title: 25_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_C1_S25/CRISPResso_on_MR912-2-MDA-MECOM-AMP_C1_S25_L001_R1_001_MR912-2-MDA-MECOM-AMP_C1_S25_L001_R2_001/Alleles_frequency_table.zip


title: 38_Mecom amplicon seq

status: Public on Nov 23 2022

type: SRA

city: Cambridge

first: Liming

last: Tao

address: 415 Main Street

country: USA

institute: Broad Institute of Harvard and MIT

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_D2_S38/CRISPResso_on_MR912-2-MDA-MECOM-AMP_D2_S38_L001_R1_001_MR912-2-MDA-MECOM-AMP_D2_S38_L001_R2_001/Alleles_frequency_table.zip

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: cell type

value: HSC

tag: chip antibody

tag: treatment

value: Mecom KO


title: S612_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR214_1.dge.txt.gz

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4 and bcl2fastq2 v2.20.0
Cumulus pipeline for SmartSeq2
Cumulus pipeline for bulkRNA
CRISPResso2
Genome_build:  Human reference genome GRCh38 and gene annotation reference Homo_sapiens.GRCh38.93.gtf
Supplementary_files_format_and_content: matrix

molecule: total RNA

extract_protocol:
mRNA isolated by  polyT beads
Smart Seq2

treatment_protocol: AAVS1  or MECOM KO

tag: genotype

value: MECOM KO


title: 30_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: S618_single cell rna seq by Smart Seq2


title: 33_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_C9_S33/CRISPResso_on_MR912-2-MDA-MECOM-AMP_C9_S33_L001_R1_001_MR912-2-MDA-MECOM-AMP_C9_S33_L001_R2_001/Alleles_frequency_table.zip


title: S616_single cell rna seq by Smart Seq2


title: S615_single cell rna seq by Smart Seq2


title: S613_single cell rna seq by Smart Seq2


title: S609_single cell rna seq by Smart Seq2


title: 22_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B10_S22/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B10_S22_L001_R1_001_MR912-2-MDA-MECOM-AMP_B10_S22_L001_R2_001/Alleles_frequency_table.zip


title: 21_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B9_S21/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B9_S21_L001_R1_001_MR912-2-MDA-MECOM-AMP_B9_S21_L001_R2_001/Alleles_frequency_table.zip


title: S607_single cell rna seq by Smart Seq2


title: S611_single cell rna seq by Smart Seq2


title: 20_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B8_S20/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B8_S20_L001_R1_001_MR912-2-MDA-MECOM-AMP_B8_S20_L001_R2_001/Alleles_frequency_table.zip


title: S606_single cell rna seq by Smart Seq2


title: S610_single cell rna seq by Smart Seq2


title: S608_single cell rna seq by Smart Seq2


title: 23_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B11_S23/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B11_S23_L001_R1_001_MR912-2-MDA-MECOM-AMP_B11_S23_L001_R2_001/Alleles_frequency_table.zip


title: S617_single cell rna seq by Smart Seq2


title: S603_single cell rna seq by Smart Seq2


title: 24_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B12_S24/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B12_S24_L001_R1_001_MR912-2-MDA-MECOM-AMP_B12_S24_L001_R2_001/Alleles_frequency_table.zip


title: S605_single cell rna seq by Smart Seq2


title: S604_single cell rna seq by Smart Seq2


title: 15_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B3_S15/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B3_S15_L001_R1_001_MR912-2-MDA-MECOM-AMP_B3_S15_L001_R2_001/Alleles_frequency_table.zip


title: 17_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-5-WTA-MECOM-AMP_F8_S356/CRISPResso_on_MR912-5-WTA-MECOM-AMP_F8_S356_L001_R1_001_MR912-5-WTA-MECOM-AMP_F8_S356_L001_R2_001/Alleles_frequency_table.zip


title: 196_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-WTA-MECOM-AMP_A4_S100/CRISPResso_on_MR912-2-WTA-MECOM-AMP_A4_S100_L001_R1_001_MR912-2-WTA-MECOM-AMP_A4_S100_L001_R2_001/Alleles_frequency_table.zip


title: 13_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B1_S13/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B1_S13_L001_R1_001_MR912-2-MDA-MECOM-AMP_B1_S13_L001_R2_001/Alleles_frequency_table.zip


title: S602_single cell rna seq by Smart Seq2


title: S599_single cell rna seq by Smart Seq2


title: 14_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B2_S14/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B2_S14_L001_R1_001_MR912-2-MDA-MECOM-AMP_B2_S14_L001_R2_001/Alleles_frequency_table.zip


title: 16_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B4_S16/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B4_S16_L001_R1_001_MR912-2-MDA-MECOM-AMP_B4_S16_L001_R2_001/Alleles_frequency_table.zip


title: S598_single cell rna seq by Smart Seq2


title: 11_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A11_S11/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A11_S11_L001_R1_001_MR912-2-MDA-MECOM-AMP_A11_S11_L001_R2_001/Alleles_frequency_table.zip


title: S601_single cell rna seq by Smart Seq2


title: S597_single cell rna seq by Smart Seq2


title: S596_single cell rna seq by Smart Seq2


title: S595_single cell rna seq by Smart Seq2


title: 12_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A12_S12/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A12_S12_L001_R1_001_MR912-2-MDA-MECOM-AMP_A12_S12_L001_R2_001/Alleles_frequency_table.zip


title: 8_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A8_S8/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A8_S8_L001_R1_001_MR912-2-MDA-MECOM-AMP_A8_S8_L001_R2_001/Alleles_frequency_table.zip


title: 9_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A9_S9/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A9_S9_L001_R1_001_MR912-2-MDA-MECOM-AMP_A9_S9_L001_R2_001/Alleles_frequency_table.zip


title: 19_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B7_S19/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B7_S19_L001_R1_001_MR912-2-MDA-MECOM-AMP_B7_S19_L001_R2_001/Alleles_frequency_table.zip


title: 18_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_B6_S18/CRISPResso_on_MR912-2-MDA-MECOM-AMP_B6_S18_L001_R1_001_MR912-2-MDA-MECOM-AMP_B6_S18_L001_R2_001/Alleles_frequency_table.zip


title: S594_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR214_1.dge.txt.gz


title: 7_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A7_S7/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A7_S7_L001_R1_001_MR912-2-MDA-MECOM-AMP_A7_S7_L001_R2_001/Alleles_frequency_table.zip


title: 6_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A6_S6/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A6_S6_L001_R1_001_MR912-2-MDA-MECOM-AMP_A6_S6_L001_R2_001/Alleles_frequency_table.zip


title: S593_single cell rna seq by Smart Seq2


title: S592_single cell rna seq by Smart Seq2


title: 5_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A5_S5/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A5_S5_L001_R1_001_MR912-2-MDA-MECOM-AMP_A5_S5_L001_R2_001/Alleles_frequency_table.zip


title: S591_single cell rna seq by Smart Seq2


title: S590_single cell rna seq by Smart Seq2


title: 4_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A4_S4/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A4_S4_L001_R1_001_MR912-2-MDA-MECOM-AMP_A4_S4_L001_R2_001/Alleles_frequency_table.zip


title: 3_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A3_S3/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A3_S3_L001_R1_001_MR912-2-MDA-MECOM-AMP_A3_S3_L001_R2_001/Alleles_frequency_table.zip


title: S589_single cell rna seq by Smart Seq2


title: S600_single cell rna seq by Smart Seq2


title: 2_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A2_S2/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A2_S2_L001_R1_001_MR912-2-MDA-MECOM-AMP_A2_S2_L001_R2_001/Alleles_frequency_table.zip


title: 10_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A10_S10/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A10_S10_L001_R1_001_MR912-2-MDA-MECOM-AMP_A10_S10_L001_R2_001/Alleles_frequency_table.zip


title: S587_single cell rna seq by Smart Seq2


title: S586_single cell rna seq by Smart Seq2


title: S585_single cell rna seq by Smart Seq2


title: 1_Mecom amplicon seq

description:
single cell genotyping:
processed data file:
./MR912-2-MDA-MECOM-AMP_A1_S1/CRISPResso_on_MR912-2-MDA-MECOM-AMP_A1_S1_L001_R1_001_MR912-2-MDA-MECOM-AMP_A1_S1_L001_R2_001/Alleles_frequency_table.zip


title: genomic DNA from TNBC patient number 97

type: genomic

city: Heidelberg

first: Dieter

last: Weichenhan

address: Im Neuenheimer Feld

department: Cancer Epigenomics

country: Germany

institute: Deutsches Krebsforschungszentrum

description: triple negative breast cancer tissue sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k/EPIC Beadchips using the standard Illumina protocol.

scan_protocol: Standard Illuminal protocol

data_processing:
To account for cell type heterogeneity, we used the Houseman algorithm for reference-based deconvolution using DNA methylation data from sorted cell types. Estimated proportions of various mammary cells (fibroblasts, epithelial, and endothelial cells), adipocytes, and immune cells (using the LUMP: leukocytes unmethylation for purity algorithm) were used as covariates to account for cell type heterogeneity in bulk tumor methylation data. Additionally, in order to minimize the false positive detection and to increase the signal-to-noise ratio in cfDNA analysis, we selected CpG sites that were almost completely methylated (β-value > 0.9) or unmethylated (β-value < 0.1) in peripheral blood DNA using methylation data from a previous genome-wide methylation study on 231 TNBC cases and 231 controls (PMID: 34789319).
RnBeads (version 1.12.1.)-normalized average Beta values, using Beta Mixture Quantile normalization (bmiq) and "enmix.oob" for background correction, both implemented in RnBeads.

label: Cy5 and Cy3

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from fresh-frozen tumor samples of TNBC cases using standard column-based extraction procedures.

tag: gender

value: Female

tag: tissue

value: Tumor tissue

tag: disease state

value: TNBC


title: genomic DNA from TNBC patient number 968


title: S583_single cell rna seq by Smart Seq2


title: S584_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1093


title: genomic DNA from TNBC patient number 916


title: genomic DNA from TNBC patient number 1828


title: S581_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1707


title: S582_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 480


title: S580_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 965


title: S578_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 944


title: S577_single cell rna seq by Smart Seq2


title: S579_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 884


title: S576_single cell rna seq by Smart Seq2

description:
single cell SS2 for AAVS1 KO
ss2_processed.tar
ss2_processed.tar/AAVS214_3.dge.txt.gz

value: AAVS1 KO


title: S588_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1603


title: genomic DNA from TNBC patient number 795


title: S575_single cell rna seq by Smart Seq2


title: S574_single cell rna seq by Smart Seq2


title: S572_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 993


title: genomic DNA from TNBC patient number 1065


title: genomic DNA from TNBC patient number 1484


title: genomic DNA from TNBC patient number 1108


title: S571_single cell rna seq by Smart Seq2


title: S573_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1778


title: genomic DNA from TNBC patient number 1796


title: S569_single cell rna seq by Smart Seq2


title: S567_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 829


title: genomic DNA from TNBC patient number 1438


title: genomic DNA from TNBC patient number 625


title: S564_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1010


title: genomic DNA from TNBC patient number 1622


title: S570_single cell rna seq by Smart Seq2


title: S561_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1048


title: genomic DNA from TNBC patient number 885


title: genomic DNA from TNBC patient number 950


title: S562_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1018


title: S565_single cell rna seq by Smart Seq2


title: S560_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1111


title: genomic DNA from TNBC patient number 1072


title: S559_single cell rna seq by Smart Seq2


title: S558_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 503


title: S568_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 525


title: S557_single cell rna seq by Smart Seq2


title: S556_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 907


title: genomic DNA from TNBC patient number 1414


title: S555_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1593


title: S566_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 639


title: S554_single cell rna seq by Smart Seq2


title: S553_single cell rna seq by Smart Seq2


title: S563_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 727


title: S552_single cell rna seq by Smart Seq2


title: S551_single cell rna seq by Smart Seq2


title: S549_single cell rna seq by Smart Seq2


title: S547_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 849


title: genomic DNA from TNBC patient number 1112


title: genomic DNA from TNBC patient number 668


title: S548_single cell rna seq by Smart Seq2


title: S545_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 980


title: genomic DNA from TNBC patient number 1109


title: S544_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 492


title: genomic DNA from TNBC patient number 721


title: S543_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 747


title: S542_single cell rna seq by Smart Seq2


title: S541_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 938


title: S538_single cell rna seq by Smart Seq2


title: S540_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1350


title: genomic DNA from TNBC patient number 951


title: genomic DNA from TNBC patient number 1030


title: S539_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 354


title: S537_single cell rna seq by Smart Seq2


title: S546_single cell rna seq by Smart Seq2


title: S536_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 933


title: genomic DNA from TNBC patient number 1697


title: S534_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 455


title: S550_single cell rna seq by Smart Seq2


title: S535_single cell rna seq by Smart Seq2


title: S533_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1592


title: S532_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 955


title: genomic DNA from TNBC patient number 1797


title: S531_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 845


title: genomic DNA from TNBC patient number 999


title: genomic DNA from TNBC patient number 261


title: S527_single cell rna seq by Smart Seq2


title: S530_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 998


title: S528_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 609


title: S526_single cell rna seq by Smart Seq2


title: S525_single cell rna seq by Smart Seq2


title: S524_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 887


title: genomic DNA from TNBC patient number 940


title: genomic DNA from TNBC patient number 1457


title: S523_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1026


title: genomic DNA from TNBC patient number 664


title: genomic DNA from TNBC patient number 966


title: S522_single cell rna seq by Smart Seq2


title: S520_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1021


title: S521_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 594


title: S515_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 424


title: genomic DNA from TNBC patient number 1537


title: S514_single cell rna seq by Smart Seq2


title: S529_single cell rna seq by Smart Seq2


title: S518_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 1355


title: S517_single cell rna seq by Smart Seq2


title: S510_single cell rna seq by Smart Seq2


title: S511_single cell rna seq by Smart Seq2


title: SAE3

city: xi'an

first: Shanfeng

last: Jiang

state: shaanxi

address: No. 127, West Youyi Road, Beilin District

department: School of Life Sciences

country: China

institute: Northwestern Polytechnical University

description: summeractive EDL

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Ictidomys tridecemlineatus
Supplementary files format and content: xllsx files include read count values

organism: Spermophilus dauricus

source_name: skletal muscle

extract_protocol:
RNA was extracted with AG RNAex ProRNA
RNAseq libraries were constructed by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).

value: skletal muscle

tag: cell line

value: WT

value: hibernarion


title: SAE1

description: summeractive EDL


title: S509_single cell rna seq by Smart Seq2


title: S513_single cell rna seq by Smart Seq2


title: SAS3

description: summeractive SOL


title: S519_single cell rna seq by Smart Seq2


title: S516_single cell rna seq by Smart Seq2


title: S507_single cell rna seq by Smart Seq2


title: SAE2

description: summeractive EDL


title: S506_single cell rna seq by Smart Seq2


title: S508_single cell rna seq by Smart Seq2


title: S505_single cell rna seq by Smart Seq2


title: S504_single cell rna seq by Smart Seq2


title: S502_single cell rna seq by Smart Seq2


title: S503_single cell rna seq by Smart Seq2


title: IBAS3

description: interboutarousal SOL


title: S512_single cell rna seq by Smart Seq2


title: SAS1

description: summeractive SOL


title: IBAE2

description: interboutarousal EDL


title: S501_single cell rna seq by Smart Seq2


title: IBAE1

description: interboutarousal EDL


title: S500_single cell rna seq by Smart Seq2


title: S498_single cell rna seq by Smart Seq2


title: IBAS2

description: interboutarousal SOL


title: S499_single cell rna seq by Smart Seq2


title: POSTE2

description: posthibernation EDL


title: POSTS3

description: post hibernation SOL


title: IBAS1

description: interboutarousal SOL


title: POSTE3

description: posthibernation EDL


title: POSTE1

description: posthibernation EDL


title: S491_single cell rna seq by Smart Seq2


title: POSTS2

description: post hibernation SOL


title: SAS2

description: summeractive SOL


title: S496_single cell rna seq by Smart Seq2


title: S490_single cell rna seq by Smart Seq2


title: HIBE2

description: hibernation EDL


title: S497_single cell rna seq by Smart Seq2


title: IBAE3

description: interboutarousal EDL


title: S495_single cell rna seq by Smart Seq2


title: S489_single cell rna seq by Smart Seq2


title: S493_single cell rna seq by Smart Seq2


title: S494_single cell rna seq by Smart Seq2


title: S492_single cell rna seq by Smart Seq2


title: HIBE3

description: hibernation EDL


title: HIBS2

description: hibernation SOL


title: S484_single cell rna seq by Smart Seq2


title: S486_single cell rna seq by Smart Seq2


title: HIBS3

description: hibernation SOL


title: POSTS1

description: post hibernation SOL


title: HIBS1

description: hibernation SOL


title: S487_single cell rna seq by Smart Seq2


title: PRES2

description: prehibernation SOL


title: S488_single cell rna seq by Smart Seq2


title: HIBE1

description: hibernation EDL


title: PRES3

description: prehibernation SOL


title: PREE3

description: prehibernation EDL


title: S480_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR912_5.dge.txt.gz


title: PREE2

description: prehibernation EDL


title: S485_single cell rna seq by Smart Seq2


title: PREE1

description: prehibernation EDL


title: S482_single cell rna seq by Smart Seq2


title: S483_single cell rna seq by Smart Seq2


title: S481_single cell rna seq by Smart Seq2


title: PRES1

description: prehibernation SOL


title: IR64-meiocyte-H3K27me3-1

city: Wuhan

first: feng

last: zhao

state: Hubei

address: No. 1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
Raw reads of all sequencing data were trimmed using fastp (v0.20.1)
The CUT&Tag clean reads were mapped to the rice IR64 reference genome (Qin P, Lu H, Du H, Wang H, Chen W, Chen Z, He Q, Ou S, Zhang H, Li X, Li X, Li Y, Liao Y, Gao Q, Tu B, Yuan H, Ma B, Wang Y, Qian Y, Fan S, Li W, Wang J, He M, Yin J, Li T, Jiang N, Chen X, Liang C, Li S. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell. 2021 Jun 24;184(13):3542-3558.e16. doi: 10.1016/j.cell.2021.04.046. Epub 2021 May 28. PMID: 34051138.) and the rice Azucena reference genome (Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N, Al-Bader N, Sobel-Sorenson C, Parakkal P, Arbelaez LJ, Franco N, Alexandrov N, Hamilton NRS, Leung H, Mauleon R, Lorieux M, Zuccolo A, McNally K, Zhang J, Wing RA. A platinum standard pan-genome resource that represents the population structure of Asian rice. Sci Data. 2020 Apr 7;7(1):113. doi: 10.1038/s41597-020-0438-2. PMID: 32265447; PMCID: PMC7138821.) with Bowtie2 aligner (Langmead and Salzberg, 2012).
scBS-seq clean reads are "paired-end" data, but when matching, the F and R sides are used to match the reference genome separately using Bismark (v0.22.3) software to obtain bam files. The F-side and R-side bam files were then merged and the duplicate reads were removed, and the methylation site file was obtained using Bismark software.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Duplications were removed, and uniquely mapped reads were retained for further analysis. Mean nuclear methylation levels were calculated by averaging methylation of individual cytosines in each context as described (Kim et al., 2019).
Supplementary files format and content: bigWig, narrowPeak,50bp/bin.map.gz,data analysis.xlsx
Library strategy: CUT&TAG

organism: Oryza sativa Indica Group

source_name: meiocytes

extract_protocol:
For collection of meiotic spikelets with meiocytes at prophase of meiosis I, tillers whose flag leaf auricle was about 3 cm under the auricle of the penultimate leaf were chosen and 0.4-0.6 cm long fresh spikelets were collected. Meiotic spikelets collected above were put on a clean slide. The anthers were gently dissected out and collected using dissecting needles under the dissection microscope.The anthers were put on a clean slide with 5 µl DEPC water/1× PBS added. Under an inverted microscope (with 10× objective), a 1 ml syringe needle was use to dissect one end of the anthers. Because the meiocytes at this stage produce callose, they stick together and form worm-like cell clusters. Gentle pressure was applied to the anthers to allow the separation of wormlike cell clusters from anther walls. The cell clusters were collected with capillary glass pipettes without taking any somatic cells.
scBS-seq libraries were constructed using a reported protocol (Clark et al., 2017). The library was constructed using the CUT&Tag kit (Hyperactive® Universal CUT&Tag Assay Kit for Illumina, Vazyme Biotech Co.,Ltd).

value: meiocytes

value: wild type


title: S477_single cell rna seq by Smart Seq2


title: IR64-flag_leaf-BS-seq-1

data_processing:
Raw reads of all sequencing data were trimmed using fastp (v0.20.1)
The CUT&Tag clean reads were mapped to the rice IR64 reference genome (Qin P, Lu H, Du H, Wang H, Chen W, Chen Z, He Q, Ou S, Zhang H, Li X, Li X, Li Y, Liao Y, Gao Q, Tu B, Yuan H, Ma B, Wang Y, Qian Y, Fan S, Li W, Wang J, He M, Yin J, Li T, Jiang N, Chen X, Liang C, Li S. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell. 2021 Jun 24;184(13):3542-3558.e16. doi: 10.1016/j.cell.2021.04.046. Epub 2021 May 28. PMID: 34051138.) and the rice Azucena reference genome (Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N, Al-Bader N, Sobel-Sorenson C, Parakkal P, Arbelaez LJ, Franco N, Alexandrov N, Hamilton NRS, Leung H, Mauleon R, Lorieux M, Zuccolo A, McNally K, Zhang J, Wing RA. A platinum standard pan-genome resource that represents the population structure of Asian rice. Sci Data. 2020 Apr 7;7(1):113. doi: 10.1038/s41597-020-0438-2. PMID: 32265447; PMCID: PMC7138821.) with Bowtie2 aligner (Langmead and Salzberg, 2012).
scBS-seq clean reads are "paired-end" data, but when matching, the F and R sides are used to match the reference genome separately using Bismark (v0.22.3) software to obtain bam files. The F-side and R-side bam files were then merged and the duplicate reads were removed, and the methylation site file was obtained using Bismark software.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Duplications were removed, and uniquely mapped reads were retained for further analysis. Mean nuclear methylation levels were calculated by averaging methylation of individual cytosines in each context as described (Kim et al., 2019).
Supplementary files format and content: bigWig, narrowPeak,50bp/bin.map.gz,data analysis.xlsx


title: S479_single cell rna seq by Smart Seq2


title: IR64-meiocyte-H3K4me3-1

value: H3K4me3(Abcam, #ab8580)


title: S478_single cell rna seq by Smart Seq2


title: IR64-flag_leaf-BS-seq-2


title: IR64-meiocyte-H3K27me3-2


title: SW_sr_TT_krh_rep_3

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

description: elongation zone of the taproot, medium root, thick root, dying root, grown in a container and then transferred to a rhizotron

data_processing:
Raw reads were subject to quality filtering and adapter trimming using BBDUK2
rRNA-mapped reads were discarded using Bowtie 2 and A. thaliana rRNAs as a reference
Oak transcriptome was assembled using StringTie and PM1N oak genome
Expression estimation was performed with RSEM
Supplementary_files_format_and_content: Expected_count  TPM

organism: Quercus robur

source_name: root

growth_protocol: The roots grew in the container system and rhizotrons. A variant was also used that initially developed in the container system and was then transferred to rhizotrons.

extract_protocol:
RNA was isolated from the taproot containing the meristematic zone and the elongation zone, and from the lateral roots using a commercial GeneAll kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage


title: S475_single cell rna seq by Smart Seq2


title: K562 - Ce-10-2 sh 2

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

description: genomic DNA from K562 transfected with Ce-10-2 sh

hyb_protocol: Standard Illumina Protocol by Diagenode

scan_protocol: Diagenode protocols

data_processing: Bioconductor package RnBeads v2.4.0

label: Standard Illumina

source_name: Ce-10-2 sh replicate 2

label_protocol: Standard Illumina Protocol by Diagenode

growth_protocol: K562 were grown in RPMI medium supplemented with 10% FBS

extract_protocol: Genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Cells were transfected with aptamers or control using Thermo Fisher Scientific Lipofectamine 2000 reagent  according to the manufacturer's protocol

tag: disease

value: chronic myelogenous leukemia

value: ce-10-2sh aptaDiR


title: IR64-meiocyte-H3K4me3-2


title: S471_single cell rna seq by Smart Seq2


title: SW_sr_TT_krh_rep_2

value: elongation zone of the taproot, medium root, thick root, dying root, grown in a container and then transferred to a rhizotron


title: IR64-meiocyte-BS-seq-2


title: S473_single cell rna seq by Smart Seq2


title: S476_single cell rna seq by Smart Seq2


title: IR64-meiocyte-BS-seq-1


title: S472_single cell rna seq by Smart Seq2


title: S470_single cell rna seq by Smart Seq2


title: SW_sr_TT_krh_rep_1


title: K562 - Ce-49 sh 1

description: genomic DNA from K562 transfected with Ce-49 sh

source_name: Ce-49 sh replicate 1

value: ce-49sh aptaDiR


title: S469_single cell rna seq by Smart Seq2

value: HSC


title: K562 - Ce-49 sh 2

source_name: Ce-49 sh replicate 2


title: S468_single cell rna seq by Smart Seq2


title: K562 - Ce-10-2 sh 1

source_name: Ce-10-2 sh replicate 1


title: S467_single cell rna seq by Smart Seq2


title: SW_sr_NT_rh_rep_3

description: elongation zone of the taproot, medium root, dying root, growing in rhizotron


title: SW_sr_TN_krh_rep_3

description: elongation zone of the taproot, medium root, thick root, grown in a container and then transferred to a rhizotron


title: SW_sr_TN_krh_rep_2

value: elongation zone of the taproot, medium root, thick root, grown in a container and then transferred to a rhizotron


title: SW_sr_TN_krh_rep_1


title: S465_single cell rna seq by Smart Seq2

value: MECOM KO


title: S464_single cell rna seq by Smart Seq2


title: SW_sr_NT_rh_rep_2

value: elongation zone of the taproot, medium root, dying root, growing in rhizotron


title: S463_single cell rna seq by Smart Seq2


title: K562 - control 1

description: genomic DNA from K562 transfected with control

source_name: control replicate 1

value: control


title: SW_sr_NN_rh_rep_3

description: elongation zone of the taproot, medium root, growing in rhizotron


title: S466_single cell rna seq by Smart Seq2


title: S461_single cell rna seq by Smart Seq2


title: S460_single cell rna seq by Smart Seq2


title: S459_single cell rna seq by Smart Seq2


title: S462_single cell rna seq by Smart Seq2


title: SW_sr_NN_rh_rep_2

value: elongation zone of the taproot, medium root, growing in rhizotron


title: S458_single cell rna seq by Smart Seq2


title: SW_sr_NN_kon_rep_3

description: elongation zone of raproot, medium root, growing in containers


title: SW_sr_NN_rh_rep_1


title: SW_sr_NT_rh_rep_1


title: SW_sr_NN_kon_rep_1

value: elongation zone of raproot, medium root, growing in containers


title: K562 - control 2

source_name: control  replicate 2


title: SW_sr_NN_kon_rep_2


title: SW_dl_NT_krh_rep_3

description: elongation zone of the taproot, long root, dying root, grown in a container and then transferred to a rhizotron


title: S457_single cell rna seq by Smart Seq2


title: S456_single cell rna seq by Smart Seq2


title: S455_single cell rna seq by Smart Seq2


title: S454_single cell rna seq by Smart Seq2


title: S453_single cell rna seq by Smart Seq2


title: SW_dl_NT_krh_rep_1

value: elongation zone of the taproot, long root, dying root, grown in a container and then transferred to a rhizotron


title: SW_dl_NT_kon_rep_3

description: elongation zone of the taproot, long root, dying root, growing in containers


title: S452_single cell rna seq by Smart Seq2


title: S451_single cell rna seq by Smart Seq2


title: SW_dl_NT_kon_rep_1

value: elongation zone of the taproot, long root, dying root, growing in containers


title: S447_single cell rna seq by Smart Seq2


title: S449_single cell rna seq by Smart Seq2


title: S450_single cell rna seq by Smart Seq2


title: S448_single cell rna seq by Smart Seq2


title: S443_single cell rna seq by Smart Seq2


title: SW_dl_NN_rh_rep_2

description: elongation zone of the taproot, long root, growing in rhizotron


title: SW_dl_NN_krh_rep_3

description: elongation zone of the taproot, long root, grown in a container and then transferred to a rhizotron


title: SW_dl_NN_kon_rep_3

description: elongation zone of the taproot, long root, growing in containers


title: SW_dl_NN_kon_rep_1

value: elongation zone of the taproot, long root, growing in containers


title: SW_dl_NN_krh_rep_1

value: elongation zone of the taproot, long root, grown in a container and then transferred to a rhizotron


title: SW_dl_NN_rh_rep_1

value: elongation zone of the taproot, long root, growing in rhizotron


title: S446_single cell rna seq by Smart Seq2


title: S440_single cell rna seq by Smart Seq2


title: S442_single cell rna seq by Smart Seq2


title: KB_sr_TT_krh_rep_3

description: lateral root, medium root, thick root, dying root, grown in a container and then transferred to a rhizotron


title: SW_dl_NN_rh_rep_3


title: S444_single cell rna seq by Smart Seq2


title: SW_dl_NN_krh_rep_2


title: KB_sr_TT_krh_rep_1

value: lateral root, medium root, thick root, dying root, grown in a container and then transferred to a rhizotron


title: SW_dl_NT_kon_rep_2


title: SW_dl_NT_krh_rep_2


title: KB_sr_NN_rh_rep_2

description: lateral root, medium root, growing in rhizotron


title: S439_single cell rna seq by Smart Seq2


title: SW_dl_NN_kon_rep_2


title: KB_sr_TT_krh_rep_2


title: S474_single cell rna seq by Smart Seq2


title: KB_sr_NN_rh_rep_3

value: lateral root, medium root, growing in rhizotron


title: S445_single cell rna seq by Smart Seq2


title: S437_single cell rna seq by Smart Seq2


title: S436_single cell rna seq by Smart Seq2


title: S433_single cell rna seq by Smart Seq2


title: S432_single cell rna seq by Smart Seq2


title: KB_sr_NN_kon_rep_3

description: lateral root, medium root, growing in containers


title: KB_sr_NN_kon_rep_2

value: lateral root, medium root, growing in containers


title: KB_sr_NN_rh_rep_1


title: KB_sr_NN_kon_rep_1


title: S441_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR912_5.dge.txt.gz


title: S438_single cell rna seq by Smart Seq2


title: KB_dl_NT_kon_rep_2

description: lateral root, long root, dying root, growing in containers


title: S431_single cell rna seq by Smart Seq2


title: S434_single cell rna seq by Smart Seq2


title: S427_single cell rna seq by Smart Seq2


title: KB_dl_NN_rh_rep_3

description: lateral root, long root, growing in rhizotron


title: KB_dl_NN_rh_rep_2

value: lateral root, long root, growing in rhizotron


title: KB_dl_NN_rh_rep_1


title: S435_single cell rna seq by Smart Seq2


title: S429_single cell rna seq by Smart Seq2


title: KB_dl_NN_krh_rep_3

description: lateral root, long root, grown in a container and then transferred to a rhizotron


title: S428_single cell rna seq by Smart Seq2


title: S430_single cell rna seq by Smart Seq2


title: KB_dl_NN_krh_rep_2

value: lateral root, long root, grown in a container and then transferred to a rhizotron


title: S425_single cell rna seq by Smart Seq2

value: HSC


title: S426_single cell rna seq by Smart Seq2


title: KB_dl_NN_krh_rep_1


title: S424_single cell rna seq by Smart Seq2


title: S423_single cell rna seq by Smart Seq2


title: KB_dl_NN_kon_rep_3

description: lateral root, long root, growing in containers


title: KB_dl_NT_kon_rep_1

value: lateral root, long root, dying root, growing in containers


title: KB_dl_NN_kon_rep_2

value: lateral root, long root, growing in containers


title: S422_single cell rna seq by Smart Seq2

value: MECOM KO


title: KB_dl_NN_kon_rep_1


title: K_sr_TT_rh_rep_2

description: meristematic zone of the taproot, medium root, thick root, dying root, growing in rhizotron


title: S415_single cell rna seq by Smart Seq2


title: S418_single cell rna seq by Smart Seq2


title: K_sr_NN_rh_rep_3

description: meristematic zone of the taproot, medium root, growing in rhizotron


title: K_sr_TT_krh_rep_3

description: meristemaric zone of the taproot, medium root, thick root, dying root, grown in a container and then transferred to a rhizotron


title: S419_single cell rna seq by Smart Seq2


title: S413_single cell rna seq by Smart Seq2


title: K_sr_NN_rh_rep_2

value: meristematic zone of the taproot, medium root, growing in rhizotron


title: S420_single cell rna seq by Smart Seq2


title: S416_single cell rna seq by Smart Seq2


title: S414_single cell rna seq by Smart Seq2


title: K_sr_TT_krh_rep_2

value: meristemaric zone of the taproot, medium root, thick root, dying root, grown in a container and then transferred to a rhizotron


title: K_sr_TT_rh_rep_1

value: meristematic zone of the taproot, medium root, thick root, dying root, growing in rhizotron


title: S412_single cell rna seq by Smart Seq2


title: K_sr_NN_krh_rep_3

description: meristematic zone of the taproot, medium root, grown in a container and then transferred to a rhizotron


title: K_sr_NN_krh_rep_2

value: meristematic zone of the taproot, medium root, grown in a container and then transferred to a rhizotron


title: S411_single cell rna seq by Smart Seq2


title: S410_single cell rna seq by Smart Seq2


title: K_sr_TT_rh_rep_3


title: S421_single cell rna seq by Smart Seq2


title: S417_single cell rna seq by Smart Seq2


title: K_sr_TT_krh_rep_1


title: S409_single cell rna seq by Smart Seq2


title: K_sr_NN_krh_rep_1


title: KB_dl_NT_kon_rep_3


title: K_sr_NN_kon_rep_3

description: meristematic zone of the taproot, medium root, growing in containers


title: K_sr_NN_rh_rep_1


title: K_sr_NN_kon_rep_2

value: meristematic zone of the taproot, medium root, growing in containers


title: K_sr_NN_kon_rep_1


title: K_kr_NN_rh_rep_3

description: meristematic zone of the taproot, short root, growing in rhizotron


title: S407_single cell rna seq by Smart Seq2


title: S405_single cell rna seq by Smart Seq2


title: S406_single cell rna seq by Smart Seq2


title: S404_single cell rna seq by Smart Seq2


title: S403_single cell rna seq by Smart Seq2


title: S402_single cell rna seq by Smart Seq2


title: S401_single cell rna seq by Smart Seq2


title: K_kr_NN_krh_rep_2

description: meristematic zone of the taproot, short root, grown in a container and then transferred to a rhizotron


title: K_kr_NN_krh_rep_1

value: meristematic zone of the taproot, short root, grown in a container and then transferred to a rhizotron


title: S399_single cell rna seq by Smart Seq2


title: K_kr_NN_krh_rep_3


title: K_kr_NN_kon_rep_2

description: meristematic zone of the taproot, short root, growing in containers


title: S400_single cell rna seq by Smart Seq2


title: K_kr_NN_kon_rep_3

value: meristematic zone of the taproot, short root, growing in containers


title: S408_single cell rna seq by Smart Seq2


title: K_kr_NN_rh_rep_1

value: meristematic zone of the taproot, short root, growing in rhizotron


title: S397_single cell rna seq by Smart Seq2


title: K_kr_NN_rh_rep_2


title: S396_single cell rna seq by Smart Seq2


title: S395_single cell rna seq by Smart Seq2


title: K_dl_NT_krh_rep_3

description: meristematic zone of the taproot, long root, grown in a container and then transferred to a rhizotron


title: S398_single cell rna seq by Smart Seq2


title: K_kr_NN_kon_rep_1


title: K_dl_NT_kon_rep_3

description: meristematic zone of the taproot, long root, dying root, growing in containers


title: S394_single cell rna seq by Smart Seq2


title: K_dl_NT_krh_rep_2

value: meristematic zone of the taproot, long root, grown in a container and then transferred to a rhizotron


title: S393_single cell rna seq by Smart Seq2


title: K_dl_NT_krh_rep_1


title: S392_single cell rna seq by Smart Seq2


title: K_dl_NT_kon_rep_1

value: meristematic zone of the taproot, long root, dying root, growing in containers


title: K_dl_NT_kon_rep_2


title: K_dl_NN_rh_rep_3

description: meristematic zone of the taproot, long root, growing in rhizotron


title: S390_single cell rna seq by Smart Seq2


title: K_dl_NN_rh_rep_2

value: meristematic zone of the taproot, long root, growing in rhizotron


title: S387_single cell rna seq by Smart Seq2


title: S388_single cell rna seq by Smart Seq2


title: K_dl_NN_krh_rep_3


title: S386_single cell rna seq by Smart Seq2


title: K_dl_NN_rh_rep_1


title: K_dl_NN_krh_rep_2


title: K_dl_NN_krh_rep_1


title: S385_single cell rna seq by Smart Seq2


title: K_dl_NN_kon_rep_3

description: meristematic zone of the taproot, long root, growing in containers


title: S384_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR912_5.dge.txt.gz


title: K_dl_NN_kon_rep_2

value: meristematic zone of the taproot, long root, growing in containers


title: K_dl_NN_kon_rep_1


title: S391_single cell rna seq by Smart Seq2


title: S382_single cell rna seq by Smart Seq2


title: S383_single cell rna seq by Smart Seq2


title: S381_single cell rna seq by Smart Seq2


title: 3KB_dl_NN_kon_rep_3

description: Third harvest date – 8-weeks old plant, lateral root, long root, growing in containers


title: S380_single cell rna seq by Smart Seq2


title: S389_single cell rna seq by Smart Seq2


title: S379_single cell rna seq by Smart Seq2


title: S378_single cell rna seq by Smart Seq2


title: 3KB_dl_NN_kon_rep_2

value: Third harvest date – 8-weeks old plant, lateral root, long root, growing in containers


title: 3K_dl_TN_rh_rep_1

description: Third harvest date – 8-weeks old plant, meristematic zone of the taproot, long root, thick root, growing in rhizotron


title: 3KB_dl_NN_kon_rep_1


title: S376_single cell rna seq by Smart Seq2

value: HSC


title: 3K_dl_TN_rh_rep_3

value: Third harvest date – 8-weeks old plant, meristematic zone of the taproot, long root, thick root, growing in rhizotron


title: 3K_dl_TN_rh_rep_2


title: 3K_dl_TN_kon_rep_3

description: Third harvest date – 8-weeks old plant, meristematic zone of the taproot, long root, thick root, growing in containers


title: S373_single cell rna seq by Smart Seq2


title: S375_single cell rna seq by Smart Seq2


title: 3K_dl_TN_kon_rep_2

value: Third harvest date – 8-weeks old plant, meristematic zone of the taproot, long root, thick root, growing in containers


title: 3K_dl_NN_rh_rep_3

description: Third harvest date – 8-weeks old plant, meristematic zone of the taproot, long root, growing in rhizotron


title: 3K_dl_TN_kon_rep_1


title: 3K_dl_NN_rh_rep_2

value: Third harvest date – 8-weeks old plant, meristematic zone of the taproot, long root, growing in rhizotron


title: 3K_dl_NN_rh_rep_1


title: S369_single cell rna seq by Smart Seq2

value: MECOM KO


title: S370_single cell rna seq by Smart Seq2


title: 3K_dl_NN_kon_rep_3

description: Third harvest date – 8-weeks old plant, meristematic zone of the taproot, long root, growing in containers


title: 3K_dl_NN_kon_rep_2

value: Third harvest date – 8-weeks old plant, meristematic zone of the taproot, long root, growing in containers


title: 3K_dl_NN_kon_rep_1


title: S368_single cell rna seq by Smart Seq2


title: S367_single cell rna seq by Smart Seq2


title: 2KB_sr_TN_rh_rep_3

description: Second harvest date - 8-weeks old plant, lateral root, medium root, thick root, growing in rhizotron


title: S363_single cell rna seq by Smart Seq2


title: S366_single cell rna seq by Smart Seq2


title: 2KB_sr_TN_rh_rep_1

value: Second harvest date - 8-weeks old plant, lateral root, medium root, thick root, growing in rhizotron


title: S374_single cell rna seq by Smart Seq2


title: 2KB_sr_TN_kon_rep_2

description: Second harvest date - 8-weeks old plant, lateral root, medium root, thick root, growing in containers


title: S364_single cell rna seq by Smart Seq2


title: 2KB_sr_TN_kon_rep_3

value: Second harvest date - 8-weeks old plant, lateral root, medium root, thick root, growing in containers


title: S371_single cell rna seq by Smart Seq2


title: 2KB_sr_TN_rh_rep_2


title: S362_single cell rna seq by Smart Seq2


title: S365_single cell rna seq by Smart Seq2


title: 2KB_sr_TN_kon_rep_1


title: S372_single cell rna seq by Smart Seq2


title: S377_single cell rna seq by Smart Seq2


title: 2KB_sr_NN_rh_rep_3

description: Second harvest date - 8-weeks old plant, lateral root, medium root, growing in rhizotron


title: S361_single cell rna seq by Smart Seq2


title: S359_single cell rna seq by Smart Seq2


title: 2KB_sr_NN_rh_rep_2

value: Second harvest date - 8-weeks old plant, lateral root, medium root, growing in rhizotron


title: 2KB_sr_NN_rh_rep_1


title: S360_single cell rna seq by Smart Seq2


title: S358_single cell rna seq by Smart Seq2


title: 2KB_sr_NN_kon_rep_1

description: Second harvest date - 8-weeks old plant, lateral root, medium root, growing in containers


title: S356_single cell rna seq by Smart Seq2


title: S355_single cell rna seq by Smart Seq2


title: 2KB_sr_NN_kon_rep_2

value: Second harvest date - 8-weeks old plant, lateral root, medium root, growing in containers


title: 2KB_sr_NN_kon_rep_3


title: 2KB_dl_NN_rh_rep_3

description: Second harvest date - 8-weeks old plant, lateral root, long root, growing in rhizotron


title: 2KB_dl_NN_kon_rep_3

description: Second harvest date - 8-weeks old plant, lateral root, long root, growing in containers


title: 2KB_dl_NN_rh_rep_2

value: Second harvest date - 8-weeks old plant, lateral root, long root, growing in rhizotron


title: 2KB_dl_NN_kon_rep_1

value: Second harvest date - 8-weeks old plant, lateral root, long root, growing in containers


title: S357_single cell rna seq by Smart Seq2


title: 2KB_dl_NN_rh_rep_1


title: S351_single cell rna seq by Smart Seq2


title: S352_single cell rna seq by Smart Seq2


title: 2KB_dl_NN_kon_rep_2


title: S353_single cell rna seq by Smart Seq2


title: S350_single cell rna seq by Smart Seq2


title: S349_single cell rna seq by Smart Seq2


title: S348_single cell rna seq by Smart Seq2


title: 2K_sr_TN_kon_rep_1

description: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, medium root, thick root, growing in containers


title: S347_single cell rna seq by Smart Seq2


title: S345_single cell rna seq by Smart Seq2


title: S354_single cell rna seq by Smart Seq2


title: S344_single cell rna seq by Smart Seq2


title: 2K_sr_NT_rh_rep_3

description: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, medium root, dying root, growing in rhizotron


title: 2K_sr_NT_rh_rep_2

value: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, medium root, dying root, growing in rhizotron


title: 2K_sr_NT_rh_rep_1


title: S342_single cell rna seq by Smart Seq2


title: 2K_sr_NN_rh_rep_1

description: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, medium root, growing in rhizotron


title: S341_single cell rna seq by Smart Seq2


title: 2K_sr_NN_rh_rep_2

value: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, medium root, growing in rhizotron


title: 2K_sr_NN_rh_rep_3


title: 2K_sr_TN_kon_rep_3

value: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, medium root, thick root, growing in containers


title: S339_single cell rna seq by Smart Seq2


title: 2K_sr_NN_kon_rep_3

description: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, medium root, growing in containers


title: 2K_kr_NN_kon_rep_3

description: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, short root, growing in containers


title: 2K_sr_NN_kon_rep_1

value: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, medium root, growing in containers


title: 2K_sr_TN_kon_rep_2


title: 2K_kr_NN_kon_rep_1

value: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, short root, growing in containers


title: S334_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR912_5.dge.txt.gz

value: HSC


title: 2K_sr_NN_kon_rep_2


title: S336_single cell rna seq by Smart Seq2


title: S337_single cell rna seq by Smart Seq2


title: S338_single cell rna seq by Smart Seq2


title: S335_single cell rna seq by Smart Seq2


title: S332_single cell rna seq by Smart Seq2


title: 2K_kr_NN_kon_rep_2


title: S343_single cell rna seq by Smart Seq2


title: S346_single cell rna seq by Smart Seq2


title: S331_single cell rna seq by Smart Seq2


title: 2K_dl_NT_kon_rep_1

description: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, long root, dying root, growing in containers


title: S333_single cell rna seq by Smart Seq2


title: 2K_dl_NT_kon_rep_3

value: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, long root, dying root, growing in containers


title: S340_single cell rna seq by Smart Seq2


title: 2K_dl_NT_kon_rep_2


title: 2K_dl_NN_rh_rep_2

description: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, long root, growing in rhizotron


title: 2K_dl_NN_rh_rep_1

value: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, long root, growing in rhizotron


title: S328_single cell rna seq by Smart Seq2


title: S329_single cell rna seq by Smart Seq2


title: 2K_dl_NN_kon_rep_2

description: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, long root, growing in containers


title: S326_single cell rna seq by Smart Seq2


title: 2K_dl_NN_kon_rep_3

value: Second harvest date - 8-weeks old plant, meristematic zone of the taproot, long root, growing in containers


title: S327_single cell rna seq by Smart Seq2

value: MECOM KO


title: S324_single cell rna seq by Smart Seq2


title: S325_single cell rna seq by Smart Seq2


title: 2K_dl_NN_kon_rep_1


title: S323_single cell rna seq by Smart Seq2


title: 1KB_sr_NN_kon_rep_1

description: First harvest date - 7-weeks old plant, lateral root, medium root, growing in containers


title: 1KB_sr_NN_kon_rep_2

value: First harvest date - 7-weeks old plant, lateral root, medium root, growing in containers


title: 2K_dl_NN_rh_rep_3


title: S321_single cell rna seq by Smart Seq2


title: S322_single cell rna seq by Smart Seq2


title: 1KB_dl_NN_kon_rep_2

description: First harvest date - 7-weeks old plant, lateral root, long root, growing in containers


title: 1KB_sr_NN_kon_rep_3


title: S320_single cell rna seq by Smart Seq2


title: S319_single cell rna seq by Smart Seq2


title: S330_single cell rna seq by Smart Seq2


title: 1K_sr_NN_kon_rep_2

description: First harvest date - 7-weeks old plant, meristematic zone of the taproot, medium root, growing in containers


title: 1KB_dl_NN_kon_rep_3

value: First harvest date - 7-weeks old plant, lateral root, long root, growing in containers


title: 1K_sr_NN_kon_rep_3

value: First harvest date - 7-weeks old plant, meristematic zone of the taproot, medium root, growing in containers


title: 1KB_dl_NN_kon_rep_1


title: S318_single cell rna seq by Smart Seq2


title: 1K_sr_NN_kon_rep_1


title: S316_single cell rna seq by Smart Seq2


title: S317_single cell rna seq by Smart Seq2


title: 1K_kr_NN_kon_rep_3

description: First harvest date - 7-weeks old plant, meristematic zone of the taproot, short root, growing in containers


title: 1K_kr_NN_kon_rep_2

value: First harvest date - 7-weeks old plant, meristematic zone of the taproot, short root, growing in containers


title: S314_single cell rna seq by Smart Seq2


title: S315_single cell rna seq by Smart Seq2


title: S312_single cell rna seq by Smart Seq2


title: S313_single cell rna seq by Smart Seq2


title: S311_single cell rna seq by Smart Seq2


title: S309_single cell rna seq by Smart Seq2


title: 1K_dl_NN_kon_rep_2


title: S310_single cell rna seq by Smart Seq2


title: 1K_dl_NN_kon_rep_3


title: 1K_dl_NT_kon_rep_2

description: First harvest date - 7-weeks old plant, meristematic zone of the taproot, long root, dying root, growing in containers


title: S307_single cell rna seq by Smart Seq2


title: S306_single cell rna seq by Smart Seq2


title: 1K_kr_NN_kon_rep_1


title: S305_single cell rna seq by Smart Seq2


title: S304_single cell rna seq by Smart Seq2


title: 1K_dl_NT_kon_rep_3

value: First harvest date - 7-weeks old plant, meristematic zone of the taproot, long root, dying root, growing in containers


title: S302_single cell rna seq by Smart Seq2


title: 1K_dl_NT_kon_rep_1


title: S301_single cell rna seq by Smart Seq2


title: 1K_dl_NN_kon_rep_1


title: S303_single cell rna seq by Smart Seq2


title: THP1, control 1

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

data_processing:
Salmon v0.11.2 was used to quantify gene expression using  a transcriptome index built from GENCODE v27.
Read counts were imported to DESeq2 for differential expression analysis. Pre-filtering excluded genes with <10 total counts across all samples.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file showing raw counts from Salmon output. Genes were filtered as described above. Column names correspond to library names.

molecule: polyA RNA

growth_protocol: THP1 were differentiated to macrophages using 100ng/mL phorbal-12-myristate-13-acetate (PMA; Sigma-Aldrich, P8139) for 24 hours in RPMI 1640+10%FBS, followed by 24-hour incubation with 20 ng/mL IL-4.

extract_protocol:
RNA from RP11-184M15.1 siRNA and control samples were extracted using Quick-RNA kit (Zymo Research; R1054).
Poly-A libraries were constructed following manufacturer's protocols.

value: WT

value: PMA differentiation

tag: time

value: 24 hours


title: THP1, RP11-184M15.1 siRNA KD3

treatment_protocol: THP1 were differentiated to macrophages using 100ng/mL phorbal-12-myristate-13-acetate (PMA; Sigma-Aldrich, P8139) for 24 hours in RPMI 1640+10%FBS, followed by 24-hour incubation with 20 ng/mL IL-4.

value: RP11-184M15.1 knockdown


title: THP1, control 3


title: THP1, control 2


title: THP1, RP11-184M15.1 siRNA KD2


title: THP1, RP11-184M15.1 siRNA KD1


title: S299_single cell rna seq by Smart Seq2


title: S300_single cell rna seq by Smart Seq2


title: S298_single cell rna seq by Smart Seq2


title: S308_single cell rna seq by Smart Seq2


title: S296_single cell rna seq by Smart Seq2


title: S297_single cell rna seq by Smart Seq2


title: S295_single cell rna seq by Smart Seq2


title: S294_single cell rna seq by Smart Seq2


title: C9ORF72 ALS iMNs treated with SYF2 siRNA-2 replicate 1

city: Los Angeles

first: Justin

last: Ichida

state: CA

address: 1425 San Pablo Street, BCC 209

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

data_processing:
Reads were aligned to the hg38 transcriptome using aligner STAR (v.2.7.8).
A gene count table was obtained using Partek E/M with Partek® Flow® software, v10.0
Differential expression analysis was performed using DESeq2 (v.1.18.1).
Pathway enirchment analysis was performed using Ingenuity Pathway Analysis (Qiagen)
Computations were performed on the High Performing-Computing Cluster supported by the University of Southern California.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized count values for each sample

source_name: neural

growth_protocol: Glia-free induced motor neurons were cultured in N3 medium.

extract_protocol:
RNA was extracted using QIAGEN RNeasy Kits according to the manufacturer's instructions.
3'-Digital Gene Expression RNAseq Library Kit (3’-DGE)
3' RNA-seq libraries were generated using the3'-Digital Gene Expression RNAseq Library Kit at Novogene Ltd, according to the manufacturers’ directions. Libraries were sequenced at the Novogene on a Illumina NovaSeq 6000 sequencer. A total of 20 million to 30 million 150-bp, paired-end reads were obtained for samples.

treatment_protocol: A lentiviral expression of NGN2, ISL1, LHX3 drives the conversion of induced motor neurons, 3 nM siRNA targetting SYF2 (or a scrambled siRNA) control was added with RNAiMAX.

value: neural

value: induced neurons

value: motor neurons

value: SYF2 siRNA-2


title: C9ORF72 isogenic control iMNs treated with scrambled siRNA replicate 2

value: C9ORF72 isogenic

value: scrambled siRNA


title: C9ORF72 isogenic control iMNs treated with scrambled siRNA replicate 1


title: C9ORF72 ALS iMNs treated with SYF2 siRNA-2 replicate 2


title: C9ORF72 isogenic control iMNs treated with SYF2 siRNA-2 replicate 1


title: C9ORF72 isogenic control iMNs treated with SYF2 siRNA-1 replicate 2

value: SYF2 siRNA-1


title: C9ORF72 ALS iMNs treated with SYF2 siRNA-1 replicate 2


title: S292_single cell rna seq by Smart Seq2

value: HSC

value: MECOM KO


title: C9ORF72 isogenic control iMNs treated with SYF2 siRNA-1 replicate 1


title: S293_single cell rna seq by Smart Seq2


title: C9ORF72 ALS iMNs treated with SYF2 siRNA-1 replicate 1


title: C9ORF72 isogenic control iMNs treated with SYF2 siRNA-2 replicate 2


title: C9ORF72 ALS induced motor neurons (iMNs) treated with scrambled siRNA replicate 1


title: C9ORF72 ALS iMNs treated with scrambled siRNA replicate 2


title: S288_single cell rna seq by Smart Seq2

description:
single cell SS2 for AAVS1 KO
ss2_processed.tar
ss2_processed.tar/AAVS912_2.dge.txt.gz

value: AAVS1 KO


title: S287_single cell rna seq by Smart Seq2


title: S286_single cell rna seq by Smart Seq2


title: hPSC-derived CMs treated with siPAX9-2

city: La Jolla

first: Georg

last: Vogler

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
nextflow run nf-core/rnaseq -r 3.0 -profile docker -params-file nf-params.json -resume
see execution_report.html and pipeline_report.txt
Differential gene expression for both knockdown conditions were determined using DESeq2 (script files: "DESeq2 Perrin VCM EGR2.R" and  "DESeq2 Perrin VCM PAX9.R")
Assembly: GRCh37
Supplementary files format and content: ENSG gene names and raw read counts per gene for each condition and replicate.

source_name: cardiomyocyte

extract_protocol:
Cells were pelleted and resuspended in 500µl TRIzol reagent followed by total RNA extraction using Qiagen RNAeasy Mini Kit.
Illumina stranded mRNA; 100ng RNA input - 13 cycles in amp step

treatment_protocol: hPSC-derived CMs were transfected with 25nM final concentrations of siRNA against EGR2, PAX9 and with scrambled control siRNAs.

tag: sirna

value: cardiomyocyte

value: PAX9 knockdown


title: hPSC-derived CMs treated with siEGR2-3

value: EGR2 knockdown


title: hPSC-derived CMs treated with siPAX9-3


title: S285_single cell rna seq by Smart Seq2


title: hPSC-derived CMs treated with siEGR2-2


title: S284_single cell rna seq by Smart Seq2


title: S290_single cell rna seq by Smart Seq2


title: S291_single cell rna seq by Smart Seq2


title: S289_single cell rna seq by Smart Seq2


title: hPSC-derived CMs treated with siCTRL-2

value: siControl

value: WT

value: siCTRL


title: hPSC-derived CMs treated with siCTRL-3


title: hPSC-derived CMs treated with siCTRL-1


title: S283_single cell rna seq by Smart Seq2


title: Azucena-flag_leaf-BS-seq-2

organism: Oryza sativa Japonica Group

value: wild type


title: S282_single cell rna seq by Smart Seq2


title: HCT116 DICER R1003Q rescue AQ-seq (dataset II) replicate 1

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: AQ-seq

data_processing:
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the mouse genome (mm10) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Assembly: hg38
Supplementary files format and content: Tab-separated values (tsv) files containing sequence variants and corresponding read counts.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Total RNAs were subjected to AQ-seq (Kim et al., 2019) except that 100 µg of total RNAs were used for library construction, and that cDNAs were amplified with NEBNext Ultra II Q5 Master Mix (NEB). The libraries were sequenced on the NovaSeq 6000 platform.


title: S278_single cell rna seq by Smart Seq2


title: S279_single cell rna seq by Smart Seq2


title: hPSC-derived CMs treated with siPAX9-1


title: S281_single cell rna seq by Smart Seq2


title: HCT116 DICER R1003Q rescue AQ-seq (dataset II) replicate 2

description: AQ-seq


title: HCT116 DICER R1855L rescue AQ-seq (dataset II) replicate 1

description: AQ-seq


title: HCT116 DICER R821H rescue AQ-seq (dataset II) replicate 1

description: AQ-seq


title: S280_single cell rna seq by Smart Seq2


title: HCT116 DICER R1855L rescue AQ-seq (dataset II) replicate 2

description: AQ-seq


title: S277_single cell rna seq by Smart Seq2


title: Azucena-flag_leaf-BS-seq-1


title: HCT116 DICER R821H rescue AQ-seq (dataset II) replicate 2

description: AQ-seq


title: S276_single cell rna seq by Smart Seq2


title: Azucena-meiocyte-H3K27me3-1

value: meiocytes


title: 293T-CUT-Tag-invivo-Hemin-PDS

first: Yin

last: Zhinang

address: Donghu road 185

institute: Wuhan University

description: CUT&Tag analysis with anti-biotin antibody

data_processing:
Assembly: Homo sapiens .hg38
Library normalized bigWig files were provided for all samples

source_name: Derived from embryonic kidney

growth_protocol: HEK293T and HeLa were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, LONSERA). Drosophila S2 cells were obtained from Invitrogen and maintained in Schneider's medium. Mouse embryonic fibroblasts (MEF) cells were grown in DMEM with 10% FBS. All cells were cultured at 37°C with 5% CO 2 . Cells were confirmed to be mycoplasma negative using MycoBlue Mycoplasma Detector (Vazyme, D101-01). Live cells were quantified using a TC20 automated cell counter (Bio-Rad).

extract_protocol:
Following Hemin treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer’s instructions.
Biotin-PEG4-Hemin was combined with the Tn5-based CUT&Tag strategy to identify Hemin binding sites in the genome. Briefly, one million HEK293T  cells were resuspended in NE1 buffer (20 mM HEPES at pH 7.9, 10 mM KCl, 0.5 mM spermidine,0.1% Triton X-100, 20% Glycerol, 1× protease inhibitors) and incubated on ice for 10 minutes. After centrifugation at 1, 300 g for 10 minutes, nuclei were isolated and collected. These nuclei were washed once with PBS and resuspended with 100 μL of wash buffer (20 mM HEPES at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors). 10 μL pre-activated concanavalin A coated magnetic beads (Smart-Lifesciences) were added to these nuclei and incubated on a rotator for 10 minutes at room temperature. The supernatant was removed and bead-bound nuclei were resuspended in 100 μL of dig-wash buffer (0.05% digitonin, 20 mM HEPES at pH 7.5,150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors) containing 2 mM EDTA.Biotin-PEG4-Hemin was added to the sample and rotated overnight at 4°C in the dark.For the control sample, biotin-PEG4-hydrazide was used to replace biotin-PEG4-Hemin. These nuclei were washed three times in 200 μL of dig-wash buffer to remove unbound biotin-PEG4-Hemin or biotin-PEG4-hydrazide. Then anti-biotin rabbit mAb was diluted 100-fold in 100 μL of dig-wash buffer with 2 mM EDTA and was added to the nuclei with one-hour rotation at room temperature in the dark. After washing once with dig-wash buffer, these nuclei were resuspended with 100 μL of dig-wash buffer with 2 mM EDTA and 1 μL of mouse anti-rabbit IgG, incubated for another one hour at room temperature in the dark, and washed three times with dig-wash buffer. A 1:250 dilution of pA-Tn5 adapter complex (~0.2 μM) was prepared in 100 μL of dig-300 buffer (0.05% digitonin, 20 mM HEPES at pH 7.5, 300 mM KCl, 0.5 mM spermidine, 1× protease inhibitors) and added to the nuclei followed by one-hour rotation at room temperature in the dark. After five washes with dig-300 buffer, the bead-bound nuclei were resuspended with 40 μL of tagmentation buffer (10 mM TAPS-NaOH at pH 8.5, 10 mM MgCl 2 , 7.5% DMF) and incubated at 37°C for one hour. To terminate the tagmentation reaction, 1.5 μL of 0.5 M EDTA, 0.5 μL of 10% SDS and 1 μL of 20 mg/mL proteinase K were added and incubated at 55°C for 1 hour and then for 15 minutes at 75°C. The DNA was extracted with Sera-Mag carboxylate-modified magnetic beads (GE Healthcare) for library preparation. 21 μL DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, and amplified with NEB Q5 high- fidelity 2× master mix. The libraries were purified with 0.56-0.85× volume of Sera- Mag carboxylate-modified magnetic beads and subjected to the Bioanalyzer DNA analysis and Illumina sequencing.
CUT&Tag
G4-CUT&Tag and R-loop CUT&Tag reads were aligned to the human genome (UCSC hg38) and Escherichia coli genome with Bowtie2 version 2.2.6 [61], using parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The aligned reads were normalized with total reads aligned (reads per million, r.p.m.) and spiked-in E.coli reads.

treatment_protocol: Following Hemin treatment for 2 hours or 6 hours, cells were collected.

value: Derived from embryonic kidney

value: Human embryonic kidney

value: treated with Hemin for 2 hours and PDS 2 hours


title: HCT116 DICER Wild-Type rescue AQ-seq (dataset II) replicate 1

description: AQ-seq


title: hPSC-derived CMs treated with siEGR2-1


title: S275_single cell rna seq by Smart Seq2


title: Azucena-meiocyte-H3K4me3-2

value: H3K4me3(Abcam, #ab8580)


title: EndoC-βH1 – Replicate 3 – Control

city: Anderlecht

first: Florian

last: Szymczak

state: Brussels

address: Route de Lennik 808 - CP618

department: Faculty of Medicine

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Reads were quality checked with fastp to excluse reads of poor quality and remove remaining adapters.
Gene expression was quantified in TPM (Transcripts per Millions) using Salmon v1.3  with additional parameters “--seqBias --gcBias --validateMappings”.
We used GENCODE v35  as the reference genome and indexed it with default k-mer values. Differential Gene Expression (DGE) analysis was performed with DESeq2 v1.30.1
Assembly: GENCODE v35 (GRCh38.p13)
Supplementary files format and content: Comma Separated Values (CSV) file containing TPM values at the gene level

extract_protocol:
Total RNA was purified from EndoC-βH1 and EndoC-βH1/ADAR1 cells using the Nucleospin miRNA Kit (Bioke) according to the manufacturer’s guidelines. RNA quality was determined by Experion RNA StdSens 1K Analysis Kit (Bio-Rad, product number 7007103) on a Experion Automated Electrophoresis System (Bio-Rad) following the manufacturer’s protocol.
Strand-specific bulk RNA sequencing was performed on a NovaSeq 6000 (2x150 paired-end with a depth of >150 million reads) by Eurofins Genomics Europe Sequencing GmbH (Kontanz, Germanty).

value: Control


title: EndoC-βH1 – Replicate 2 – Control


title: Azucena-meiocyte-H3K27me3-2


title: S274_single cell rna seq by Smart Seq2


title: EndoC-βH1 – Replicate 3 – ADAR overexpression

value: ADAR overexpression


title: EndoC-βH1 – Replicate 1 – ADAR overexpression


title: Azucena-meiocyte-H3K4me3-1


title: 476_wound

city: Indianapolis

first: Julie

last: Brothwell

state: IN

address: 635 Barnhill Dr., MS420

department: Department of Microbiology & Immunology

institute: Indiana University

data_processing:
Basecalling was performed with Illumina RTA v3.4.4 and bcl2fastq v2.20.
Sequenced reads were aligned to the Haemophilus ducreyi 35000HP genome (AE017143.1) using Bowtie2 or human genome (hg38) using STAR.
Human reads in pustule samples were subsampled to 125 million reads. H. ducreyi reads in cultures were subsampled to 1 million reads.
Count matricies were made for human and H. ducreyi reads using featureCounts.
Library normalization and statistical analysis was performed in R v4.1.0 with the DESeq2 package.
Assembly: hg38; AE017143.1
Supplementary files format and content: txt file for the count matrix of the 12 H. ducreyi samples from this study and the reanalyzed samples from 8 H. ducreyi samples from GSE130901
Supplementary files format and content: txt file for the count matrix of the 16 human samples from this study and the reanalyzed samples from 8 human samples from GSE130901

source_name: skin

growth_protocol: The inocula consisted of H. ducreyi cultured in GC broth supplemented with 1% IsoVitaleX, 50 𝜇g/mL hemin, and 5% heat-inactivated fetal bovine serum and shaken at 33°C in ambient air to mid-log phase (OD660 0.200-0.250). 10 mL of mid-log (OD660 0.200-0.250) culture was pelleted and stored in 2 mL of RNALater at -80°C. The culture was processed and diluted in PBS so that ~70 CFU of H. ducreyi would be delivered to the upper arm skin of volunteers using a allergy testing device. Volunteers were both infected with the inoculum and sham inoculated with PBS. The infection progressed for 6-8 days, at which point painful pustules had developed at the infected sites. A 6 mm punch biopsy was taken of both the pustule and wound. Biopsies were placed in 2 mL of RNALater at the bedside and then stored at -80°C.

extract_protocol:
RNA was extracted from samples the day after collection using the Qiagen RNeasy Fibrous Tissue Mini Kit with on-column DNase digestion. RNA was eluted from the column with nuclease free water and then treated with Turbo DNase (Invitrogen) for an in-solution DNase digestion.
Purified RNA was treated with Qiagen FastSelect for bacteria and human rRNA depletion. Libraries were prepared with a Roche KAPA kit.

value: skin

value: wound


title: S272_single cell rna seq by Smart Seq2

value: HSC

value: AAVS1 KO


title: Azucena-meiocyte-BS-seq-3


title: 477_wound


title: S273_single cell rna seq by Smart Seq2


title: S271_single cell rna seq by Smart Seq2


title: EndoC-βH1 – Replicate 2 – ADAR overexpression


title: Azucena-meiocyte-BS-seq-2


title: 473_wound


title: EosACs6

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: HTseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.26.0
Assembly: Input: We used the Mus musculus, GRCm38 genome Reference to the source of the genome and gtf files
Supplementary files format and content: gene_counts.normalized.csv (Matrix table with normalized gene counts for every gene and every sample)

organism: Mus musculus

source_name: eosinophils

extract_protocol:
RNA was extracted using TRIzol™ Reagent (Invitrogen,Thermo Fisher) according to the manufacturer’s instructions.The RNA integrity number (RIN) was analyzed using  Typestation (Agilent) and only samples of RIN>8 were used
2 ng of purified RNA was obtained from 10^6 eosinophils and used for library construction according to the CEL-Seq2 protocol

tag: strain

value: eosinophils

value: ACs


title: HCT116 DICER Wild-Type rescue AQ-seq (dataset II) replicate 2

description: AQ-seq


title: 474_wound


title: 475_wound


title: EosACs4


title: 471_wound


title: EosACs5


title: 470_wound


title: 469_wound


title: S269_single cell rna seq by Smart Seq2


title: EosIL4ACs3


title: S268_single cell rna seq by Smart Seq2


title: EndoC-βH1 – Replicate 1 – Control


title: 293T-TFIIB-ChIP-Rx-Hemin

description: 293T cells ChIP-seq analysis with TFIIB and Hemin

data_processing:
library strategy: ChIP-seq-Rx
Biotin CUT&Tag Reads were aligned to the human genome (UCSC hg38) and Escherichia coli genome with Bowtie2 version 2.2.6, using parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The aligned reads were normalized with total reads aligned (reads per million, r.p.m.) and spiked-in E.coli reads
ChIP-Rx reads were aligned to the human genome (UCSC hg38) and mouse genome (mm10) with Bowtie2 version2 2.2.6 , using parameters: --local --very-sensitive. The resulting reads were normalized with the aligned mouse reads.
qPRO-seq reads were aligned to the human hg38 genome. The resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m.) and converted to bigwig files for visualization in the UCSC genome browser. Heatmap and metagene plots were made for the indicated windows using the average coverage (r.p.m.).
G4-CUT&Tag and R-loop CUT&Tag reads were aligned to the human genome (UCSC hg38) and Escherichia coli genome with Bowtie2 version 2.2.6 [61], using parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The aligned reads were normalized with total reads aligned (reads per million, r.p.m.) and spiked-in E.coli reads.
RNA-seq reads were aligned to the human genome (UCSC hg38) or mouse genome (mm10) (the RNA-seq were normalized with the spiked-in Drosophila reads), respectively. Alignments were processed with HISAT2, allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads. The read counts across each gene were counted with featureCounts version 2.0.0.
Assembly: Homo sapiens .hg38
Assembly: Mus musculus.mm10
Assembly: Escherichia coli K-12 substr. MG1655
Supplementary files format and content: Library normalized bigWig files were provided for all samples

extract_protocol:
Following Hemin treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer’s instructions.
Biotin-PEG4-Hemin was combined with the Tn5-based CUT&Tag strategy to identify Hemin binding sites in the genome. Briefly, one million HEK293T  cells were resuspended in NE1 buffer (20 mM HEPES at pH 7.9, 10 mM KCl, 0.5 mM spermidine,0.1% Triton X-100, 20% Glycerol, 1× protease inhibitors) and incubated on ice for 10 minutes. After centrifugation at 1, 300 g for 10 minutes, nuclei were isolated and collected. These nuclei were washed once with PBS and resuspended with 100 μL of wash buffer (20 mM HEPES at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors). 10 μL pre-activated concanavalin A coated magnetic beads (Smart-Lifesciences) were added to these nuclei and incubated on a rotator for 10 minutes at room temperature. The supernatant was removed and bead-bound nuclei were resuspended in 100 μL of dig-wash buffer (0.05% digitonin, 20 mM HEPES at pH 7.5,150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors) containing 2 mM EDTA.Biotin-PEG4-Hemin was added to the sample and rotated overnight at 4°C in the dark.For the control sample, biotin-PEG4-hydrazide was used to replace biotin-PEG4-Hemin. These nuclei were washed three times in 200 μL of dig-wash buffer to remove unbound biotin-PEG4-Hemin or biotin-PEG4-hydrazide. Then anti-biotin rabbit mAb was diluted 100-fold in 100 μL of dig-wash buffer with 2 mM EDTA and was added to the nuclei with one-hour rotation at room temperature in the dark. After washing once with dig-wash buffer, these nuclei were resuspended with 100 μL of dig-wash buffer with 2 mM EDTA and 1 μL of mouse anti-rabbit IgG, incubated for another one hour at room temperature in the dark, and washed three times with dig-wash buffer. A 1:250 dilution of pA-Tn5 adapter complex (~0.2 μM) was prepared in 100 μL of dig-300 buffer (0.05% digitonin, 20 mM HEPES at pH 7.5, 300 mM KCl, 0.5 mM spermidine, 1× protease inhibitors) and added to the nuclei followed by one-hour rotation at room temperature in the dark. After five washes with dig-300 buffer, the bead-bound nuclei were resuspended with 40 μL of tagmentation buffer (10 mM TAPS-NaOH at pH 8.5, 10 mM MgCl 2 , 7.5% DMF) and incubated at 37°C for one hour. To terminate the tagmentation reaction, 1.5 μL of 0.5 M EDTA, 0.5 μL of 10% SDS and 1 μL of 20 mg/mL proteinase K were added and incubated at 55°C for 1 hour and then for 15 minutes at 75°C. The DNA was extracted with Sera-Mag carboxylate-modified magnetic beads (GE Healthcare) for library preparation. 21 μL DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, and amplified with NEB Q5 high- fidelity 2× master mix. The libraries were purified with 0.56-0.85× volume of Sera- Mag carboxylate-modified magnetic beads and subjected to the Bioanalyzer DNA analysis and Illumina sequencing.
ChIP-Rx was performed with 1×10 7 human cells and 1×10 6 MEF cells for spike-in normalization as described in a previous study [21]. For immunoprecipitation, sonicated chromatin was incubated with 10 μg specific antibodies and 15 μL of pre- blocked Protein A/G beads (Smart-Lifesciences). After extensive washes, the captured DNA was eluted for library preparation using the NEBNext Ultra II DNA library prep kit for Illumina before sequencing on a NovaSeq 6000.
G4-CUT&Tag and R-loop CUT&Tag were performed as previously described( Wang et al. 2021; Li et al. 2021)

value: treated with Hemin for 2 hours

tag: antibody

value: TFIIB


title: EosIL4ACs2


title: 293T-CUT-Tag-4Rloop-IgG

description: CUT&Tag analysis with IgG antibody

data_processing:
library strategy: CUT&Tag
Biotin CUT&Tag Reads were aligned to the human genome (UCSC hg38) and Escherichia coli genome with Bowtie2 version 2.2.6, using parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The aligned reads were normalized with total reads aligned (reads per million, r.p.m.) and spiked-in E.coli reads
ChIP-Rx reads were aligned to the human genome (UCSC hg38) and mouse genome (mm10) with Bowtie2 version2 2.2.6 , using parameters: --local --very-sensitive. The resulting reads were normalized with the aligned mouse reads.
qPRO-seq reads were aligned to the human hg38 genome. The resulting reads were normalized to the total reads used for alignment (reads per million, r.p.m.) and converted to bigwig files for visualization in the UCSC genome browser. Heatmap and metagene plots were made for the indicated windows using the average coverage (r.p.m.).
G4-CUT&Tag and R-loop CUT&Tag reads were aligned to the human genome (UCSC hg38) and Escherichia coli genome with Bowtie2 version 2.2.6 [61], using parameters: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The aligned reads were normalized with total reads aligned (reads per million, r.p.m.) and spiked-in E.coli reads.
RNA-seq reads were aligned to the human genome (UCSC hg38) or mouse genome (mm10) (the RNA-seq were normalized with the spiked-in Drosophila reads), respectively. Alignments were processed with HISAT2, allowing only uniquely mapping reads with up to three mismatches within the 150 bp reads. The read counts across each gene were counted with featureCounts version 2.0.0.
Assembly: Homo sapiens .hg38
Assembly: Mus musculus.mm10
Assembly: Escherichia coli K-12 substr. MG1655
Supplementary files format and content: Library normalized bigWig files were provided for all samples

value: untreated

value: IgG


title: S267_single cell rna seq by Smart Seq2

data_processing:
Basecalls performed using CASAVA version 1.4 and bcl2fastq2 v2.20.0
Cumulus pipeline for SmartSeq2
Cumulus pipeline for bulkRNA
CRISPResso2
Genome_build:  Human reference genome GRCh38 and gene annotation reference Homo_sapiens.GRCh38.93.gtf
Supplementary_files_format_and_content: matrix


title: 293T-CUT-Tag-4G4-IgG

description: CUT&Tag analysis with IgG antibody


title: EosIL4ACs1


title: EosINFgEcoliACs3

value: IFNgEcoliACs


title: S265_single cell rna seq by Smart Seq2


title: 293T-CUT-Tag-invivo-Hemin-Vehicle

value: Derived from embryonic kidney

value: anti-biotin


title: 293T-CUT-Tag-invivo-IgG

description: CUT&Tag analysis with IgG antibody


title: S264_single cell rna seq by Smart Seq2


title: 293T-CUT-Tag-invivo-Hemin-80


title: 293T-CUT-Tag-invitro-Hemin

description: CUT&Tag analysis with biotin-PEG4-Hemin


title: EosINFgEcoliACs1


title: 293T-CUT-Tag-invitro-Hemin-TMPyP4

description: CUT&Tag analysis with biotin-PEG4-Hemin


title: S270_single cell rna seq by Smart Seq2


title: SLR22

city: Freiburg

first: Kyra

last: Zodel

address: Breisacher Straße 115

department: Center for Translational Cell Research

institute: University Hospital Freiburg

data_processing:
genome build/assembly: GRCh37
Sequence reads were trimmed for adapter sequences and low-quality sequences using trimmomatic (v 0.38) (parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 HEADCROP:3 TRAILING:10 MINLEN:25)
Sequences were aligned to respective Ensembl references using the STAR aligner (v 2.5.2b) (parameters: --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --quantMode GeneCounts)
Supplementary files format and content: tab-delimited text file of raw counts of all samples

source_name: kidney

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey Nagel)
RNA libraries were prepared using the Illumina TruSeq Stranded RNA library preparation kit

value: kidney

value: ccRCC

value: WT

value: male


title: RCC4

value: female


title: S262_single cell rna seq by Smart Seq2


title: A498


title: EosIFNgACs2

value: IFNgACs


title: S261_single cell rna seq by Smart Seq2

value: HSC


title: 786-O


title: 769-P


title: EosIFNgACs1


title: Pregnant women with GDM-3 [lncRNA]

first: yin

middle: di

last: Bao

address: 238 Jiefang Rd

institute: Renmin Hospital of Wuhan

data_processing:
Illumina PE150  software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples
Assembly: hg38

source_name: placenta

extract_protocol:
Total RNA was isolated from 3 NC and 3 GDM cases using TRIzol reagent (Thermo Fisher Scientific, 15596026) and then treated with DNase I following the manufacturer’s instructions.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: Pregnant women with GDM


title: S266_single cell rna seq by Smart Seq2

source_name: HSC

extract_protocol:
mRNA isolated by  polyT beads
Smart Seq2

value: AAVS1 KO


title: Pregnant women with GDM-2 [lncRNA]


title: 293T-CUT-Tag-invivo-Hemin-TMPyP4

value: treated with Hemin for 2 hours and TMPyP4 2 hours


title: EosEcoliACs3

value: eosinophils

value: EcoliACs


title: Pregnant women with GDM-1 [lncRNA]


title: S260_single cell rna seq by Smart Seq2


title: RPTEC

value: RPTEC

value: renal epithelial cell


title: EosINFgEcoliACs2

value: IFNgEcoliACs


title: 293T-CUT-Tag-invtro-IgG

description: CUT&Tag analysis with IgG antibody

value: Derived from embryonic kidney

value: untreated

value: IgG


title: EosIFNgACs3


title: Healthy pregnant women-3 [lncRNA]

value: Healthy pregnant women


title: Healthy pregnant women-2 [lncRNA]


title: S258_single cell rna seq by Smart Seq2


title: EosEcoliACs2


title: EosEcoliACs1


title: HCT116 DICER R821A rescue AQ-seq replicate 2

description: AQ-seq

value: DICER R821A rescue


title: Healthy pregnant women-1 [lncRNA]


title: S257_single cell rna seq by Smart Seq2


title: S263_single cell rna seq by Smart Seq2


title: EosACs3

value: ACs


title: HCT116 DICER R821A rescue AQ-seq replicate 1

description: AQ-seq


title: HCT116 DICER R821E rescue AQ-seq replicate 2

description: AQ-seq

value: DICER R821E rescue


title: S256_single cell rna seq by Smart Seq2


title: HCT116 DICER ΔPAZ helix rescue AQ-seq replicate 2

description: AQ-seq

value: DICER {delta}PAZ helix rescue


title: EosACs2


title: HCT116 DICER R821E rescue AQ-seq replicate 1

description: AQ-seq


title: S255_single cell rna seq by Smart Seq2

value: HSC


title: HCT116 DICER ΔPAZ helix rescue AQ-seq replicate 1

description: AQ-seq


title: S259_single cell rna seq by Smart Seq2


title: HCT116 DICER A5 rescue AQ-seq replicate 2

description: AQ-seq

value: DICER A5 rescue


title: S254_single cell rna seq by Smart Seq2

value: AAVS1 KO


title: HCT116 DICER A5 rescue AQ-seq replicate 1

description: AQ-seq


title: EosACs1


title: HEK 293T cells, wildtype, biol rep 3 (miRNA-seq)

city: London

first: Pengcheng

last: Zhang

state: Ontario

address: 1151 Richmond St

department: Biochemistry

country: Canada

institute: The University of Western Ontario

data_processing:
Partek Flow v10.0.22
Reads were trimmed to 18 bp in length
fastq files were aligned to hg38 using Bowtie 1.0.0 and annotated with hg38 - miRBase mature microRNAs version 22 deduplicated
Features were excluded if maximum reads <= 7.0
Reads were normalized using Counts Per Million and adding 1.0
Fold changes and p-values were caluclated using Partek's Gene-specific analysis (GSA), a statistical modeling approach.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including fold change and statistical significance value for each miRNA
Supplementary files format and content: tab-delimited text file including miRNA counts

source_name: HEK 293T

growth_protocol: HEK 293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
Total RNA samples were processed using the QIAseq miRNA Library Kit (Qiagen, Canada).

value: HEK 293T

value: immortalized human embryonic kidney cells

value: WT


title: HCT116 DICER E5 rescue AQ-seq replicate 2

description: AQ-seq

value: DICER E5 rescue


title: HCT116 DICER E5 rescue AQ-seq replicate 1

description: AQ-seq


title: HCT116 DICER wild-type rescue AQ-seq replicate 1

description: AQ-seq

value: DICER WT rescue


title: S251_single cell rna seq by Smart Seq2

first: Liming

last: Tao

institute: Broad Institute of Harvard and MIT


title: HEK 293T cells, wildtype, biol rep 2 (miRNA-seq)


title: HCT116 DICER wild-type rescue AQ-seq replicate 2

description: AQ-seq


title: S252_single cell rna seq by Smart Seq2


title: HEK 293T cells, TENT3A/B double knockout, biol rep 3 (miRNA-seq)

value: TENT3A/B knockout


title: HEK 293T cells, wildtype, biol rep 1 (miRNA-seq)


title: HEK 293T cells, TENT3A/B double knockout, biol rep 2 (miRNA-seq)


title: S250_single cell rna seq by Smart Seq2


title: S249_single cell rna seq by Smart Seq2


title: AML_155

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

institute: SHANGH RUIJIN HOSPITAL

data_processing:
Trim-galore was employed to remove the adapter sequences.
The clean reads were aligned with STAR and quantified with HT-Seq using the GRCh38 human assembly.
Novel and annotated splice junctions were quantified by rMATS and filtered for coverage and variance.
The differential expression assessment was conducted using the DESeq2 package.
Gene expression levels were normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM) using a customed script.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw count values for each Sample; Tab-delimited text files include splice junction raw count for each Sample.

source_name: Bone marrow

extract_protocol:
Bone marrow mononuclear cells from AML patients were isolated after Ficoll–Isopaque density gradient centrifugation. Genomic mRNA were extracted from the patients’ BM using the AllPrep PowerFecal RNA Kit in accordance with the manufacturer’s instructions.
The DNase I-treated total RNA preparations were qualitatively validated by Agilent RNA 6000 Nano Kit with the 2100 Bioanalyzer system, and libraries were prepared using the KAPA RNA HyperPrep kit in accordance with the manufacturer’s instructions (KAPA). High-throughput sequencing was performed on the NovaSeq 6000 platform in accordance with the manufacturer’s protocol (paired-end 2 × 150 bp).

value: Bone marrow

value: Bone marrow mononuclear cells

value: Acute myeloid leukemia

value: Treatment-Naïve

value: Diagnosis

tag: age

value: Male


title: AML_156

value: Female


title: AML_152


title: AML_154


title: AML_151


title: S248_single cell rna seq by Smart Seq2

address: 415 Main Street


title: HEK 293T cells, TENT3A/B double knockout, biol rep 1 (miRNA-seq)


title: HEK 293T cells, wildtype, biol rep 3 (RNA-seq)

data_processing:
Partek Flow v10.0.22
fastq files were aligned to hg38 using STAR 2.7.3a and annotated with Ensembl Transcripts release 102
Features were excluded if maximum reads <= 12.0
Reads were normalized using Counts Per Million and adding 1.0
Fold changes and p-values were caluclated using Partek's Gene-specific analysis (GSA), a statistical modeling approach.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including fold change and statistical significance value for each mRNA
Supplementary files format and content: tab-delimited text file including gene counts

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
Total RNA samples were processed using the Vazyme VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, Nanjing, China) which includes rRNA reduction.


title: AML_149


title: AML_148


title: S253_single cell rna seq by Smart Seq2


title: AML_147


title: HEK 293T cells, wildtype, biol rep 2 (RNA-seq)


title: S247_single cell rna seq by Smart Seq2


title: S246_single cell rna seq by Smart Seq2


title: AML_157


title: AML_145


title: AML_144


title: S245_single cell rna seq by Smart Seq2


title: AML_146


title: AML_143


title: HEK 293T cells, wildtype, biol rep 1 (RNA-seq)


title: HEK 293T cells, TENT3A/B double knockout, biol rep 3 (RNA-seq)


title: S244_single cell rna seq by Smart Seq2


title: AML_153


title: AML_142


title: AML_141


title: HEK 293T cells, TENT3A/B double knockout, biol rep 2 (RNA-seq)


title: S243_single cell rna seq by Smart Seq2


title: AML_139


title: AML_140


title: S242_single cell rna seq by Smart Seq2


title: AML_150


title: AML_138


title: AML_137


title: ZIP3

city: Shenyang

first: Xiao

last: Dong

state: Liaoning

address: 155 Nanjing North Street, Heping District

department: Department of Urology

institute: The first hospital of China Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: OSRC-2 renal cell carcinoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) 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.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: renal cell carcinoma cells

value: SLC39A1 overexpressed


title: AML_136


title: S241_single cell rna seq by Smart Seq2

city: Cambridge

value: HSC


title: AML_134


title: AML_135


title: S240_single cell rna seq by Smart Seq2

value: AAVS1 KO


title: ZIP1


title: AML_133


title: AML_132


title: S239_single cell rna seq by Smart Seq2


title: AML_130


title: NC3

value: negative control


title: AML_131


title: S238_single cell rna seq by Smart Seq2


title: NC2


title: S237_single cell rna seq by Smart Seq2


title: AML_128


title: HEK 293T cells, TENT3A/B double knockout, biol rep 1 (RNA-seq)

value: HEK 293T

value: immortalized human embryonic kidney cells


title: AML_129


title: AML_124


title: NC1


title: AML_127


title: MECOM_16K

data_processing:
Basecalls performed using CASAVA version 1.4 and bcl2fastq2 v2.20.0
Cumulus pipeline for 10x
Genome_build:  Human reference genome GRCh38 and gene annotation reference Homo_sapiens.GRCh38.93.gtf
Supplementary_files_format_and_content: h5

source_name: single cell rna seq by 10x Genomics V3

extract_protocol:
mRNA isolated by  polyT beads
10X RNA V3

value: Mecom KO


title: S236_single cell rna seq by Smart Seq2


title: AML_123


title: AAVS1_11K


title: S234_single cell rna seq by Smart Seq2


title: ZIP2


title: AML_122


title: AML_126


title: AML_125


title: AML_121


title: S235_single cell rna seq by Smart Seq2


title: p73.KO rep3

first: Arthur

middle: W.

last: Lambert

state: MA

address: 455 Main street

institute: Whitehead Institute

data_processing:
The 40-nt long single-end reads had very good quality as checked with FastQC. Reads were mapped with STAR 2.5.4b to hg38 version of human genome using the “sjdbOverhang” parameter set to 39, and the annotation file from ENSEMBL GRCh38.90. At least 79% of reads were uniquely mapped, corresponding to at least 22 millions uniquely mapped reads. The samples were stranded, and counts for the 2nd read strand aligned with RNA were used for calculating the number of counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file with raw gene counts for every gene

source_name: ITGB4-hi with KO of p73

growth_protocol: RNA was isolated from cells grown under standard tissue culture conditions

extract_protocol:
Total RNA was isolated with a modified Trizol protocol. Libraries were prepared for RNA-Seq using KAPA Biosystems KAPA mRNA HyperPrep Kit, according to manufacturer’s directions. Briefly, total RNA (0.1-1 ug) is enriched for polyadenylated sequences using oligo-dT magnetic bead capture. The enriched mRNA fraction is then fragmented, and first-strand cDNA is generated using random primers. Strand specificity is achieved during second-strand cDNA synthesis by replacing dTTP with dUTP, which quenches the second strand during amplification. The resulting cDNA is A-Tailed and ligated with indexed adapters. Finally, the library is amplified using a DNA Polymerase which cannot incorporate past dUTPs, effectively quenching the second strand during PCR.
KAPAHyperPrepmRNA

treatment_protocol: CRISPR was used to generated the various KO lines and a non-targeting sgRNA (NT) was used as a control.

tag: parental line

tag: subline

value: mammary carcinoma cells


title: S233_single cell rna seq by Smart Seq2

tag: cell type


title: p73.KO rep2


title: AML_119

tag: treatment


title: AML_120

tag: genotype


title: AML_118

tag: gender


title: AML_117

tag: tissue


title: AML_116

tag: disease state


title: p73.KO rep1


title: p63.KO rep3

source_name: ITGB4-hi with KO of p63


title: S230_single cell rna seq by Smart Seq2


title: AML_114


title: AML_113


title: AML_112


title: p63.KO rep2


title: p63.KO rep1


title: S228_single cell rna seq by Smart Seq2


title: S227_single cell rna seq by Smart Seq2


title: AML_109