffer prepared in advance, and single-cell cDNA was synthesized. Then, the obtained cDNA was purified using XP magnetic beads and DNA Clean and Concentrator Kit-5 (Zymo) and quantified. After that, the cDNA was interrupted into 200bp short fragments after being ligated to the biotin index sequences. Finally, RNA-seq libraries for the purified biotin-labled DNA fragments constructed following the NEB DNA Library Prep kit instructions were sequenced on the Illumina HiSeq X-Ten platform.

value: Ovary

value: db/db

value: somatic cell


title: RNA_mOocy_b153

value: ob/ob


title: DETC_isotype_treated_scRNA-seq

status: Public on Dec 12 2021

city: London

first: Duncan

last: McKenzie

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

source_name: FACS sorted CD45+EpCAM-MHC-II- epidermal cells

growth_protocol: Ear tissue was processed immediately following sacrifice of mice, 7d subsequent to antibody injection

extract_protocol:
Ears were split and floated upon Trypsin-GNK (2.5mg/ml trypsin (Sigma), 7.35mg/ml NaCl, 0.35mg/ml KCl, 0.85mg/ml glucose) for 1 hr at 37 degrees C. Epidermis was separated and digested in trypsin-GNK with 100 ug/ml DNase I (Roche) and 1X Dnase buffer (1.21 mg/ml Tris base, 0.5mg/ml MgCl2, 73ug/ml CaCl2) for 20 min at 37 degrees C with agitation. Isolated cells were washed in medium and stained with Live/Dead Fixable Near-IR Dye (Molecular Probes), followed by mouse Fc block (BD) and anti-CD45-APC (30-F11, BioLegend), anti-MHC-II I-A/I-E-FITC (M5/114.15.2, BioLegend) and anti-EpCAM-PE (G8.8, eBioscience). Live CD45+EpCAM-MHC-II- cells were sorted with a FACS Aria Fusion.
RNA libraries were prepared for sequencing using Chromium Single Cell 3' GEM, Library and Gel Bead Kit v3 (10x Genomics)

treatment_protocol: Ear epidermis was separated and digested to yield a single cell suspension, from which epidermal T cells were FACS purified

value: Dendritic Epidermal T Cells (DETC)

value: 8 week old

value: FVB/NJ

tag: Sex

value: Female

tag: treatment

value: Treated 7d prior with intradermal injection of isotype control antibody


title: RNA_mOocy_b150


title: RNA_mOocy_b149


title: RNA_mOocy_b148


title: RNA_mOocy_b146


title: RNA_mOocy_b147


title: RNA_mOocy_b143


title: RNA_mOocy_b144

value: oocyte


title: RNA_mOocy_b145


title: Rspo WT vs KI 14d non infected

status: Public on Jan 01 2022

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: polarity(+)

hyb_protocol: Whole mouse genome 4x44k and 8x60k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm  and extended range (XDR) for 4x44K microarrays and 3µm for 8x60K microarrays using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 for 4x44K microarrays and GE2_1200_Dec17 for 8x60K microarrays extraction protocol by the mean of trimmed positive non-flagged/non-control reporters.

source_name: Rspo WT 14d non infected

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: All animals were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum. Male, 6- to 8-week-old mice were used for this study.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method according the manufacturer´s protocol.

treatment_protocol: Mouse glands from H. pylori infected Rspo3 WT and KI animals were treated with tamoxifen 2 month before euthanasia. Cells  were isolated from the corpus  as previously described.

value: non infected

value: wildtype

value: corpus

source_name: Rspo KI 14d non infected

value: RSPO3 knock-in (KI) mutant


title: RNA_mOocy_b139


title: RNA_mOocy_b140


title: RNA_mOocy_b141


title: RNA_mOocy_b137


title: RNA_mOocy_b138


title: Rspo KI vs WT 14d non infected

description: polarity(-)


title: RNA_mOocy_b135


title: RNA_mOocy_b136


title: RNA_mOocy_b134


title: RNA_mOocy_b133


title: RNA_mOocy_b132


title: RNA_mOocy_b131


title: Rspo  KO vs WT 2m infected

description: polarity(-)

source_name: Rspo  KO 2m infected

value: 2 months infected

value: RSPO3 knock-out (KO) mutant

source_name: Rspo WT 2m infected


title: RNA_mOocy_b130


title: RNA_mOocy_b129


title: DETC_anti-Skint1_treated_scRNA-seq

value: WT

value: Treated 7d prior with intradermal injection of anti-Skint1 antibody


title: RNA_mOocy_b142

value: Ovary


title: RNA_mOocy_b152

value: db/db, ob/ob


title: RNA_mOocy_b127

value: db/db

value: somatic cell


title: RNA_mOocy_b124


title: RNA_mOocy_b116


title: RNA_mOocy_b119


title: RNA_mOocy_b121


title: RNA_mOocy_b128

value: ob/ob


title: RNA_mOocy_b118


title: RNA_mOocy_b126


title: RNA_mOocy_b120


title: RNA_mOocy_b114


title: RNA_mOocy_b117


title: RNA_mOocy_b112


title: RNA_mOocy_b123


title: RNA_mOocy_b111


title: RNA_mOocy_b110

value: somatic cell, oocyte


title: RNA_mOocy_b109


title: RNA_mOocy_b113


title: RNA_mOocy_b108


title: RNA_mOocy_b105


title: RNA_mOocy_b106


title: RNA_mOocy_b104


title: Rspo  WT vs KO 2m infected

description: polarity(+)

source_name: Rspo  WT 2m infected

source_name: Rspo KO 2m infected


title: RNA_mOocy_b107


title: RNA_mOocy_b125


title: RNA_mOocy_b103


title: RNA_mOocy_b122


title: RNA_mOocy_b101


title: RNA_mOocy_b115


title: RNA_mOocy_b102


title: RNA_mOocy_b100


title: RNA_mOocy_b98


title: RNA_mOocy_b95


title: RNA_mOocy_b99


title: RNA_mOocy_b97


title: RNA_mOocy_b94


title: RNA_mOocy_b96


title: RNA_mOocy_b93


title: RNA_mOocy_b91


title: RNA_mOocy_b92


title: RNA_mOocy_b90


title: RNA_mOocy_b89


title: RNA_mOocy_b88


title: RNA_mOocy_b87


title: RNA_mOocy_b86


title: RNA_mOocy_b84


title: RNA_mOocy_b83


title: RNA_mOocy_b82


title: RNA_mOocy_b57

value: wild type


title: RNA_mOocy_b58


title: RNA_mOocy_b59


title: RNA_mOocy_b56


title: RNA_mOocy_b53


title: RNA_mOocy_b55


title: RNA_mOocy_b54


title: RNA_mOocy_b51


title: RNA_mOocy_b52


title: RNA_mOocy_b48


title: RNA_mOocy_b47


title: RNA_mOocy_b49


title: RNA_mOocy_b46


title: RNA_mOocy_b50


title: RNA_mOocy_b44


title: RNA_mOocy_b42


title: RNA_mOocy_b41


title: RNA_mOocy_b45


title: RNA_mOocy_b40


title: RNA_mOocy_b43


title: RNA_mOocy_b32


title: RNA_mOocy_b85


title: RNA_mOocy_b39


title: RNA_mOocy_b29


title: RNA_mOocy_b31


title: RNA_mOocy_b24


title: RNA_mOocy_b23


title: RNA_mOocy_b21


title: RNA_mOocy_b13


title: RNA_mOocy_b14


title: RNA_mOocy_b12


title: RNA_mOocy_b11


title: RNA_mOocy_b30


title: RNA_mOocy_b6


title: RNA_mOocy_b8


title: RNA_mOocy_b7


title: RNA_mOocy_b4


title: RNA_mOocy_b5


title: RNA_mOocy_b3


title: RNA_mOocy_b1


title: LNCap cells_siGATA2_D_SOX9_rep2

city: San Antonio

first: Tianbao

last: Li

state: Texas

address: 7703 Floyd Curl

department: Molecular Medicine

institute: University of Texas Health Science Center at San Anotnio

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version with parameters '-k 2 -v 2' to report up to two valid alignments
Read with multiple valid alignments were removed using a Perl program
Uniquely mapped reads from replicates of the same sample were pooled
Peaks were called using MACS2 with default parameters
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed (MACS2_peak)

growth_protocol: LNCaP cells were cultured in 10% FBS RPMI 1640 medium, 1:3 split every 4 days. Cells are cultured in 5% charcoal stripped FBS RPMI-1640 medium for 3 days before hormone treatment.

extract_protocol:
For ATAC-seq, 50,000 cells were resuspended in cold ATAC-seq resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2). Cell nuclei were then prepared by incubation in 50 μl of ATAC-seq resuspendsion buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin on ice for 3 min. After centrifugation, nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer ,2.5 μl Nextera Tn5 transposase (Illuminar), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water), and incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 rpm. Transposed fragments were then purified with a Zymo DNA Clean and Concentrator-5 Kit. All libraries showed sufficient amplification after the 5 pre-amplification cycles and quantified using the KAPA Library Quantification Kit.
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min on horizontal rotator at room temperature and cell pellets were collected and subjected to sonication. The sheared chromatin was then diluted and immunoprecipitated with 4 µg of specific antibodies at 4°C overnight. After washing, chromatin complexes were eluted with elution buffer and crosslinking was reversed at 65°C overnight. DNA fragments were purified with the QIAquick PCR purification kit.
For ATAC-seq, the library preparation was performed with Nextera DNA Library Prep Kit for Illumina following the manufacturer’s instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina Novaseq 6000 at the Duke sequencing core.
For ChIP-seq, the eluted ChIP DNA was used for library preparation with NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer’s protocol. The library was ampliﬁed with 12 PCR cycles and prepared with gel-based size selection.

treatment_protocol: 10 nM DHT was added before cell collection for ATAC-seq/ ChIP-seq of histone markers assay.

value: LNCap

tag: chip antibody

tag: vendor

value: Chemicon

tag: catalog #

tag: sirna

value: siGATA2 (Horizon Discovery, Catalog ID:L-009024-02-0020)

value: DHT


title: LNCap cells_siGATA2_D_SOX9_rep1


title: LNCap cells_siCon_V_GATA2_rep2

value: Santa Cruz

value: siCon (Horizon Discovery, Catalog ID:D-001810-10-20)

value: DMSO


title: LNCap cells_siCon_V_GATA2_rep1


title: LNCap cells_siCon_V_SOX9_rep2


title: LNCap cells_siGATA2_V_SOX9_rep2


title: LNCap cells_siSox9_D_GATA2_rep2

value: siSox9 (Horizon Discovery, Catalog ID:L-021507-00-0020)


title: LNCap cells_siSox9_V_GATA2_rep1


title: LNCap cells_siSox9_D_GATA2_rep1


title: LNCap cells_siCon_D_SOX9_rep2


title: LNCap cells_siCon_V_SOX9_rep1


title: LNCap cells_siSox9_V_GATA2_rep2


title: RNA_mOocy_b22

tag: strain

tag: genotype

tag: cell type


title: LNCap cells_siCon_D_SOX9_rep1

tag: cell line


title: LNCap cells_siGATA2_ATAC_rep2


title: LNCap cells_siGATA2_ATAC_rep1


title: LNCap cells_siCon_D_GATA2_rep2


title: RNA_mOocy_b10

tag: tissue


title: RNA_mOocy_b9


title: LNCap cells_siCon_D_GATA2_rep1


title: LNCap cells_siCon_ATAC_rep1


title: LNCap cells_siCon_ATAC_rep2


title: HEK293T_flavopiridol_timecourse

status: Public on Dec 01 2021

city: Seattle

first: Hyeon-Jin

last: Kim

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: sci-RNA-seq profiles and hash ladder calibration lines of HEK293T cells exposed to 300 nM of flavopiridol for increasing amounts of time or DMSO control

data_processing:
Illumina RTA software used for basecalling.
The sci-RNA-seq libraries were processed according to the protocol described in Srivatsan et al. First, Illumina reads were demultiplexed using bcl2fastq (v2.20). Custom scripts were used to extract barcodes that match reverse transcription (RT) indices within Levenstein distance cutoff of 2. After RT barcode matching, poly(A) sequences were trimmed using trim-galore, and the trimmed reads were aligned to  hg38  using STAR aligner (v2.5.2b) with default settings. The aligned reads were filtered with MAPQ >= 30, deduplicated, and collapsed by unique molecular identifiers (UMIs). The deduplicated reads were then assigned to genes using bedtools intersect function with an annotated human gene model. Knee plots were then generated from UMI counts per cell barcode to filter out true cell barcodes from debris. Thresholds were selected on a per-experiment basis and gene expression profiles from cell barcodes with total UMI counts greater than the knee threshold were used to generate a CDS object for downstream analysis.
The hash IDs were assigned sample labels as described in Srivatsan et al. In summary, reads from hash oligos were extracted from the demultiplexed read files by matching the first 10 bp of read 2 to the hash barcodes with the Levenstein distance of 2 and looking for trailing poly(A) sequences from position 12-16 bp. These reads were deduplicated and collapsed by UMIs, which were then used for sample assignment and hash ladder calibration line construction.
Genome_build: GRCh38
Supplementary_files_format_and_content: _UMI.count.matrix: single cell gene expression data in a sparse matrix format (gene_index | cell_index | gene_count).
Supplementary_files_format_and_content: _cell.annotations: Cell annotation file (cell_barcode | experiment name).
Supplementary_files_format_and_content: _gene.annotations: Gene annotation file (gene_id | gene_short_name).
Supplementary_files_format_and_content: _hashLadderSampleSheet.txt: Sample sheet for hash oligos used for calibration.
Supplementary_files_format_and_content: _hashIDSampleSheet.txt: Sample sheet for hash oligos used for labeling different treatment conditions.
Supplementary_files_format_and_content: _hash-ladder-exp.txt: Sample sheet for hash oligos used for labeling different treatment conditions.
Supplementary_files_format_and_content: _hashID-annotation.txt: Sample sheet for hash oligos used for labeling different treatment conditions.
Supplementary_files_format_and_content: _hashTable.out: Table that contains hash ladder oligo counts for each cell in the experiment.
Supplementary_files_format_and_content: _hashTable-labels-filtered.out: Table that contains hash ID oligo counts for each cell in the experiment.
Supplementary_files_format_and_content: _hashTable_unique_filtered.txt: Table that summarizes hash ladder calibration lines in each cell
Supplementary_files_format_and_content: _cds_conv.rds: Monocle3 cds object constructed with conventional size factor normalization.
Supplementary_files_format_and_content: _cds_hash_ladder.rds: Monocle3 cds object constructed with hash ladder based size factor normalization.

source_name: Cell line

growth_protocol: A549 and HEK293T cells were cultured in DMEM (Gibco) media containing 10% fetal bovine serum (Invitrogen) and 1% penicillin and streptomycin (Gibco) at 37°C with 5% CO2.

extract_protocol:
After drug treatment, cells were harvested via trypLE incubation and lysed with ice cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Extracted nuclei were then labeled with hash oligos by paraformaldehyde fixation with appropriate hash oligos and subjected to sci-RNA-seq (Cao et al. 2017). Detailed protocol is described in the method section of the manuscript.
sci-RNA-seq libraries were prepared by following the protocol described in Cao et al. 2017 and Srivatsan et al. 2020.

treatment_protocol: For the proof of concept experiment, HEK293T cells were grown in a T-75 flask. For the flavopiridol time course experiment, HEK293T cells were seeded onto a 6-well culture plate at a density of 400,000 cells per well in 2 mL of media. For the HDAC inhibitor time course and HDAC inhibitor and dexamethasone co-treatment experiments, A549 cells were seeded onto a 96-well culture plate at a density of 25,000 cells per well in 100 μL of media.

value: mixed sample (non-demultiplexed):300 nM of flavopiridol for 0 (DMSO),1,3,6,12,24 hours


title: Swim Bladder1

status: Public on Nov 22 2021

city: Hangzhou

first: Mengmeng

last: Jiang

address: Yuhangtang Road 866, Xihu Distric

institute: Zhejiang University

data_processing:
The drop-seq core computational tool was used for preprocessing of the Microwell-seq data. The implementation is described in the Drop-seq computational cookbook (http://mccarrolllab.org/dropseq/).
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: http://dec2017.archive.ensembl.org/Danio_rerio/Info/Index
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

organism: Danio rerio

source_name: swim  bladder

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: Tubingen

value: swim bladder


title: RNA_mOocy_b2

value: Ovary


title: Leaf, high phytotoxic potential, A1

status: Public on Oct 27 2021

city: Mlochow

first: Dorota

last: Sołtys-Kalina

address: Platanowa 19

department: Mlochow Research Centre

country: Poland

institute: IHAR-PIB

data_processing:
Zebracall process Version 0.5.0.13875 used for basecalling.
The index of the reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000226075.1) was built using Bowtie v2.1.0.
Poor quality and to short reads (<30 nt) were removed from analysis.
Paired-end clean reads obtained for bulks A and B were aligned to the reference genome using TopHat v2.0.9.
Assembly: GCF_000226075.1
Supplementary files format and content: csv files were generated using DESeq2 package.
Supplementary files format and content: all_samples_raw_count.xlsx: Excel file includes abundance measurements.

organism: Solanum tuberosum

source_name: Leaf

growth_protocol: Potato plants were planted in plastic pots filled with soil. Plants grew in greenhouse from May to October.

extract_protocol:
Total RNA was isolated using TRIZol method as described Chomczyński and Sacchi (1987).
The mRNA was isolated using Dynabeads® mRNA Purification Kit for mRNA enrichment (Ambion, 61006), and cDNA libraries were prepared using MGIEasy RNA Directional Library Prep Set (MGI, 1000006386). The established cDNA libraries were sequenced on the BGISEQ-500 sequencing platform (BGI Genomics, China) to generate 100-bp paired-end reads (PE100).

treatment_protocol: At stage of full anthesis, leaves were collected, ground in liquid nitrogen and freezed in -80°C until use.

value: Leaf

tag: population

value: Diploid hybrid 15-1

tag: developmental stage

value: Full anthesis

tag: phenotype

value: High glycoalkaloids, high phytotoxic potential

value: untreated


title: Leaf, high phytotoxic potential, A3


title: Leaf, low phytotoxic potential, B2

value: High glycoalkaloids, low phytotoxic potential


title: LNCap cells_siGATA2_V_SOX9_rep1

value: LNCap

value: Chemicon


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate9.

status: Public on Oct 25 2021

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive, Room 3700

department: Department of Genetics

institute: Stanford University School of Medicine

description:
STARR-seq library reporter-derived mRNA
HS-STARR-seq-promoters_counts.txt.gz

data_processing:
Library strategy: STARR-seq
Illumina bcl2fastq2-v2.20.0 used for basecalling.
STARR-seq: bowtie2 was used to align sequences to custom indices with options: --maxins 2000 -p 16 --no-discordant --no-mixed --fast
motif modification STARR-seq: bowtie2 was used to align sequences to custom indices with options: --maxins 2000 -p 16 --no-discordant --no-mixed --fast --score-min L,-0.7,-0.7
PRO-Seq: bowtie was used to align sequences to hg19 with options: --wrapper basic-0 -p 4
ExP 1Kx1K barcode to promoter aligned reads were counted with a custom python script to associate ExP barcodes to promoter sequences.
ExP 1Kx1K DNA and RNA reads were demultiplexed with the Je-suite demultiplex version 2.0 and counted with a custom python script.
HS-STARR-seq DNA and RNA reads were counted with a custom python script.
Motif modification STARR-seq Promoter + barcode aligned reads were counted with a custom python script to associate motif_modification barcodes to promoter sequences and quality filtered.
PRO-Seq: bowtie was used to align sequences to hg19 with options: --wrapper basic-0 -p 4, and reads were counted in gene bodies with a custom script.
Motif modification STARR-seq DNA and RNA reads were counted with a custom python script.
Genome_build: hg19
Supplementary_files_format_and_content: tabular separated values - promoter and barcode read count
Supplementary_files_format_and_content: tab separated values - K562 ExP 1Kx1K DNA and RNA counts
Supplementary_files_format_and_content: tab separated values - Hybrid-selected K562 Enhancer regions STARR-seq DNA and RNA counts
Supplementary_files_format_and_content: tab separated values - Hybrid-selected Promoter regions STARR-seq DNA and RNA counts

source_name: transfected plasmid reporter

growth_protocol: We maintained cells at a density between 100,000 and 1,000,000 cells per ml in RPMI-1640 (Thermo Fisher Scientific) with 10% heat-inactivated FBS, 2 mM L-glutamine and 100 units per ml streptomycin and 100 mg ml−1 penicillin by diluting cells 1:8 in fresh medium every 3 days. Cell lines were regularly tested for mycoplasma.

extract_protocol:
STARR-seq: We extracted RNA using 3 RNAeasy columns per 50-million cell replicate and isolated polyA+ mRNA using the Qiagen Oligotex mRNA kit.
Motif-modification STARR-seq: We extracted RNA using 3 RNAeasy columns per 50-million cell replicate and isolated polyA+ mRNA using the Poly(A)Purist MAG kit from Thermo Fisher Scientific.
PRO-Seq: We performed PRO-Seq essentially as described in Kwak H et al. Science 2013.
We performed reverse transcription using SuperScript IV, then performed a junction PCR using intron-spanning primers, then finally a sequence-ready PCR.

tag: library type

value: STARR-seq transcript RNA


title: Leaf, low phytotoxic potential, B1


title: Leaf, low phytotoxic potential, B3


title: Promoter_hybrid_select_DNA_input.

description:
STARR-seq library transfected DNA
HS-STARR-seq-promoters_counts.txt.gz

value: STARR-seq transcript DNA


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate8.


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate5.


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate6.


title: SAMPLE 8_hCDL (0.01%)

status: Public on Nov 16 2021

city: Macau

first: Guokai

last: Chen

address: University of Macau Avenida da Universidade Taipa, Macau, China

institute: University of Macau

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina).

data_processing:
Data was normalized by quantile normalization.
www.arrayanalysis.org computed the normalized signal intensity.

source_name: Human embryonic stem cell H1

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio).

growth_protocol: Human ESCs (H1) were maintained in E8 medium on matrigel-coated plates with daily medium change. Cells are passaged at 70% confluence by 1:12 with 5 μM ROCK inhibitor Y27632. Y27632 was romoved after 24 hrs. Cells were given treatments for 2 days and then collected for analysis.

extract_protocol: Toatal RNA was isolated by Qiagen Rneasy kit.

treatment_protocol: E8: normal E8 medium. AlbuMAX: E8 medium supplemented with 1.6% AlbuMAX. Albumin: E8 medium supplemented with 1% Albumin. CDL: E8 medium supplemented with 1% chemically defined lipid concentrate. hCDL (0.1x): E8 medium supplemented with 0.1x homemade chemically defined lipid mixture. LPA: E8 medium supplemented with 1 μM lysophosphatidic acid (18:1). LPA + Albumin: E8 medium supplemented with 1 μM LPA + 1% albumin.

value: H1 hESC cell line

value: hCDL (0.1x)


title: SAMPLE 3_LPA (1 μM)

value: LPA


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate9.


title: SAMPLE 9_Albumin (1%)

value: Albumin


title: SAMPLE 1_E8


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate7.


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate1.


title: SAMPLE 2_AlbuMAX (1.6%)

value: AlbuMAX


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate7.


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate3.


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate4.


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate8.


title: SAMPLE 10_LPA (1 μM) + Albumin (1%)

value: LPA + Albumin


title: SAMPLE 5_CDL (1%)

value: CDL


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate6.


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate2.


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate4.


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate10.


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate5.


title: ExP_Promoter_to_BC_map.

description: STARR-seq plasmid DNA barcode-promoter dictionary

value: STARR-seq plasmid DNA


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate2.


title: Leaf, high phytotoxic potential, A2

value: Leaf

value: Diploid hybrid 15-1


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate3.


title: Promoter_hybrid_select_BioReplicate4_TechnicalReplicate10.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate8.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate7.


title: Promoter_hybrid_select_BioReplicate3_TechnicalReplicate1.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate5.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate6.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate4.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate1.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate2.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate8.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate10.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate7.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate3.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate9.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate6.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate5.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate4.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate3.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate10.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate1.


title: K562_ExP_1Kx1K_DNA_input.

description:
STARR-seq library transfected DNA
ExP_1Kx1K_counts.txt.gz


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate9.

description:
STARR-seq library reporter-derived mRNA
ExP_1Kx1K_counts.txt.gz


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate8.


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate7.


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate5.


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate6.


title: Promoter_hybrid_select_BioReplicate2_TechnicalReplicate9.


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate7.


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate9.


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate3.


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate6.


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate4.


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate2.


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate4.


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate5.


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate8.


title: Promoter_hybrid_select_BioReplicate1_TechnicalReplicate2.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate7.


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate2.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate6.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate9.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate5.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate4.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate1.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate8.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate3.


title: K562_ExP_1Kx1K_BioReplicate2_TechnicalReplicate2.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate8.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate7.


title: K562_ExP_1Kx1K_BioReplicate4_TechnicalReplicate1.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate9.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate5.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate4.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate3.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate2.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate8.

description:
STARR-seq library reporter-derived mRNA
HS-STARR-seq-enhancers_counts.txt.gz


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate1.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate9.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate1.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate5.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate7.


title: K562_ExP_1Kx1K_BioReplicate3_TechnicalReplicate3.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate9.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate8.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate3.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate10.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate6.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate2.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate7.


title: K562_ExP_1Kx1K_BioReplicate1_TechnicalReplicate6.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate5.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate4.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate9.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate8.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate1.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate1.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate7.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate10.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate4.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate3.


title: Enhancer_hybrid_select_DNA_input.

description:
STARR-seq library transfected DNA
HS-STARR-seq-enhancers_counts.txt.gz


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate3.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate2.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate6.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate4.


title: Enhancer_hybrid_select_BioReplicate4_TechnicalReplicate6.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate10.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate8.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate9.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate1.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate6.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate3.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate10.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate5.


title: Enhancer_hybrid_select_BioReplicate3_TechnicalReplicate2.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate1.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate4.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate7.


title: Enhancer_hybrid_select_BioReplicate1_TechnicalReplicate2.


title: Enhancer_hybrid_select_BioReplicate2_TechnicalReplicate5.


title: P120_IN

status: Public on Oct 08 2021

data_processing:
Raw sequencing data was demultiplexed and converted into FASTQ files using CASAVA (v1.8.2), and quality tested with FASTQC v0.11.2.
Alignment to the mm10 genome was performed using the STAR aligner version 2.5.1b (Dobin et al., 2013). Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read), and a high ratio of uniquely mapped reads (>75%) was confirmed with exonic alignment inspected to ensure that reads were mapped predominantly to annotated exons.
Raw and normalized (FPKM) gene expression was quantified across all genes (RNAseq) using the top-expressed isoform as proxy for gene expression using HOMER v4.10 (Heinz et al.,2010),resulting in 10-55 million uniquely mapped reads in exons.
Principal Component Analysis was carried out with prcomp in R 3.4.3 on normalized counts. Differential gene expression was carried out using the DESeq2[1] package version 1.14.1 using the HOMER getDiffExpression.pl script with default normalization and using replicates to compute within-group dispersion. Significance for differential expression was defined as adjusted P<0.05, calculated using Benjamini-Hochberg's procedure for multiple comparison adjustment.
Genome_build: mm10
Supplementary_files_format_and_content: Excel Table with normalized gene counts

source_name: whole ROI homogenate (input)

growth_protocol: 12 hour light/dark cycle with ad lib access to standard mouse chow

extract_protocol:
1% PFA perfusion then brain microdissection in cold physiological buffer, then RNA extracted (input) or ribosomal pulldown via Ribotag protocol (Sanz et al PNAS 2009): HA-tagged ribosome pulled down with Cst Rb anti-HA antibody, isolated via Pierce IgG beads. All RNA extracted with Qiagen RNeasy Micro kit.
standard Illumina protocol (PolyA beads)

tag: age

value: post natal day 120

value: 73.12 GFAP-cre x RPL22-HA

value: visual cortex


title: P120_4

source_name: from astrocyte ribome pulldown


title: P120_5


title: P28_IN

value: post natal day 28


title: P120_1


title: P28_4


title: P28_5


title: P14_IN

value: post natal day 14


title: P28_2


title: P28_1


title: P14_2


title: P14_3


title: P14_4


title: P7_IN2

value: post natal day 7


title: P7_3


title: P7_2


title: P14_1


title: P7_1