title: Mock CoLoC-seq replicate #2 sample 3 µg/ml RNase A

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_3_S12_R1_001

data_processing:
Library strategy: CoLoC-seq
Read libraries were trimmed off adapters with cutadapt v(2.8)
Read alignment and Feature quantification was done with READemption version: 0.4.3. Parameters for alignment -p 20, -a 95, -l 30, --fastq, --progress. Parameters for Feature quantification -p 20, --features CDS,gene,rRNA,tRNA,scRNA,snoRNA,miRNA,lnc_RNA,snRNA,antisense_RNA
Genome_build: Genome Reference Consortium Human Build 38 patch release 13
Supplementary_files_format_and_content: Coverage files are in wig format and gene quantification files are in CSV format

source_name: Cultured Flp-In T-REx 293 cells

growth_protocol: Cells were cultivated at 37°C in the presence of 5% CO2 in Eagle’s Minimum Essential Medium (EMEM) containing 1 g/L glucose and supplemented with 1.5 g/L sodium bicarbonate and 0.11 g/L sodium pyruvate. Cells were harvested at ~80% confluency.

extract_protocol:
Crude mitochondria were purified from mechanically disrupted cells by differential centrifugation and treated with varying concentrations of RNase A, as specified in sample descriptions. Mock CoLoC-seq samples had been lysed with β-dodecyl maltoside prior to RNase treatment.
Cap structures were removed with RNA 5’-pyrophosphohydrolase. The 5’-adapter was ligated to 5’-phosphorylated ends. Then the 3’-adapter was ligated to 3’-hydroxyl ends. The first-strand cDNA synthesis was performed with M-MLV reverse transcriptase with a 3’-adapter-annealing primer. The resulting cDNA was PCR-amplified (15 cycles) with a high-fidelity DNA polymerase and barcoded TruSeq primers. cDNA was purified with the AMPure XP kit, fragmented, end-repaired, and subjected to another round of adapter ligation and PCR amplification. The cDNA samples were pooled equimolarly and size-selected on an agarose gel in the range 10-to-220 nt (excluding the flanking sequences). The pool was sequenced on an Illumina NextSeq 500 instrument (75-nt single-end reads).
Single-end RNA-seq selecting against RNase A-cleaved transcripts.

tag: cell line

value: Cultured Flp-In T-REx 293 cells

tag: protocol

value: Mock CoLoC-seq

tag: pre-treatment

value: 3 µg/ml RNase A


title: 27_49_AM_5ASA

status: Public on Nov 24 2022

type: SRA

city: Marseille

first: Franck

last: Galland

address: 163 avenue de Luminy

country: France

institute: centre d'immunologie de Marseille Luminy

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto the hg38 assembly of the Homo sapiens genome using Tophat 2.0.14 and bowtie version 2-2.1.0.
Quantification of gene expression has been performed using HTSeq-0.6.1 with annotations coming from Ensembl 87. Only no-ambiguously assigned reads have been retained for further analyses.
Genome_build: hg38
Supplementary_files_format_and_content: a text file, containing ENSembl ID and associated raw counts.

molecule: polyA RNA

organism: Homo sapiens

source_name: intestinal biopsy

extract_protocol: RNA extraction from colonic biopsies was performed using the Qiagen AllPrep RNA/DNA Mini Kit. RNA integrity was measure by AGILENT bioanalyzer.

tag: tissue

value: intestinal biopsy

tag: disease state

value: Ulcerative colitis (UC)

tag: disease activity

value: moderate activity (AM)

tag: treatment


title: 35_68_AM_TNF

value: anti-TNFbiologics  (TNF)


title: Mock CoLoC-seq replicate #2 sample 1.6 µg/ml RNase A

country: Germany

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_16_S10_R1_001

library_source: genomic

molecule: other

value: lysed with β-dodecyl maltoside prior to RNase treatment

value: 1.6 µg/ml RNase A


title: 26_49_AM_5ASA


title: 21_1_Q_5ASA

value: quiescent (Q)


title: Mock CoLoC-seq replicate #2 sample 1.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_13_S9_R1_001

value: 1.3 µg/ml RNase A


title: Mock CoLoC-seq replicate #2 sample 1 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_1_S8_R1_001

value: 1 µg/ml RNase A


title: 15_94_AM_TNF

value: Crohn's disease (CD)


title: 19_83_Q_IS

value: immunosuppressors (IS)


title: ErbB4_mut_P15_S1_2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Assembly: Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq2
Supplementary files format and content: mm10
Supplementary files format and content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2021_1 were also provided

molecule: total RNA

organism: Mus musculus

source_name: cerebral cortex synaptosomes

extract_protocol:
Cortices from P15 Lhx6-Cre;Erbb4+/+;Rpl22HA/HA and Lhx6-Cre;Erbb4F/F;Rpl22HA/HA mice were rapidly dissected in ice-cold RNase-free PBS and immediately homogenized in SynPER Synaptic Protein Extraction Reagent (ThermoScientific) supplemented with 1x cOmplete EDTA-free protease inhibitors (Sigma-Aldrich), 1 mg/ml Heparin (Sigma-Aldrich), 200 U/ml RNAsin (Promega), 100 μg/ml cycloheximide, and 1 mM DTT (Sigma-Aldrich). Synaptosomes were then prepared according to the manufacturer’s instructions. The final synaptosome pellets were resuspended in supplemented SynPER, and Igepal-CA630 (Sigma-Aldrich) was added to the samples to a final concentration of 1%. 100 μl of anti-HA magnetic beads (Pierce #88837) were washed in supplemented SynPER and added to the samples for 3-4 h at 4ºC with gentle rotation. After incubation, beads were washed 3 times in ice-cold washing buffer (300 mM KCl, 1% Igepal- CA630, 50 mM Tris-HCl pH 7.5, 12mM MgCl2, 1mM DTT and 100 μg/ml cycloheximide) and eluted in 350 μl of RLT Plus buffer from the RNAeasy Plus Micro kit (Qiagen) supplemented with 2-mercaptoethanol (Bio-Rad). RNA purification of immunoprecipitated RNA was performed using the RNeasy Plus Micro kit (Qiagen) following the manufacturer’s protocol.
Library preparation for all samples was performed with 1 ng of total RNA using the SMARTer Ultra Low RNAkit for ultra-low RNA. Samples were then sequenced paired-end using an Illumina HiSeq 2500 platform to approximately 60-80 million mapped reads per sample.

value: cerebral cortex synaptosomes

tag: development stage

tag: cell type

value: MGE-derived interneurons

tag: genotype


title: 5_82_AM_NT

value: Non treated (NT)


title: Mock CoLoC-seq replicate #2 sample 0.6 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_06_S7_R1_001

value: Cultured Flp-In T-REx 293 cells

value: 0.6 µg/ml RNase A


title: 4_80_Q_NT


title: Mock CoLoC-seq replicate #2 sample 0.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_03_S6_R1_001

value: Mock CoLoC-seq

value: 0.3 µg/ml RNase A


title: 1_28_Q_NT

value: intestinal biopsy


title: Mock CoLoC-seq replicate #2 sample 0.1 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_01_S5_R1_001

value: 0.1 µg/ml RNase A


title: 18_7_Q_IS


title: Ctrl_P15_C1_4


title: Mock CoLoC-seq replicate #2 sample 0.05 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_005_S4_R1_001

value: 0.05 µg/ml RNase A


title: 39_93_AS_Cort

value: Ulcerative colitis (UC)

value: severe activity (AS)

value: corticoids (Cort)


title: 11_100_Q_TNF

value: quiescent (Q)

value: anti-TNFbiologics  (TNF)


title: Mock CoLoC-seq replicate #2 sample 2 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_2_S11_R1_001

value: lysed with β-dodecyl maltoside prior to RNase treatment

value: 2 µg/ml RNase A


title: 2_57_Q_NT

value: Crohn's disease (CD)


title: Mock CoLoC-seq replicate #1 sample 3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_3_S31_R1_001

value: 3 µg/ml RNase A


title: Mock CoLoC-seq replicate #1 sample 2.6 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_26_S30_R1_001

value: 2.6 µg/ml RNase A


title: 17_3_Q_IS

value: immunosuppressors (IS)


title: Mock CoLoC-seq replicate #1 sample 2.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_23_S29_R1_001

value: Cultured Flp-In T-REx 293 cells

value: 2.3 µg/ml RNase A


title: 13_54_AM_TNF

value: moderate activity (AM)


title: Mock CoLoC-seq replicate #1 sample 2 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_2_S28_R1_001

value: Mock CoLoC-seq


title: Mock CoLoC-seq replicate #2 sample 0 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
44bis_0_S3_R1_001

value: 0 µg/ml RNase A


title: 10_99_Q_TNF

value: intestinal biopsy


title: Mock CoLoC-seq replicate #1 sample 1.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_13_S27_R1_001

value: 1.3 µg/ml RNase A


title: 7_91_AM_NT

value: Non treated (NT)


title: WT_V_J4_4

type: RNA

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.0. CEL files were further processed with Affymetrix Expression Console software version 1.3.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label: biotin

source_name: WT

label_protocol: Biotinylated double strand cDNA targets were prepared from 3 to 20 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit according to manufacturer recommendations.

extract_protocol: After 4 days of DSS administration mice were sacrificed and a 1 cm segment of the distal colon was recovered and frozen embedded in OCT. HE stained 5 µm colon sections were used to capture the epithelial cell layer from the colonic mucosa using the ArcturusXT Laser Capture Microdissection (LCM) System (Applied Biosystems) following manufacturer’s procedures. Total RNA was afterwards extracted from purified epithelial mucosal cells using the Arcturus PicoPure RNA Isolation kit (Applied Biosystems). RNAs samples were validated by Agilent 2001 bioanalyzer (Agilent Technologies)

treatment_protocol: mice were exposed to 4 days of oral administration of 2% DSS (dextran sodium sulfate)(MP Biomedical) in the drinking water

tag: strain

value: colon

tag: cell category

value: intestinal epithelial cells

tag: Sex

value: female

value: WT control

value: DSS 2% (Dextran Sodium Sulfate) 4 days


title: WT_V_CT_4


title: Mock CoLoC-seq replicate #1 sample 1 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_1_S26_R1_001

value: lysed with β-dodecyl maltoside prior to RNase treatment

value: 1 µg/ml RNase A


title: WT_V_J4_1


title: 20_84_Q_IS

value: Crohn's disease (CD)

value: quiescent (Q)


title: WT_CT_4


title: WT_J4_2


title: Mock CoLoC-seq replicate #1 sample 0.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_03_S25_R1_001

value: Cultured Flp-In T-REx 293 cells

value: 0.3 µg/ml RNase A


title: WT_J4_5


title: WT_V_CT_1


title: 12_54_AM_TNF

value: moderate activity (AM)

value: anti-TNFbiologics  (TNF)


title: VIVA_J4_5

source_name: VIVA

value: transgenic mice with over-expression of vnn1


title: WT_CT_1


title: Mock CoLoC-seq replicate #1 sample 0.1 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_01_S24_R1_001

value: Mock CoLoC-seq

value: 0.1 µg/ml RNase A


title: 9_23_Q_TNF

value: intestinal biopsy


title: VIVA_J4_4

value: colon


title: VIVA_J4_3

value: intestinal epithelial cells


title: VIVA_J4_2

value: female


title: WT_CT_3

value: WT control


title: Mock CoLoC-seq replicate #1 sample 0 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41bis_0_S23_R1_001

value: 0 µg/ml RNase A


title: 6_24_AM_NT

value: Non treated (NT)


title: CoLoC-seq replicate #2 sample 3 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-3_S13_R1_001

value: CoLoC-seq

value: 3 µg/ml RNase A


title: VIVA_CT_5


title: VIVA_CT_4


title: WT_J4_4

value: DSS 2% (Dextran Sodium Sulfate) 4 days


title: VIVA_J4_1


title: CoLoC-seq replicate #2 sample 1.6 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-16_S11_R1_001

value: Cultured Flp-In T-REx 293 cells

value: 1.6 µg/ml RNase A


title: CoLoC-seq replicate #2 sample 1 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-1_S9_R1_001

value: 1 µg/ml RNase A


title: CoLoC-seq replicate #2 sample 1.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-13_S10_R1_001

value: 1.3 µg/ml RNase A


title: CoLoC-seq replicate #2 sample 0.6 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-06_S8_R1_001

value: 0.6 µg/ml RNase A


title: VIVA_CT_1

value: transgenic mice with over-expression of vnn1


title: KO_J4_5

source_name: KO

value: Mouse deficient for gene vnn1


title: KO_J4_1


title: CoLoC-seq replicate #2 sample 2 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-2_S12_R1_001

value: 2 µg/ml RNase A


title: KO_J4_2

value: colon


title: 19R018_zygotene spermatocytes-Dhx36-cKO-rep2

city: Shanghai

first: Zhang

middle: ke

last: jia

state: Shanghai

address: Xuhui district yueyang road 320

country: China

institute: CAS

data_processing:
Libraries were sequenced using single reads on Illumina HiSeq 2000 (Illumina).
Quality control (QC) of the reads from high throughput sequencing pipelines was carried out by FastQC (v0.11.9).
Low-quality bases and adapter-containing reads were then trimmed from raw data by Trim Galore (v0.6.7) with default parameters.
The remaining trimmed sequences were further mapped against the ENSEMBL mouse reference genome (mm9) with HISAT2(version 2.2.1), which allowed mapping across splicing junctions by read segmentation.
The subsequent mapped reads were quantified by FeatureCounts (available in Subread software package, version 2.0.3).
Assembly: ENSEMBL mouse reference genome (mm9)
Supplementary files format and content: The file was named 'raw_counts.txt' containing  the count numbers of all genes for each Sample.

source_name: mouse synchronous zygotene spermatocytes

growth_protocol: Animals were fed by the Animal Care at Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Science

extract_protocol:
Testes from from wild-type and Dhx36 mutant spermatogenesis synchronous mice were collected in PBS on ice. After removal of the tunica albuginea, the testes were incubated in 5mL of PBS with 120 U/mL of collagenase type I (Worthington) at 32 °C with gentle agitation for 5 min. The dispersed seminiferous tubules were then digested with 5mL of 0.25% trypsin (Gibco), 0.1 mL of DNase I (5 mg/mL; Sigma) at 32 °C for 8 min, and then terminated by adding 0.5 mL of fetal bovine serum (FBS; Gibco) to inactivate trypsin. The resulting dissociated testicular cells were filtered through a PBS-prewetted cellular filter (70 μm). After spin down at 500 g for 5 min at 4 °C, the cells in the pellet were resuspended at a concentration of 106 cells/mL in DMEM with Hoechst 33342 (3 mg/mL; Sigma) and 5 μl DNase I followed by rotating for 20 min at 32 °C in the oven at 10 r.p.m./min speed. Zygotene spermatocytes were collected based on their fluorescent label with Hoechst 33342 staining using FACS (BD Biosciences). Cell purity was further examined by meiotic nuclear spreading with immunofluorescence staining as described above. The purity of isolated zygotene is about 95%
Total RNA was extracted from zygotene spermatocytes isolated from wild-type and Dhx36 mutant spermatogenesis synchronous mice using Trizol reagent (Invitrogen). RNA quality was determined by Qubit Fluorometer and Agilent Bioanalyzer 2100. rRNAs were removed from total RNAs by the NEBNext rRNA Depletion Kit (NEB). The remaining RNAs were fragmented and then reverse transcribed. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol:
2-day-old animals were pipette-fed with WIN18,466 (100μg/g body weight) suspended in 1% gum tragacanth for 7 consecutive days. WIN18,466 treated mice were then received an i.p. injection of all-trans-RA (Sigma) (33μg/g body weight) in dimethyl sulfoxide (DMSO; Sigma), left to recover for 216 hours, and testes then were collected in PBS on ice. After removal of the tunica albuginea, the testes were incubated in 5mL of PBS with 120 U/mL of collagenase type I (Worthington) at 32 °C with gentle agitation for 5 min. The dispersed seminiferous tubules were then digested with 5mL of 0.25% trypsin (Gibco), 0.1 mL of DNase I (5 mg/mL; Sigma) at 32 °C for 8 min, and then terminated by adding 0.5 mL of fetal bovine serum (FBS; Gibco) to inactivate trypsin. The resulting dissociated testicular cells were filtered through a PBS-prewetted cellular filter (70 μm). After spin down at 500 g for 5 min at 4 °C, the cells in the pellet were resuspended at a concentration of 106 cells/mL in DMEM with Hoechst 33342 (3 mg/mL; Sigma) and 5 μl DNase I followed by rotating for 20 min at 32 °C in the oven at 10 r.p.m./min speed. Zygotene spermatocytes were collected based on their fluorescent label with Hoechst 33342 staining using FACS (BD Biosciences). Cell purity was further examined by meiotic nuclear spreading with immunofluorescence staining as described above. The purity of isolated zygotene is about 98%
The conditional knockout alleles for Dhx36 (Dhx36flox/flox) and the Stra8-GFPCre knock-in mouse line were generated as described previously. All animals were maintained on the C57BL/6J genetic background. The germ cell-specific deletion of Dhx36 was produced by crossing Dhx36flox/flox mice with the Stra8-GFPCre line. Animal experiments were approved by the Animal Care and Use Committee at Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Science, and were performed according to the relevant regulations and guidelines. 2-day-old animals were pipette-fed with WIN18,466 (100μg/g body weight) suspended in 1% gum tragacanth for 7 consecutive days. WIN18,466 treated mice were then received an i.p. injection of all-trans-RA (Sigma) (33μg/g body weight) in dimethyl sulfoxide (DMSO; Sigma), left to recover for 216 hours, and testes then were collected.  Zygotene spermatocytes were isolated from these testes.

value: testis

value: zygotene spermatocytes

value: Dhx36flox/flox Stra8-GFPCre+


title: VIVA_CT_2

value: intestinal epithelial cells

value: female


title: KO_J4_4


title: VIVA_CT_3


title: S. cerevisiae, empty vector, urolithin B treatment, rep1

city: Lisboa

first: Regina

last: Menezes

address: Campo Grande 376

country: Portugal

institute: Universidade Lusófona de Humanidades e Tecnologias

data_processing:
assessment of the quality of the data using FastQC program
sequence trimming was performed with Seqtk tool and re-assessment of the quality using FastQC program
reads were mapped using Bowtie2
files were transformed to BAM and sorted using Samtools
quantification of the transcripts expression using Artemis
Assembly: sac64
Supplementary files format and content: raw counts of sequencing reads for the features of interest

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in synthetic dropout (SD)-glucose medium 108 [0.67% (w/v) yeast nitrogen base (YNB) without amino acids (Difco, United States), 0.77 g/L single 109 amino acid dropout CSM-URA (MP Biomedicals, United States), and 2% (w/v) glucose (Sigma-110 Aldrich, United States)] for 24 h at 30°C under orbital shaking.

extract_protocol:
RNA was harvested by lyticase incubation, followed by High Pure RNA Isolation Kit
RNA libraries for RNA-seq were prepared using QuantSeq 3prime mRNA FWD (Standard) following manufacturer's protocols.

treatment_protocol: ppIAPP-GFP and empty vector expression was induced using galactose medium for 12h in the presence or absence of 50 uM of urolithin B

value: 12h of urolitin B


title: S. cerevisiae, human ppIAPP fused to GFP expression, urolithin B treatment, rep2


title: S. cerevisiae, human ppIAPP fused to GFP expression, urolithin B treatment, rep3


title: S. cerevisiae, empty vector, urolithin B treatment, rep3


title: CoLoC-seq replicate #2 sample 0.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-03_S7_R1_001

value: CoLoC-seq

value: 0.3 µg/ml RNase A


title: KO_CT_3


title: KO_CT_4


title: 19R016_zygotene spermatocytes-Control-rep2

treatment_protocol:
2-day-old animals were pipette-fed with WIN18,466 (100μg/g body weight) suspended in 1% gum tragacanth for 7 consecutive days. WIN18,466 treated mice were then received an i.p. injection of all-trans-RA (Sigma) (33μg/g body weight) in dimethyl sulfoxide (DMSO; Sigma), left to recover for 216 hours, and testes then were collected in PBS on ice. After removal of the tunica albuginea, the testes were incubated in 5mL of PBS with 120 U/mL of collagenase type I (Worthington) at 32 °C with gentle agitation for 5 min. The dispersed seminiferous tubules were then digested with 5mL of 0.25% trypsin (Gibco), 0.1 mL of DNase I (5 mg/mL; Sigma) at 32 °C for 8 min, and then terminated by adding 0.5 mL of fetal bovine serum (FBS; Gibco) to inactivate trypsin. The resulting dissociated testicular cells were filtered through a PBS-prewetted cellular filter (70 μm). After spin down at 500 g for 5 min at 4 °C, the cells in the pellet were resuspended at a concentration of 106 cells/mL in DMEM with Hoechst 33342 (3 mg/mL; Sigma) and 5 μl DNase I followed by rotating for 20 min at 32 °C in the oven at 10 r.p.m./min speed. Zygotene spermatocytes were collected based on their fluorescent label with Hoechst 33342 staining using FACS (BD Biosciences). Cell purity was further examined by meiotic nuclear spreading with immunofluorescence staining as described above. The purity of isolated zygotene is about 96%
The conditional knockout alleles for Dhx36 (Dhx36flox/flox) and the Stra8-GFPCre knock-in mouse line were generated as described previously. All animals were maintained on the C57BL/6J genetic background. The germ cell-specific deletion of Dhx36 was produced by crossing Dhx36flox/flox mice with the Stra8-GFPCre line. Animal experiments were approved by the Animal Care and Use Committee at Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Science, and were performed according to the relevant regulations and guidelines. 2-day-old animals were pipette-fed with WIN18,466 (100μg/g body weight) suspended in 1% gum tragacanth for 7 consecutive days. WIN18,466 treated mice were then received an i.p. injection of all-trans-RA (Sigma) (33μg/g body weight) in dimethyl sulfoxide (DMSO; Sigma), left to recover for 216 hours, and testes then were collected.  Zygotene spermatocytes were isolated from these testes.

value: mouse synchronous zygotene spermatocytes

value: wild type


title: KO_CT_5


title: S. cerevisiae, human ppIAPP fused to GFP expression, rep3

value: no treatment


title: 19R015_zygotene spermatocytes-Control-rep1

treatment_protocol:
2-day-old animals were pipette-fed with WIN18,466 (100μg/g body weight) suspended in 1% gum tragacanth for 7 consecutive days. WIN18,466 treated mice were then received an i.p. injection of all-trans-RA (Sigma) (33μg/g body weight) in dimethyl sulfoxide (DMSO; Sigma), left to recover for 216 hours, and testes then were collected in PBS on ice. After removal of the tunica albuginea, the testes were incubated in 5mL of PBS with 120 U/mL of collagenase type I (Worthington) at 32 °C with gentle agitation for 5 min. The dispersed seminiferous tubules were then digested with 5mL of 0.25% trypsin (Gibco), 0.1 mL of DNase I (5 mg/mL; Sigma) at 32 °C for 8 min, and then terminated by adding 0.5 mL of fetal bovine serum (FBS; Gibco) to inactivate trypsin. The resulting dissociated testicular cells were filtered through a PBS-prewetted cellular filter (70 μm). After spin down at 500 g for 5 min at 4 °C, the cells in the pellet were resuspended at a concentration of 106 cells/mL in DMEM with Hoechst 33342 (3 mg/mL; Sigma) and 5 μl DNase I followed by rotating for 20 min at 32 °C in the oven at 10 r.p.m./min speed. Zygotene spermatocytes were collected based on their fluorescent label with Hoechst 33342 staining using FACS (BD Biosciences). Cell purity was further examined by meiotic nuclear spreading with immunofluorescence staining as described above. The purity of isolated zygotene is about 95%
The conditional knockout alleles for Dhx36 (Dhx36flox/flox) and the Stra8-GFPCre knock-in mouse line were generated as described previously. All animals were maintained on the C57BL/6J genetic background. The germ cell-specific deletion of Dhx36 was produced by crossing Dhx36flox/flox mice with the Stra8-GFPCre line. Animal experiments were approved by the Animal Care and Use Committee at Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Science, and were performed according to the relevant regulations and guidelines. 2-day-old animals were pipette-fed with WIN18,466 (100μg/g body weight) suspended in 1% gum tragacanth for 7 consecutive days. WIN18,466 treated mice were then received an i.p. injection of all-trans-RA (Sigma) (33μg/g body weight) in dimethyl sulfoxide (DMSO; Sigma), left to recover for 216 hours, and testes then were collected.  Zygotene spermatocytes were isolated from these testes.


title: KO_CT_2


title: S. cerevisiae, empty vector, urolithin B treatment, rep2


title: KO_CT_1


title: KO_J4_3

value: DSS 2% (Dextran Sodium Sulfate) 4 days


title: CoLoC-seq replicate #2 sample 0.1 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-01_S6_R1_001

value: Cultured Flp-In T-REx 293 cells

value: 0.1 µg/ml RNase A


title: S. cerevisiae, human ppIAPP fused to GFP expression, rep2


title: 19R017_zygotene spermatocytes-Dhx36-cKO-rep1

treatment_protocol:
2-day-old animals were pipette-fed with WIN18,466 (100μg/g body weight) suspended in 1% gum tragacanth for 7 consecutive days. WIN18,466 treated mice were then received an i.p. injection of all-trans-RA (Sigma) (33μg/g body weight) in dimethyl sulfoxide (DMSO; Sigma), left to recover for 216 hours, and testes then were collected in PBS on ice. After removal of the tunica albuginea, the testes were incubated in 5mL of PBS with 120 U/mL of collagenase type I (Worthington) at 32 °C with gentle agitation for 5 min. The dispersed seminiferous tubules were then digested with 5mL of 0.25% trypsin (Gibco), 0.1 mL of DNase I (5 mg/mL; Sigma) at 32 °C for 8 min, and then terminated by adding 0.5 mL of fetal bovine serum (FBS; Gibco) to inactivate trypsin. The resulting dissociated testicular cells were filtered through a PBS-prewetted cellular filter (70 μm). After spin down at 500 g for 5 min at 4 °C, the cells in the pellet were resuspended at a concentration of 106 cells/mL in DMEM with Hoechst 33342 (3 mg/mL; Sigma) and 5 μl DNase I followed by rotating for 20 min at 32 °C in the oven at 10 r.p.m./min speed. Zygotene spermatocytes were collected based on their fluorescent label with Hoechst 33342 staining using FACS (BD Biosciences). Cell purity was further examined by meiotic nuclear spreading with immunofluorescence staining as described above. The purity of isolated zygotene is about 97%
The conditional knockout alleles for Dhx36 (Dhx36flox/flox) and the Stra8-GFPCre knock-in mouse line were generated as described previously. All animals were maintained on the C57BL/6J genetic background. The germ cell-specific deletion of Dhx36 was produced by crossing Dhx36flox/flox mice with the Stra8-GFPCre line. Animal experiments were approved by the Animal Care and Use Committee at Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Science, and were performed according to the relevant regulations and guidelines. 2-day-old animals were pipette-fed with WIN18,466 (100μg/g body weight) suspended in 1% gum tragacanth for 7 consecutive days. WIN18,466 treated mice were then received an i.p. injection of all-trans-RA (Sigma) (33μg/g body weight) in dimethyl sulfoxide (DMSO; Sigma), left to recover for 216 hours, and testes then were collected.  Zygotene spermatocytes were isolated from these testes.


title: S. cerevisiae, human ppIAPP fused to GFP expression, urolithin B treatment, rep1


title: CoLoC-seq replicate #2 sample 0.05 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-005_S5_R1_001

value: 0.05 µg/ml RNase A


title: PM2.5_treated_2

first: Hai

last: Lin

address: No. 600, Yishan Road, Xuhui District

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were filtered with Seqtk to remove adaptor sequence and low-quality sequence.
Genome mapping was performed by "splices mapping" algorithm in Hista2 (version:2.0.4).
Annotation genome used was GRCh38.p4 (hg38).
Assembly: mm10
Supplementary files format and content: count and FPKM values for each Sample

source_name: nasal mucosa

growth_protocol: Cells were cultured in DMEM containing 20% fetal calf serum, 100 IU/mL penicillin, 100μg/mL streptomycin and 2μg/mL amphotericin B at 37 ℃ with 5% CO2.

extract_protocol:
RNA was extracted using MagBeads Total RNA Extraction Kit（Cat#T02-096) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Cells were treated with 100 μg/ml PM2.5 or  same amount of normal culture medium for 24h.

value: nasal mucosa

value: fibroblasts


title: PM2.5_treated_3


title: PM2.5_treated_1


title: Control_3

value: Control


title: CoLoC-seq replicate #2 sample 0 µg/ml RNase A

description:
gene_feature_quantification_non_mock.csv
CoLoC44-0_S4_R1_001

value: 0 µg/ml RNase A


title: Control_2


title: S. cerevisiae, human ppIAPP fused to GFP expression, rep1


title: others, replicate 5 [451]

city: Reims

first: Brisebarre

last: Audrey

address: 45 rue Cognacq-Jay

institute: INSERM

data_processing:
Image analysis and base calling was performed using Illumina Real Time Analysis (3.4.4) with default parameters.
Quality control of raw sequence data was performed using FastQC (version 0.11.5).
Head bases were trimmed for adaptor sequences, and low-complexity or low-quality sequence was removed with Trimmomatic (version 0.39).
The remaining sequences were mapped to the Homo sapiens hg38 reference genome assembly (hg38.fa) using tophat2 (version 2.1.1) with stringent parameters generating bam format.
The quality of alignment was checked using metrics provided by qualimap (version 2.2.1) and low quality alignments removed.
Raw counts were obtained using htseq-count (version 0.6.1).
Raw counts were normalized using a scalling factor based on median gene expression across the samples and filtered to exclude genes with fewer than 5 counts across the samples.
Assembly: hg38
Supplementary files format and content: matrix including normalized counts for each sample

source_name: lung

growth_protocol: After the proliferation phase, cells were cultured in bronchial epithelial cell growth medium (BEGM) (Lonza, Walkersville, MD).

extract_protocol:
Total RNA was purified from frozen primary tumor cell pellets with RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s specifications.
Libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations. Briefly the key stages of this protocol are successively, the purification of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 100ng total RNA (with the Magnetic mRNA Isolation Kit from NEB), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing.

value: lung

tag: tumor type

value: Non Small Cell Lung Cancer

tag: histological diagnosis

value: Adenocarcinoma

value: primary tumor cells

tag: phenotype

value: others


title: CoLoC-seq replicate #1 sample 2 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_2_S21_R1_001

value: CoLoC-seq

value: 2 µg/ml RNase A


title: others, replicate 6 [469]

value: Squamous Cell Carcinoma


title: CoLoC-seq replicate #1 sample 3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_3_S22_R1_001

value: 3 µg/ml RNase A


title: S. cerevisiae, empty vector, rep1

value: no treatment


title: CoLoC-seq replicate #1 sample 1.6 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_16_S20_R1_001

value: Cultured Flp-In T-REx 293 cells

value: 1.6 µg/ml RNase A


title: S. cerevisiae, empty vector, rep2


title: others, replicate 4 [422]


title: vel1_2

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

data_processing:
FastQC v0.11.5
STAR_2.6.0c
Stringtie v1.3.3
DEseq2 v1.16.1
Assembly: C. neoformans XL280α
Supplementary files format and content: tpm TPM of all strains after mating inducing

organism: Cryptococcus deneoformans XL280

extract_protocol:
The level and integrity of RNA in each sample were evaluated using a Qubit RNA Assay Kit on a Qubit 2.0 Flurometer (Life Technologies, CA, USA) and RNA Nano 6000 Assay Kit with the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively. RNA purity was assessed using a Nano Photometer spectrophotometer (IMPLEN, CA, USA).
The transcriptome libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) according to the manufacturer’s instructions.

value: V8 medium at 30°C, 12h


title: CoLoC-seq replicate #1 sample 1.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_13_S19_R1_001

value: 1.3 µg/ml RNase A


title: others, replicate 2 [413]


title: FHITlow/pHER2high, replicate 5 [401]


title: CoLoC-seq replicate #1 sample 1 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_1_S18_R1_001

value: 1 µg/ml RNase A


title: vel1_1


title: others, replicate 1 [363]


title: FHITlow/pHER2high, replicate 4 [395]


title: FHITlow/pHER2high, replicate 3 [321]


title: FHITlow/pHER2high, replicate 2 [294]


title: nrg1_1


title: Control_1

value: nasal mucosa

value: fibroblasts

value: Control


title: CoLoC-seq replicate #1 sample 0.6 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_06_S17_R1_001

value: 0.6 µg/ml RNase A


title: FHITlow/pHER2high, replicate 1 [291]

value: lung

value: Non Small Cell Lung Cancer

value: Adenocarcinoma


title: S. cerevisiae, empty vector, rep3


title: CoLoC-seq replicate #1 sample 0.3 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_03_S16_R1_001

value: CoLoC-seq

value: 0.3 µg/ml RNase A


title: others, replicate 3 [420]

value: Squamous Cell Carcinoma

value: primary tumor cells

value: others


title: hob7_2


title: FHITlow/pHER2high, replicate 6 [405]


title: NP2

city: shanghai

first: li

last: mingqing

address: NO.419 fangxie Road, Shanghai

institute: Affiliated obstetrics and Gynecology Hospital of Fudan University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: decidua

extract_protocol:
Sample washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

value: decidua

tag: Stage

value: first trimester of pregnancy

tag: group

value: NP


title: NP1


title: hob7_1

value: V8 medium at 30°C, 12h


title: gat6_2


title: NP3


title: CoLoC-seq replicate #1 sample 0.1 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_01_S15_R1_001

tag: cell line

value: Cultured Flp-In T-REx 293 cells

tag: protocol

value: 0.1 µg/ml RNase A


title: X0 hiPSCs

city: Jerusalem

first: Ithai

last: Waldhorn

address: Kiryat Hadassah

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hebrew University

data_processing:
Trimming the first 9 bases with fastx_trimmer (FASTX package) and removing low quality (under 32) bases from both ends.
Removing adapter sequences from the 3' end with cutadapt, v1.12, using -O 1, -m 15 and --match-read-wildcards.
Filtering out low quality reads with fastq_quality_filter (FASTX package), using -q 20 and -p 90.
Alignment with Tophat, v2.0.14, using parameters -N 5, --read-gap-length 5, --read-edit-dist 10, --read-realign-edit-dist 3, --segment-length 22, --no-coverage-search, --library-type fr-firststrand and supplying genes annotations file (-G parameter) from Ensembl release 89. Htseq-count, v0.6.0, using parameter -s 'reverse', was used for getting raw counts.
Normalization and differential expression analysis with DESeq2, v1.12.4. Genes with less than 10 reads were discarded prior to normalization. Testing was done with default parameters, adding the date of preparation as a batch factor in the statistical model.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel with DESeq2 results. First row is a header, then each row is for a gene. Columns A to I have general gene details; columns J to R have raw counts for each sample; columns S to AA have DESeq2 normalized counts for each sample; column AB is DESeq2's calculated baseMean; columns AC to AG are the results of comparing samples with two copies of X to samples with a single copy of X; columns AH to AL have results for comparing samples with a Y chromosome to samples without Y chromosome; columns AM to AQ have results for comparing XY samples to XX samples.

source_name: X0 hiPSCs

growth_protocol: EBV-immortalized B-cells were reprogrammed using B-cell Nucleofector Kit with 4 plasmids containing the following genes: SOX2, OCT4, KLF4, LIN28, L-MYC, SV40LT, shP53. hiPSCs were cultured on human foreskin fibroblasts with KnockOut medium supplemented with serum replacement and bFGF.

extract_protocol:
Total RNA was extracted from hiPSCs using the miRNeasy Micro Kit (QIAGEN, Hilden, Germany).
Libraries were prepared using LEXOGEN's SENSE mRNA-Seq Library Prep Kit V2, with poly-A selection.

value: human induced pluripotent stem cells (hiPSCs)

tag: sex chromosome complement


title: CoLoC-seq replicate #1 sample 0 µg/ml RNase A

description:
gene_feature_quantification_non_mock_and_mock.csv
41_0_S14_R1_001

value: 0 µg/ml RNase A


title: XXY2 hiPSCs

source_name: XXY hiPSCs

value: 47, XXY


title: hepatic mRNA-m6A LPS 2

city: Xinxiang

first: Yanhong

last: Zhang

state: Henan

address: 90, Huanlan road

institute: Henan institute of science and technology

data_processing:
Fastp software was used to remove low-quality bases, undetermined bases and reads containing adaptor contamination
Hisat2 software was applied to align reads to the reference genome of chicken
Mapped reads of IP and Input libraries were provided for R package exomePeak for m6A peak identified. MEME and HOMER were used for de novo and known motif finding, followed by localization of the motif with respect to peak summit
Called peaks were annotated by intersection with gene architecture by using R package ChIPseeker
StringTie was applied to determine the expression level for all mRNAs from Input libraries by calculating FPKM
Genome_build: Gallus gallus Ensembl_v96 ftp://ftp.ensembl.org/pub/release-96/fasta/gallus_gallus/dna/
Supplementary_files_format_and_content: fpkm expression, peak

organism: Gallus gallus

source_name: hepatic mRNA-m6A LPS

growth_protocol: Liver tissue samples were obtained frome 21-day-old broilers

extract_protocol:
Approximately 400 ug of total RNA was extracted from liver using TRIzol .  The mRNA was  purified by using oligo(dT)-coupled magnetic beads. Following purification, the poly(A) mRNA fractions was then fragmented into ~100 nt-long oligonucleotides . The cleaved RNA fragments were subjected to m6A immunoprecipitation with anti-m6A antibody. Rabbit normal IgG was used as the negative control. An equal amount of fragmented mRNA from each biological sample was reserved as the input control (Input).
The eluted m6A-containing fragments (IP) and the input were converted by SuperScriptTM Ⅱ Reverse Transcriptase (Invitrogen, cat.1896649, USA) to obtain cDNA, which was then used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase Ⅰ (NEB, cat.m0209, USA), RNaseH (NEB, cat.m0297, USA) and dUTP solution (Thermo Fisher, cat. R0133, USA). A-bases were then added to the blunt ends of each strand for the subsequent ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; eight cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 ± 50 bp. At last, a 2×150bp paired-end sequencing were performed on an illumina Novaseq™ 6000 (LC-BioTechnology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
MeRIP Seq

treatment_protocol: Chicks were intraperitoneally injected with LPS from Escherichia coli 055:B5 (L4524, Sigma-Aldrich) at a dose of 1 mg/kg body weight. Chicks in the Control group were injected with the same volume of PBS. Two hours after the treatment, livers were obtained and frozen in liquid nitrogen and stored at -80°C.

tag: tissue

value: liver

value: LPS

tag: merip antibody

value: anti-m6A  (No. 202003, Synaptic Systems, Germany)

tag: library

value: IP


title: nrg1_2

tag: treatment


title: fzc49_2


title: XY3 hiPSCs

source_name: XY hiPSCs

tag: cell type


title: hepatic mRNA-m6A LPS 1


title: hepatic mRNA-m6A control 2

source_name: hepatic mRNA-m6A control

value: control


title: fzc49_1

tag: genotype


title: E-301 LOF + ICI

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

country: USA

institute: Johns Hopkins University

description: 3' mRNA Library

library_source: transcriptomic single cell

data_processing:
Samples were demultiplexed and aligned using Cell Ranger 6.1 (10X Genomics) to genome build mm10 to obtain a raw read count matrix of barcodes corresponding to cells and features corresponding to detected genes.
Mapped read counts were analysed using Seurat v.4 and harmonized to remove biological replicate associated effects using harmony.
Assembly: mm10
Supplementary files format and content: Processed data are matrices with raw counts for features in sequenced cells (matrix.mtx). A list of cell barcodes and detected genes is also included for each sample (barcodes.tsv, features.tsv).

source_name: B16D5-HER2 tumor

extract_protocol:
Tumors were resected, mechanically dissected and enzymatically digested. Following a gradient centrifugation, single-cell suspensions were sorted for viable CD45+ cells.
The Chromium Next GEM Single Cell 3' v3.1 kit was used and library construction was performed according to the manufacturer's protocol.

treatment_protocol: Mice carrying established B16D5-Her2 tumors were treated every 2nd day and tumors harvested 7 days post initial treatment.

value: B16D5-HER2 tumor

value: CD45+ cells

tag: strain

value: E-301 LOF + ICI


title: XY2 hiPSCs


title: hepatic mRNA-m6A control 1


title: E-301 + ICI

description: 3' mRNA Library


title: ada2_2


title: ada2_1


title: hepatic mRNA-LPS 1

source_name: hepatic mRNA-LPS

value: input


title: E-301 LOF

description: 3' mRNA Library

value: E-301 LOF


title: Renal tissue, DN, rep3

city: Guangzhou

first: Xiaoyan

last: Bai

address: No. 106, Zhongshan 2nd Road Yuexiu District Guangzhou

department: Nephrology

institute: Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences

hyb_protocol: 1.5 ug of Cy3-labelled cRNA  was fragmented and hybridized using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and 1 minute with Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Renal tissue, Ctrl

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNA purification (RNeasy Mini Kit (Qiagen p/n 74104). RNA was quantified and quality was monitored by NanoDrop ND-1000.

extract_protocol: RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations. RNA was quantified and quality was monitored by NanoDrop ND-1000.

tag: disease state

value: diabetic nephropathy

tag: gender

value: female

tag: age

value: kidney


title: Renal tissue, DN, rep1

source_name: Renal tissue, DN

value: male


title: Renal tissue, Ctrl, rep3


title: WT_sex_2

value: WT

value: V8 medium at 30°C, 12h


title: hepatic mRNA-LPS 2


title: Renal tissue, DN, rep2


title: XX3 hiPSCs

source_name: XX hiPSCs

value: human induced pluripotent stem cells (hiPSCs)


title: XY1 hiPSCs


title: Renal tissue, Ctrl, rep2


title: E-301

description: 3' mRNA Library


title: Renal tissue, Ctrl, rep1


title: hepatic mRNA-control 2

source_name: hepatic mRNA-control

value: liver


title: XXY1 hiPSCs

value: 47, XXY


title: XX2 hiPSCs


title: Untreated

description: 3' mRNA Library

value: Untreated


title: XX1 hiPSCs


title: hepatic mRNA-control 1


title: R9_A10_PB

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

data_processing:
Droplet-based scRNA-seq datasets were aligned and quantified using the CellRanger software package (version 4.0.0)
Datasets were subjected to Seurat3(version 3.2.3) for further analysis
To pass quality control, cells were required to have at least 200 detected, and less than 10% of aligned reads mapping to mitochondrial genes. And genes were required to express in > 3 cells.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: matrix.tsv.gz

source_name: Peripheral blood

growth_protocol: We identified that synergistic and inducible expression of specific genes in pluripotent stem cells gave rise to engraftable iHPC capable of generating blood cells.

extract_protocol:
Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics) following manufacture’s instruction.
Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics) following manufacture’s instruction.

treatment_protocol: At 16 weeks after iHPC transplantation, we sorted the GFP+CD45.2+ cells from the peripheral blood of recipients for Droplet-based scRNA-seq.  Droplet-based scRNA-seq datasets were produced using a Chromium system (10x Genomics) following manufacture’s instruction.

value: GFP+CD45.2+ cells


title: pre-Puberty

city: Nanning

first: Liangfeng

last: Huang

state: Guangxi

address: No. 100, East University Road

department: Animal Reproduction Institute

institute: Guangxi University

description: 10x scRNA-seq

data_processing:
10x Genomics
Genome_build: UOA_WB_1
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx, and expression.txt files.

organism: Bubalus bubalis

source_name: Testis

extract_protocol:
After the gel beads containing barcode information are combined with a mixture of cells and enzymes, entering a reservoir divided by oil to form GEMs, the gel beads are dissolved to release the capture sequence containing the barcode sequence, reverse transcribe the cDNA fragment, and label the sample. Following breakage of the gel beads and breaking of the oil droplets, PCR amplification is performed using the cDNA as template. The products of all GEMs are mixed and a standard sequencing library is constructed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Testis

value: Germline and somatic cells

value: postnatal month 3


title: peri-Puberty

description: 10x scRNA-seq

value: postnatal month 24


title: gat6_1


title: SLN91_NT_2 SLN91, Human melanoma cell line, not treated

status: Public on Nov 23 2022

city: Milan

first: Andrea

last: Anichini

address: Via Venezian 1

department: Research

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: The Gene expression assay was performed on the NanoString nCounter platform (FLEX) using the PanCancer Immune Profiling Panel. Overnight hybridization of Reporter and Capture Probes occurred for 18 hours at 65°C, then reactions were held at 4°C until they were placed on the nCounter Prep Station. 12 samples (input of 200 ng/sample) were run per cartridge following the manufacturer’s protocol

scan_protocol: The specific amount of target molecules was quantified performing the nCounter Digital Analyzer. Each assay was scanned at 555 field of view (FOV) with a CCD camera.

data_processing: nSolver 4.0 software (NanoString Technologies) was used for quality control  (QC) with default setting. Negative control probes were used for background subtraction. For normalization geometric mean of 6 positive controls and 40 housekeeping genes were used.

label: No label is used in Nanostring

source_name: Human Melanoma cell line, control, untreated

label_protocol: No label is used in Nanostring

growth_protocol: Melanoma cell lines were seeded at 1.25x10^4/mL in T75 flasks with RPMI-1640 medium supplemented with 4% FCS without antibiotics.

extract_protocol: RNA was extracted from melanoma cell lines by TRIzol (Invitrogen). Melanin removal was carried out by the CTAB-UREA method. Samples were treated with DNase 1 and purified by RNeasy MinElute Cleanup Kit (Invitrogen). The quality of total RNA was assessed by agarose gel electrophoresis.

treatment_protocol: Melanoma cell lines were treated twice with epigenetic drugs (at T=24h and T=72h) and then evaluated for gene modulation at T=144h.

value: Female

tag: type of lesion

value: nodal metastasis

tag: mutational subset

value: BRAF-MUTANT


title: WT_sex_1


title: SLN91_2_2 SLN91, Human melanoma cell line, treated with OTX015

source_name: Human Melanoma cell line, treated with epigenetic drug, for 144 h


title: FRN39_2_2 FRN39, Human melanoma cell line, treated with OTX015

value: Male

value: BRAF/NRAS WILD TYPE


title: FRN39_NT_2 FRN39, Human melanoma cell line, not treated


title: CPN20_2_2 CPN20, Human melanoma cell line, treated with OTX015

value: NRAS-MUTANT


title: GRD43_2_2 GRD43, Human melanoma cell line, treated with OTX015


title: GRD43_NT_2 GRD43, Human melanoma cell line, not treated


title: VRG100_2_2 VRG100, Human melanoma cell line, treated with OTX015

value: primary tumor


title: VRG100_NT_2 VRG100, Human melanoma cell line, not treated


title: MNT59_8 MNT59, Human melanoma cell line, treated with combination of guadecitabine and GSK126

source_name: Human Melanoma cell line, treated with two epigenetic drugs, for 144 h


title: MNT59_10 MNT59, Human melanoma cell line, treated with combination of givinostat and GSK126


title: MNT59_7 MNT59, Human melanoma cell line, treated with combination of guadecitabine and JQ1


title: BRM17_2_2 BRM17, Human melanoma cell line, treated with OTX015


title: BRM17_NT_2 BRM17, Human melanoma cell line, not treated


title: MNT59_11 MNT59, Human melanoma cell line, treated with combination of JQ1 and GSK126


title: MNT59_12 MNT59, Human melanoma cell line, treated with abemaciclib


title: MNT59_6 MNT59, Human melanoma cell line, treated with combination of guadecitabine and givinostat


title: MNT59_2 MNT59, Human melanoma cell line, treated with guadecitabine


title: MNT59_5 MNT59, Human melanoma cell line, treated with GSK126


title: MNT59_4 MNT59, Human melanoma cell line, treated with JQ1


title: MNT59_3 MNT59, Human melanoma cell line, treated with givinostat


title: CPN20_NT_2 CPN20, Human melanoma cell line, not treated


title: GLM41_5 GML41, Human melanoma cell line, treated with GSK126


title: MNT59_NT MNT59, Human melanoma cell line, not treated


title: GML41_NT GML41, Human melanoma cell line, not treated


title: GLM41_2 GML41, Human melanoma cell line, treated with guadecitabine


title: MNT59_9 MNT59, Human melanoma cell line, treated with combination of givinostat and JQ1


title: CST30_4 CST30, Human melanoma cell line, treated with JQ1


title: GLM41_4 GML41, Human melanoma cell line, treated with JQ1


title: GLM41_6 GML41, Human melanoma cell line, treated with abemaciclib


title: CST30_NT CST30, Human melanoma cell line, not treated


title: GLM41_3 GML41, Human melanoma cell line, treated with givinostat


title: CST30_6 CST30, Human melanoma cell line, treated with abemaciclib


title: VRG100_4 VRG100, Human melanoma cell line, treated with JQ1


title: CST30_2 CST30, Human melanoma cell line, treated with guadecitabine


title: VRG100_3 VRG100, Human melanoma cell line, treated with givinostat


title: CST30_3 CST30, Human melanoma cell line, treated with givinostat


title: VRG100_6 VRG100, Human melanoma cell line, treated with abemaciclib


title: BRM17_6 BRM17, Human melanoma cell line, treated with abemaciclib


title: CST30_5 CST30, Human melanoma cell line, treated with GSK126


title: BRM17_5 BRM17, Human melanoma cell line, treated with GSK126


title: BRM17_NT BRM17, Human melanoma cell line, not treated


title: SLN91_10 SLN91, Human melanoma cell line, treated with combination of givinostat and GSK126


title: VRG100_5 VRG100, Human melanoma cell line, treated with GSK126


title: SLN91_12 SLN91, Human melanoma cell line, treated with abemaciclib


title: SLN91_9 SLN91, Human melanoma cell line, treated with combination of givinostat and JQ1


title: SLN91_11 SLN91, Human melanoma cell line, treated with combination of JQ1 and GSK126


title: VRG100_NT VRG100, Human melanoma cell line, not treated


title: BRM17_3 BRM17, Human melanoma cell line, treated with givinostat


title: SLN91_6 SLN91, Human melanoma cell line, treated with combination of guadecitabine and givinostat


title: SLN91_5 SLN91, Human melanoma cell line, treated with GSK126


title: SLN91_8 SLN91, Human melanoma cell line, treated with combination of guadecitabine and GSK126


title: SLN91_7 SLN91, Human melanoma cell line, treated with combination of guadecitabine and JQ1


title: SLN91_4 SLN91, Human melanoma cell line, treated with JQ1


title: BRM17_4 BRM17, Human melanoma cell line, treated with JQ1


title: SLN91_3 SLN91, Human melanoma cell line, treated with givinostat


title: VRG100_2 VRG100, Human melanoma cell line, treated with guadecitabine


title: SLN91_NT SLN91, Human melanoma cell line, not treated


title: CPN20_11 CPN20, Human melanoma cell line, treated with combination of JQ1 and GSK126


title: SLN91_2 SLN91, Human melanoma cell line, treated with guadecitabine


title: CPN20_9 CPN20, Human melanoma cell line, treated with combination of givinostat and JQ1


title: CPN20_12 CPN20, Human melanoma cell line, treated with abemaciclib


title: CPN20_8 CPN20, Human melanoma cell line, treated with combination of guadecitabine and GSK126


title: CPN20_10 CPN20, Human melanoma cell line, treated with combination of givinostat and GSK126


title: CPN20_5 CPN20, Human melanoma cell line, treated with GSK126


title: CPN20_2 CPN20, Human melanoma cell line, treated with guadecitabine


title: CPN20_6 CPN20, Human melanoma cell line, treated with combination of guadecitabine and givinostat


title: CPN20_7 CPN20, Human melanoma cell line, treated with combination of guadecitabine and JQ1


title: CPN20_4 CPN20, Human melanoma cell line, treated with JQ1


title: CPN20_3 CPN20, Human melanoma cell line, treated with givinostat


title: CPN20_NT CPN20, Human melanoma cell line, not treated


title: BRM17_2 BRM17, Human melanoma cell line, treated with guadecitabine


title: FRN39_7 FRN39, Human melanoma cell line, treated with combination of guadecitabine and JQ1


title: FRN39_8 FRN39, Human melanoma cell line, treated with combination of guadecitabine and GSK126


title: FRN39_9 FRN39, Human melanoma cell line, treated with combination of givinostat and JQ1


title: FRN39_6 FRN39, Human melanoma cell line, treated with combination of guadecitabine and givinostat


title: FRN39_5 FRN39, Human melanoma cell line, treated with GSK126


title: FRN39_4 FRN39, Human melanoma cell line, treated with JQ1


title: FRN39_3 FRN39, Human melanoma cell line, treated with givinostat


title: BNV13_12 BNV13, Human melanoma cell line, treated with combination of decitabine, givinostat and GSK126

source_name: Human Melanoma cell line, treated with three epigenetic drugs, for 144 h


title: FRN39_NT FRN39, Human melanoma cell line, not treated


title: FRN39_2 FRN39, Human melanoma cell line, treated with guadecitabine


title: BNV13_10 BNV13, Human melanoma cell line, treated with combination of givinostat and GSK126


title: BNV13_11 BNV13, Human melanoma cell line, treated with combination of JQ1 and GSK126


title: BNV13_8 BNV13, Human melanoma cell line, treated with combination of decitabine and GSK126


title: BNV13_9 BNV13, Human melanoma cell line, treated with combination of givinostat and JQ1


title: BNV13_7 BNV13, Human melanoma cell line, treated with combination of decitabine and JQ1


title: BNV13_5 BNV13, Human melanoma cell line, treated with GSK126


title: FRN39_10 FRN39, Human melanoma cell line, treated with combination of givinostat and GSK126


title: FRN39_11 FRN39, Human melanoma cell line, treated with combination of JQ1 and GSK126


title: BNV13_3 BNV13, Human melanoma cell line, treated with givinostat


title: BNV13_2 BNV13, Human melanoma cell line, treated with decitabine


title: BNV13_NT BNV13, Human melanoma cell line, not treated


title: GRD43_12 GRD43, Human melanoma cell line, treated with combination of decitabine, givinostat and GSK126


title: GRD43_9 GRD43, Human melanoma cell line, treated with combination of givinostat and JQ1


title: GRD43_11 GRD43, Human melanoma cell line, treated with combination of JQ1 and GSK126


title: GRD43_10 GRD43, Human melanoma cell line, treated with combination of givinostat and GSK126


title: GRD43_7 GRD43, Human melanoma cell line, treated with combination of decitabine and JQ1


title: GRD43_4 GRD43, Human melanoma cell line, treated with JQ1


title: GRD43_NT GRD43, Human melanoma cell line, not treated


title: GRD43_2 GRD43, Human melanoma cell line, treated with decitabine


title: BNV13_4 BNV13, Human melanoma cell line, treated with JQ1


title: GRD43_5 GRD43, Human melanoma cell line, treated with GSK126


title: GRD43_8 GRD43, Human melanoma cell line, treated with combination of decitabine and GSK126


title: GRD43_6 GRD43, Human melanoma cell line, treated with combination of decitabine and givinostat


title: GRD43_3 GRD43, Human melanoma cell line, treated with givinostat


title: E13.5-KO 3

city: Scarborough

first: Arturo

last: Hernandez

state: ME

address: 81 Research Drive

department: Center for Molecular Medicine

institute: Maine Medical Center Research Institute

data_processing:
Raw sequence data in Fastq format were assessed for quality (FastQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and ribosomal RNA content. NovoAlign version 2.08 (Novocraft, http://novocraft.com) was used to align reads to the reference genome.
Alignments were combined to create clusters of reads (or patches), which represent nonredundant genomic regions in the reference genome sequence. Cluster boundaries are created by taking all samples into account during the cluster generation to define the leftmost and right-most end coordinates of each cluster. Only uniquely mapping reads are taken into consideration. While clusters represent expressed loci regardless of genomic location, clusters overlapping known genes (as defined by the reference genome assembly annotation), they were labeled as such for downstream analysis. After clusters are created in this way, they undergo linear normalization by multiplying each sample’s locus coverage by the total reads of the lowest read-count sample divided by the respective sample's total reads.

source_name: Fetal Heart

extract_protocol:
Qiagen RNAeasy mini kit
Standard Illumina protocols

tag: embryonic age


title: E13.5-KO 2


title: E13.5-KO 4


title: E13.5-KO 1


title: HeLa WT siCasp8 Thy 3h Rep 3

city: Essen

first: Samuel

last: Peña-Llopis

address: Hufelandstr. 55, Augenklinik 1.UG, Rm 69-71

department: Ophthalmology

institute: University Hospital Essen

description: Gene expression profiling wild-type HeLa cells treated with thymidine for 3 h and silencing of CASP8

hyb_protocol: 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray according to the Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide).

data_processing: The data were normalized using quantile normalization with R using function normalize.quantiles from Bioconductor package preprocessCore.

label: Biotin, Cy3-Streptavidin

source_name: HeLa WT siCasp8 Thy 3h Rep 3

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) is used to generate single-stranded cRNA from input amounts of 500ng total RNA.

growth_protocol: Cells were cultured in their respective culture media at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy Plus kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Non-synchronized or synchronized with double-thymidine and released for 3 hours.

value: HeLa

value: Wild-Type

value: Thy 3h

tag: additional treatment

tag: replicate

value: Replicate 3


title: HeLa KO FlagCasp8 Thy 3h Rep 1

description: Gene expression profiling of HeLa cells with knockout of CASP8 and treated with thymidine for 3 h and overexpression of Flag-Casp8

source_name: HeLa KO FlagCasp8 Thy 3h Rep 1

tag: cell line

value: CASP8 knockout

value: Replicate 1


title: HeLa WT Thy 3h Rep 3

description: Gene expression profiling wild-type HeLa cells treated with thymidine for 3 h

source_name: HeLa WT Thy 3h Rep 3


title: HeLa WT Thy 3h Rep 2

source_name: HeLa WT Thy 3h Rep 2

value: Replicate 2


title: HeLa KO UT Rep 1

description: Gene expression profiling of untreated HeLa cells with knockout of CASP8

source_name: HeLa KO UT Rep 1

value: Untreated


title: E13.5-Wild type 2


title: E13.5-Wild type 4


title: E13.5-Wild type 3


title: E13.5-Wild type 1


title: HeLa KO Thy 3h Rep 1

description: Gene expression profiling of HeLa cells with knockout of CASP8 and treated with thymidine for 3 h

source_name: HeLa KO Thy 3h Rep 1


title: HeLa KO Thy 3h Rep 3

source_name: HeLa KO Thy 3h Rep 3


title: HeLa KO Thy 3h Rep 2

source_name: HeLa KO Thy 3h Rep 2


title: Plp iKO-3

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: format:xls ; Contain the estimated expression values produced by Cufflinks.

source_name: Mutant

extract_protocol:
RNA from control and Olig2 mutant spinal cord were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

value: spinal cord

tag: timepoint

value: 14 days after injury

value: Olig2 fl/fl; Plp creERT


title: HeLa KO UT Rep 2

source_name: HeLa KO UT Rep 2


title: HeLa WT Thy 3h Rep 1

source_name: HeLa WT Thy 3h Rep 1


title: Plp iKO-2

tag: tissue


title: HeLa KO FlagCasp8 Thy 3h Rep 2

source_name: HeLa KO FlagCasp8 Thy 3h Rep 2


title: HeLa WT UT Rep 2

description: Gene expression profiling of untreated wild-type HeLa cells

source_name: HeLa WT UT Rep 2


title: HeLa WT siCasp8 Thy 3h Rep 2

source_name: HeLa WT siCasp8 Thy 3h Rep 2


title: HeLa WT UT Rep 1

source_name: HeLa WT UT Rep 1


title: Control-3

source_name: Control

value: Olig2 fl/+; Plp creERT


title: Plp iKO-1


title: Control-2


title: HeLa WT UT Rep 3

source_name: HeLa WT UT Rep 3


title: HeLa WT siCasp8 Thy 3h Rep 1

source_name: HeLa WT siCasp8 Thy 3h Rep 1


title: BF-D3

city: Nanjing

first: Jiawei

last: Li

state: Jiangsu

address: Zhongshan road No.321

department: State Key Laboratory of Pharmaceutical Biotechnology, Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery

institute: Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School Nanjing

data_processing:
illumina Casava1.7 software used for basecalling
Sequence reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabases of library size (RPKM) using a protocal from Chepelev et.al., Nucleic Acids Research, 2009.
Assembly: Rn6
Supplementary files format and content: RPKM values for each Sample

organism: Rattus norvegicus

source_name: bone marrow

growth_protocol: BMSCs were maintained in DMEM-LG; 1 g/L with chondrogenic induced medium and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) .

treatment_protocol:
Then the cells of BMSC_CT groups were treated with CTGF for 1 weeks followed by TGF-β1.
The cells of BF-D groups were treated with docetaxels

value: bone marrow

value: BMSCs

value: fibrotic Bone marrow-mesenchymal stem cells (BMSCs)

value: WT

value: Docetaxel treatment


title: BF-C2

value: Control


title: BF-D1


title: BF-C3


title: HeLa KO FlagCasp8 Thy 3h Rep 3

source_name: HeLa KO FlagCasp8 Thy 3h Rep 3

value: HeLa


title: BMSC-CT3

value: Bone marrow-mesenchymal stem cells (BMSCs)

value: CTGF+TGFβ1 treatment


title: BMSC-C3


title: BMSC-C2


title: Control-1


title: Input library sequencing; RNA-seq

city: Durham

first: Craig

middle: Barrett

last: Lowe

state: North Carolina

address: 213 Research Dr

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

description: FS DNA Library Prep Kit

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cluster analysis was performed using Seurat v4.0 (https://satijalab.org/seurat/). For each library, cells were removed which contained 200 or fewer genes or more than 5,000 genes. Each library was independently normalized and 2,000 highly variable features were identified for each library. Cells across independent libraries at were integrated for joint analysis via canonical correlation analysis. Variation in gene expression based on cell-cycle related genes was regressed from cluster analysis in dataset scaling using an annotated set of G2M and S phase related genes provided in Seurat. k-nearest neighbors (k=20) were calculated in the space of significant principal components (in this case, 30 principal components) and clustering was performed with the Louvain-Jaccard method. Cell type cluster and metacluster identities were assigned on the basis of marker gene expression.
For input normalization, fastq reads from the input library were aligned using the Burrows-Wheeler Aligner (https://github.com/lh3/bwa) to a custom reference genome including the mouse assembly mm10 with additional fasta records containing the sequences of each STARR-seq library construct (constructList.txt)
To measure enhancer activity in pseudo-bulk tissue, we we implemented gonomics: fastqFilter - collapseUmi (available from https://github.com/vertgenlab/gonomics) to remove unique molecular identifier (UMI) duplicates from our 10x libraries. We then used gonomics: fastqFormat -singleCell to parse the cell barcode and UMI from R1 into the read name for the R2 fastq. We then used the BWA to align reads to our custom STARR-seq reference genome described above. The enhancer activity score for each construct was then calculated as the input- normalized UMI count per 1000 total reporter UMI counts.
To perform cell-type specific enhancer activity quantification (as seen in pooledClusterCounts.txt), reads from each library aligned to the custom STARR-seq reference genome described above were sorted by cell barcode using gonomics: mergeSort -singleCellBx and input-normalized count matrices were generated with gonomics: scCount. Input-normalized count matrices were then partitioned by metacluster using cluster identities determined for each cell barcode by Seurat. Cells with fewer than 4 pCAG-GFP UMIs were discarded. The input-normalized reporter UMI counts for each cell were then further normalized to the pCAG-GFP UMI count for that cell. The cell type enhancer activity score was then calculated as the average transfection-normalized, input-normalized UMI count per cell in each cluster.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: genomic DNA

organism: synthetic construct

source_name: Synthetic plasmid library

extract_protocol:
Electroporated brains were harvested and dissected in ice-cold sterile PBS. Meninges were removed and GFP+ portions of the cortices were incubated at 37◦C for 10 minutes in 0.25% trypsin-EDTA supplemented with 0.1% DNAse I. Following incubation, the trypsin solution was removed and replaced with ice- cold 10% FBS/HBSS/Propidium iodide supplemented with 0.01% DNAse I. A single cell suspension was then generated by trituration with a fire-polished glass pipette and filtered with a 30 μm cell strainer. Cells were then stained with the LIVE/DEAD Near-IR Dead Cell Stain per manufacturer’s instructions. Following staining, viable GFP+ cells were bulk sorted using a FACS Aria II cytometer.
For input normalization: input plasmid libraries were fragmented and sequenced with the NEBNext Ultra II FS DNA Library Prep Kit per manufacturer's instrutions.
For scRNA-seq: library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
scRNA-seq/WGS

treatment_protocol: Input STARR-seq plasmid libraries were delivered to developing mouse cerebral cortices (E14.5/E15.5) via in utero electroporation and harvested 18 hours post electroporation.

value: Synthetic plasmid library


title: 1344_Mecom amplicon seq

city: Cambridge

first: Liming

last: Tao

address: 415 Main Street

institute: Broad Institute of Harvard and MIT

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H12_S672/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H12_S672_L001_R1_001_MR912_3_MDA_MECOM_AMP_H12_S672_L001_R2_001/Alleles_frequency_table.zip

data_processing:
Library strategy: amplicon-seq
Basecalls performed using CASAVA version 1.4 and bcl2fastq2 v2.20.0
CRISPResso2
Genome_build:  Human reference genome GRCh38 and gene annotation reference Homo_sapiens.GRCh38.93.gtf
Supplementary_files_format_and_content: txt

source_name: HSC

growth_protocol: cells were cultured at 37oC and 5%O2 in serum-free HSC media comprised of StemSpan  II medium (Stem Cell Technologies) supplemented with CC100 cytokine cocktail (Stem Cell Technologies), 100ng/ml TPO (Peprotech) and 35nM UM171 (Stem Cell Technologies). Confluency was maintained between 2e5-1e6 cells/ml.

extract_protocol: genomic DNA or cDNA  isolated by  beads

treatment_protocol: MECOM KO

value: HSC

tag: chip antibody

value: Mecom KO


title: 1341_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H9_S669/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H9_S669_L001_R1_001_MR912_3_MDA_MECOM_AMP_H9_S669_L001_R2_001/Alleles_frequency_table.zip


title: 1342_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_Cat_D7_S43/CRISPResso_on_MR214_1_Cat_D7_S43_L001_R1_001_MR214_1_Cat_D7_S43_L001_R2_001/Alleles_frequency_table.zip


title: 1337_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H5_S665/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H5_S665_L001_R1_001_MR912_3_MDA_MECOM_AMP_H5_S665_L001_R2_001/Alleles_frequency_table.zip


title: 1340_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H8_S668/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H8_S668_L001_R1_001_MR912_3_MDA_MECOM_AMP_H8_S668_L001_R2_001/Alleles_frequency_table.zip


title: 1338_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_H4_S88/CRISPResso_on_MR912-2-MDA-MECOM-AMP_H4_S88_L001_R1_001_MR912-2-MDA-MECOM-AMP_H4_S88_L001_R2_001/Alleles_frequency_table.zip


title: BF-D2


title: 1335_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H3_S663/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H3_S663_L001_R1_001_MR912_3_MDA_MECOM_AMP_H3_S663_L001_R2_001/Alleles_frequency_table.zip


title: 1336_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H9_S381/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H9_S381_L001_R1_001_MR912-5-WTA-MECOM-AMP_H9_S381_L001_R2_001/Alleles_frequency_table.zip


title: 1334_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_C5_S125/CRISPResso_on_MR912-2-WTA-MECOM-AMP_C5_S125_L001_R1_001_MR912-2-WTA-MECOM-AMP_C5_S125_L001_R2_001/Alleles_frequency_table.zip


title: 1332_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_H6_S282/CRISPResso_on_MR912_3_Dog_H6_S282_L001_R1_001_MR912_3_Dog_H6_S282_L001_R2_001/Alleles_frequency_table.zip


title: BNV13_6 BNV13, Human melanoma cell line, treated with combination of decitabine and givinostat

source_name: Human Melanoma cell line, treated with two epigenetic drugs, for 144 h

value: Female

value: nodal metastasis

value: BRAF-MUTANT


title: BMSC-CT2


title: 1330_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G10_S658/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G10_S658_L001_R1_001_MR912_3_MDA_MECOM_AMP_G10_S658_L001_R2_001/Alleles_frequency_table.zip


title: 1327_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G7_S655/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G7_S655_L001_R1_001_MR912_3_MDA_MECOM_AMP_G7_S655_L001_R2_001/Alleles_frequency_table.zip


title: 1331_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_H1_S85/CRISPResso_on_MR912-2-MDA-MECOM-AMP_H1_S85_L001_R1_001_MR912-2-MDA-MECOM-AMP_H1_S85_L001_R2_001/Alleles_frequency_table.zip


title: BMSC-C1


title: 1328_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G8_S656/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G8_S656_L001_R1_001_MR912_3_MDA_MECOM_AMP_G8_S656_L001_R2_001/Alleles_frequency_table.zip


title: HeLa KO UT Rep 3

description: Gene expression profiling of untreated HeLa cells with knockout of CASP8

source_name: HeLa KO UT Rep 3

value: CASP8 knockout

value: Untreated

value: Replicate 3


title: 1329_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G9_S657/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G9_S657_L001_R1_001_MR912_3_MDA_MECOM_AMP_G9_S657_L001_R2_001/Alleles_frequency_table.zip


title: 1343_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_H11_S671/CRISPResso_on_MR912_3_MDA_MECOM_AMP_H11_S671_L001_R1_001_MR912_3_MDA_MECOM_AMP_H11_S671_L001_R2_001/Alleles_frequency_table.zip


title: 1326_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G6_S654/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G6_S654_L001_R1_001_MR912_3_MDA_MECOM_AMP_G6_S654_L001_R2_001/Alleles_frequency_table.zip


title: 1325_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G5_S653/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G5_S653_L001_R1_001_MR912_3_MDA_MECOM_AMP_G5_S653_L001_R2_001/Alleles_frequency_table.zip


title: 1339_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Dog_E3_S243/CRISPResso_on_MR912_3_Dog_E3_S243_L001_R1_001_MR912_3_Dog_E3_S243_L001_R2_001/Alleles_frequency_table.zip


title: 1322_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_E2_S242/CRISPResso_on_MR912-5-MDA-MECOM-AMP_E2_S242_L001_R1_001_MR912-5-MDA-MECOM-AMP_E2_S242_L001_R2_001/Alleles_frequency_table.zip


title: 1324_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G4_S652/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G4_S652_L001_R1_001_MR912_3_MDA_MECOM_AMP_G4_S652_L001_R2_001/Alleles_frequency_table.zip


title: 1323_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G3_S651/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G3_S651_L001_R1_001_MR912_3_MDA_MECOM_AMP_G3_S651_L001_R2_001/Alleles_frequency_table.zip


title: 1321_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_G6_S174/CRISPResso_on_MR912-2-WTA-MECOM-AMP_G6_S174_L001_R1_001_MR912-2-WTA-MECOM-AMP_G6_S174_L001_R2_001/Alleles_frequency_table.zip


title: 1333_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_E12_S156/CRISPResso_on_MR912_3_Bird_E12_S156_L001_R1_001_MR912_3_Bird_E12_S156_L001_R2_001/Alleles_frequency_table.zip


title: 1319_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C9_S609/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C9_S609_L001_R1_001_MR912_3_MDA_MECOM_AMP_C9_S609_L001_R2_001/Alleles_frequency_table.zip


title: 1320_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_F12_S648/CRISPResso_on_MR912_3_MDA_MECOM_AMP_F12_S648_L001_R1_001_MR912_3_MDA_MECOM_AMP_F12_S648_L001_R2_001/Alleles_frequency_table.zip


title: 1315_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_C9_S225/CRISPResso_on_MR912-5-MDA-MECOM-AMP_C9_S225_L001_R1_001_MR912-5-MDA-MECOM-AMP_C9_S225_L001_R2_001/Alleles_frequency_table.zip


title: 1316_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_F8_S644/CRISPResso_on_MR912_3_MDA_MECOM_AMP_F8_S644_L001_R1_001_MR912_3_MDA_MECOM_AMP_F8_S644_L001_R2_001/Alleles_frequency_table.zip


title: 1318_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_F10_S646/CRISPResso_on_MR912_3_MDA_MECOM_AMP_F10_S646_L001_R1_001_MR912_3_MDA_MECOM_AMP_F10_S646_L001_R2_001/Alleles_frequency_table.zip


title: 1317_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_D8_S44/CRISPResso_on_MR912-2-MDA-MECOM-AMP_D8_S44_L001_R1_001_MR912-2-MDA-MECOM-AMP_D8_S44_L001_R2_001/Alleles_frequency_table.zip


title: 1313_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_F5_S641/CRISPResso_on_MR912_3_MDA_MECOM_AMP_F5_S641_L001_R1_001_MR912_3_MDA_MECOM_AMP_F5_S641_L001_R2_001/Alleles_frequency_table.zip


title: 1312_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_Bird_B6_S114/CRISPResso_on_MR912_3_Bird_B6_S114_L001_R1_001_MR912_3_Bird_B6_S114_L001_R2_001/Alleles_frequency_table.zip


title: 1314_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_D1_S37/CRISPResso_on_MR912-2-MDA-MECOM-AMP_D1_S37_L001_R1_001_MR912-2-MDA-MECOM-AMP_D1_S37_L001_R2_001/Alleles_frequency_table.zip


title: 1309_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_F1_S637/CRISPResso_on_MR912_3_MDA_MECOM_AMP_F1_S637_L001_R1_001_MR912_3_MDA_MECOM_AMP_F1_S637_L001_R2_001/Alleles_frequency_table.zip


title: 1310_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A1_S385/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A1_S385_L001_R1_001_MR214_1_MDA_MECOM_AMP_A1_S385_L001_R2_001/Alleles_frequency_table.zip


title: 1311_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B3_S591/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B3_S591_L001_R1_001_MR912_3_MDA_MECOM_AMP_B3_S591_L001_R2_001/Alleles_frequency_table.zip


title: 1305_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_E9_S633/CRISPResso_on_MR912_3_MDA_MECOM_AMP_E9_S633_L001_R1_001_MR912_3_MDA_MECOM_AMP_E9_S633_L001_R2_001/Alleles_frequency_table.zip


title: 1307_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G8_S560/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G8_S560_L001_R1_001_MR912_3_MDA_MECOM_AMP_G8_S560_L001_R2_001/Alleles_frequency_table.zip


title: 1306_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_F10_S454/CRISPResso_on_MR214_1_MDA_MECOM_AMP_F10_S454_L001_R1_001_MR214_1_MDA_MECOM_AMP_F10_S454_L001_R2_001/Alleles_frequency_table.zip


title: 1304_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_E8_S632/CRISPResso_on_MR912_3_MDA_MECOM_AMP_E8_S632_L001_R1_001_MR912_3_MDA_MECOM_AMP_E8_S632_L001_R2_001/Alleles_frequency_table.zip


title: 1303_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C7_S607/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C7_S607_L001_R1_001_MR912_3_MDA_MECOM_AMP_C7_S607_L001_R2_001/Alleles_frequency_table.zip


title: 1302_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_E6_S630/CRISPResso_on_MR912_3_MDA_MECOM_AMP_E6_S630_L001_R1_001_MR912_3_MDA_MECOM_AMP_E6_S630_L001_R2_001/Alleles_frequency_table.zip


title: 1300_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_G6_S174/CRISPResso_on_MR912-2-WTA-MECOM-AMP_G6_S174_L001_R1_001_MR912-2-WTA-MECOM-AMP_G6_S174_L001_R2_001/Alleles_frequency_table.zip


title: 1299_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A12_S492/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A12_S492_L001_R1_001_MR912_3_MDA_MECOM_AMP_A12_S492_L001_R2_001/Alleles_frequency_table.zip


title: 1298_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_D12_S144/CRISPResso_on_MR912-2-WTA-MECOM-AMP_D12_S144_L001_R1_001_MR912-2-WTA-MECOM-AMP_D12_S144_L001_R2_001/Alleles_frequency_table.zip


title: 1297_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B8_S596/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B8_S596_L001_R1_001_MR912_3_MDA_MECOM_AMP_B8_S596_L001_R2_001/Alleles_frequency_table.zip


title: 1296_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_D12_S48/CRISPResso_on_MR912-2-MDA-MECOM-AMP_D12_S48_L001_R1_001_MR912-2-MDA-MECOM-AMP_D12_S48_L001_R2_001/Alleles_frequency_table.zip


title: 1301_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A4_S484/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A4_S484_L001_R1_001_MR912_3_MDA_MECOM_AMP_A4_S484_L001_R2_001/Alleles_frequency_table.zip


title: 1295_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_G10_S178/CRISPResso_on_MR912-2-WTA-MECOM-AMP_G10_S178_L001_R1_001_MR912-2-WTA-MECOM-AMP_G10_S178_L001_R2_001/Alleles_frequency_table.zip


title: 1289_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_E2_S338/CRISPResso_on_MR912-5-WTA-MECOM-AMP_E2_S338_L001_R1_001_MR912-5-WTA-MECOM-AMP_E2_S338_L001_R2_001/Alleles_frequency_table.zip


title: 1293_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D9_S621/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D9_S621_L001_R1_001_MR912_3_MDA_MECOM_AMP_D9_S621_L001_R2_001/Alleles_frequency_table.zip


title: 1288_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A6_S390/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A6_S390_L001_R1_001_MR214_1_MDA_MECOM_AMP_A6_S390_L001_R2_001/Alleles_frequency_table.zip


title: 1294_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D10_S622/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D10_S622_L001_R1_001_MR912_3_MDA_MECOM_AMP_D10_S622_L001_R2_001/Alleles_frequency_table.zip


title: 1291_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D7_S619/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D7_S619_L001_R1_001_MR912_3_MDA_MECOM_AMP_D7_S619_L001_R2_001/Alleles_frequency_table.zip


title: 1292_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D8_S620/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D8_S620_L001_R1_001_MR912_3_MDA_MECOM_AMP_D8_S620_L001_R2_001/Alleles_frequency_table.zip


title: 1287_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D3_S615/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D3_S615_L001_R1_001_MR912_3_MDA_MECOM_AMP_D3_S615_L001_R2_001/Alleles_frequency_table.zip


title: 1308_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C3_S315/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C3_S315_L001_R1_001_MR912-5-WTA-MECOM-AMP_C3_S315_L001_R2_001/Alleles_frequency_table.zip


title: 1286_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_C6_S30/CRISPResso_on_MR912-2-MDA-MECOM-AMP_C6_S30_L001_R1_001_MR912-2-MDA-MECOM-AMP_C6_S30_L001_R2_001/Alleles_frequency_table.zip


title: 1290_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D6_S618/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D6_S618_L001_R1_001_MR912_3_MDA_MECOM_AMP_D6_S618_L001_R2_001/Alleles_frequency_table.zip


title: 1285_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-MDA-MECOM-AMP_F1_S253/CRISPResso_on_MR912-5-MDA-MECOM-AMP_F1_S253_L001_R1_001_MR912-5-MDA-MECOM-AMP_F1_S253_L001_R2_001/Alleles_frequency_table.zip


title: 1284_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_B8_S404/CRISPResso_on_MR214_1_MDA_MECOM_AMP_B8_S404_L001_R1_001_MR214_1_MDA_MECOM_AMP_B8_S404_L001_R2_001/Alleles_frequency_table.zip


title: 1283_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C11_S611/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C11_S611_L001_R1_001_MR912_3_MDA_MECOM_AMP_C11_S611_L001_R2_001/Alleles_frequency_table.zip


title: 1281_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C9_S609/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C9_S609_L001_R1_001_MR912_3_MDA_MECOM_AMP_C9_S609_L001_R2_001/Alleles_frequency_table.zip


title: 1279_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C7_S607/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C7_S607_L001_R1_001_MR912_3_MDA_MECOM_AMP_C7_S607_L001_R2_001/Alleles_frequency_table.zip


title: 1280_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_E9_S153/CRISPResso_on_MR912-2-WTA-MECOM-AMP_E9_S153_L001_R1_001_MR912-2-WTA-MECOM-AMP_E9_S153_L001_R2_001/Alleles_frequency_table.zip


title: 1282_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C10_S610/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C10_S610_L001_R1_001_MR912_3_MDA_MECOM_AMP_C10_S610_L001_R2_001/Alleles_frequency_table.zip


title: 1278_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C6_S606/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C6_S606_L001_R1_001_MR912_3_MDA_MECOM_AMP_C6_S606_L001_R2_001/Alleles_frequency_table.zip


title: 1276_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C4_S604/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C4_S604_L001_R1_001_MR912_3_MDA_MECOM_AMP_C4_S604_L001_R2_001/Alleles_frequency_table.zip


title: 1277_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_C5_S605/CRISPResso_on_MR912_3_MDA_MECOM_AMP_C5_S605_L001_R1_001_MR912_3_MDA_MECOM_AMP_C5_S605_L001_R2_001/Alleles_frequency_table.zip


title: 1275_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_H3_S471/CRISPResso_on_MR214_1_MDA_MECOM_AMP_H3_S471_L001_R1_001_MR214_1_MDA_MECOM_AMP_H3_S471_L001_R2_001/Alleles_frequency_table.zip


title: 1274_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_G8_S560/CRISPResso_on_MR912_3_MDA_MECOM_AMP_G8_S560_L001_R1_001_MR912_3_MDA_MECOM_AMP_G8_S560_L001_R2_001/Alleles_frequency_table.zip


title: 1273_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H12_S384/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H12_S384_L001_R1_001_MR912-5-WTA-MECOM-AMP_H12_S384_L001_R2_001/Alleles_frequency_table.zip


title: 1272_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_A8_S392/CRISPResso_on_MR214_1_MDA_MECOM_AMP_A8_S392_L001_R1_001_MR214_1_MDA_MECOM_AMP_A8_S392_L001_R2_001/Alleles_frequency_table.zip


title: 1271_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_E4_S52/CRISPResso_on_MR912-2-MDA-MECOM-AMP_E4_S52_L001_R1_001_MR912-2-MDA-MECOM-AMP_E4_S52_L001_R2_001/Alleles_frequency_table.zip


title: 1270_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_D11_S431/CRISPResso_on_MR214_1_MDA_MECOM_AMP_D11_S431_L001_R1_001_MR214_1_MDA_MECOM_AMP_D11_S431_L001_R2_001/Alleles_frequency_table.zip


title: 1269_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_C8_S320/CRISPResso_on_MR912-5-WTA-MECOM-AMP_C8_S320_L001_R1_001_MR912-5-WTA-MECOM-AMP_C8_S320_L001_R2_001/Alleles_frequency_table.zip


title: 1268_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B8_S596/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B8_S596_L001_R1_001_MR912_3_MDA_MECOM_AMP_B8_S596_L001_R2_001/Alleles_frequency_table.zip


title: 1263_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B3_S591/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B3_S591_L001_R1_001_MR912_3_MDA_MECOM_AMP_B3_S591_L001_R2_001/Alleles_frequency_table.zip


title: 1264_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_H1_S373/CRISPResso_on_MR912-5-WTA-MECOM-AMP_H1_S373_L001_R1_001_MR912-5-WTA-MECOM-AMP_H1_S373_L001_R2_001/Alleles_frequency_table.zip


title: 1266_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B6_S594/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B6_S594_L001_R1_001_MR912_3_MDA_MECOM_AMP_B6_S594_L001_R2_001/Alleles_frequency_table.zip


title: 1262_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_B2_S590/CRISPResso_on_MR912_3_MDA_MECOM_AMP_B2_S590_L001_R1_001_MR912_3_MDA_MECOM_AMP_B2_S590_L001_R2_001/Alleles_frequency_table.zip


title: 1261_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_D1_S517/CRISPResso_on_MR912_3_MDA_MECOM_AMP_D1_S517_L001_R1_001_MR912_3_MDA_MECOM_AMP_D1_S517_L001_R2_001/Alleles_frequency_table.zip


title: 1260_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A12_S588/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A12_S588_L001_R1_001_MR912_3_MDA_MECOM_AMP_A12_S588_L001_R2_001/Alleles_frequency_table.zip


title: 1258_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR214_1_MDA_MECOM_AMP_E1_S433/CRISPResso_on_MR214_1_MDA_MECOM_AMP_E1_S433_L001_R1_001_MR214_1_MDA_MECOM_AMP_E1_S433_L001_R2_001/Alleles_frequency_table.zip


title: 1256_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A8_S584/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A8_S584_L001_R1_001_MR912_3_MDA_MECOM_AMP_A8_S584_L001_R2_001/Alleles_frequency_table.zip


title: 1251_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_B7_S115/CRISPResso_on_MR912-2-WTA-MECOM-AMP_B7_S115_L001_R1_001_MR912-2-WTA-MECOM-AMP_B7_S115_L001_R2_001/Alleles_frequency_table.zip


title: 1255_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_G12_S372/CRISPResso_on_MR912-5-WTA-MECOM-AMP_G12_S372_L001_R1_001_MR912-5-WTA-MECOM-AMP_G12_S372_L001_R2_001/Alleles_frequency_table.zip


title: 1252_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A4_S580/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A4_S580_L001_R1_001_MR912_3_MDA_MECOM_AMP_A4_S580_L001_R2_001/Alleles_frequency_table.zip


title: 1254_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A6_S582/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A6_S582_L001_R1_001_MR912_3_MDA_MECOM_AMP_A6_S582_L001_R2_001/Alleles_frequency_table.zip


title: 1250_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912_3_MDA_MECOM_AMP_A2_S578/CRISPResso_on_MR912_3_MDA_MECOM_AMP_A2_S578_L001_R1_001_MR912_3_MDA_MECOM_AMP_A2_S578_L001_R2_001/Alleles_frequency_table.zip