title: Wild type.rep.2

value: Wild type


title: MUTZ5_Rux_1

status: Public on Sep 22 2021

type: SRA

city: Philadelphia

first: Ruitao

last: Zhang

state: PA

address: 2930 Chestnut St. Apt. 1709-B

department: Pediatrics

country: USA

institute: Children's Hospital of Philadelphia

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the human genome hg38 reference sequence using STAR v3.5.3a
Gene-based FPKM and read count matrices were performed with Cufflinks v2.2.1 and featureCounts v1.3.6.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: leukemia cell line

growth_protocol: B-cell acute lymphoblastic leukemia cell lines MHHCALL4, MUTZ5, and TVA1 were grown in suspension typically 10-20 × 106 cells into a T75 flask in RPMI 1640 (31870-025; Invitrogen) supplemented with 20% FBS, 1% Glutamax, 1% HEPES, 1% NEAA, and 100 unit/ml penicillin/streptomycin (MUTZ5 and MHH-cALL4) or RPMI supplemented with 10% FBS and 100 unit/ml penicillin/streptomycin (TVA1).

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen) and treated with DNAse, and SMART-seq v4 Ultra Low input RNA kit (Takara) and Nextera XT DNA library prep kit (Illumina) were used for library preparation using 10 ng of total RNA as input.
RNA libraries were prepared for sequencing using standard Illumina protocols
Paired-end sequencing was performed using the Illumina NovaSeq 6000 platform with a 150-bp read length

treatment_protocol: Two technical replicates per condition were treated with 0.1% DMSO vehicle, venetoclax, tyrosine kinase inhibitor (ruxolitinib or dasatinib), or combination for 72 hours

tag: cell type

value: B cell precursor leukemia


title: Lung-Mtb-Aggregates 3

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren St, Rm# W250.Q

department: New Jersey Medical School,

institute: Rutgers Biomedical and Health Sciences, Rutgers The State University of NJ

data_processing:
QuantSeq FWD followed by Trimming using reference 'polyA' and "truseq"
The STAR aligner (Spliced Transcripts Alignment to a Reference) is Lexogens aligner of choice for aligning reads which were generated in a QuantSeq FWD or QuantSeq REV experiment.
The STAR aligner aligns reads directly to a reference genome via the utilization of a pre-generated index of the reference. A reference consists of sequences in FASTA format and, optionally, information about genes and transcripts stored in a GFF/GTF file. The reads are provided in a text file in the FASTQ format, which is then aligned by the tool. The results of this alignment are the aligned reads in SAM or binary SAM (BAM) format, optionally the unmapped reads in SAM/BAM format and mapping statistics for the alignment.
The STAR aligners key feature is that it maps reads directly against the reference in notable short time, with an inherent drawback of requiring a relatively high amount of short term memory (RAM) compared to other alignment tools to do so.
The differential expression analysis was performed with DESeq2. DESeq2 is a bioconducter package implemented in R.
Genome_build: OryCun2.0 (GCA_000003625.1)
Supplementary_files_format_and_content: There are 3 groups; Group-1=Singles; Group-2=Aggregates; Group-3=Normal  (control). Group 1 and 2 were normalized to Group-3 (control) and the resulting data (log2 fold change) is presented as Differentially Expressed list of entities in Excel file

organism: Oryctolagus cuniculus

source_name: Lung

extract_protocol:
Total RNA from uninfected, Mtb-SC and -AG-infected rabbit lungs was isolated (n=3) at T=24 h time point. Briefly, portions of frozen lung tissue (0.5g) were thawed in the presence of 10x volume (wt/vol) of TRIzol reagent (Life Technologies, Grand Island, NY, USA) and homogenized on ice. RNA was extracted once with 0.1 volumes (vol/vol) of BCP solution (Molecular Research Center Inc, Cincinnati, OH, USA), and the aqueous phase, containing RNA, was mixed with an equal volume of 70% ethanol and passed through mini spin columns from the Qiagen RNeasy Mini Kit (Qiagen Inc, Germantown, MD, USA).  Following on-column digestion of the contaminating DNA using DNaseI, RNA was purified and eluted with sterile water, as described by the manufacturer.  The quality and quantity of the purified RNA were assessed by using the NanoDrop instrument (NanoDrop products, Wilmington, DE, USA), and by Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
RNAseq experiment was performed by Lexogen (Lexogen, Inc, Greenland, NH, USA). Briefly, cDNA libraries were prepared using Lexogen QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina using standard protocols (Lexogen, Inc, Greenland, NH, USA), and sequencing was performed with NextSeq protocol. The quality of sample reads, mapping, alignment, and read counts were performed using the STAR (Spliced Transcripts Alignment to a Reference) tool and the RSEQC quality control package (Lexogen, Inc, Greenland, NH, USA). After removing genes without reads in all the tested samples, data normalization and differential expression of transcripts were performed with DESeq2 from the Bioconductor package implemented in R. The output data were filtered to select transcripts with Benjamini-Hochberg adjusted p <0.05 using FASTQ/MULTIQC tool (Lexogen, Inc, Greenland, NH, USA).

tag: strain

value: NZW

tag: agent

value: Mycobacterium tuberculosis as aggregates

tag: tissue

value: Lung

tag: time point

value: 24 hrs post infection


title: TVA1_Combo_1


title: MUTZ5_Combo_1


title: MCF7_ING1_siRNA_rep3

type: RNA

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: Gene expression data from  MCF7 cells treated with 0.025 µm ON-TARGETplus Human ING1 siRNA pool (Dharmacon)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Clariom_S_Human GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Annotation: https://bioconductor.org/packages/release/data/annotation/html/pd.clariom.s.human.html Gene expression data were analysed using Partek Genomics Suite 6.6 software (Partek Incorporated). The raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes (DEG) were identified by a two-way ANOVA. Untreated samples were first compared with samples treated with the mock siRNA and identified DEG were discarded from future analysis. Then DEG between cells treated with mock siRNA and cells treated with ING1 siRNA were detected. DEG were were considered significant if p-value ≤ 0.01, FDR ≤ 0.05 and fold change of >1.5 or <-1.5.

label: biotin

source_name: MCF-7 cells, ING1 siRNA, harvested 01.06.18

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 human breast carcinoma cells were cultured in RPMI medium without phenol red (Invitrogen) supplemented with 2 mM L-glu (Sigma-Aldrich) and 10% fetal bovine serum (Sigma-Aldrich) and grown in T75 culture flasks at 37oC in a 5% CO2 atmosphere.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 30x10000  MCF-7 cells were seeded in single wells of a 6-well plate (9 cm2) in antibiotic-free medium and incubated at 37oC with 5% CO2 until they reached 60-80% confluency (overnight). Afterwards, the MCF-7 cells were incubated for 48 hours with transfection media containing 3 µl/well DharmaFect1 (Dharmacon) and 0.025 µm ON-TARGETplus Human ING1 siRNA pool (Dharmacon) or ON-TARGETplus Non-targeting siRNA. Post-transfection, cells were harvested with 1% Trypsin in PBS, rinsed with PBS and homogenated in Trizol solution (GibcoBRL). The cell homogenate was stored at -20oC until RNA extraction was performed.

tag: cell line

tag: knock-down level (qpcr)


title: HeLa siGl3-3 snRNA-seq

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Adapters, polyA tails and the 3 most 5' bases were removed, and reads < 15 nt removed, using Cutadapt
Transcript expression (GENCODE v. 26 annotation) was quantified using Salmon v0.8.2
Genome_build: hg19
Supplementary_files_format_and_content: transcript level quant.sf files from Salmon output

source_name: HeLa

growth_protocol: Cells were maintained at 37°C in the presence of 5% CO2 in Dulbecco's Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol:
RNeasy Mini Kit (QIAGEN)
Clontech SMARTer smRNA-Seq Kit for Illumina protocol, with size selection to enrich for transcripts in the snRNA/snoRNA size range

treatment_protocol: Cells were plated 24h before transfection and then transfected using the Calcium phosphate method at a confluence of ~50% with either siTFIP11 or siGl3 (control: targeting Gl3 luciferase) with a final concentration of 40 nm.

value: HeLa

tag: treatment


title: Lung-Normal 3


title: Wild type.rep.1

city: Cuernavaca

first: David

last: Romero

state: Morelos

address: Ave. Universidad 2001. Col. Chamilpa

department: Center for Genomic Sciences

country: Mexico

institute: National Autonomous University of Mexico

data_processing:
Quality checking of the sequencing raw reads was done using fastq.gzC
Sequence reads were trimmed using Trimmomatic v.0.36
Paired-end reads were mapped towards R. etli CFN42 reference genome (GenBank accession number GCF_000092045.1) using Bowtie2 aligner v.2.2.6.
Read counts were generated using featureCounts software. The hit counts were summarized using the gene_id for the total CDS features of the reference genome (6226), allowing MultiMapping and MultiOverlap reads
Determination of differential gene expression was done using NOISeqBIO with TMM normalization
Genome_build: R. etli CFN42 (GenBank accession number GCF_000092045.1)
Supplementary_files_format_and_content: Excel Workbook, a single file for all samples containing: the number of raw and normalized mean reads (TMM) for each gene, as well as, the differential expression analysis using NOISeqBIO

organism: Rhizobium etli

source_name: Bacterial cells

growth_protocol: Uninduced R. etli strains were grown in minimal medium Y (MMY) supplemented with biotin at 1 mg l-1. MMY at 30°C to an A620 of 0.5 (9 h)

extract_protocol:
Cell pellets (10^8 cells) were stored on RNAlater (Thermo-Fisher).  Further RNA extraction, rRNA depletion, was done by GeneWiz (South Plainfield, NJ, USA).
cDNA library was made according to the protolocols of GeneWiz (South Plainfield, NJ, USA).

tag: genotype

tag: depletion time


title: Lung-Normal 1


title: MUTZ5_DMSO_2


title: Lung-Mtb-Aggregates 2


title: MCF7_non-targeting_siRNA_rep3

description: Gene expression data from  MCF7 cells treated with 0.025 µm ON-TARGETplus Non-targeting siRNA

source_name: MCF-7 cells, non-targeting siRNA, harvested 01.06.18


title: MHHCALL4_Ven_2


title: Wild type.rep.3


title: MHHCALL4_Ven_1


title: MUTZ5_Combo_2


title: HeLa siTFIP11_3 RNA-seq

data_processing:
Adapter sequences and/or low-quality ends were identified and trimmed using bbduk 35.59
Reads were mapped to the human genome (hg19) using STAR v2.5.2b
PCR duplicates were removed from aligned files using Picard tools
Gene expression was quantified using featureCounts v1.4.6-p5 and GENCODE v. 26 annotation
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated file of read counts per gene per sample

molecule: polyA RNA

extract_protocol:
RNA was isolated using a Nucleospin kit from Macherey/Nagel.
Illumina TruSeq stranded mRNA protocol


title: Lung-Mtb-Aggregates 1


title: HeLa siTFIP11-2 snRNA-seq


title: Lung-Mtb-singles 2

value: Mycobacterium tuberculosis as single cells


title: HeLa siTFIP11-1 snRNA-seq


title: HeLa siGl3-1 snRNA-seq


title: MCF7_untreated_rep2

description: Gene expression data from untreated MCF7 cells grew at the same time and kept in the same conditions as the treated ones

source_name: MCF-7 cells, untreated, harvested 25.05.18


title: HeLa siGI3_3 RNA-seq


title: MHHCALL4_Rux_1


title: Lung-Mtb-singles 3


title: MCF7_untreated_rep3

source_name: MCF-7 cells, untreated, harvested 01.06.18


title: HeLa siTFIP11_1 RNA-seq


title: MCF7_ING1_siRNA_rep2

source_name: MCF-7 cells, ING1 siRNA, harvested 25.05.18


title: diffuse large B-cell lymphoma_rep5

city: Urumqi

first: Xinxia

last: Li

state: Xinjiang

address: The First Affiliated Hospital of Xinjiang Medical University

department: Department of Pathology

country: China

description: Gene expression none of them received radiation or chemotherapy prior to surgery in human fresh tissue

hyb_protocol: After purification the labeled RNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 12.5; Agilent Technologies) was employed to finish the basic analysis with the raw data.

source_name: diffuse large B-cell lymphoma tissue_rep5

label_protocol: total RNA was dephosphorylated, denaturated and then labeled with Cyanine-3-CTP

extract_protocol: Total RNA was extracted from fresh frozen tissue by using mirVanaTM RNA Isolation Kit (AM1561) according to the operation instructions.

treatment_protocol: All fresh tissues were collected from untreated patients that none of them received radiation or chemotherapy prior to surgery at the First Affiliated Hospital of Xinjiang Medical University,

value: diffuse large B-cell lymphoma


title: MHHCALL4_Rux_2


title: HeLa siGI3_2 RNA-seq


title: MCF7_non-targeting_siRNA_rep2

source_name: MCF-7 cells, non-targeting siRNA, harvested 25.05.18


title: diffuse large B-cell lymphoma_rep4

institute: The First Affiliated Hospital of Xinjiang Medical University

source_name: diffuse large B-cell lymphoma tissue_rep4


title: Lung-Mtb-singles 1


title: MCF7_ING1_siRNA_rep1

source_name: MCF-7 cells, ING1 siRNA, harvested 24.05.18,


title: HeLa siTFIP11_2 RNA-seq


title: MHHCALL4_DMSO_2


title: MHHCALL4_DMSO_1


title: HeLa siGI3_1 RNA-seq


title: HuRKO_LZ_MDM_20 [LZ_KO3]

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

country: France

institute: INSERM

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_LZ_WT_LZ.csv
lane5681_CTGGCATA_HuRKO_LZ_MDM_20
lane5719_TGGCATA_HuRKO_LZ_MDM_20
lane5718_TGGCATA_HuRKO_LZ_MDM_20

data_processing:
Sample demultiplexing (all samples were loaded in 3 different lane). Data from each sample was then merged.
Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.4.4). Example: command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC lane2_L1_CGATGT_L002_R1.fastq.gz
Remaining sequences were and aligned to the mouse genome (GRCm38) with HiSat (v2.1.0)
Bam files were merged using SamTools (v1.8) and counted using FeatureCounts (v1.6.3), Mus_musculus.GRCm38.89.gtf annotation and default parameters.
R (v3.4.1) and DESeq2 (v1.24.0) was used for differential expression analysis. NA omit. Cut off: padj<0.05
Differential alternative splicing (AS) was analysed with rMATS (v4.0.2) after reprocessing sequencing data as follow.  Data trimmed with Flexbar (v3.0) and SamTools (v1.8) and remapped using STAR (v 2.5.1b), an splicing aware tool (Python (v2.7.2)). Read length was 101, parameter -paired and annotation  Mus_musculus.GRCm38.90.gtf. Differentially spliced events in pairwise comparison were considered significant if FDR<0.05 and have an absolute inclusion level of >0.1.
Genome_build: mm10
Supplementary_files_format_and_content: csv files. DESeq2 results, DESeq2 normalized gene counts, rMATs results.

organism: Mus musculus

source_name: LZ GC B cells

extract_protocol:
Total RNA from FACs-sorted DZ and LZ GC B cells was isolated using the Rneasy Microkit from Qiagen.
Libraries were generated using 10 ng of total RNA and the SureSelect Strand Specific RNA-Seq Library Preparation kit for the Illumina platform (Agilent)

tag: genotype/variation

value: HuRfl/fl AIDCre (HuR KO)

tag: cell type source

value: light zone (LZ, CD19+ IgD- CD38- CD95+ CXCR4- CD86+ cells)

value: primary germinal centre B cells

tag: illumina index

value: CTGGCATA


title: MHHCALL4_Combo_1


title: MHHCALL4_Combo_2


title: HCT 116 infected with V. parahaemolyticus serotype O3:K6 at MOI-100 replicate 2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description:
Infection at MOI 100 Replicate 2
I100_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Microsoft Excel file that include FPKM values for each Sample

source_name: Human colon tumor cells

growth_protocol: V. parahaemolyticus serotype O3:K6 culture grown to exponential phase

extract_protocol:
Trizol method of RNA isolation
Illumina TrueSeq cDNA Library Preparation Protocol

treatment_protocol: Infection on HCT 116 cells at MOI 10 and MOI 100 and post 4h infection cells were harvested for total mRNA isolation

value: HCT 116

value: colorectal carcinoma derived cells

value: colon

tag: infection


title: HCT 116 infected with V. parahaemolyticus serotype O3:K6 at MOI-10 replicate 2

description:
Infection at MOI 10 Replicate 2
I10_2


title: diffuse large B-cell lymphoma_rep1

source_name: diffuse large B-cell lymphoma tissue_rep1


title: diffuse large B-cell lymphoma_rep3

source_name: diffuse large B-cell lymphoma tissue_rep3


title: WT_LZ_MDM_18 [LZ_WT3]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_LZ_WT_LZ.csv
lane5681_GCCACATA_WT_LZ_MDM_18
lane5719_CCACATA_WT_LZ_MDM_18
lane5718_CCACATA_WT_LZ_MDM_18

value: HuRfl/fl (control WT)

value: GCCACATA


title: WT_LZ_MDM_14 [LZ_WT2]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_LZ_WT_LZ.csv
lane5681_GATAGACA_WT_LZ_MDM_14
lane5719_ATAGACA_WT_LZ_MDM_14
lane5718_ATAGACA_WT_LZ_MDM_14

value: GATAGACA


title: HCT 116 infected with V. parahaemolyticus serotype O3:K6 at MOI-10 replicate 1

description:
Infection at MOI 10 Replicate 1
I10_1


title: HuRKO_LZ_MDM_12 [LZ_KO1]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_LZ_WT_LZ.csv
lane5681_GAGTTAGC_HuRKO_LZ_MDM_12
lane5719_AGTTAGC_HuRKO_LZ_MDM_12
lane5718_AGTTAGC_HuRKO_LZ_MDM_12

value: GAGTTAGC


title: diffuse large B-cell lymphoma_rep2

source_name: diffuse large B-cell lymphoma tissue_rep2


title: HuRKO_LZ_MDM_16 [LZ_KO2]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_LZ_WT_LZ.csv
lane5681_GACAGTGC_HuRKO_LZ_MDM_16
lane5719_ACAGTGC_HuRKO_LZ_MDM_16
lane5718_ACAGTGC_HuRKO_LZ_MDM_16

value: GACAGTGC


title: Dmxr1::MXR1N400-OE B

first: Aditi

last: Gupta

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

institute: Indian Institute of Science

description: Deletion mutant of Mxr1 complemented with Mxr1N400 expressed under GAPDH promoter

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent Pichia pastoris Gene Expression Microarray 8X15K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift normalization method. Gene based analysis was performed.

organism: Komagataella pastoris

source_name: Cells cultured in YNBM for 14 hrs

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit. The concentration and purity of the RNA was evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 2000). The integrity of the RNA was analyzed on the Bioanalyzer (Agilent; 2100 expert). We considered RNA to be of good quality based on the 260/280 values (Nanodrop) and optimal RNA integrity profile in Bioanalyzer.

tag: auxotrophic selection marker

value: Histidine Auxotroph

tag: antibiotic resistance marker

value: ZeocinTM and BlasticidinTM


title: Dmxr1::MXR1N400-OE A


title: UnInfected HCT 116 replicate 2

description:
Untreated Replicate 2
U1_2

value: Untreated


title: WT_LZ_MDM_10 [LZ_WT1]

description:
processed data file:
DESeq2_Normalised_counts.csv
DESeq2_KO_LZ_WT_LZ.csv
lane5681_GAGCTGAA_WT_LZ_MDM_10
lane5719_AGCTGAA_WT_LZ_MDM_10
lane5718_AGCTGAA_WT_LZ_MDM_10

value: GAGCTGAA


title: Dmxr1::MXR1-OE B

description: Deletion mutant of Mxr1 complemented with  full length Mxr1 expressed under GAPDH promotor


title: HCT 116 infected with V. parahaemolyticus serotype O3:K6 at MOI-100 replicate 1

description:
Infection at MOI 100 Replicate 1
I100_1


title: lymph node reactive hyperplasia_rep5

source_name: lymph node reactive hyperplasia tissue_rep5

value: lymph node reactive hyperplasia


title: lymph node reactive hyperplasia_rep3

source_name: lymph node reactive hyperplasia tissue_rep3


title: GS115 B

description: Wild Type

value: wildtype


title: MCF7_non-targeting_siRNA_rep1

source_name: MCF-7 cells, non-targeting siRNA, harvested 24.05.18


title: MCF7_untreated_rep1

source_name: MCF-7 cells, untreated, harvested 24.05.18


title: SCNT_8c_rep3

status: Public on Sep 21 2021

city: Wuhan

first: Jing-Jing

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

data_processing:
Illumina Casava (v1.8.2) was used for basecalling.
Low-quality reads were removed by Trimmomatic (v0.39).
The filtered reads were mapped to the pig reference genome (Sscrofa11.1) with STAR (v2.5.3a).
Transcripts were reconstructed by StringTie (v2.1.2) to define protein-coding novel transcripts by GffCompare (v0.10.2) and CPC2.
Gene differential expression analysis using DESeq2 based on the reads count file obtained by htseq-count.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each transcripts in different samples.

organism: Sus scrofa

source_name: somatic cell nuclear transfer embryos

extract_protocol:
The total RNA of 6-well PFFs is extracted by TRIzol. The total RNA of 30 SCNT embryos is extracted by PicoPure RNA Isolation Kit. Double-stranded cDNA was then synthesized by SMARTer Pico PCR cDNA Synthesis Kit and Advantage 2 PCR Kit, and purified by AMPure XP beads.
After fragmentation with a Bioruptor Sonication System, cDNA libraries were generated by VAHTS Universal V6 RNA-seq Library Prep Kit.

value: somatic cell nuclear transfer embryos

tag: developmental stage


title: Dmxr1 B

description: Deletion mutant of Mxr1

value: ZeocinTM


title: Dmxr1::MXR1-OE A


title: lymph node reactive hyperplasia_rep2

source_name: lymph node reactive hyperplasia tissue_rep2


title: SCNT_8c_rep2


title: Dmxr1 A

description: Deletion mutant of Mxr1


title: SCNT_4c_KG_rep3


title: UnInfected HCT 116 replicate 1

description:
Untreated Replicate 1
UI_1

tag: cell type


title: PFF_rep1

source_name: primary porcine fetal fibroblasts

value: primary porcine fetal fibroblasts

value: 2-5 passages


title: SCNT_4c_rep3


title: SCNT_8c_rep1


title: lymph node reactive hyperplasia_rep1

source_name: lymph node reactive hyperplasia tissue_rep1


title: GS115 A

description: Wild Type


title: H3K4me3_SCNT_4cell_rep1

library_source: genomic

data_processing:
Illumina Casava (v1.8.2) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads.
ChIP-seq reads were mapped to Sscrofa11.1 reference genome using Bowtie2 (v2.3.3.1).
Multiple mapped reads, PCR duplicates, and reads that have a map quality score less than 30 were removed.
Peak calling was performed by MACS2 (v2.2.5) with the parameters "macs2 callpeak –n Sample –g 2.2e9 -B -p 0.05" relative to input samples.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: bigwig files were generated using deeptools.

molecule: genomic DNA

extract_protocol:
The DNA extraction of 200 PFFs or 50 4-cell SCNT embryos are performed by using ULI-NChIP protocol as previously described (Brind'Amour et al., 2015).
Raw ChIP DNA material is used for library construction by KAPA HyperPrep Kit.

tag: chip antibody

value: H3K4me3 (ab8580, Abcam)


title: H3K9me3_SCNT_4cell_rep2

value: H3K9me3 (ab8898, Abcam)


title: H3K9me3_SCNT_4cell_rep1


title: H3K27me3_SCNT_4cell_rep2


title: lymph node reactive hyperplasia_rep4

source_name: lymph node reactive hyperplasia tissue_rep4


title: H3K27me3_SCNT_4cell_rep1


title: H3K27me3_PFF_rep2


title: SCNT_4c_KG_rep2


title: SCNT_4c_rep2


title: H3K27me3_PFF_rep1


title: PFF_rep2


title: G1

city: Xi'an

first: Hai

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart_seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases. scRNA-seq data was processed using stander CellRanger pipeline.
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12. scRNA-seq data was processed using stander CellRanger pipeline.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1. scRNA-seq data was processed using stander CellRanger and Seurat pipeline.
Genome_build: Anas_platyrhynchos.BGI_duck_1.0.90
Genome_build: ftp://ftp.ensembl.org/pub/release-90/fasta/anas_platyrhynchos/dna/Anas_platyrhynchos.BGI_duck_1.0.dna.toplevel.fa.gz
Genome_build: ftp://ftp.ensembl.org/pub/release-90/gtf/anas_platyrhynchos/Anas_platyrhynchos.BGI_duck_1.0.90.gtf.gz
Supplementary_files_format_and_content: The BAM (Binary Alignment/Map) file format is a generic and highly compressed format for storing alignments.txt file could use as BAMs in Cuffquant to quantifies gene and transcript expression levels. Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.

organism: Anas platyrhynchos

source_name: PWBC scRNA-seq

growth_protocol: Seperated cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L_glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols

treatment_protocol: Peripheral blood samples from 45-week-old male specific pathogen-free (SPF) ducks and removed erythrocytes from blood samples using erythrocyte lysis solution. Then, cells were first separated by density gradient centrifugation using a duck lymphocyte isolation kit.The peripheral blood mononuclear cells (PBMCs), which were located in the middle layer, were further separated by differential adhesion in culture dishes preloaded with sterilized glass coverslips according to the different adherent properties of PBMCs.

value: peripheral white blood cells


title: SCNT_4c_KG_rep1


title: SCNT_4c_rep1


title: comm_ts2

city: Lausanne

first: Franziska

last: Gruhl

address: University of Lausanne, Quartier Sorge

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt

data_processing:
Read quality assessment and mapping: Basecalling was performed with the Illumina Casava software (v 1.9) and read quality assessed with FastQC (v 0.10.1). The ensembl annotations for opossum (monDom5), mouse (mm10), rat (rn5), rhesus macaque (rheMac2) and human (hg38) were used to build transcriptome indexes for mapping with TopHat2 (v 2.0.11). TopHat2 was run with default settings and the --mate-inner-dist and --mate-std-dev options set to 50 and 200 respectively. The mate-inner-distance parameter was estimated based on the fragment analyzer report.
CircRNA annotation: We developed a custom pipeline to detect circRNAs, which performs the following steps: Unmapped reads with a phred quality value of at least 25 are used to generate 20 bp anchor pairs from the terminal 3' and 5'-ends of the read. Anchors are remapped with bowtie2 (v 2.1.0) on the reference genome. Mapped anchor pairs are filtered for 1) being on the same chromosome, 2) being on the same strand and 3) for having a genomic mapping distance to each other of a maximum of 100 kb. Next, anchors are extended upstream and downstream of their mapping locus. They are kept if pairs are extendable to the full read length. During this procedure a maximum of two mismatches is allowed. Next, all unpaired reads are selected from the accepted_hits.bam file generated by TopHat2 (singletons) and assessed for whether the mate read (second read of a paired-end sequencing read) of the anchor pair mapped between the backsplice coordinates. All anchor pairs for which 1) the mate did not map between the genomic backsplice coordinates, 2) the mate mapped to another backsplice junction or 3) the extension procedure could not reveal a clear breakpoint are removed. Based on the remaining candidates, a backsplice index is built with bowtie2 and all reads are remapped on this index to increase the read coverage by detecting reads that cover the BSJ with less than 20 bp, but at least 8 bp. Candidate reads that were used to build the backsplice index and now mapped to another backsplice junction are removed. Upon this procedure, the pipeline provides a first list of backsplice junctions. The set of scripts, which performs the identification of putative BSJs, as well as a short description of how to run the pipeline are reposited on GitHub (https://github.com/Frenzchen/ncSplice_circRNAdetection).
CircRNA expression levels: CPM (counts per million) values for backsplice junctions were calculated for each tissue as follows: counts = mean(counts_rep1, counts_rep2, counts_rep3); totalMappedReads =mean(mappedReads_rep1, mappedReads_rep2, mappedReads_rep3); CPM= counts*10^6/totalMappedReads  To distinguish putative backsplice junctions from the technical and biological noise background, the enrichment of the previously defined junctions in RNase R treated samples was calculated. The enrichment was defined as CPM increase in RNase R treated versus untreated samples: enrichment = CPM_RNase R/CPM_untreated  Candidates with a log2-enrichment of smaller 1.5 were removed. Expression levels for all circRNAs can be found in the files mdCircRNA_cpms.txt (opossum), mmCircRNA_cpms.txt (mouse), rnCircRNA_cpms.txt (rat), rmCircRNA_cpms.txt (rhesus macaque) and hsCircRNA_cpms.txt (human).
CircRNA transcript reconstruction: To reconstruct the exon structure of circRNA transcripts in each tissue, we made use of the junction enrichment in RNase R treated samples. To normalize junction reads across libraries, the size factors ( size factor = median(x/geometric mean) ) based on the geometric mean ( geometric mean = product(x)^(1/length(x)) ) of common junctions in untreated and treated samples was calculat, with x being a vector containing the number of reads per junction. We then compared read coverage for junctions outside and inside the BSJ for each gene and used the log2-change of junctions outside the backsplice junction to construct the expected background distribution of change in junction coverage upon RNase R treatment. The observed coverage change of junctions inside the backsplice was then compared to the expected change in the background distribution and junctions with a log2-change outside the 90% confidence interval were assigned as circRNA junction. A loose cut-off was chosen here, because involved junctions can show a decrease in coverage if their linear isoform was present at high levels before (degradation levels of linear isoforms do not correlate with the enrichment levels of circRNAs). Next, we reconstructed a splicing graph for each circRNA candidate, in which network nodes are exons connected by splice junctions (edges). Connections between nodes are weighted by the coverage in the RNase R treated samples. The resulting network graph is directed (because of the known circRNA start and stop coordinates), acyclic (because splicing always proceeds in one direction), weighted and relatively small. We used a simple breadth-first-search algorithm to traverse the graph and to define the strength for each possible isoform by its mean coverage. For further analyses, only the strongest isoform was considered.  A gtf-file with the circRNA annotation for each species has been deposited (mdCircRNAs.gtf, mmCircRNA.gtf, rnCircRNAs.gtf, rmCircRNAs.gtf, hsCircRNAs.gtf).
Genome_build: opossum: monDom5 (ensembl release 75, feb 2014); mouse: mm10 (ensembl release 75, feb 2014); rat: rn5 (ensembl release 75, feb 2014); rhesus macaque: rheMac2 (ensembl release 77, oct 2014); human: hg38 (ensembl release 77, oct 2014)
Supplementary_files_format_and_content: tab-delimited text files include CPM values for all circRNAs.
Supplementary_files_format_and_content: gtf-files contain the circRNA annotation (genes, transcripts and exons) for each species.

source_name: Testis

extract_protocol:
Tissue was dissected at indicated ages (see section ”Samples” in GEO metadata). RNA for mouse, rat, rhesus and human was extracted using the RNeasy protocol from QIAGEN; for opossum, a TRIzol/chloroform-based protocol was used. Tissues were stored at -80 C until library preparation.
We used 5µg of RNA per tissue as starting material for library preparation, which were treated with RNase R for 1 h at 37 ̊C to degrade linear RNAs, followed by RNA purification with RNA Clean & Concentrator-5 kit (Zymo Research) according to the manufacturer’s protocol. Libraries were prepared from the purified RNA with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold according to the protocol with the following modifications to select larger fragments: 1). Instead of the recommended 8 min at 68 ̊C for fragmentation, we incubated samples for only 4 min at 68 ̊C to increase the fragment size; 2). In the final PCR clean-up after enrichment of the DNA fragments, we changed the 1:1 ratio of DNA to AMPure XP Beads to a 0.7:1 ratio to select for binding of larger fragments. Libraries were analyzed on the fragment analyzer for their quality and sequenced with the Illumina HiSeq 2500 platform.

value: Testis

value: wild type

tag: age

value: 9 weeks

value: untreated


title: input_SCNT_4cell

tag: tissue


title: H3K9me3_PFF_rep2


title: H3K4me3_PFF_rep2


title: H3K9me3_PFF_rep1


title: rrmm_ce2

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt

source_name: Cerebellum

value: Cerebellum

value: RNase R-treated


title: PFF_rep3


title: H3K4me3_SCNT_4cell_rep2


title: rrmm_ts1

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: comm_ce3

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: input_PFF


title: rrmm_ts2

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: H3K4me3_PFF_rep1


title: comm_ts3

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: comm_lv3

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt

source_name: Liver

value: Liver


title: comm_lv2

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: CS8FP5iCTR_CTL2_human_E3/E4_Healthy_iMicroglia

city: Los Angeles

first: Michael

last: Workman

state: CA

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

description:
processed data file: Human_iMicroglia_counts.csv
CS8FP5iCTR_CTL2_S45_R1_001

data_processing:
Demultiplexing and conversion of raw sequencing data to FASTQ was performed with Illumina bcl2fastq software
FastQC was used to assess sequence quality and reads were aligned to either human GRCh38.p13 (GENCODE 32) or mouse GRCm38.p6 (GENCODE M23) genome assemblies using Salmon (v1.1.0)
Transcript abundance estimates were quantified with Salmon (v1.1.0) and summarized to gene-level counts with tximport in R
Genome_build: Human GRCh38.p13 (GENCODE 32) or Mouse GRCm38.p6 (GENCODE M23)
Supplementary_files_format_and_content: counts.csv

growth_protocol: Human iPSC-derived microglia were differentiated following the protocol of Douvaras et al., Stem Cell Reports (2017)

extract_protocol:
Total RNA was extracted using a Direct-zol RNA Miniprep kit (#R2051, Zymo Research) with on-column DNAse digestion, according to the manufacturer’s instructions
RNA libraries were generated using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and prepared for sequencing using standard Illumina protocols

treatment_protocol: For metal-treated iMicroglia samples, cells were incubated with 30 uM zinc or 7.5 uM cadmium for 24 h

tag: background

value: Healthy Control

tag: Sex

value: Male

tag: tissue/cell type

value: iPSC-derived microglia

value: CTL

tag: sequencing batch

value: Batch 3


title: comm_ce2

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt

tag: genotype

tag: treatment


title: rrmm_ce1

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: rrmm_lv2

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: rrmm_lv3

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: rrmm_ce3

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: rrmm_ts3

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: CS8FP5iCTR_Zn_human_E3/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
CS8FP5iCTR_Zn_S46_R1_001

value: Zn


title: comm_lv1

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: comm_ce1

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: EDi023-A_CTL2_human_E4/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi023-A_CTL2_S39_R1_001

value: Female


title: comm_ts1

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: CS8FP5iCTR_Cd_human_E3/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
CS8FP5iCTR_Cd_S47_R1_001

value: Cd


title: EDi023-A_Zn_human_E4/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi023-A_Zn_S40_R1_001


title: EDi036-A_Cd_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi036-A_Cd_S50_R1_001


title: EDi023-A_Cd_human_E4/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi023-A_Cd_S41_R1_001


title: EDi035-A_Zn_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi035-A_Zn_S43_R1_001


title: EDi036-A_CTL2_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi036-A_CTL2_S48_R1_001


title: EDi036-A_CTL1_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi036-A_CTL1_S33_R1_001


title: EDi029-A_Zn_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi029-A_Zn_S52_R1_001


title: rrmm_lv1

description:
mmCircRNAs.gtf
mmCircRNA_cpms.txt


title: CS8FP5iCTR_CTL1_human_E3/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
CS8FP5iCTR_CTL1_S27_R1_001


title: EDi029-A_CTL1_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi029-A_CTL1_S30_R1_001


title: EDi044-A_CTL_human_E3/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi044-A_CTL_S16_R1_001

value: Batch 2


title: EDi042-A_CTL_human_E3/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi042-A_CTL_S13_R1_001


title: EDi035-A_CTL2_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi035-A_CTL2_S42_R1_001


title: EDi035-A_CTL1_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi035-A_CTL1_S36_R1_001


title: EDi029-A_CTL2_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi029-A_CTL2_S51_R1_001


title: EDi022-A_CTL_human_E3/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi022-A_CTL_S19_R1_001


title: EDi035-A_Cd_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi035-A_Cd_S44_R1_001


title: EDi036-A_Zn_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi036-A_Zn_S49_R1_001


title: EDi028-A_CTL_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi028-A_CTL_S1_R1_001


title: EDi023-A_CTL1_human_E4/E4_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi023-A_CTL1_S24_R1_001


title: EDi034-A_CTL_human_E3/E3_Healthy_iMicroglia

description:
processed data file: Human_iMicroglia_counts.csv
EDi034-A_CTL_S10_R1_001


title: R1-AD1_shKLF5-2_ETH rep1

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

description:
AD1_shKLF5-2_ETH rep1
processed data file: counts_KLF5.txt

data_processing:
Fastq files containing 75 bp paired-end reads were aligned to the hg19 reference genome using HiSat2 (v. 2.1.0).
Subread (v. 1.4.6) featureCounts was used to quantify gene expression using the version 87 GRCh37 annotation from Ensembl.
Count data were filtered for differential gene expression testing to only keep genes that had a cpm (counts per million) value greater than 1 cpm in at least 2 samples across all experimental conditions.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: counts_KLF5_allsamples.txt: Tab-delimited txt file containing gene counts for all study samples.

source_name: R1-AD1 prostate cancer cells

growth_protocol: R1-AD1 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco) with 10% fetal bovine serum (FBS) and antibiotics (penicillin and streptomycin). R1-D567 were cultured in RPMI1640 medium with 10% charcoal stripped FBS (CSS).

extract_protocol:
ReliaPrep RNA miniprep systems (Promega) according to manufacturer instructions.
Illumina TruSeq Stranded mRNA kit.

treatment_protocol: R1-AD1 and R1-D567 cells were seeded at 5 x 10e5 per well of 6-well plate and infected with indicated lentivirus containing shRNAs against KLF5 (shKLF5-1, shKLF5-2) or a negative control (shCon) for 48 hrs. For R1-D567 cells, the cells were directly lysed and proceeded for RNA extraction by using the ReliaPrep RNA miniprep systems (Promega) according to manufacturer instructions. For R1-AD1 cells, each infected cells with indicated shRNA were split into duplicate wells in RPMI1640 medium with 10% CSS for 72 hrs and stimulated with 1 nM DHT or 0.1% (v/v) ethanol as vehicle control for 24 hrs in RPMI 1640 containing 5% CSS prior to RNA extraction.

tag: cell line

value: Prostate cancer

tag: shRNA

tag: hormone treatment

value: 0.1% (v/v) ethanol

tag: passages


title: R1-AD1_shKLF5-1_DHT rep3

description:
AD1_shKLF5-1_DHT rep3
processed data file: counts_KLF5.txt

value: 1 nM DHT


title: R1-AD1_shKLF5-2_ETH rep2

description:
AD1_shKLF5-2_ETH rep2
processed data file: counts_KLF5.txt


title: R1-AD1_shCon_ETH rep3

description:
AD1_shCon_ETH rep3
processed data file: counts_KLF5.txt

value: shCon


title: R1-AD1_shKLF5-2_ETH rep3

description:
AD1_shKLF5-2_ETH rep3
processed data file: counts_KLF5.txt


title: M2: stromal cells sorted from leukemic mice at M phase, biological rep2

city: shanghai

first: hezhou

last: guo

address: Shanghai, P. R. China.  No. 197 Rui Jin Er Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: Gene expression data from stromal cells sorted from leukemic mice at M phase

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: bone marrow

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

tag: strain

value: FVB/NJ

value: bone marrow

value: bone marrow stromal cells (CD45.1-Ter119-)


title: M3: stromal cells sorted from leukemic mice at M phase, biological rep3


title: R1-AD1_shKLF5-2_DHT rep3

description:
AD1_shKLF5-2_DHT rep3
processed data file: counts_KLF5.txt


title: WT3: stromal cells sorted from wild type mice, biological rep3

description: Gene expression data from stromal cells sorted from wild type mice


title: E3: stromal cells sorted from leukemic mice at E phase, biological rep3

description: Gene expression data from stromal cells sorted from leukemic mice at E phase


title: E1: stromal cells sorted from leukemic mice at E phase, biological rep1


title: M1: stromal cells sorted from leukemic mice at M phase, biological rep1


title: R1-AD1_shKLF5-1_ETH rep2

description:
AD1_shKLF5-1_ETH rep2
processed data file: counts_KLF5.txt


title: E2: stromal cells sorted from leukemic mice at E phase, biological rep2


title: WT2: stromal cells sorted from wild type mice, biological rep2


title: R1-AD1_shCon_DHT rep1

description:
AD1_shCon_DHT rep1
processed data file: counts_KLF5.txt


title: R1-AD1_shCon_DHT rep3

description:
AD1_shCon_DHT rep3
processed data file: counts_KLF5.txt


title: R1-AD1_shCon_DHT rep2

description:
AD1_shCon_DHT rep2
processed data file: counts_KLF5.txt


title: R1-AD1_shKLF5-2_DHT rep2

description:
AD1_shKLF5-2_DHT rep2
processed data file: counts_KLF5.txt


title: R1-D567_shKLF5-2 rep3

description:
D567_ETH_shKLF52_3
processed data file: counts_KLF5.txt

source_name: R1-D567 prostate cancer cells


title: R1-AD1_shKLF5-1_ETH rep3

description:
AD1_shKLF5-1_ETH rep3
processed data file: counts_KLF5.txt


title: R1-AD1_shKLF5-1_ETH rep1

description:
AD1_shKLF5-1_ETH rep1
processed data file: counts_KLF5.txt


title: R1-D567_shKLF5-2 rep1

description:
D567_ETH_shKLF52_1
processed data file: counts_KLF5.txt


title: R1-AD1_shKLF5-2_DHT rep1

description:
AD1_shKLF5-2_DHT rep1
processed data file: counts_KLF5.txt


title: R1-AD1_shKLF5-1_DHT rep2

description:
AD1_shKLF5-1_DHT rep2
processed data file: counts_KLF5.txt


title: R1-D567_shKLF5-1 rep3

description:
D567_ETH_shKLF51_3
processed data file: counts_KLF5.txt


title: WT1: stromal cells sorted from wild type mice, biological rep1


title: R1-AD1_shKLF5-1_DHT rep1

description:
AD1_shKLF5-1_DHT rep1
processed data file: counts_KLF5.txt


title: R1-AD1_shCon_ETH rep2

description:
AD1_shCon_ETH rep2
processed data file: counts_KLF5.txt


title: R1-D567_shKLF5-2 rep2

description:
D567_ETH_shKLF52_2
processed data file: counts_KLF5.txt


title: HCT116 WT RNA-seq Replicate 3

city: Darlinghurst

first: Qian

last: Du

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Paired-end reads were processed using Trim Galore (v0.4.0, parameter settings: --fastqc --paired --retain_unpaired --length 16).
STAR (Dobin et al., 2013) was used to map reads to the hg19 human transcriptome build (STAR v2.5.3a, parameter settings: --quantMode TranscriptomeSAM).
Mapped reads where counted into genes and transcripts using rsem (v1.2.21) (Li and Dewey, 2011).
TMM normalization was applied using edgeR (v3.12.1) (Robinson et al., 2010). Fold changes (FC) were computed as the log2 ratio of normalized reads per gene using edgeR. Genes with fold change ± 1.5 and FDR < 0.01 were considered as significantly altered.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Table of gene-level TPM values calculated by RSEM in replicates of HCT116 and DKO1.

source_name: colorectal cancer cell line

growth_protocol: Cell lines were cultured in McCoy’s 5A modified medium (Gibco, #16600-082) supplemented with heat inactivated foetal bovine serum (10%, Gibco, 16000-044).

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol (Life Technologies, #15596018).
Libraries were constructed with the Illumina TruSeq Stranded mRNA library preparation kit (Illumina, #RS-122-2102) and sequenced on the Illumina HiSeq X Ten.


title: R1-AD1_shCon_ETH rep1

description:
AD1_shCon_ETH rep1
processed data file: counts_KLF5.txt


title: HCT116 DKO1 RNA-seq Replicate 1


title: N2

city: Guangzhou

first: Beibei

last: Zhu

state: Guangdong

address: No. 613 W. Huangpu Avenue, Tianhe

department: Department of Infectious Diseases

institute: The First Affiliated Hospital of Jinan University

description: Sex: MMMFF

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by DESEQ2
Genome_build: Genome_build: hg19

source_name: individual human

extract_protocol:
leukocyte-depleted platelets were collected and prepared by magnetic bead sorting column to obtain high purity platelets.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

tag: disease state

value: healthy


title: N5

description: Sex: MMMFF


title: SingleCell-F

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger (v1.0.0) pipeline.
The single-cell RNA-seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger (v3.1.0) pipeline
Genome_build: GRCz10.88
Supplementary_files_format_and_content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline, including gene expression and spatial contents. For 10x Genomics single-cell RNA-Seq: output of CellRanger pipeline, including gene expression, features and barcodes.

organism: Danio rerio

source_name: Zebrafish melanomas (BRAF-V600E)

extract_protocol:
For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor-bearing fish were euthanized on ice and washed in 1X PBS. After dissection of the head and tail, the remaining tissue was equilibrated in cold OCT for 2 minutes, before transfer to a tissue mold filled with fresh OCT for snap-freezing in liquid nitrogen-chilled isopentane. Tissue blocks were stored at -80°C. For cryosectioning, both the tissue block and the ST slide were equilibrated inside the cryostat for 15-30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide (Visium Spatial Gene Expression Slides, 10X Genomics). ST slides containing sections were stored at -80°C for a maximum of one week before use. For single-cell RNA-seq using the 10X genomics 3’ GEX (v3) platform: Adult tumor-bearing fish were dissected to obtain only the tumor and surrounding tissues (i.e head and tail were removed). Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase (Sigma-Aldrich #5401020001) in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide-bore P1000, followed by incubation for an additional 15 minutes at RT. After adding 500 uL FBS to stop the dissociation reaction, samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS, and cells were sorted at room temperature to remove debris and doublets, using a BD FACSAria III cell sorter (BD Biosciences). Equal numbers of GFP+ (tumor) and GFP- (macroenvironment) cells were collected.
For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide (10X Genomics) and all reagents were from the Visium Spatial Gene Expression Kit (10X Genomics). Briefly, sections were fixed in chilled methanol for 30 min at -20°C, stained with hematoxylin and eosin, and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole-slide scanner at 40X magnification. After imaging, sections were permeabilized at 37°C for 45 minutes. After permeabilization, the on-slide reverse transcription (RT) reaction was performed at 53°C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit (10X Genomics). Second strand synthesis was subsequently performed on-slide for 15 minutes at 65°C. All on-slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis, samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip (Agilent). For single-cell RNA-seq using the 10X genomics 3’ GEX (v3) platform: Equal numbers of sorted GFP+ (tumor) and GFP- (macroenvironment) cells were centrifuged at 300g for 5 minutes at RT, and resuspended in DMEM + 10% FBS. Droplet-based scRNA-seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics) and Chromium Single Cell 3’ Chip G (10X Genomics). Approximately 10,000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.

tag: sample type

value: Single cell suspension


title: N1

description: Sex: MMMFF


title: T4

description: Sex: MMMMF

source_name: hepatocellular carcinoma patient

value: hepatocellular carcinoma patient


title: T5

description: Sex: MMMMF


title: HCT116 DKO1 RNA-seq Replicate 3


title: R1-D567_shKLF5-1 rep2

description:
D567_ETH_shKLF51_2
processed data file: counts_KLF5.txt

tag: cell type


title: SingleCell-E


title: R1-D567_shCon rep2

description:
D567_ETH_shCon_2
processed data file: counts_KLF5.txt


title: R1-D567_shCon rep1

description:
D567_ETH_shCon_1
processed data file: counts_KLF5.txt


title: HCT116 WT RNA-seq Replicate 2


title: HCT116 DKO1 WGBS R2

data_processing:
Sequencing reads from WGBS data were aligned to the human genome using v1.2 of an internally developed pipeline Meth10X (Nair et al. 2018). This is publicly available and can be downloaded from https://github.com/luuloi/Meth10X. The pipeline backbone is built based on workflow control Bpipe (v0.9.9.2) (Sadedin et al. 2012). Briefly, adaptor sequences were removed using in-house bash script in paired-end mode following library prep kit guide. Bwa-meth (v0.20) (Pedersen et al. 2014) was then used to align reads to hg19 using default parameters. The generated bam files were marked for duplicates using Picard (v2.3.0) (http://broadinstitute.github.io/picard). Bam files were then quality checked using Qualimap (v2.2.1) (Okonechnikov et al. 2016). Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using MethylDackel (https://github.com/dpryan79/MethylDackel) and Biscuit (https://github.com/zwdzwd/biscuit). Biscuit was used to call SNPs that were discounted from the final table.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bigwig files containing methylation ratios (C/(C + T)) at each CpG site with a minimum coverage of 5.

extract_protocol:
Genomic DNA was extracted from cells using QIAamp Mini Kit (QIAGEN, #51304).
Library preparation was performed using the CEGX TrueMethyl Whole-Genome kit (v3.1) with minor improvements as described in Nair et al., 2018.


title: HCT116 DKO1 WGBS R1


title: N4

description: Sex: MMMFF


title: R1-D567_shKLF5-1 rep1

description:
D567_ETH_shKLF51_1
processed data file: counts_KLF5.txt


title: T3

description: Sex: MMMMF


title: R1-D567_shCon rep3

description:
D567_ETH_shCon_3
processed data file: counts_KLF5.txt


title: HCT116 WT WGBS R1


title: T2

description: Sex: MMMMF


title: HCT116 DKO1 Hi-C Replicate 2

description:
DKO1_Hi-C_allValidPairs.hic
DKO1_40kb_TADs.bed
pcaOut_DKO1.PC1.txt

data_processing:
HiC-Pro (Servant et al. 2015) was used to align and filter the Hi-C data, identify chromatin interactions, and generate Hi-C heatmaps. To generate filtered Hi-C contact matrices, the Hi-C reads were aligned against the human reference genome (hg19) and corrected using the ICE “correction” algorithm (Imakaev et al. 2012) built into HiC-Pro.
Contact matrices used in down-stream analysis were KR-normalized using JuiceBox tools (Durand et al. 2016, Durand et al. 2016) using Hi-C contact matrices in .hic format generated by hicpro2juciebox script in HiC-Pro as input.
Chromatin domains and boundaries were identified using TADtool (Kruse et al. 2016) at 40kb bin resolution with an insulating window of 103kb and 500kb using pooled Hi-C filtered contact matrices as input.
Compartment analysis was performed using the Homer pipeline (Heinz et al. 2010) (v4.6) with Hi-C filtered contact matrices as input.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: allValidPairs files contain all valid interactions identified at multiple resolutions (10kb, 20kb, 40kb, 100kb, 150kb, 500kb and 1Mb) using HiC-Pro pipeline. hic files contain compressed contact matrices at all resolutions. hic format can also be used to visualise Hi-C data in Juicebox (Durand et al., 2016; Robinson et al., 2018) or WashU Epigenome Browser (Zhou et al., 2013). TADs.bed files contain domain calls generated via TADtool in a bed format. pcaOut files contain sub-nuclear compartment calls created by Homer software.

extract_protocol:
Hi-C data was generated using the Arima-HiC kit (Cat. #A510008), according to manufacturer's protocols. Cells were cross-linked with 2% formaldehyde and 1-5 μg of DNA was used per Hi-C reaction.
The Arima kit uses two restriction enzymes: ^GATC (DpnII), G ^ANTC (N can be either of the 4 genomic bases) (HinfI), which after ligation of DNA ends generates 4 possible ligation junctions in the chimeric reads: GATC-GATC, GANT-GATC, GANT-ANTC, GATC-ANTC. Hi-C libraries were prepared using the KAPA Hyper Library Prep Kit with a modified protocol provided by Arima.


title: N3

description: Sex: MMMFF


title: T1

description: Sex: MMMMF


title: HCT116 WT WGBS R2


title: HCT116 DKO1 Hi-C Replicate 1


title: HCT116 WT Hi-C Replicate 1

description:
HCT116_Hi-C_allValidPairs.hic
HCT116_40kb_TADs.bed
pcaOut_HCT116.PC1.txt


title: HCT116 DKO1 Hi-C Replicate 3


title: HCT116 DKO1 RNA-seq Replicate 2


title: HCT116 WT Hi-C Replicate 2


title: Cell_1117_E10.5_FACS-HE_Runx1_KO

city: manchester

first: Muhammmad

middle: Zaki

last: Fadlullah Wilmot

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

data_processing:
Basecall files generated from NextSeq sequencing run were converted to FASTQ format with Illumina’s bcl2fastq. Alignment was performed by STAR 2.4.2a to ensemble reference genome (GRCm38 release 87) with default parameters. Read counts from BAM files were extracted using htseq (version 0.6.1p1) with the following setting --format=bam --stranded=no --type=exon --idattr=gene_id. Count table was loaded into the R environment (R version 3.6.2).
Genome_build: Mus musculus.GRCm38 release 87

source_name: Aorta gonad mesonephros

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)

tag: developmental stage

value: ICR


title: Cell_1113_E10.5_FACS-HE_Runx1_KO


title: Cell_1106_E10.5_FACS-Mes_KO


title: Cell_1108_E10.5_FACS-Mes_KO


title: Cell_1109_E10.5_FACS-Mes_KO


title: Cell_1107_E10.5_FACS-Mes_KO


title: Cell_1118_E10.5_FACS-HE_Runx1_KO


title: Cell_1110_E10.5_FACS-HE_Runx1_KO


title: Cell_1111_E10.5_FACS-HE_Runx1_KO


title: Cell_1116_E10.5_FACS-HE_Runx1_KO


title: Cell_1114_E10.5_FACS-HE_Runx1_KO


title: Cell_1104_E10.5_FACS-Mes_KO


title: Cell_1103_E10.5_FACS-Endo_Runx1_het


title: Cell_1119_E10.5_FACS-HE_Runx1_KO


title: Cell_1101_E10.5_FACS-Endo_Runx1_het


title: Cell_1115_E10.5_FACS-HE_Runx1_KO


title: Cell_1112_E10.5_FACS-HE_Runx1_KO


title: Cell_1100_E10.5_FACS-Endo_Runx1_het


title: HCT116 WT RNA-seq Replicate 1


title: Cell_1102_E10.5_FACS-Endo_Runx1_het


title: HCT116 WT Hi-C Replicate 3


title: Cell_1097_E10.5_FACS-Endo_Runx1_het


title: Cell_1099_E10.5_FACS-Endo_Runx1_het


title: Cell_1098_E10.5_FACS-Endo_Runx1_het


title: Cell_1095_E10.5_FACS-HE_Runx1_KO


title: Cell_1105_E10.5_FACS-Mes_KO


title: Cell_1096_E10.5_FACS-HE_Runx1_KO


title: Cell_1093_E10.5_FACS-HE_Runx1_KO


title: Cell_1094_E10.5_FACS-HE_Runx1_KO


title: Cell_1092_E10.5_FACS-HE_Runx1_KO


title: Cell_1090_E10.5_FACS-HE_Runx1_KO


title: Cell_1089_E10.5_FACS-HE_Runx1_KO


title: Cell_1085_E10.5_FACS-HE_Runx1_KO


title: Cell_1075_E10.5_FACS-HE_Runx1_KO


title: Cell_1084_E10.5_FACS-HE_Runx1_KO


title: Cell_1086_E10.5_FACS-HE_Runx1_KO


title: Cell_1088_E10.5_FACS-HE_Runx1_KO


title: HCT116 DKO1 Nanopore-Seq

data_processing:
Reads were base called with Guppy v3.3.0 on a GPU-enabled Sun Grid Engine high performance computing server (parameters “--chunks_per_runner 1500 --gpu_runners_per_device 1 --cpu_threads_per_caller 4 -x "cuda:0 cuda:1 cuda:2 cuda:3" -r” and configuration “dna_r9.4.1_450bps_hac_prom.cfg”).
Base called reads (fastq) were aligned to hg19 using minimap2 (Li 2018) (v.2.17-r943-dirty) with parameters “-ax map-ont”. Mapped reads were sorted and indexed with SAMtools (v1.9).
Variants were called and phased with medaka_variant (v0.11.4, https://nanoporetech.github.io/medaka) with the options “-t 36 -s r941_prom_high_g330  -m r941_prom_high_g330 -p -b 100”.
Genome_build: GRCh37/hg19

extract_protocol:
HCT116 and DKO1 DNA (1 μg) was sheared using the Covaris g-TUBE spun at 3400 x g in 2 x 60 sec spins.
Sheared DNA was prepared for Nanopore sequencing using the Ligation 1D kit (SQK-LSK109) according to manufacturer’s instructions. Each cell line was sequenced on one PromethION flow cell.


title: Cell_1091_E10.5_FACS-HE_Runx1_KO


title: Cell_1081_E10.5_FACS-HE_Runx1_KO


title: Cell_1076_E10.5_FACS-HE_Runx1_KO


title: Cell_1082_E10.5_FACS-HE_Runx1_KO


title: Cell_1077_E10.5_FACS-HE_Runx1_KO


title: Cell_1087_E10.5_FACS-HE_Runx1_KO


title: Cell_1079_E10.5_FACS-HE_Runx1_KO


title: Cell_1080_E10.5_FACS-HE_Runx1_KO


title: Cell_1074_E10.5_FACS-HE_Runx1_KO


title: Cell_1071_E10.5_FACS-HE_Runx1_KO


title: Cell_1072_E10.5_FACS-HE_Runx1_KO


title: Cell_1083_E10.5_FACS-HE_Runx1_KO


title: Cell_1078_E10.5_FACS-HE_Runx1_KO


title: SCNT_4c_TDG_rep3

last: Zhang

source_name: somatic cell nuclear transfer embryos

tag: cell/tissue type

value: somatic cell nuclear transfer embryos


title: Cell_1073_E10.5_FACS-HE_Runx1_KO


title: HCT116 WT Nanopore-Seq


title: Cell_1070_E10.5_FACS-HE_Runx1_KO


title: SCNT_4c_TDG_rep2


title: SCNT_4c_TDG_rep1


title: Cell_1069_E10.5_FACS-HE_Runx1_KO


title: Cell_1068_E10.5_FACS-HE_Runx1_KO


title: WGBS_SCNT_4c_TDG_rep2

data_processing:
Illumina Casava (v1.8.2) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads.
PBAT-seq reads were mapped to Sscrofa11.1 reference genome using bismark (v0.22.3).
Multiple mapped reads, PCR duplicates, and reads that have a map quality score less than 30 were removed.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: bigwig files were generated using deeptools.

source_name: somatic cell nuclear transfer embryos

extract_protocol:
The DNA extraction of PFFs or 4-cell SCNT embryos (50 cells) are performed Bisulfite-seq by using PBAT protocol as previously described (Miura et al., 2012; Smallwood et al., 2014).
Bisulfite converted DNA is used for library construction using the index primer and the universal primer (NEB), and 2× KAPA HiFi HotStart ReadyMix.

value: somatic cell nuclear transfer embryos


title: WGBS_SCNT_4c_rep2


title: WGBS_SCNT_4c_TDG_rep1


title: Cell_1067_E10.5_FACS-HE_Runx1_KO


title: WGBS_PFF_rep2

source_name: primary porcine fetal fibroblasts

value: primary porcine fetal fibroblasts

value: 2-5 passages


title: Cell_1064_E10.5_FACS-HE_Runx1_KO


title: Cell_1066_E10.5_FACS-HE_Runx1_KO


title: Cell_1063_E10.5_FACS-HE_Runx1_KO


title: Cell_1065_E10.5_FACS-HE_Runx1_KO


title: WGBS_SCNT_4c_rep3


title: Cell_1060_E10.5_FACS-HE_Runx1_KO


title: Cell_1059_E10.5_FACS-HE_Runx1_KO


title: Cell_1061_E10.5_FACS-HE_Runx1_KO


title: Cell_1056_E10.5_FACS-HE_Runx1_KO


title: WGBS_PFF_rep1


title: SM-D9EPW_S95_E1-50

city: Seattle

first: Bosiljka

last: Tasic

state: WA

address: 615 Westlake Ave N.

department: Molecular Genetics

institute: Allen Institute for Brain Science

description:
human_LGN_2021_exon-matrix.csv
human_LGN_2021_intron-matrix.csv

data_processing:
Processing of SSv4 libraries was performed as described previously (Tasic et al., 2018). Briefly, libraries were sequenced on an Illumina HiSeq 2500 platform (paired-end with read lengths of 50 bp) to a target read depth of 0.5M reads per cell (range 100,275-12,329,698, median 1,003,867). The Illumina sequencing reads were aligned to GRCm38.p3 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 18 January 2016
Sequence alignment was performed using STAR v2.5.3. (Dobin et al., 2013) in the two-pass mode. PCR duplicates were masked and removed using STAR option ‘bamRemoveDuplicates’. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) and summarizeOverlaps function in ‘IntersectionNotEmpty’ mode for exonic and intronic regions separately. For the SSv4 dataset, we only used exonic regions for gene quantification. Cells that met any one of the following criteria were removed: < 100,000 total reads, < 1,000 detected genes (with CPM > 0), < 75% of reads aligned to genome, or CG dinucleotide odds ratio > 0.5. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E. coli genome (version ASM584v2) and were used as a QC metric.
Genome_build: GRCh38.p2

source_name: Human - dLGN - PC

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia. The brain tissues of two adult M. nemestrina (southern pig-tailed macaque) and one M. fascicularis  (crab-eating macaque) were obtained through the Tissue Distribution Program of the Washington  National Primate Research Center and conformed to the guidelines provided by the US National  Institutes of Health. All procedures were approved by the Institutional Animal Care and Use Commit-  tee of the University of Washington under protocol number 4277-01.

extract_protocol:
We isolated single cells and nuclei as previously described (Tasic et al., 2016, Bakken et al., 2018) with modifications. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C. For nuclei isolation, dissected regions of interest were transferred to microcentrifuge tubes, snap frozen in a slurry of dry ice and ethanol, and stored at -80°C until the time of use. To isolate nuclei, frozen tissues were placed into a homogenization buffer that consisted of 10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNasin Plus RNase inhibitor (Promega), 1X protease inhibitor (Promega), and 0.1mM DTT. Tissues were placed into a 1ml dounce homogenizer (Wheaton) and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei. Homogenate was strained through a 30μm cell strainer (Miltenyi Biotech) and centrifuged at 900xg for 10 minutes to pellet nuclei. Nuclei were then resuspended in staining buffer containing 1X PBS supplemented with 0.8% nuclease-free BSA and 0.5% RNasin Plus RNase inhibitor.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

tag: donor

value: M

tag: age

value: PC

tag: facs gating

value: NeuN-pos

tag: cell class

value: GABA

tag: cell cluster


title: SM-D9EPW_S96_E1-50

tag: Sex

value: NeuN-neg

tag: sequencing batch

value: Non-Neuronal

value: Astro


title: SM-D9EPW_S94_E1-50

value: Glut

value: MP


title: Cell_1062_E10.5_FACS-HE_Runx1_KO

tag: genotype


title: Cell_1057_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S92_E1-50


title: Cell_1055_E10.5_FACS-HE_Runx1_KO


title: WGBS_SCNT_4c_TDG_rep3


title: Cell_1054_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S91_E1-50


title: WGBS_SCNT_4c_rep1


title: SM-D9EPW_S90_E1-50


title: WGBS_PFF_rep3


title: Cell_1053_E10.5_FACS-HE_Runx1_KO


title: Cell_1058_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S93_E1-50


title: SM-D9EPW_S89_E1-50


title: Cell_1052_E10.5_FACS-HE_Runx1_KO


title: Cell_1051_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S86_E1-50


title: SM-D9EPW_S84_E1-50


title: SM-D9EPW_S85_E1-50


title: Cell_1049_E10.5_FACS-HE_Runx1_KO


title: Cell_1044_E10.5_FACS-HE_Runx1_KO


title: Cell_1047_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S83_E1-50


title: SM-D9EPW_S82_E1-50


title: Cell_1048_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S78_E1-50


title: SM-D9EPW_S80_E1-50

value: Oligo


title: Cell_1050_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S81_E1-50


title: SM-D9EPW_S79_E1-50


title: Cell_1042_E10.5_FACS-HE_Runx1_KO


title: Cell_1045_E10.5_FACS-HE_Runx1_KO


title: Cell_1043_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S77_E1-50


title: Cell_1046_E10.5_FACS-HE_Runx1_KO


title: Cell_1041_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S75_E1-50


title: SM-D9EPW_S76_E1-50


title: Cell_1038_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPW_S73_E1-50


title: SM-D9EPV_S95_E1-50


title: Cell_1037_E10.5_FACS-HE_Runx1_KO


title: SM-D9EPV_S91_E1-50


title: Cell_1040_E10.5_FACS-HE_Runx1_KO


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