title: AML_108


title: NT rep3

status: Public on Nov 23 2022

type: SRA

city: Cambridge

first: Arthur

middle: W.

last: Lambert

state: MA

address: 455 Main street

country: USA

institute: Whitehead Institute

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

source_name: ITGB4-hi with non-targeting guide

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

tag: cell type

value: mammary carcinoma cells


title: AML_106

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

country: China

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.

molecule: total RNA

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).

tag: tissue

value: Bone marrow

value: Bone marrow mononuclear cells

tag: disease state

value: Acute myeloid leukemia

tag: treatment

value: Treatment-Naïve

tag: time

value: Diagnosis

tag: age

tag: gender

value: Male

tag: genotype


title: S226_single cell rna seq by Smart Seq2

first: Liming

last: Tao

address: 415 Main Street

institute: Broad Institute of Harvard and MIT

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

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

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:
mRNA isolated by  polyT beads
Smart Seq2

treatment_protocol: AAVS1  or MECOM KO

value: HSC

value: AAVS1 KO


title: NT rep2


title: NT rep1


title: AML_105

value: Female


title: S232_single cell rna seq by Smart Seq2


title: AML_104


title: S231_single cell rna seq by Smart Seq2


title: AML_103


title: AML_115


title: AML_102


title: dKO rep3

source_name: ITGB4-hi with KO of p63/p73


title: S224_single cell rna seq by Smart Seq2


title: S223_single cell rna seq by Smart Seq2


title: AML_101


title: dKO rep2


title: S229_single cell rna seq by Smart Seq2


title: AML_100


title: AML_99


title: dKO rep1


title: AML_110


title: S222_single cell rna seq by Smart Seq2


title: AML_98


title: AML_96


title: AML_97


title: S221_single cell rna seq by Smart Seq2


title: lo_EV rep1

data_processing:
The 40-nt long single-end reads from Illumina had very good quality as checked with FastQC. Reads were mapped with STAR 2.6.1a to hg38 version of human genome using the “sjdbOverhang” parameter set to 39, and the annotation file from ENSEMBL GRCh38.90. At least 70% of reads were uniquely mapped, corresponding to at least 32 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-lo cells with expression of a control empty vector

treatment_protocol: ITGB4-hi dKO or ITGB4-lo cells were engineered to constitutively express the indicated vectors through stable selection.


title: lo_EV rep2


title: AML_94


title: AML_95


title: S220_single cell rna seq by Smart Seq2


title: S225_single cell rna seq by Smart Seq2


title: AML_93


title: AML_92


title: lo_dNp63 rep2

source_name: ITGB4-lo cells with ectopic expression of dNp63


title: S219_single cell rna seq by Smart Seq2


title: AML_91


title: lo_dNp63 rep1


title: AML_90


title: S217_single cell rna seq by Smart Seq2


title: S218_single cell rna seq by Smart Seq2


title: AML_87


title: dKO_TAp73 rep2

source_name: dKO cells with ectopic expression of TAp73


title: AML_88


title: dKO_TAp73 rep1


title: AML_89


title: AML_85


title: S216_single cell rna seq by Smart Seq2


title: dKO_EV rep2

source_name: dKO cells with expression of control empty vector


title: AML_83


title: S215_single cell rna seq by Smart Seq2


title: S214_single cell rna seq by Smart Seq2


title: AML_81


title: AML_82


title: AML_84


title: S213_single cell rna seq by Smart Seq2


title: dKO_EV rep1


title: dKO_dual rep1

source_name: dKO cells with ectopic expression of dNp63/TAp73


title: dKO_dual rep2


title: AML_79


title: S212_single cell rna seq by Smart Seq2


title: AML_78


title: AML_80


title: AML_77


title: dKO_dNp63 rep2

source_name: dKO cells with ectopic expression of dNp63


title: S211_single cell rna seq by Smart Seq2


title: AML_86


title: AML_74


title: S210_single cell rna seq by Smart Seq2


title: AML_75


title: AML_73


title: dKO_dNp63 rep1


title: AML_76


title: Ad-SIRT6-2

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
DIFFERENTIAL EXP. - EdgeR-3.6.8 exactTest + benjamini-hochberg (multiple test correction) with and without a cpm > 1 for all samples filter
Assembly: GRCh38.p3 + Gencode-23 Annotation
Supplementary files format and content: Raw gene counts TSV

source_name: Umbilical Vein

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC, passage 3 to passage 5) were seeded in 0.2% gelatin-coated dishes the day before experiment.

extract_protocol:
After treatment, RNA was extracted using an RNeasy Mini kit (Qiagen, Valencia, CA) per manufacturer's instructions.
High-quality RNA samples (pre-assessed by Nanodrop 2000) were further processed in the Genomics Research Center of the University of Rochester. Briefly, RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer's protocols. mRNA was purified from 100 ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3′ adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500 bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8 pM per lane. Single end reads of 100 nt are generated for each sample and aligned to the organism specific reference genome. The sequencing was performed using the Illumina high-throughput HiSeq 4000.

treatment_protocol: HUVECs at 100% confluence were infected with control adenoviral LacZ or adenoviral SIRT6 for 48 h.

value: Umbilical Vein

value: endothelial cells

tag: transfected with


title: Ad-SIRT6-1


title: AML_71


title: S209_single cell rna seq by Smart Seq2


title: AML_72


title: AML_70


title: AML_69


title: AD-ctrl-2

value: control


title: AML_68


title: Ad-ctrl-1


title: AML_67


title: S206_single cell rna seq by Smart Seq2


title: AML_66


title: S205_single cell rna seq by Smart Seq2


title: hMSCs, shCTR9#5 OD D7 Rep3

city: Madison

first: NGAI TING

last: CHAN

state: WI

address: 4849 Sheboygan Ave

department: Oncology

institute: University of Wisconsin -- Madison

data_processing:
Basecalls performed using CASAVA version 1.8
Trimmed RNA sequencing reads were aligned to the transcript annotation of human reference genome (hg38.ncbiRefSeq.gtf) using STAR (v2.7.9a).
Duplicated reads and reads with low mapping quality were eliminated by sambamba tools (v0.7.1).
FeatureCounts (Subread package, v2.0.1) was used to count reads as a measure of gene expression.
Differential expressed genes were identified by DESeq2 (v1.36.0) in R with FDR <0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: human primary mesenchymal stem cells

growth_protocol: Isolated hMSCs were cultured in basal medium composed of low-glucose MEMα (Corning), 10% fetal bovine serum (FBS, VWR), and 1% antibiotics (Gibco™ Penicillin-Streptomycin, ThermoFisher Scientific) and maintained at 37°C under a humidified atmosphere of 5% CO2.

extract_protocol:
total RNA was extracted from cells using the E.Z.N.A™ HP Total RNA extraction kit (Omega) under manufacturer’s protocol. 100ng total RNA as starter input for library prep.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
1 x 50bp

treatment_protocol: For osteogenesis, hMSCs were induced in osteogenic medium composed of 1x MEMα (Corning), 10% FBS, 1% antibiotics, 10 mM β-glycerophosphate, 50 mg/ml L-ascorbic acid–2-phosphate, and 0.1 mM dexamethasone (Sigma Aldrich) for up to 28 days.

value: human primary mesenchymal stem cells

value: CTR9 Knockdown

value: osteogenic differentiation

value: Day 7


title: hMSCs, shCTR9#5 OD D7 Rep2


title: AML_64


title: AML_63


title: S204_single cell rna seq by Smart Seq2


title: AML_61


title: AML_62


title: AML_60


title: S203_single cell rna seq by Smart Seq2


title: hMSCs, shCTR9#3 OD D7 Rep3


title: AML_59


title: S208_single cell rna seq by Smart Seq2


title: S202_single cell rna seq by Smart Seq2


title: hMSCs, shCTR9#3 OD D7 Rep2


title: AML_57


title: S207_single cell rna seq by Smart Seq2


title: AML_56


title: AML_55


title: S200_single cell rna seq by Smart Seq2


title: hMSCs, shCTR9#3 OD D7 Rep1


title: AML_65


title: AML_54


title: AML_53


title: S199_single cell rna seq by Smart Seq2


title: hMSCs, shControl OD D7 Rep3

value: Control Knockdown


title: AML_52

value: Bone marrow


title: AML_51

value: Bone marrow mononuclear cells


title: hMSCs, shControl OD D7 Rep2


title: AML_50

value: Acute myeloid leukemia


title: hMSCs, shCTR9#5 OD D7 Rep1


title: hMSCs, shControl OD D7 Rep1


title: S198_single cell rna seq by Smart Seq2


title: S197_single cell rna seq by Smart Seq2


title: AML_58

value: Treatment-Naïve


title: AML_49

value: Diagnosis


title: AML_48

value: Male


title: S201_single cell rna seq by Smart Seq2

value: HSC


title: AML_47


title: S196_single cell rna seq by Smart Seq2

value: AAVS1 KO


title: LX22_425L, NHWD-870, 5 days

city: Bethesda

first: Haobin

last: Chen

state: MD

address: 10 Center Drive, Room 3-5888

department: Thoracic Surgery Branch

institute: National Institutes of Health

description:
BETi6
LX22_425L
mRNA

data_processing:
CCBR Pipeliner. Details can be found at https://ccbr.github.io/pipeliner-docs/RNA-seq/Gene-and-isoform-expression-overview/
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt.
Trimmed sequence reads were mapped to hg19 using STAR for two passes.
Read count extraction and normalization were performed using RSEM.
Assembly: hg19
Supplementary files format and content: *.txt: Tab-delimited text files include normalized counts or FPKM values for all samples.

source_name: patient-derived xenograft (LX22 PDX)

growth_protocol: LX22 PDX was inoculated subcutaneously in 6-wk-old NSG mice (Charles River Laboratories). Once the tumor volume reached around 250 mm3, mice were treated with NHWD-870 or vehicle via oral gavage daily for 5 days.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen) by following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Library Prep following the manufacturer's protocols.

treatment_protocol: Tumor cells were separated from mouse stromal cells using a magnetic-activated cell sorting method (Schneeberger et al.PLoS ONE 2016, 11:e0160587).

value: patient-derived xenograft (LX22 PDX)

value: small cell lung cancer SCLC-N subtype

value: WT

value: 5 days


title: AML_45

value: Female


title: AML_46


title: S195_single cell rna seq by Smart Seq2


title: AML_44


title: AML_43


title: S194_single cell rna seq by Smart Seq2


title: AML_41


title: AML_42


title: LX22_395L, NHWD-870, 5 days

description:
BETi3
LX22_395L
mRNA


title: AML_40


title: S193_single cell rna seq by Smart Seq2


title: LX22_425R, NHWD-870, 5 days

description:
BETi2
LX22_425R
mRNA


title: AML_39


title: S192_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR912_2.dge.txt.gz

value: MECOM KO


title: LX22_395R, NHWD-870, 5 days

description:
BETi1
LX22_395R
mRNA


title: AML_38


title: AML_37


title: S191_single cell rna seq by Smart Seq2


title: AML_36


title: AML_35


title: LX22_392L, NHWD-870, 5 days

description:
BETi5
LX22_392L
mRNA


title: S190_single cell rna seq by Smart Seq2


title: LX22_399R, vehicle, 5 days

description:
Ctr6
LX22_399R
mRNA

value: Vehicle


title: AML_34


title: LX22_397R, vehicle, 5 days

description:
Ctr5
LX22_397R
mRNA


title: AML_33


title: AML_31


title: S189_single cell rna seq by Smart Seq2


title: AML_32


title: LX22_399L, vehicle, 5 days

description:
Ctr4
LX22_399L
mRNA


title: LX22_392R, NHWD-870, 5 days

description:
BETi4
LX22_392R
mRNA


title: S188_single cell rna seq by Smart Seq2


title: AML_30


title: LX22_326L, vehicle, 5 days

description:
Ctr3
LX22_326L
mRNA


title: S187_single cell rna seq by Smart Seq2


title: AML_29


title: AML_28


title: LX22_397L, vehicle, 5 days

description:
Ctr2
LX22_397L
mRNA


title: AML_27


title: AML_25


title: S185_single cell rna seq by Smart Seq2


title: AML_24


title: AML_111


title: LX22_326R, vehicle, 5 days

description:
Ctr1
LX22_326R
mRNA


title: AML_22


title: S183_single cell rna seq by Smart Seq2


title: COR-L279 cells, 1.5µM JQ1, 24hrs, biol rep 3

description:
JQ1_high3
JQ1_1_5uM_3_S59
Biological replicate 3

growth_protocol: COR-L279 cells were maintained in RPMI supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ⁰C.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded total RNA Library Prep kit (RS-122-2201) following the manufacturer's protocols.

treatment_protocol: Cells were treated with JQ1 (0.5 or 1.5µM) or DMSO for 24 hours.

tag: cell line


title: AML_20


title: COR-L279 cells, 1.5µM JQ1, 24hrs, biol rep 2

description:
JQ1_high2
JQ1_1_5uM_2_S58
Biological replicate 2


title: S182_single cell rna seq by Smart Seq2


title: AML_17


title: COR-L279 cells, 1.5µM JQ1, 24hrs, biol rep 1

description:
JQ1_high1
JQ1_1_5uM_1_S57
Biological replicate 1


title: COR-L279 cells, 0.5µM JQ1, 24hrs, biol rep 3

description:
JQ1_low3
JQ1_0_5uM_3_S56
Biological replicate 3


title: AML_21


title: AML_19


title: AML_16


title: AML_15


title: S180_single cell rna seq by Smart Seq2


title: AML_26


title: AML_107


title: AML_13


title: AML_14


title: COR-L279 cells, 0.5µM JQ1, 24hrs, biol rep 1

description:
JQ1_low1
JQ1_0_5uM_1_S54
Biological replicate 1


title: AML_23


title: S179_single cell rna seq by Smart Seq2


title: AML_12


title: S184_single cell rna seq by Smart Seq2


title: COR-L279 cells, DMSO, 24hrs, biol rep 3

description:
DMSO3
DMSO3_S53
Biological replicate 3

value: DMSO


title: AML_11


title: S178_single cell rna seq by Smart Seq2


title: AML_10


title: AML_9


title: S181_single cell rna seq by Smart Seq2


title: AML_18


title: COR-L279 cells, DMSO, 24hrs, biol rep 2

description:
DMSO2
DMSO2_S52
Biological replicate 2


title: AML_7


title: S177_single cell rna seq by Smart Seq2


title: AML_8


title: AML_6


title: COR-L279 cells, DMSO, 24hrs, biol rep 1

description:
DMSO1
DMSO1_S51
Biological replicate 1


title: S176_single cell rna seq by Smart Seq2


title: AML_5


title: COR-L279 cells, 0.5µM JQ1, 24hrs, biol rep 2

description:
JQ1_low2
JQ1_0_5uM_2_S55
Biological replicate 2


title: S175_single cell rna seq by Smart Seq2


title: AML_4


title: H446 cells, NEUROD1 gRNA #297, clone 2-1, JQ1, biol rep 2

description:
H446_ND1_KO_cl_2-1_JQ1_2
Biological replicate 2
mRNA

growth_protocol: H446 NEUROD1-knockout derivatives and control cell clones were maintained in RPMI supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ⁰C.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Library Prep following the manufacturer's protocols.

treatment_protocol: Cells were treated with JQ1 (1µM) or DMSO for 24 hours.

value: NEUROD1 knockout

value: 24 hours


title: H446 cells, NEUROD1 gRNA #297, clone 2-1, JQ1, biol rep 3

description:
H446_ND1_KO_cl_2-1_JQ1_3
Biological replicate 3
mRNA


title: S186_single cell rna seq by Smart Seq2


title: S174_single cell rna seq by Smart Seq2


title: H446 cells, NEUROD1 gRNA #297, clone 2-1, JQ1, biol rep 1

description:
H446_ND1_KO_cl_2-1_JQ1_1
Biological replicate 1
mRNA


title: AML_3

value: Bone marrow

value: Bone marrow mononuclear cells


title: H446 cells, NEUROD1 gRNA #297, clone 15, JQ1, biol rep 3

description:
H446_ND1_KO_cl_15_JQ1_3
Biological replicate 3
mRNA


title: circBtnl1_WT

city: Beijing

first: Hui

last: Guo

address: Datun road 15

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: mm10
Supplementary files format and content: Matrix table with FPKM and TPM values for each gene and each sample.

organism: Mus musculus

source_name: small intestine

extract_protocol:
RNA was harvested using RNAprep Pure Micro Kit (Tiangen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using MGIEasy RNA Library Prep Kit V3.0 (MGI-tech) following manufacturer's protocols.

value: small intestine

value: small Intestinal stem cells

value: Intestinal stem cells

value: circBtnl1 wild-type


title: S173_single cell rna seq by Smart Seq2

value: HSC


title: circBtnl1_KO

value: circBtnl1 knockout


title: H446 cells, NEUROD1 gRNA #297, clone 15, JQ1, biol rep 2

description:
H446_ND1_KO_cl_15_JQ1_2
Biological replicate 2
mRNA

value: small cell lung cancer SCLC-N subtype


title: AML_1

value: Acute myeloid leukemia

value: Treatment-Naïve

value: Diagnosis


title: HLF cells, siUSP1-2

city: xinxing

first: huijie

last: yang

address: Hongqi District, Xinxiang City

institute: Xinxiang Medical University

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: GRCh38
Supplementary files format and content: xlsx files include FPKM value for each Sample

source_name: Hepatocellular carcinoma

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

extract_protocol:
Lysis of cells with Trizol regent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using BGISEQ-500 protocols.

treatment_protocol: HLF cells were transfected with siControl and siUSP1 for 48 h.

value: Hepatocellular carcinoma

value: HLF

value: Hepatocellular carcinoma cell


title: HLF cells, siUSP1-1


title: H446 cells, NEUROD1 gRNA #297, clone 15, JQ1, biol rep 1

description:
H446_ND1_KO_cl_15_JQ1_1
Biological replicate 1
mRNA

value: NEUROD1 knockout


title: HLF cells, siControl-3

value: siControl


title: rep4_96h_ATV:TREM2 [DRN-21490]

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Sequencing adapters were trimmed using skewer (Jiang et al., 2014) (version 0.2.2) with default parameters. Unique molecular identifiers (UMIs) were extracted from each read with the umi2index tool (Lexogen). Quality control of the trimmed reads was performed using FastQC (version 0.11.5: www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the human genome version GRCh38_p12. A STAR index (version 2.7.1a) (Dobin et al., 2013); was built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release release_28) were provided via the --sjdbGTFfile argument. STAR alignments were generated with the following parameters: --outFilterType BySJout, --quantMode TranscriptomeSAM, -- outFilterIntronMotifs RemoveNoncanonicalUnannotated, --outSAMstrandField intronMotif, -- outSAMattributes NH HI AS nM MD XS and --outSAMunmapped Within. Alignments were obtained with the following parameters: --readFilesCommand zcat --outFilterType BySJout -- outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- outFilterMismatchNmax 999 - outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 -- alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode GeneCounts -- outSAMunmapped Within --outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outBAMcompression 6. Unique molecular identifiers (UMIs) were extracted from each read with the umi2index tool (Lexogen). Gene level counts were obtained using featureCounts from the subread package (version 2.0.0) (Liao et al., 2014).
To calculate normalized counts per million (CPM) TMM normalization was applied across all genes with the edgeR R package.
Assembly: GRCh38
Supplementary files format and content: Excel (XLSX) file with sample annotations, raw counts and TMM-normalized counts per million (CPM)

source_name: iPSC derived microglia

growth_protocol: Human iPSCs were maintained in mTESR-Plus (Stemcell Technologies #100-0276) until seeding for differentiation. On Day 3 primary human astrocyte feeder cells were thawed and seeded into poly-L-Lysine coated 10cm2 tissue culture dishes using Lonza AGM (CC-3186) as growth medium. On Day 8 primary human astrocytes were dissociate using 0.05% Trypsin-EDTA (ThermoFisher,  25300062) counted in the Nexcelom cellometer and seeded at 10,000 cells/cm2 (approximately 100,000 cells per well of a 6-well tissue culture plate was used). On Day 10 floating colonies of hematopoietic progenitor cells (HPCs) were visible and collected. To collect the cells, medium from each well was collected and added to a 15mL conical tube. Any remaining medium in the conical tube was then aspirated and HPCs were resuspended in microglia differentiation medium (IMDM base medium containing 10% FBS, and 20ng/mL each of GM-CSF (Peprotech, AF-300-03), IL3 (Peprotech, AF-200-03), and M-CSF (Peprotech, AF-30-25)). AGM was aspirated from the astrocyte feeder cell plates and HPCs collected from an entire 12-well plate were seeded evenly across 2, 6-well plates containing astrocyte feeder cells. After one week of culture numerous cells are seen proliferating in suspension with some firmly attaching to astrocyte feeder cells.  On Day 20 2mL medium was collected from each well and suspension cells were pelleted at 300xg for five minutes. Medium was aspirated and pelleted cells were resuspended in 24mL microglia differentiation medium (see above) and 2mL of the cell suspension was added back to each well. By Day 42 cells were harvested and seeded in an assay dependent manner.

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) and resuspended in 14 µl nuclease-free water. RNA quantity and quality were assessed with a RNA 6000 Pico chip (Agilent, #5067-1513) on a 2100 Bioanalyzer (Agilent).
Libraries were generated using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with Qubit 1X dsDNA HS Assay Kits (Invitrogen Q33231) and Bioanalyzer High Sense DNA chip (Agilent 5067-4626). Libraries were pooled in equimolar ratios for sequencing.

treatment_protocol: iMG were plated at 30,000 cells / well in microglia differentiation media (see below) on 96-well Cell Carrier Ultra plates, and allowed to adhere for 3 days.  Subsequently, media was exchanged for microglia differentiation media diluted 1:3 with microglia differentiation media without growth factors, and treated with 100nM ATV:ISO or ATV:TREM2, or 10 ng/mL LPS (Sigma L2880), 20 ng/mL TGFb (RnD 7754-BH), or 20 ng/mL IFNg (RnD 285-IF/CF).  After 4 days of treatment, RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, 74034).  RNA quality was assessed with a RNA 6000 Pico chip (Agilent 5067-1513) on a 2100 Bioanalyzer (Agilent) and quantified with Qubit RNA HS Assay Kits (Life Technologies, Q32855).

tag: batch

value: WT

value: nM

value: 96 hours

value: iPSC derived microglia


title: S170_single cell rna seq by Smart Seq2

value: MECOM KO


title: H446 cells, NEUROD1 gRNA #297, clone 12, JQ1, biol rep 3

description:
H446_ND1_KO_cl_12_JQ1_3
Biological replicate 3
mRNA

value: 24 hours


title: HLF cells, siControl-2


title: H446 cells, NEUROD1 gRNA #297, clone 12, JQ1, biol rep 2

description:
H446_ND1_KO_cl_12_JQ1_2
Biological replicate 2
mRNA


title: S168_single cell rna seq by Smart Seq2

value: HSC


title: HLF cells, siUSP1-3


title: HLF cells, siControl-1


title: rep4_16h_ATV:TREM2 [DRN-21489]

value: 16 hours


title: rep3_96h_ATV:TREM2 [DRN-21488]


title: genomic DNA from TNBC patient number 847

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

molecule: genomic DNA

label_protocol: Standard Illumina protocol

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

value: Female

value: Tumor tissue

value: TNBC


title: H446 cells, NEUROD1 gRNA #297, clone 12, JQ1, biol rep 1

description:
H446_ND1_KO_cl_12_JQ1_1
Biological replicate 1
mRNA

value: small cell lung cancer SCLC-N subtype


title: S172_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR912_2.dge.txt.gz


title: AML_2

value: Bone marrow

value: Bone marrow mononuclear cells

value: Acute myeloid leukemia

value: Treatment-Naïve

value: Diagnosis

value: Male


title: H446 cells, NEUROD1 gRNA #297, clone 2-1, DMSO, biol rep 3

description:
H446_ND1_KO_cl_2-1_3
Biological replicate 3
mRNA

value: NEUROD1 knockout

value: DMSO


title: S167_single cell rna seq by Smart Seq2


title: S166_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 83


title: genomic DNA from TNBC patient number 846


title: rep2_96h_ATV:TREM2 [DRN-21486]

value: WT

value: nM

value: 96 hours

value: iPSC derived microglia


title: rep3_16h_ATV:TREM2 [DRN-21487]

value: 16 hours


title: H446 cells, NEUROD1 gRNA #297, clone 2-1, DMSO, biol rep 2

description:
H446_ND1_KO_cl_2-1_2
Biological replicate 2
mRNA

value: 24 hours


title: rep2_16h_ATV:TREM2 [DRN-21485]


title: S165_single cell rna seq by Smart Seq2

value: HSC

value: MECOM KO


title: S171_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 819

value: Female

value: Tumor tissue

value: TNBC


title: H446 cells, NEUROD1 gRNA #297, clone 2-1, DMSO, biol rep 1

description:
H446_ND1_KO_cl_2-1_1
Biological replicate 1
mRNA

value: small cell lung cancer SCLC-N subtype


title: S169_single cell rna seq by Smart Seq2


title: S164_single cell rna seq by Smart Seq2


title: rep1_96h_ATV:TREM2 [DRN-21484]


title: genomic DNA from TNBC patient number 781


title: rep1_16h_ATV:TREM2 [DRN-21483]


title: H446 cells, NEUROD1 gRNA #297, clone 15, DMSO, biol rep 2

description:
H446_ND1_KO_cl_15_2
Biological replicate 2
mRNA


title: genomic DNA from TNBC patient number 739


title: S162_single cell rna seq by Smart Seq2


title: rep4_96h_LPS [DRN-21466]

value: LPS


title: S161_single cell rna seq by Smart Seq2


title: H446 cells, NEUROD1 gRNA #297, clone 15, DMSO, biol rep 3

description:
H446_ND1_KO_cl_15_3
Biological replicate 3
mRNA


title: rep4_16h_LPS [DRN-21465]


title: genomic DNA from TNBC patient number 719


title: H446 cells, NEUROD1 gRNA #297, clone 12, DMSO, biol rep 3

description:
H446_ND1_KO_cl_12_3
Biological replicate 3
mRNA


title: H446 cells, NEUROD1 gRNA #297, clone 12, DMSO, biol rep 2

description:
H446_ND1_KO_cl_12_2
Biological replicate 2
mRNA


title: H446 cells, NEUROD1 gRNA #297, clone 15, DMSO, biol rep 1

description:
H446_ND1_KO_cl_15_1
Biological replicate 1
mRNA


title: S160_single cell rna seq by Smart Seq2


title: S159_single cell rna seq by Smart Seq2


title: H446 cells, NEUROD1 gRNA #297, clone 12, DMSO, biol rep 1

description:
H446_ND1_KO_cl_12_1
Biological replicate 1
mRNA


title: genomic DNA from TNBC patient number 706


title: rep3_16h_LPS [DRN-21463]


title: S158_single cell rna seq by Smart Seq2


title: rep2_96h_LPS [DRN-21462]


title: S163_single cell rna seq by Smart Seq2


title: H446 cells, Non-targeting gRNA, clone 13, JQ1, biol rep 2

description:
H446_NTgRNA_cl_13_JQ1_2
Biological replicate 2
mRNA


title: H446 cells, Non-targeting gRNA, clone 13, JQ1, biol rep 3

description:
H446_NTgRNA_cl_13_JQ1_3
Biological replicate 3
mRNA


title: S156_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 697


title: genomic DNA from TNBC patient number 696


title: genomic DNA from TNBC patient number 778


title: rep1_96h_LPS [DRN-21460]


title: rep3_96h_LPS [DRN-21464]


title: S155_single cell rna seq by Smart Seq2


title: H446 cells, Non-targeting gRNA, clone 13, JQ1, biol rep 1

description:
H446_NTgRNA_cl_13_JQ1_1
Biological replicate 1
mRNA


title: genomic DNA from TNBC patient number 69


title: H446 cells, Non-targeting gRNA, clone 10, JQ1, biol rep 3

description:
H446_NTgRNA_cl_10_JQ1_3
Biological replicate 3
mRNA


title: genomic DNA from TNBC patient number 670


title: rep1_16h_LPS [DRN-21459]


title: rep4_96h_TGFb [DRN-21458]

value: TGFb


title: H446 cells, Non-targeting gRNA, clone 10, JQ1, biol rep 2

description:
H446_NTgRNA_cl_10_JQ1_2
Biological replicate 2
mRNA


title: S153_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 666

description: triple negative breast cancer tissue sample


title: genomic DNA from TNBC patient number 658


title: S152_single cell rna seq by Smart Seq2


title: H446 cells, Non-targeting gRNA, clone 10, JQ1, biol rep 1

description:
H446_NTgRNA_cl_10_JQ1_1
Biological replicate 1
mRNA


title: genomic DNA from TNBC patient number 70


title: rep3_96h_TGFb [DRN-21456]


title: H446 cells, Non-targeting gRNA, clone 3, JQ1, biol rep 3

description:
H446_NTgRNA_cl_3_JQ1_3
Biological replicate 3
mRNA


title: S151_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR912_2.dge.txt.gz


title: genomic DNA from TNBC patient number 65


title: H446 cells, Non-targeting gRNA, clone 3, JQ1, biol rep 2

description:
H446_NTgRNA_cl_3_JQ1_2
Biological replicate 2
mRNA


title: S150_single cell rna seq by Smart Seq2


title: rep3_16h_TGFb [DRN-21455]


title: rep2_96h_TGFb [DRN-21454]


title: H446 cells, Non-targeting gRNA, clone 3, JQ1, biol rep 1

description:
H446_NTgRNA_cl_3_JQ1_1
Biological replicate 1
mRNA


title: S157_single cell rna seq by Smart Seq2


title: S154_single cell rna seq by Smart Seq2


title: S149_single cell rna seq by Smart Seq2


title: S148_single cell rna seq by Smart Seq2


title: H446 cells, Non-targeting gRNA, clone 13, DMSO, biol rep 3

description:
H446_NTgRNA_cl_13_3
Biological replicate 3
mRNA


title: rep2_16h_TGFb [DRN-21453]


title: rep4_16h_TGFb [DRN-21457]


title: genomic DNA from TNBC patient number 637


title: H446 cells, Non-targeting gRNA, clone 13, DMSO, biol rep 2

description:
H446_NTgRNA_cl_13_2
Biological replicate 2
mRNA


title: S147_single cell rna seq by Smart Seq2


title: H446 cells, Non-targeting gRNA, clone 13, DMSO, biol rep 1

description:
H446_NTgRNA_cl_13_1
Biological replicate 1
mRNA


title: S146_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 626


title: rep1_16h_TGFb [DRN-21451]


title: genomic DNA from TNBC patient number 656


title: rep4_96h_IFNg [DRN-21450]

value: IFNg


title: genomic DNA from TNBC patient number 624


title: genomic DNA from TNBC patient number 649


title: S145_single cell rna seq by Smart Seq2


title: H446 cells, Non-targeting gRNA, clone 10, DMSO, biol rep 3

description:
H446_NTgRNA_cl_10_3
Biological replicate 3
mRNA


title: genomic DNA from TNBC patient number 622


title: rep4_16h_IFNg [DRN-21449]


title: S144_single cell rna seq by Smart Seq2


title: S143_single cell rna seq by Smart Seq2


title: H446 cells, Non-targeting gRNA, clone 10, DMSO, biol rep 2

description:
H446_NTgRNA_cl_10_2
Biological replicate 2
mRNA


title: genomic DNA from TNBC patient number 599


title: H446 cells, Non-targeting gRNA, clone 10, DMSO, biol rep 1

description:
H446_NTgRNA_cl_10_1
Biological replicate 1
mRNA


title: rep3_96h_IFNg [DRN-21448]


title: H446 cells, Non-targeting gRNA, clone 3, DMSO, biol rep 3

description:
H446_NTgRNA_cl_3_3
Biological replicate 3
mRNA


title: rep1_96h_TGFb [DRN-21452]


title: genomic DNA from TNBC patient number 642


title: rep3_16h_IFNg [DRN-21447]


title: genomic DNA from TNBC patient number 574


title: S142_single cell rna seq by Smart Seq2


title: rep2_96h_IFNg [DRN-21446]


title: H446 cells, Non-targeting gRNA, clone 3, DMSO, biol rep 2

description:
H446_NTgRNA_cl_3_2
Biological replicate 2
mRNA


title: S141_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 512


title: rep2_16h_IFNg [DRN-21445]


title: rep1_96h_IFNg [DRN-21444]


title: genomic DNA from TNBC patient number 510


title: genomic DNA from TNBC patient number 484


title: genomic DNA from TNBC patient number 466


title: rep1_16h_IFNg [DRN-21443]


title: S139_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 460


title: S137_single cell rna seq by Smart Seq2


title: S138_single cell rna seq by Smart Seq2


title: rep4_96h_PBS [DRN-21442]

value: PBS


title: genomic DNA from TNBC patient number 432


title: S136_single cell rna seq by Smart Seq2


title: rep4_16h_PBS [DRN-21441]


title: WT_1

city: chongqing

first: Zhongwei

last: He

address: xinqiao

institute: Xinqiao Hospital

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the GRCz11 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCz11
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Danio rerio

source_name: kidney

growth_protocol: Zebrafish were maintained at 28.5 ℃ in the system water with a dark/light cycle of 10h/14h and fed two times daily.

extract_protocol:
The total DNA was sheared into 100-500 bp fragments using ultrasonic crusher. The ChIP pull down assay was performed by incubating 25 µg of chromatin samples (in equal volume) with 2.5 µg of antibodies (anti-H3K4me3 (CST, 9751) or Rabbit IgG (CST, 66326, as negative control)) for 24 hours at 4 °C on a vertical rotor
ChIP-seq libraries were prepared using the  CUT&RUN Assay kit (CST, 86652) following an agarose bead wash and incubating the complex with the beads for 3 hours at 4 °C.The ChIP pull down assay was performed by incubating 25 µg of chromatin samples (in equal volume) with 2.5 µg of antibodies (anti-H3K4me3 (CST, 9751) or Rabbit IgG (CST, 66326, as negative control)) for 24 hours at 4 °C on a vertical rotor.Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Intraperitoneal injection of gentamicin in zebrafish

tag: antibody

value: kidney

tag: group

value: Intraperitoneal injection of 0.9%NaCl


title: WT_Input

value: input

value: WT


title: rep3_96h_PBS [DRN-21440]

value: nM

value: 96 hours

value: iPSC derived microglia


title: genomic DNA from TNBC patient number 423


title: WT_3


title: S135_single cell rna seq by Smart Seq2

value: HSC


title: RD5_3

value: 5 dpi

value: Intraperitoneal injection of gentamicin


title: RD5_Input


title: genomic DNA from TNBC patient number 421

value: Female

value: Tumor tissue


title: S140_single cell rna seq by Smart Seq2

value: MECOM KO


title: RD5_2


title: S134_single cell rna seq by Smart Seq2


title: H446 cells, Non-targeting gRNA, clone 3, DMSO, biol rep 1

description:
H446_NTgRNA_cl_3_1
Biological replicate 1
mRNA

value: small cell lung cancer SCLC-N subtype

value: DMSO

value: 24 hours


title: rep3_16h_PBS [DRN-21439]

value: PBS

value: 16 hours


title: rep2_96h_PBS [DRN-21438]


title: RD3_Input

value: kidney


title: genomic DNA from TNBC patient number 374

value: TNBC


title: S133_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 357


title: RD3_2


title: S132_single cell rna seq by Smart Seq2


title: rep2_16h_PBS [DRN-21437]

value: WT


title: rep1_96h_PBS [DRN-21436]

value: nM


title: genomic DNA from TNBC patient number 340


title: S131_single cell rna seq by Smart Seq2


title: RD3_1


title: T1a1b3

city: Wuhan

first: Danna

last: Jia

address: 1037 Luoyu Road

institute: Huazhong University of Science and Technology

data_processing:
Illumina Novaseq 6000 software used for basecalling.
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 poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 and paired-end clean reads were aligned to the reference genome using Hisat2.
TPM conversion was performed to obtain the standardized gene/transcript expression level.
Assembly: GRCz11
Supplementary files format and content: *_TPM.csv: Comma-separated text files include TPM values.

source_name: head

extract_protocol:
The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: head

tag: strain

value: AB

value: tulp1a&tulp1b knockout

tag: developmental stage

value: 4 dpf


title: S130_single cell rna seq by Smart Seq2

value: HSC


title: genomic DNA from TNBC patient number 294

value: Female


title: genomic DNA from TNBC patient number 287

value: Tumor tissue


title: S129_single cell rna seq by Smart Seq2

value: MECOM KO


title: rep4_96h_ISO-ATV [DRN-21419]

value: ISO-ATV

value: 96 hours

value: iPSC derived microglia


title: rep1_16h_PBS [DRN-21435]

value: PBS


title: T1a1b2


title: T1a1b1


title: genomic DNA from TNBC patient number 237


title: S128_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 249


title: WT3

value: wild type


title: S127_single cell rna seq by Smart Seq2


title: rep3_96h_ISO-ATV [DRN-21417]


title: rep4_16h_ISO-ATV [DRN-21418]

value: 16 hours


title: genomic DNA from TNBC patient number 199

value: TNBC


title: WT2


title: genomic DNA from TNBC patient number 198


title: S125_single cell rna seq by Smart Seq2


title: WT1


title: genomic DNA from TNBC patient number 195


title: S124_single cell rna seq by Smart Seq2


title: Col-0-rep3.mRNA-seq

city: Hangzhou

first: Fengli

last: Zhao

state: Zhejiang

address: No. 28 of Shuidaosuo Road

department: State Key Laboratory of Rice Biology and Breeding

institute: China National Rice Research Institute

description:
mRNA-seq data
Col-0.mRNA.intron.SS-ratio.txt
Col-0.mRNA.5bp.bw

data_processing:
The adapters, Ns and low-quality bases were removed from raw data using the Trimmomatic package (version 0.39). Then, the reads shorter than 36 bp were also removed.
The clean reads were mapped to the TAIR10 genome using the HISAT2 (version 2.2.0) with default parameters.
The reads with more than one reported alignment were excluded. The mapped reads were sorted and indexed by SAMtools (version 1.3.1).
The Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) of each gene were calculated by StringTie [4] (version 2.1.4). Genes with FPKM ≥ 1 were used for the calculation of 5’SS or 3’SS ratio.
Assembly: TAIR10 genome
Supplementary files format and content: BigWig, useful for dense, continuous data that will be displayed in the Genome Browser as a graph.
Supplementary files format and content: SS-ratio, tab-separated text that contains splicing efficiency values for introns of each expressed gene

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol:
Honda buffer and nuclei resuspension buffer extract the nuclear component. Trizol reagent,chloroform and RNeasy kit extract the RNAs.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: seedling

tag: ecotype

value: mRNA


title: Col-0-rep2.mRNA-seq


title: genomic DNA from TNBC patient number 188


title: S123_single cell rna seq by Smart Seq2

source_name: HSC


title: Col-0-rep1.mRNA-seq


title: genomic DNA from TNBC patient number 18


title: rep1_16h_ISO-ATV [DRN-21412]

value: WT

value: nM


title: S122_single cell rna seq by Smart Seq2


title: rep1_96h_ISO-ATV [DRN-21413]


title: genomic DNA from TNBC patient number 177


title: genomic DNA from TNBC patient number 154


title: Col-0-rep1.cb-RNA-seq

description:
CB-RNA-seq data
Col-0.cb-RNA.intron.SS-ratio.txt
Col-0.cb-RNA.5bp.bw

data_processing:
The adapters, Ns and low-quality bases were removed from raw data using the Trimmomatic package (version 0.39). Then, the reads shorter than 36 bp were also removed.
The clean reads were mapped to the TAIR10 genome using the HISAT2 (version 2.2.0) with default parameters.
The reads with more than one reported alignment were excluded. The mapped reads were sorted and indexed by SAMtools (version 1.3.1).
The Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) of each gene were calculated by StringTie [4] (version 2.1.4). Genes with FPKM ≥ 1 were used for the calculation of 5’SS or 3’SS ratio.
Assembly: TAIR10 genome
Supplementary files format and content: BigWig, useful for dense, continuous data that will be displayed in the Genome Browser as a graph.
Supplementary files format and content: SS-ratio, tab-separated text that contains splicing efficiency values for introns of each expressed gene
Library strategy: CB-RNA-seq

molecule: nuclear RNA

value: CB-RNA (rRNA removed)


title: 293T-Pol_II-ChIP-NaOH-merge

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

institute: Wuhan University

description: ChIP-seq-Rx

data_processing:
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
Assembly: Drosophila melanogaster.dm6
Supplementary files format and content: Library normalized bigWig files were provided for all samples

source_name: ChIP-seq analysis with Pol_II and Hemin merge data

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 for 6 hours, 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 or HeLa 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.
qPRO-seq was performed as previously reported (Judd et al. 2020; Li et al. 2021).
G4-CUT&Tag and R-loop CUT&Tag were performed as previously described( Wang et al. 2021; Li et al. 2021)
RNA Sequencing (RNA-seq) Following Hemin treatment for 6 hours, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer’s instructions. 1 μg total RNA was spike-in with 100 ng Drosophila S2 RNA and was further used for mRNA isolation with VAHTS mRNA Capture Beads (Vazyme, N401) following the manufacturer's instructions. Then library preparation was done using the NEBNext Ultra II Directional RNA Library Prep Kit, followed by sequencing on a NovaSeq 6000.

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

tag: tag

value: Derived from embryonic kidney

value: untreated


title: Col-0-rep2.cb-RNA-seq


title: rep3_16h_ISO-ATV [DRN-21416]

tag: cell type


title: S120_single cell rna seq by Smart Seq2

value: HSC


title: S121_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 137

description: triple negative breast cancer tissue sample

value: Female

tag: tissue

value: Tumor tissue


title: Col-0.G3-rep2.cb-RNA-seq

description:
CB-RNA-seq data
Col-0.G3.cb-RNA.intron.SS-ratio.txt
Col-0.G3.cb-RNA.5bp.bw

value: CB-RNA (only polyA RNA)


title: rep2_96h_ISO-ATV [DRN-21415]

value: ISO-ATV

value: 96 hours


title: S126_single cell rna seq by Smart Seq2

value: MECOM KO


title: rep2_16h_ISO-ATV [DRN-21414]

value: iPSC derived microglia


title: Col-0.G3-rep1.cb-RNA-seq


title: S119_single cell rna seq by Smart Seq2


title: S118_single cell rna seq by Smart Seq2


title: 293T-RNA-seq-Hemin-80uM-6h-rep2

description: RNA-seq

source_name: 293T cells RNA-seq with Hemin replicate2

value: treated with Hemin for 6 hours


title: S117_single cell rna seq by Smart Seq2


title: genomic DNA from TNBC patient number 128

tag: disease state

value: TNBC


title: Col-0.G2-rep2.cb-RNA-seq

description:
CB-RNA-seq data
Col-0.G2.cb-RNA.intron.SS-ratio.txt
Col-0.G2.cb-RNA.5bp.bw

value: seedling

tag: treatment


title: genomic DNA from TNBC patient number 105


title: S116_single cell rna seq by Smart Seq2

description:
single cell SS2 for MECOM KO
ss2_processed.tar
ss2_processed.tar/MR912_2.dge.txt.gz


title: 293T-RNA-seq-Hemin-80uM-6h-rep1

description: RNA-seq

source_name: 293T cells RNA-seq with Hemin replicate1


title: Col-0.G2-rep1.cb-RNA-seq


title: 293T-RNA-seq-Hemin-0uM-6h-rep2

description: RNA-seq

source_name: 293T cells RNA-seq replicate2


title: 293T-Pol_II-ChIP-Hemin-80uM-rep1

description: ChIP-seq-Rx

source_name: ChIP-seq analysis with Pol_II and Hemin replicate1

value: treated with Hemin for 2 hours


title: 293T-Pol_II-ChIP-Hemin-80uM-rep2

description: ChIP-seq-Rx

source_name: ChIP-seq analysis with Pol_II and Hemin replicate2


title: S115_single cell rna seq by Smart Seq2


title: Kasumi-1 cells, Control knockdown replicate 2

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

data_processing:
Library strategy: Ribometh-Seq
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina NextSeq 500 or HiScanSQ respectively
Adapter sequences were removed using Cutadapt with a minimum length of 15 nt
Reads were mapped using Bowtie2 to a reference sequence file containing rDNA sequences of U18, U28 and U5.8S and splicosomal RNA U1, U12, U2, U4, U5 and U6
For each position the number of 5’-read ends was counted.
2’O-methyation was calculated as scoreC based on 5’-end frequencies as described before by Birkedal et al., 2015
Genome_build: Annotation of modification sites as well as rRNA & snRNA sequence were downloaded from https://www-snorna.biotoul.fr. Furthermore we considered novel sites reported by Krogh 2016, Jorjani 2016 and Sharma 2017
Supplementary_files_format_and_content: RiboMethSeq_scoreC.txt contains calculated scoreC for annotated modification sites: subunit TAB pos TAB annotation TAB sample_scoreC

growth_protocol: The cells were cultured in RPMI1640 with 20% FBS and 1% Penicillin-Streptomycin. For FBL knockdown, the cells were induced with 100 ng/ml doxycycline.

extract_protocol:
Total RNA was extracted with mirRNeasy mini kit (NEB).
100 ng total RNA was fragmented by alkaline hydrolysis at 95°C for 12 min. to achieve a fragment length of about 30 nucleotides. Libraries were prepared using the NEBNext® Small RNA library prep kit.

value: AML cell

value: 100 ng/ml doxycycline

tag: expression

value: Ctrl knockdown

tag: re-expression

value: no re-expression


title: Col-0.G1-rep2.cb-RNA-seq

description:
CB-RNA-seq data
Col-0.G1.cb-RNA.intron.SS-ratio.txt
Col-0.G1.cb-RNA.5bp.bw

value: CB-RNA (mRNA and rRNA removed)

tag: age


title: Kasumi-1 cells, Control knockdown replicate 1


title: Col-0.G1-rep1.cb-RNA-seq


title: 293T-NRF2-ChIP-Hemin

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with NRF2 and Hemin

value: Derived from embryonic kidney


title: vil1-1 R3

city: Austin

first: Wei

last: Zong

state: Texas

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Raw reads wer mapped to the TAIR10 Arabidopsis genome using Bowtie 2 with default parameters
Featurecount was used to count read numbers of each gene
edgeR was used to identify differentially expressed genes
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include counted reads  of each gene for each sample

source_name: seedlings

growth_protocol: For seed germination, seeds were sterilized and placed on filter paper and then stratified for 3 days at 4 ℃ under dark condition; seeds were germinated on 1/2 Murashige and Skoog (MS) plates containing 0.8% Phytagel. Seedlings were grown in growth chamber with 16-h light/8-h dark cycles at 22℃.

extract_protocol:
Total RNA was isolaed from 1-day-old seedlings using Purelink Plant RNA Regent (Invitrogen) according to manufacturer's instructions.
RNA-Seq libraries were prepared by Genomic Sequencing and Analysis Facility at Univeristy of Texas at Austin

tag: genotype

value: vil1 mutant

value: 1 day old

value: whole seedling


title: S114_single cell rna seq by Smart Seq2

value: HSC


title: 293T-NRF2-ChIP-Ctrl

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with NRF2

value: untreated


title: vil1-1 R2


title: Kasumi-1 cells, FBL knockdown replicate 2

value: FBL knockdown


title: 293T-ChIP-Bach1-Hemin

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with Bach1 and Hemin


title: S113_single cell rna seq by Smart Seq2

value: MECOM KO


title: S112_single cell rna seq by Smart Seq2


title: Kasumi-1 cells, FBL knockdown replicate 1


title: genomic DNA from TNBC patient number 122

tag: gender

value: Female

value: Tumor tissue


title: rep2_16h_LPS [DRN-21461]

value: WT

value: LPS

value: nM

value: 16 hours

value: iPSC derived microglia


title: vil1-1 R1


title: 293T-ChIP-Bach1-Ctrl

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with Bach1

tag: cell line


title: 293T-RNA-seq-Hemin-0uM-6h-rep1

description: RNA-seq

source_name: 293T cells RNA-seq replicate1


title: S111_single cell rna seq by Smart Seq2


title: Col-0 R3

value: wild type


title: S109_single cell rna seq by Smart Seq2


title: Col-0 R2


title: 293T-ChIP-RBBP5-Hemin

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with RBBP5 and Hemin

value: treated with Hemin for 2 hours


title: S110_single cell rna seq by Smart Seq2


title: 293T-ChIP-RBBP5-Ctrl

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with RBBP5

value: Derived from embryonic kidney


title: 293T-ChIP-P300-Hemin

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with P300 and Hemin


title: Col-0 R1


title: S108_single cell rna seq by Smart Seq2


title: 293T-ChIP-P300-Ctrl

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with P300


title: S106_single cell rna seq by Smart Seq2

source_name: HSC


title: WT+AA_Rep2

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was converted into FASTQ files using Cell Ranger mkfastq (version 3.0.2)
FASTQ files were aligned to the mm10 genome (downloaded from the 10X Genomics website) using Cell Ranger count (version 3.0.2)
Cell Ranger output was analyzed using Seurat (version 2.3.4)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
The tissues were minced and digested with Liberase TM (0.5 mg/ml with 100U/mL of DNAse) for 20 min at room temperature and GFP+ cells were sorted by BD FACSAria SORP system
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: 8-week-old SARATg or WT mice crossed with PDGFRb-Cre and Z/EG reporter mice were subjected to either repeated subcutaneous bleomycin (20mg/kg BW 3x week for 2 weeks) or intraperitoneal injection of aristolochic acid (5mg/kg BW 3x week for 3 weeks) to induce skin or kidney fibrosis respectively, and skin an kiney were harvested.

value: kidney

value: PDGFRb+GFP+

value: Wildtype

value: Aristolochic acid IP injection


title: P3-904

city: Harbin

first: Zhang

last: Yi

address: xiangan street num 766

institute: The Fourth Affiliated Hospital of Harbin Medical University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp 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. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Brain

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Brain

value: Slc20a2 homozygous (HO) knockout

value: Placebo treatment


title: F3-612

value: FTY720 treatment


title: P3-612


title: S107_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

extract_protocol:
mRNA isolated by  polyT beads
Smart Seq2

value: HSC

value: MECOM KO


title: P1-623


title: F3-908


title: P3-907


title: WT+AA_Rep3


title: OE-AA_Rep2

value: Sara Transgene

value: Vehicle IP injection


title: 293T-ChIP-H3K4me3-NaOH

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with H3K4me1

value: untreated


title: 293T-ChIP-H3K4me3-Hemin

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with H3K4me1 and Hemin


title: F3-609


title: F1-918


title: S105_single cell rna seq by Smart Seq2


title: S104_single cell rna seq by Smart Seq2


title: OE+AA_Rep1


title: F1-624


title: WT-AA_Rep3


title: F1-622


title: S102_single cell rna seq by Smart Seq2


title: WT+AA_Rep1


title: 293T-ChIP-H3K4me2-NaOH

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with H3K4me2


title: 293T-ChIP-H3K4me2-Hemin

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with H3K4me2 and Hemin


title: 2iSL_40hr_2

city: New York

first: Lydia

last: Finley

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Quality control and filtering of raw fastq files was performed using fastp.
Sequencing reads were aligned to mm10 using STAR.
Raw counts were generated using featurecounts.
Assembly: mm10
Supplementary files format and content: Processed data files include raw counts for each sample in CSV format.

source_name: mouse embryonic stem cells

growth_protocol: ES cells were maintained on gelatin-coated plates in the following media: serum/LIF, serum/LIF+2i or 2i/LIF. Serum/LIF medium contained knockout DMEM (10829018; Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Gemini), 0.1 mM 2-mercaptoethanol, 2 mM l-glutamine and 1,000 U ml−1 LIF (Gemini). To generate serum/LIF+2i maintenance medium, serum/LIF medium was supplemented with 3 μM CHIR99021 (Stemgent) and 1 μM PD0325901 (Stemgent) (2i). 2i/LIF medium contained a 1:1 mix of DMEM/F-12 (11320033; Gibco) and Neurobasal medium (21103049; Gibco) including N-2 supplement (17502048; Gibco), B-27 supplement (17504044; Gibco), 2-mercaptoethanol, 2 mM l-glutamine, LIF and 2i. To generate ES cells in the naive ground state of pluripotency, serum/LIF-cultured ES cells were adapted for three passages to serum/LIF+2i medium or 2i/LIF medium. Adapted cells were used for a maximum of nine passages.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: For exit from naive pluripotency, serum/LIF+2i-cultured ES cells were seeded at least 24 h before washing with PBS and changing into medium containing a 1:1 mix of glutamine-free DMEM (11960051; Gibco) and Neurobasal medium including N-2 supplement, B-27 supplement, 2-mercaptoethanol and 2 mM l-glutamine at the indicated time before collection (24 or 40 h). 2i/LIF-cultured ES cells were seeded at least 24 h before being washed with PBS and changed into serum-free maintenance medium without 2i or LIF at the indicated time before collection (12, 24 or 40 h).

value: mESC

value: 2i + serum/LIF media, 40 hours after exit from pluripotency


title: 293T-ChIP-H3K4me1-Hemin

description: ChIP-seq-Rx

value: treated with Hemin for 2 hours


title: WT-AA_Rep1


title: S101_single cell rna seq by Smart Seq2

first: Liming

last: Tao

institute: Broad Institute of Harvard and MIT


title: 2iSL_40hr_1


title: 2iSL_24hr_2

value: 2i + serum/LIF media, 24 hours after exit from pluripotency


title: S98_single cell rna seq by Smart Seq2


title: 293T-ChIP-H3K4me1-NaOH

description: ChIP-seq-Rx

value: Derived from embryonic kidney


title: S99_single cell rna seq by Smart Seq2


title: 293T-ChIP-H3K27ac-NaOH

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with H3K27ac


title: 2iSL_24hr_1


title: OE-AA_Rep1

value: kidney

value: PDGFRb+GFP+


title: WT_Bleomycin_Rep3

source_name: skin

value: skin

value: Wildtype

value: Bleomycin Sub-Q injection


title: 293T-ChIP-H3K27ac-Hemin

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with H3K27ac and Hemin


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

description: ChIP-seq-Rx

source_name: 293T cells ChIP-seq analysis with TFIIB

value: TFIIB


title: S97_single cell rna seq by Smart Seq2


title: S103_single cell rna seq by Smart Seq2


title: 293T-PROseq-NaOH-rep2

description: qPRO-seq

source_name: qPRO-seq  analysis with 293T replicate2


title: 2iSL_12hr_2

value: 2i + serum/LIF media, 12 hours after exit from pluripotency


title: SaraTG_Bleomycin_Rep1


title: 293T-PROseq-NaOH-rep1

description: qPRO-seq

source_name: qPRO-seq  analysis with 293T replicate1


title: S96_single cell rna seq by Smart Seq2

description:
single cell SS2 for AAVS1 KO
ss2_processed.tar
ss2_processed.tar/AAVS912_1.dge.txt.gz

value: HSC

value: AAVS1 KO


title: S100_single cell rna seq by Smart Seq2

value: MECOM KO


title: WT-AA_Rep2

value: Vehicle IP injection


title: WT_PBS_Rep3

value: PBS Sub-Q injection


title: SaraTG_PBS_Rep1

value: Sara Transgene


title: S94_single cell rna seq by Smart Seq2


title: S95_single cell rna seq by Smart Seq2


title: 293T-PROseq-Hemin-80ul-rep1

description: qPRO-seq

source_name: qPRO-seq  analysis 293T with hemin treatment replicate1


title: 2iSL_0hr_1

value: mESC

value: 2i + serum/LIF media


title: 2iLIF_40hr_2

value: 2i/LIF media, 40 hours after exit from pluripotency


title: 2iSL_0hr_2


title: WT_PBS_Rep2


title: 2iLIF_40hr_1


title: WT_Bleomycin_Rep1


title: 293T-R-loop-CUT-Tag-CTRL

description: CUT&Tag

source_name: R-Loop CUT&Tag analysis with 2HBD

value: Derived from embryonic kidney

value: untreated


title: 2iLIF_24hr_2

value: 2i/LIF media, 24 hours after exit from pluripotency


title: S91_single cell rna seq by Smart Seq2


title: 293T-G4-Hemin-80uM-CUT-Tag

description: CUT&Tag

source_name: G4 CUT&Tag hemin treatment, analysis with Flag-BG4 antibody

value: treated with Hemin for 2 hours


title: 293T-G4-CUT-Tag

description: CUT&Tag

source_name: G4 CUT&Tag analysis with Flag-BG4 antibody


title: 2iLIF_24hr_1


title: WT_PBS_Rep1

value: skin

value: PDGFRb+GFP+

value: Wildtype


title: S90_single cell rna seq by Smart Seq2

source_name: HSC


title: 2iSL_12hr_1

value: 2i + serum/LIF media, 12 hours after exit from pluripotency


title: 516_primary_cell_line

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: GRCm38
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: normal primary renal epithelial cells

value: WT

value: male


title: HeLa-biotin-PEG4-hemin-CUT-Tag

description: CUT&Tag

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

value: HeLa

value: Derived from uterus adenocarcinoma


title: 515_primary_cell_line


title: 293T-PROseq-Hemin-80ul-rep2

description: qPRO-seq

source_name: qPRO-seq  analysis 293T with hemin treatment replicate2


title: 2iLIF_12hr_2

value: mESC

value: 2i/LIF media, 12 hours after exit from pluripotency


title: S89_single cell rna seq by Smart Seq2

city: Cambridge

address: 415 Main Street

value: HSC

value: AAVS1 KO


title: acute myeloid leukemia (AML)_DR99

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from Ensembl genome browser website. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups  (three biological replicates per condition) was performed using DESeq2 R package.
The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially  expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts, FPKMs

source_name: leukemia blast cells

extract_protocol:
Total RNA was extracted with miRNeasy Kits (NEB).
A total amount of 1µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for lliumina® (NEB, USA) following manufacturer 's recommendations.
Transcriptomic RNA-sequencing of poylA enrichmed molecules

value: leukemia blast cells

value: AML

tag: aml status

value: de novo

tag: fab type

tag: Sex

value: f


title: 293T-R-loop-CUT-Tag-Hemin

description: CUT&Tag

source_name: R-Loop CUT&Tag hemin treatment ,analysis with 2HBD

value: Derived from embryonic kidney

value: treated with Hemin for 2 hours

tag: antibody


title: S93_single cell rna seq by Smart Seq2


title: WT_Bleomycin_Rep2

value: skin

value: PDGFRb+GFP+

value: Wildtype

value: Bleomycin Sub-Q injection


title: 513_primary_cell_line

value: kidney

value: normal primary renal epithelial cells

value: WT

value: male


title: 2iLIF_12hr_1

source_name: mouse embryonic stem cells

value: mESC

value: 2i/LIF media, 12 hours after exit from pluripotency


title: 286_T1_tumour_cell_line

value: VpR tumour cell line

value: ccRCC

value: Vhl, Trp53, Rb1 knockout


title: acute myeloid leukemia (AML)_DR96

value: leukemia blast cells

value: AML

value: de novo


title: acute myeloid leukemia (AML)_DR98

value: m


title: 2iLIF_0hr_2

value: 2i/LIF media


title: S87_single cell rna seq by Smart Seq2

value: HSC

value: AAVS1 KO


title: S86_single cell rna seq by Smart Seq2


title: S92_single cell rna seq by Smart Seq2


title: 126_T2_tumour_cell_line


title: S85_single cell rna seq by Smart Seq2


title: 2iLIF_0hr_1


title: acute myeloid leukemia (AML)_DR95


title: S84_single cell rna seq by Smart Seq2


title: 244_T2_tumour_cell_line


title: Output mouse scSTARR-seq, E15.5 Injection; scRNA-seq

city: Durham

first: Craig

middle: Barrett

last: Lowe

state: North Carolina

address: 213 Research Dr

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

description: 10x Genomics

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

source_name: Cerebral Cortex

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

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

value: Cerebral Cortex

value: E15.5 Injection; E16.5 Sequencing

value: In utero electroporation


title: 83_T1_tumour_cell_line

value: kidney

value: female


title: acute myeloid leukemia (AML)_DR94

value: f


title: acute myeloid leukemia (AML)_DR93


title: BMDM, Wdfy3 knockout, replicate 4

first: Hanrui

last: Zhang

state: United States

address: 630 West 168th Street

institute: Columbia University Irving Medical Center

data_processing:
Raw sequencing reads were mapped to the mouse genome version GRCm39 (M27) using Salmon (version 1.5.1) to obtain transcript abundance counts. MultiQC was used to generate quality control reports based on Salmon read mapping results.
The transcript-level count information was summarized to the gene level using tximport (version 1.20.0).
Differential expression was assessed using DESeq2 (version 1.34.0). Genes with an absolute fold change > 1.5 and false discovery rate (FDR)-adjusted P value < 0.05 were considered as differentially expressed (DE).
Assembly: mm10
Supplementary files format and content: tab-delimited text file for salmon counts
Supplementary files format and content: tab-delimited text file for DESeq2 normalized counts by rld

source_name: BMDM

growth_protocol: Bone marrow (BM) cells from 9-10 week old mice were isolated by flushing femurs and tibia with DMEM basal medium using 10 mL syringes with 22G needles (day 0). The isolated BM cells were cultured at 37°C, 5% CO2 on non-tissue-culture-treated vessels for 7-10 days in BMDM culture medium containing DMEM supplemented with 10% (vol/vol) heat-activated fetal bovine serum (HI-FBS), 20% (vol/vol) L-929 fibroblast conditioned medium, and 2 mM L-Glutamine. During differentiation, the growth medium was replaced with fresh medium 96 h after seeding and then every 2-3 days. BMDMs were harvested at day 8 for RNA extraction.

extract_protocol:
Total RNAs were extracted from BMDMs (9-10 weeks old male mice: 4 Cre- and 4 Cre+) using the Quick-RNA miniprep plus kit (Zymo).
With a minimum of 300 ng input RNA, strand-specific, poly(A)+ libraries were prepared and sequenced at 20 million 100-bp paired-end reads per sample.

value: BMDM

value: LysMCre+ Wdfy3 knockout

value: Male

value: 9-10 weeks


title: S83_single cell rna seq by Smart Seq2


title: 99_T1_tumour_cell_line

value: VpR tumour cell line

value: ccRCC

value: Vhl, Trp53, Rb1 knockout


title: acute myeloid leukemia (AML)_DR92

value: leukemia blast cells

value: AML

value: de novo

value: m


title: Group_4_inoculum

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

organism: [Haemophilus] ducreyi

source_name: culture

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: culture


title: BMDM, Wdfy3 knockout, replicate 3


title: S88_single cell rna seq by Smart Seq2

value: HSC

value: AAVS1 KO


title: Group_3_inoculum


title: S82_single cell rna seq by Smart Seq2


title: BMDM, Wdfy3 knockout, replicate 2


title: acute myeloid leukemia (AML)_DR91


title: S81_single cell rna seq by Smart Seq2


title: S80_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR90


title: Group_2_inoculum


title: Output mouse scSTARR-seq, E14.5 Injection; scRNA-seq

description: 10x Genomics

value: Cerebral Cortex

value: E14.5 Injection; E15.5 Sequencing

value: In utero electroporation


title: acute myeloid leukemia (AML)_DR09


title: BMDM, Wdfy3 knockout, replicate 1

value: BMDM


title: BMDM, Control, replicate 4

value: LysMCre- Control


title: S79_single cell rna seq by Smart Seq2


title: S78_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR87


title: acute myeloid leukemia (AML)_DR88

value: f


title: acute myeloid leukemia (AML)_DR89


title: S77_single cell rna seq by Smart Seq2


title: S76_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR86


title: BMDM, Control, replicate 3

value: Male

value: 9-10 weeks


title: BMDM, Control, replicate 1


title: S75_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR85

value: sAML


title: S74_single cell rna seq by Smart Seq2


title: microglia, ATV:4D9-7-Day (NH35G)

data_processing:
BCL files output by the sequencer were demultiplexed with 10X Genomics' cellranger mkfastq command (version 3.1.0)
Raw reads (FASTQ files) were processed with 10X Genomics' cellranger count command (version 4.0.0) with the following arguments: --transcriptome=refdata-gex-mm10-2020-A --expect-cells=10000
Assembly: mm10
Supplementary files format and content: HDF5 files with raw counts per gene per droplet, produced by cellranger (version 4.0.0) as raw_feature_bc_matrix.h5
Supplementary files format and content: filtered counts for all droplets that passed QC in Matrix Market (mtx) format, gzip-compressed
Supplementary files format and content: 3 CSV files with metadata accompanying the mtx file: cell_barcodes.csv, gene_symbols.csv, filtered_counts_metadata.csv

source_name: Cortex and hipocampus

growth_protocol: hTfR KI mice were used for this study and this mouse model was originally generated at Denali. Animals were bred at JAX Laboratories and transferred to Denali at least two weeks before the initiation of the study for acclimation. Animals were housed in standard conditions in Denali’s vivarium with ad libitum access to food and water.

extract_protocol:
Sixteen mice were divided into three batches for processing, each batch contains all five conditions, and a 16th animal was added to the third batch as a control sample.  Mice were perfused with PBS and each hemibrain was dissociated using the Adult Brain Dissociation kit Mouse and Rat (Miltenyi, 130-107-677).  Single cell suspensions were labeled with CD45 MicroBeads Mouse (Miltenyi, 130-052-301) for MACS sorting of microglia.  The enriched microglia cells stored in PBS with 1% BSA were filtered through a 30 μm strainer and counted via hemocytometer for single cell capture using the Chromium Controller (10X Genomics).  Each sample was loaded with a target recovery of 10,000 cells.
Single cell libraries were constructed using the Chromium Single Cell 3ʹ Reagent Kits v3 (10X Genomics, PN-1000075).  Each library was barcoded with single indexing using the Chromium i7 Multiplex Kit (10X Genomics, PN-120262), and combined equimolar into a pool for sequencing on a MiSeq sequencer (Illumina) to determine actual single cell capture rate.  A final sequencing pool was combined using the MiSeq cell count values to target a minimum of 20,000 read pairs per cell.  The final sequencing pool was shipped to SeqMatic (Fremont) for sequencing on a NovaSeq 6000 with an S2 flowcell (28X91X8).

treatment_protocol: Mice were dosed with ATV:4D9 (10mg/kg) or ATV:RSV (10 mg/kg) antibodies a single time.

value: brain

tag: tissue region

value: Cortex and hipocampus

value: microglia

tag: strain

tag: age unit

value: months

tag: batch

value: hTfR KI

tag: treatment dose

tag: treatment dose unit

value: mg/kg

tag: treatment duration

tag: treatment duration unit

value: days


title: microglia, ATV:RSV-1-Day (NH34G)

tag: tissue

tag: cell type

tag: treatment


title: Group_1_inoculum

value: culture


title: acute myeloid leukemia (AML)_DR84

value: leukemia blast cells

tag: disease state

value: AML

value: de novo

tag: age

value: m


title: S73_single cell rna seq by Smart Seq2

value: HSC

tag: genotype

value: AAVS1 KO


title: acute myeloid leukemia (AML)_DR83

tag: aml status

tag: fab type

value: f


title: microglia, ATV:4D9-14-Day (NH32G)

tag: Sex

value: Male


title: microglia, ATV:4D9-28-Day (NH33G)

tag: tissue region


title: S72_single cell rna seq by Smart Seq2


title: BMDM, Control, replicate 2

value: BMDM

value: LysMCre- Control

value: 9-10 weeks


title: acute myeloid leukemia (AML)_DR82


title: acute myeloid leukemia (AML)_DR80


title: ELN.TNF_E_1

type: RNA

city: Dallas

first: William

middle: R

last: Swindell

state: TX

address: 6201 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

description: Gene expression data from TNF+ELN-treated KCs

hyb_protocol: Microarray hybridizations were performed using standard protocols by ThermoFisher (Waltham, MA).

scan_protocol: The standard Affymetrix protocol was following using the GeneChip™ Scanner.

data_processing: Raw CEL files were normalized using the robust multichip average (RMA) algorithm to generate log2-scaled signal intensities (Irizarry et al., 2003).

label: biotin

source_name: Keratinocytes

label_protocol: Biotinylated cDNA was prepared following the standard Affymetrix protocol using the GeneChip WT labeling kit.

growth_protocol: Neonatal human epidermal KCs (passage 8) were plated in KC growth medium at late subconfluence density (~220,000 cells/well).

extract_protocol: RNA was extracted using the Qiagen (Hilden, Germany) RNAeasy Mini Plus kit with QIAcube Connect automated nucleic acid purification instrument.

treatment_protocol: Cells were incubated with test materials in KC maintenance medium for 24 hours.

value: Keratinocytes

value: TNF+ELN

tag: replicate


title: ELN.TNF_E_2


title: BAK.TNF_D_2

description: Gene expression data from TNF+BAK-treated KCs

value: TNF+BAK


title: S70_single cell rna seq by Smart Seq2

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.


title: BAK.ELN.TNF_F_1

description: Gene expression data from TNF+BAK+ELN-treated KCs

value: TNF+BAK+ELN


title: BAK.ELN.TNF_F_2


title: CBD.TNF_C_2

description: Gene expression data from TNF+CBD-treated KCs

value: TNF+CBD


title: BAK.TNF_D_1


title: acute myeloid leukemia (AML)_DR79

value: tAML


title: microglia, ATV:4D9-28-Day (NH25G)

first: Thomas

last: Sandmann

institute: Denali Therapeutics

value: brain

value: Cortex and hipocampus

value: microglia

tag: strain

tag: age unit

value: months

value: hTfR KI

value: mg/kg

value: days


title: S69_single cell rna seq by Smart Seq2

value: HSC

value: AAVS1 KO


title: microglia, ATV:RSV-1-Day (NH24G)

value: Male

tag: batch

tag: treatment dose


title: acute myeloid leukemia (AML)_DR78

value: leukemia blast cells

value: AML

value: f


title: S68_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR77

value: de novo

value: m


title: microglia, ATV:4D9-14-Day (NH23G)

tag: treatment dose unit

tag: treatment duration


title: acute myeloid leukemia (AML)_DR76


title: CBD.TNF_C_1

value: Keratinocytes

value: TNF+CBD


title: TNF_B_2

description: Gene expression data from TNF-treated KCs

value: TNF


title: S71_single cell rna seq by Smart Seq2


title: TNF_B_1


title: microglia, ATV:4D9-1-Day (NH22G)

tag: tissue

value: brain

value: Cortex and hipocampus

tag: treatment duration unit


title: microglia, ATV:4D9-7-Day (NH21G)

tag: cell type

value: microglia

value: months

tag: treatment


title: microglia, ATV:4D9-1-Day (NH31G)

tag: age

value: hTfR KI

value: mg/kg


title: acute myeloid leukemia (AML)_DR75

tag: disease state


title: CTL_A_2

description: Gene expression data from non-treated control (CTL) KCs

value: CTL


title: S66_single cell rna seq by Smart Seq2

value: HSC

tag: genotype

value: AAVS1 KO


title: S65_single cell rna seq by Smart Seq2


title: S64_single cell rna seq by Smart Seq2


title: acute myeloid leukemia (AML)_DR74

value: leukemia blast cells

tag: aml status

value: tAML

tag: fab type


title: microglia, ATV:4D9-7-Day (NH4G)

tag: Sex

value: Male

tag: tissue region

value: days


title: CTL_A_1

tag: replicate


title: S63_single cell rna seq by Smart Seq2