title: ToxoR1A

city: Guangzhou

first: Kexing

last: Huang

state: Guangdong

address: Southern Medical University, Sha Tai North Road, Baiyun District

department: Department of Pathogen Biology

institute: School of Public Health, Southern Medical University

data_processing:
Illumina Casava1.4 software was used for basecalls
Raw reads produced from sequencing machines contain dirty reads which contain adapters, unknown or low quality bases. These data will negatively affect following bioinformatics analysis.Therefore, dirty raw reads are discarded: Remove reads with adaptors;Remove reads with unknown nucleotides larger than 5%;Remove low quality reads (The rate of reads which quality value <= 10 is more than 20%); Get the clean reads eventually. After filtering the low quality reads, clean reads were aligned to the T.gondii GT1 strain whole genome
Fragments Per Kilobase per Million fragments (FPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008.
Genome_build: TGGT1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values (log2-transformed with an offset value of 1.0) for each Sample,ToxoR1A_FPKM for the FPKM of each All-Unigene in sample ToxoR1A. ToxoR5A_FPKM for the FPKM of each All-Unigene in sample ToxoR5A. Nr-ID for Nr sequence ID.Nr-Score for blast score. Nr-Evalue for blast E value. Nr-annotation for Nr sequence annotation. Swissprot-ID for Swissprot sequence ID. Swissprot-Score for blast score. Swissprot-Evalue for blast E value. Swissprot-annotation for Swissprot sequence annotation. NT-ID for NT sequence ID. NT-Score for blast score. NT-Evalue for blast E value. NT-annotation for NT sequence annotation. COG-Protein-or-Domain for Aligned Protein-or-Domain. COG-Score for blast score. COG-Evalue for blast E value. COG-ID for COG ID. COG-Function-Description for COG function description. KO_id for KO ID.KEGG-Evalue for blast E value. KEGG-Score for blast score. KEGG-Gene for KEGG sequence ID. KO_definition for KO definition. GO-BiologicalProcess for GO Biological Process. GO-MolecularFunction for GO Molecular Function. Go-CellularComponent for GO Cellular Component.

organism: Toxoplasma gondii RH

source_name: tachyzoites

growth_protocol: The RH strain of T. gondii ( genotype I lineage, ToxoDB#10 ) is preserved in liquid nitrogen and passaged in HFF cells or mice in our laboratory. Mice were provided non-medicated feed and water ad libitum throughout the experiment.

extract_protocol:
Tachyzoites were collected and RNA was harvested using Trizol reagent. IlluminaTruSeq™ RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After recovering Toxoplasma gondii RH strain previously stored in liquid nitrogen for more than one month, each of the six mice of the first generation was intraperitoneally inoculated with RH strain tachyzoites contained in 0.5 ml frozen liquid. After being sacrificed, the mice were peritoneally injected with 3ml PBS and then collected the peritoneal fluid that contained the tachyzoites. A total of six tachyzoites samples were collected from the six mice.Peritoneally infecting another six mice of the second generation with 0.5 ml tachyzoites dilution and conducting the methods and steps as described in the first generation, until the tachyzoites from the the six mice of the fifth generation were collected.

value: RH strain

tag: passages

value: collected from peritoneal fluid of the 1st generation infected mice

value: wild type


title: ToxoR5A

status: Public on May 14 2021

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: strain

value: collected from peritoneal fluid of the 5th generation infected mice

tag: genotype


title: MX1356-C6RGTANXX-3-TGACAT

city: Vancouver

first: Wan

middle: L

last: Lam

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

data_processing:
Raw fastq files were processed by the miRMaster platform (March 2018, miRBase v21), using its default settings.
Predicted novel miRNA precursor sequences were excluded if not classified by miRMaster as ‘novel’. Predicted mature novel miRNA sequences were also excluded if they were present in miRBase v22.
For kno-sncRNA files: for mature sncRNAs derived from multiple precursor sequences, only the most highly-expressed precursor-mature pair is reported
For nov-miRNA files: for putative mature miRNA sequences that could be derived from multiple putative miRNA precursor sequences, only the precursor-mature pair with the highest probability (as assigned by miRMaster) is reported.
Genome_build: hg38
Supplementary_files_format_and_content: isomiR files: precursor (name of miRNA precursor), miRNA (name of mature miRNA from which isomiR is derived), iso_type (description of modifications to mature miRNA sequence [Fehlmann et al., 2017, PMID: 28911107]), RPM (expression of isomiR, normalized to reads-per-million); nov-miR files: chromosome, start (nucleotide position of the start of the putative miRNA precursor), stop (nucleotide position of the end of the putative miRNA precursor), probability (probability of the precursor being a true miRNA precursor), novomirank_score (novoMiRank score for the precursor [Backes et al., 2016, PMID: 26635395]), sequence (sequence of the putative mature miRNA), RPM (expression of the putative mature miRNA, normalized to reads-per-million); kno-sncRNA files: Reference (for miRNAs, piRNAs, and tRNAs: the name of the sncRNA sequence. For snRNAs and snoRNAs: Ensembl transcript ID of the sncRNA sequence), Subtype (type of sncRNA; one of miRNA, piRNA, snRNA, snoRNA, or tRNA), RPM (expression of sncRNA, normalized to reads-per-million); supplementary file: Reference (for known sncRNAs, identical to the sncRNA processed data files; for novel miRNAs, has the format chromosome|start|stop|sequence; for isomiRs, has the format precursor|miRNA|iso_type), Subtype (one of miRNA, piRNA, snRNA, snoRNA, tRNA, isomiR, nov-miR), subsequent columns denote reads-per-million expression in different samples.

organism: Homo sapiens

source_name: Chorionic villi

extract_protocol:
Thirty milligram samples were taken from the chorionic villi on the fetal-facing side of the placenta. TRIzol was used to extract total RNA.
Sequencing was performed using the standard ribodepleted strand-specific RNA sequencing protocol of Canada’s Michael Smith Genome Sciences Centre in Vancouver, in line with The Cancer Genome Atlas miRNA sequencing protocol (Chu et al., 2015, PMID: 26271990). Briefly, after adaptor ligation, amplification was achieved through 15 cycles of PCR (98˚C for 15s, 62˚C for 30s, 72˚C for 15s), concluded by 5 minutes at 72˚C. Gel extraction from a 3% MetaPhor Agarose gel was used to select for RNAs shorter than 200 nucleotides, and hybridization was used to deplete the rRNA fraction. RNA quality was confirmed on an Agilent Bioanalyzer 2100 (Agilent, USA). Sequencing was performed on an Illumina HiSeq 2500.

tag: developmental stage

value: Term

tag: neural tube defect

tag: tissue

value: placenta (chorionic villi)


title: Kidney, sham 1

type: RNA

city: Saitama

first: Akinori

last: Aomatsu

address: 1-847 Amanuma-cho, Omiya-ku

department: Nephrology

country: Japan

institute: Saitama Medical Center, Jichi Medical University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Ver.2.0 Microarray (Agilent, G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 074809_D_F_20171030). Quantile normalization was performed by the GeneSpring GX software using Agilent.SingleColor.74809 technology. Data were baseline shifted to the median of all samples.

organism: Mus musculus

source_name: sham model

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The kidney samples weighing 30 mg were homogenized using a glass homogenizer. Total RNA, including messenger RNA (mRNA), was purified from the kidney samples using an RNeasy Mini Kit (Qiagen).

value: kidney

tag: disease state

value: sham model


title: mESC_DNA_cell36

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

molecule: genomic DNA

source_name: cell line

growth_protocol: mESCs were cultured at 37 °C with 5% CO2 and was maintained in high glucose DMEM

extract_protocol:
folloing CoTECH protocol
After PCR enrichment using Q5 polymerase, the 300-1,000 bp fragments were isolated using the 1.5% (w/v) agarose gel and purified once with 0.8 x AMpure XP beads

treatment_protocol: The mESCs were dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for CoTECH

tag: cell type

value: cultured mouse embryonic stem cells

tag: chip antibody


title: mESC_DNA_cell43


title: Kidney, sham 4


title: MX1357-C6RGTANXX-4-AGTCTT


title: mESC_DNA_cell32


title: MX1356-C6RGTANXX-3-GCTGTA


title: MX1356-C6RGTANXX-3-ATGGCA


title: mESC_DNA_cell33


title: mESC_DNA_cell31


title: mESC_DNA_cell29


title: mESC_DNA_cell35


title: Kidney, IRI-3

hyb_protocol: The hybridization mixture was denatured at 100°C for 5 minutes in a reaction volume of 45 ul containing 2x Agilent GE hybridization buffer HI-RPM and 10x Agilent blocking agent following the manufacturers instructions and immediately transferred to ice water bath. Each sample was hybridized to SurePrint G3 Mouse miRNA microarray 8 x 60K Rel.21.0 (Agilent, G4859C) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using miRNA setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters(protocol miRNA_1200_Jun14 and Grid 070155_D_F_20141006). The 90th percentile shift normalization was performed by the GeneSpring GX software using Agilent.miRNA.70155_v21_0 technology. Data were baseline shifted to the median of all samples.

source_name: IRI-AKI model

label_protocol: RNA labeling was performed using miRNA Complete Labeling Reagent & Hybridization Kit (Agilent, 5190-0456) following the Agilent protocols v.2.4. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase for 30 min at 37°C. After adding DMSO, the reaction mixture was incubated at 100°C for 7 minutes and immediately transferred to ice water bath.Ligation was performed with pCp-Cy3 at 16 °C for 2 hours.The labeled RNA were dried completely in a vacuum concentrator and resuspended in 18 ul of nuclease free water.

extract_protocol: Kidney samples weighing 30 mg were homogenized using a glass homogenizer. Total RNA, including miRNA, was purified from the kidney samples using an miRNeasy Mini Kit (Qiagen) .

value: IRI-AKI model


title: Kidney, IRI-18


title: Kidney, IRI-1


title: mESC_DNA_cell34


title: mESC_DNA_cell28


title: Kidney, IRI-2


title: mESC_DNA_cell27


title: MX1356-C6RGTANXX-3-GTATAG

value: Second trimester


title: mESC_DNA_cell26


title: Kidney, control-6


title: MX1357-C6RGTANXX-4-AATTAT


title: MX1355-C6RGTANXX-2-GGAACT


title: MX1357-C6RGTANXX-4-TCTGAG


title: mESC_DNA_cell22


title: MX1356-C6RGTANXX-3-CCTTGC


title: mESC_DNA_cell30


title: MX1355-C6RGTANXX-2-CATTCA


title: mESC_DNA_cell24


title: mESC_DNA_cell21


title: Kidney, control-3


title: mESC_DNA_cell23


title: mESC_DNA_cell25


title: mESC_DNA_cell20


title: Kidney, control-2


title: MX1356-C6RGTANXX-3-GCGTGG


title: mESC_DNA_cell17


title: mESC_DNA_cell19


title: mESC_DNA_cell18


title: MX1310-C5JC1ACXX-4-CTCTAC


title: MX1310-C5JC1ACXX-4-GGACGG


title: mESC_DNA_cell15


title: MX1307-C5JC4ACXX-7-CAGGCC


title: mESC_DNA_cell14


title: Kidney, LPS-10

source_name: LPS-AKI model

value: LPS-AKI model


title: Kidney, control-1


title: Kidney, LPS-11


title: Kidney, LPS-12


title: Kidney, control-miRNA 5

source_name: IRI-AKI+control-miRNA-PEI-NPs model

value: IRI-AKI+control-miRNA-PEI-NPs model


title: mESC_DNA_cell13


title: MX1303-C5JC4ACXX-3-TAGGAT


title: mESC_DNA_cell12


title: mESC_DNA_cell11


title: mESC_DNA_cell9


title: MX1310-C5JC1ACXX-4-TGACAT

value: Anencephaly


title: MX1310-C5JC1ACXX-4-GGAACT


title: mESC_DNA_cell10


title: MX1307-C5JC4ACXX-7-AGCATC

value: Spina bifida


title: mESC_DNA_cell16


title: mESC_DNA_cell7


title: mESC_DNA_cell6


title: mESC_DNA_cell5


title: MX1306-C5JC4ACXX-6-GTATAG


title: MX1305-C5JC4ACXX-5-TGTTGG


title: mESC_DNA_cell4


title: Kidney, LPS-6


title: Kidney, Mock6


title: Kidney, Mock8


title: Kidney, Mock7


title: mESC_DNA_cell2


title: mESC_DNA_cell3


title: mESC_DNA_cell1


title: K562 siSAFB&B2 H3K9me3 ChIP-Seq

city: HOUSTON

first: Ruoyu

last: Wang

state: Texas

address: 6431 Fannin St

country: USA

institute: UTHealth McGovern Medical School

data_processing:
MINT-Seq, TT-Seq, MeRIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
ChIP-seq: All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: K562 cell

growth_protocol: K562 and HeLa cells were grown in RPMI 1640 medium (Corning) or DMEM (Corning) supplemented with 10% heat-inactivated FBS(Gibco), respectively.  Cells were grown at 37°C under 5% CO2.

extract_protocol:
1 million cells were resuspended in hypotonic buffer (10 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2 and protease inhibitor cocktail) and homogenized through a G25 syringe. Chromatin was digested in 0.2 U μl−1 MNase (NEB) at 37 °C for 10 min, and the reaction was quenched by 0.5 M EDTA. Chromatin was resuspended in hypotonic buffer (0.2 mM EDTA, pH 8.0, 0.1 mM benzamidine, 0.1 mM phenylmethylsulfonyl fluoride, 1.5 mM dithiothreitol and 1 × protease inhibitor cocktail (PIC) and incubated for 1 h on ice. Cellular debris was pelleted and the supernatant was recovered. Chromatin was pre-cleared with 20 μl of 1:1 protein A:protein G Dynabeads (Life Technologies) and immunoprecipitation was carried out with antibody–bead complexes (2ug H3K9me3 antibody and 20 μl 1:1 protein A:protein G Dynabeads) overnight at 4 °C. IPed complexes were washed twice with 400 μl of ChIP wash buffer I (20 mM Tris-HCl, pH 8.0, 0.1% SDS, 1% Triton X-100, 2 mM EDTA and 150 mM NaCl) and twice with 400 μl of ChIP wash buffer II (20 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2 mM EDTA and 500 mM NaCl). Protein–DNA complexes were eluted in 200 μl of elution buffer (100 mM NaHCO3 and 1% SDS) for 2 h at 68 °C. IPed material was purified by phenol chloroform and was processed for library construction.
DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for illumina according to manufactorer's instructions

treatment_protocol: Cells were labeled in media for 4 min with 700 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.

value: immortalized myelogenous leukemia cell line

value: H3K9me3, Abcam ab8898


title: K562-PSMA1-MIL-inversion-clone1-TT-Seq

description: nuclear RNA

data_processing:
Library strategy: TT-seq
MINT-Seq, TT-Seq, MeRIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
ChIP-seq: All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Duffy et al., Mol Cell, 2015.  M6A methylated RNA was immunoprecipitated by anti-m6A antibodies (202003, SYSY).
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions


title: K562-PSMA1-MIL-inversion-clone2-TT-Seq

description: nuclear RNA


title: MX1304-C5JC4ACXX-4-CCGGTG


title: MX1356-C6RGTANXX-3-CGGCCT

value: First trimester


title: Kidney, Mock5


title: Follicular B cell, H1_S33

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description:
Follicular_vs_ActB.xlsx
Follicular_vs_GC.xlsx
Follicular_vs_MBC_negative.xlsx
Follicular_vs_MBC_positive.xlsx
TPM_values.xlsx

data_processing:
Kallisto (v.0.46) was used to map sequence reads to Mus musculus transcriptome (GRCm38/ Ensembl release 99). Kallisto TPM values were converted to absolute counts using tximport (v1.12.3) R package and DESeq2 (v.1.24.0) [3] was utilized for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files with TPM expression and differential expression

source_name: B cells

extract_protocol:
RNA was isolated using RNAClean XP Beads (Beckman Coulter, A63987). Near full-length mRNA was reverse transcribed as previously described (Islam et al., 2014) (Trombetta et al., 2014).
Multiplexed libraries were prepared for sequencing using a Nextera XT DNA Library Preparation Kit (Illumina). Libraries were sequenced on an Illumina NovaSeq 6000 at the Rockefeller University Genomics Core.

treatment_protocol: Cells were sorted directly into a solution of 1% 2-β-mercaptoethanol (Sigma) in TCL Buffer (Qiagen, 1031576).

value: lymph node

tag: cell subset

value: Follicular B cell


title: Activated B cell, H5_S37

description:
Follicular_vs_ActB.xlsx
GC_vs_ActB.xlsx
MBC_negative_vs_ActB.xlsx
MBC_positive_vs_ActB.xlsx
TPM_values.xlsx

value: Activated B cell


title: MX1355-C6RGTANXX-2-CAAGTT


title: MX1356-C6RGTANXX-3-TAGTTG


title: Activated  B cell, G5_S32


title: K562 siCTL H3K9me3 ChIP-Seq


title: Memory B cell -, H4_S36

description:
Follicular_vs_MBC_negative.xlsx
GC_vs_MBC_negative.xlsx
MBC_negative_vs_ActB.xlsx
MBC_positive_vs_MBC_negative.xlsx
TPM_values.xlsx

value: Memory B cell -


title: Memory B cell +, G3_S30

description:
Follicular_vs_MBC_positive.xlsx
GC_vs_MBC_positive.xlsx
MBC_positive_vs_ActB.xlsx
MBC_positive_vs_MBC_negative.xlsx
TPM_values.xlsx

value: Memory B cell +


title: Germinal Center B cell, G2_S29

description:
Follicular_vs_GC.xlsx
GC_vs_ActB.xlsx
GC_vs_MBC_negative.xlsx
GC_vs_MBC_positive.xlsx
TPM_values.xlsx

value: Germinal Center B cell


title: mESC_DNA_cell8


title: Memory B cell +, H3_S35


title: Germinal Center B cell, H2_S34


title: K562-PSMA1-MIL-KO-clone2-TT-Seq

description: nuclear RNA


title: Memory B cell -, G4_S31


title: K562-PSMA1-MIL-KO-clone1-TT-Seq

description: nuclear RNA


title: MX1355-C6RGTANXX-2-ACATCG

value: placenta (chorionic villi)


title: MCF7 TT-Seq

description: nuclear RNA

source_name: MCF7 cell

value: breast cancer cell


title: Follicular B cell, G1_S28


title: Follicular B cell, F1_S25


title: MX1355-C6RGTANXX-2-AAGCTA


title: MCF7 MINT-Seq

description: nuclear RNA

data_processing:
Library strategy: MINT-seq
MINT-Seq, TT-Seq, MeRIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
ChIP-seq: All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig


title: Germinal Center B cell, F2_S26


title: Memory B cell -, F4_S27


title: Memory B cell -, E4_S23


title: Germinal Center B cell, E2_S21


title: Activated B cell, E5_S24


title: pir1_catalytic_dead_rep2_L4-YA_pRNA_pppRNA

city: Riverside

first: Weifeng

last: Gu

state: California

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

data_processing:
The samples are debarcoded using the 8 nt barcodes
The 3' AGATCGGAA and beyond are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
Genome_build: C. elegans WS215
Supplementary_files_format_and_content: tabbed txt file containing sequence and read number for the analysis

organism: Caenorhabditis elegans

source_name: pRNA+pppRNA in pir-1 catalytic mutant

growth_protocol: Worms were grown on NGM or Ivermectin-containing NGM plates with OP50 at 20 °C.

extract_protocol:
RNAs were extracted with TRIzol
RNAs were linked with Truseq LT/V1/V2 linkers using the standard 5' and 3' ligation methods. Amplicons with ~20 nt inserts were selected for sequencing. The samples were multiplexed with 8 nt indexes in the 3' linker. Please refer to Li L et al. RNA. 2020 Feb;26(2):218-227.

treatment_protocol: For cloning ppp-RNAs, the sample is treated with 0.5 μM PIR-1 at 20 °C for 2 hours and for cloning only p-RNAs, no PIR-1 is required.

value: whole worm

tag: rna fraction

value: All RNA


title: K562-siSAFB&B2-TT-Seq

data_processing:
Library strategy: TT-Seq
MINT-Seq, TT-Seq, MeRIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

molecule: nuclear RNA

tag: cell line

value: immortalized myelogenous leukemia cell line K562


title: K562-WT-TT-Seq rep2

description: nuclear RNA


title: avr3x_L4-YA_rep2_pRNA_pppRNA

source_name: pRNA+pppRNA in avr3x


title: Follicular B cell, E1_S20


title: K562-ZRANB3-MIL-KO-c1-TT-Seq


title: pir1_catalytic_dead_rep2_L4-YA_pRNA_only

source_name: pRNA in pir-1 catalytic mutant

value: pRNA


title: K562-WT-TT-Seq


title: Memory B cell +, E3_S22


title: Activated B cell, D5_S19


title: K562-siSAFB&B2-RNA-Seq

data_processing:
MINT-Seq, TT-Seq, MeRIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig


title: avr3x_L4-YA_rep2_pRNA_only

source_name: pRNA in avr3x


title: Memory B cell -, D4_S18


title: Memory B cell +, D3_S17


title: K562-siSAFB-TT-Seq


title: pir1_catalytic_dead_rep1_L4-YA_pRNA_pppRNA


title: K562-siCTLT-TT-Seq


title: K562-siSAFB-RNA-Seq


title: pir1_catalytic_dead_rep1_L4-YA_pRNA_only


title: Follicular B cell, D1_S15


title: hNPC-siSAFB&B2-RNA-Seq-rep2

source_name: hNPC cell

value: neural progenitor cells


title: Germinal Center B cell, D2_S16


title: K562-ZRANB3-MIL-KO-c2-TT-Seq


title: K562-siCTL-RNA-Seq


title: N2_embryo_rep2_for_ERGO-1_26G_metagene_analysis

source_name: small RNA in embryo

value: embryo


title: N2_embryo_rep1_for_ERGO-1_26G_metagene_analysis


title: Activated B cell, C5_S14


title: avr3x_L4-YA_rep1_pRNA_only


title: Memory B cell +, C3_S12


title: Germinal Center B cell, C2_S11


title: Perturb_CD4_stim_intra_D6_HTO

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: antibody oligos

data_processing:
Library strategy: Cell Hashing
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
The two sequencing lanes (C6 and D6) were combined using CellRanger-ATAC aggr
For ADT and HTO count libraries, tag abundances were quantified per barcode using the kallisto/kite framework. gRNA-based KOs were assigned based on a modified version of HTO Demux.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library

molecule: other

source_name: T-cells from peripheral blood mononuclear cells

growth_protocol: Cells were stimulated for 72 hours, followed by 4 days resting and then electroporation with Cas9 protein. Samples were treated with distinct gRNAs based on the overall design. Cells were further expanded an additional 7 days

extract_protocol:
Samples were stained with hashing antibodies for multiplexing gRNAs and surface marker antibodies, fixed with 1% PFA and then extracted using the 10x protocol (Omni-ATAC)
ATAC libraries were constructed according to the 10x Genomics scATAC-seq v1.1 protocol while antibody tags were captured via the bridge oligo spiked-in the barcoding reaction and amplfied using tag-specific handles.
10x Genomics scATAC-seq v1.1

treatment_protocol: Cells were re-stimulated for 72 hours and then enriched for live cells by cell sorting

tag: donor #

value: One biological donor

tag: ab treatment

value: CD298/β2 microglobulin hash antibodies corresponding to CRISPR gRNA

tag: asap-seq protocol

value: silane elute + SPRI supernatant


title: Memory B cell -, B4_S9

value: lymph node


title: hNPC-siCTL-RNA-Seq-rep2


title: hNPC-siSAFB&B2-RNA-Seq-rep1


title: hNPC-siCTL-RNA-Seq-rep1


title: HMC3-TT-Seq

source_name: HMC3 cell

value: microglial cell line HMC3


title: Follicular B cell, C1_S10

value: Follicular B cell


title: Germinal Center B cell, B2_S7


title: HMC3-RNA-Seq


title: avr3x_L4-YA_rep1_pRNA_pppRNA


title: Perturb_CD4_stim_intra_D6_ATAC

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
The two sequencing lanes (C6 and D6) were combined using CellRanger-ATAC aggr
For ADT and HTO count libraries, tag abundances were quantified per barcode using the kallisto/kite framework. gRNA-based KOs were assigned based on a modified version of HTO Demux.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library


title: SH-SY5Y untreated cells, mRNA_library

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

description:
SH-SY5Y Split 1, tagged with Hashtag-1,A0251
SH-SY5Y Split 1, tagged with Hashtag-2,A0252
SY5Y.csv
filtered_feature_bc_matrix.h5
raw_feature_bc_matrix.h5
feature_reference.csv

data_processing:
Raw reads were mapped to the human genome version hg38/GRCh38 using the STAR aligner version 2.7.
The resulting aligned reads data were saved in BAM format, which also included unaligned reads.
BAM file was then processed with Cell Ranger v4.0.0, in order to obtain matrices of gene counts per cell in CSV (comma-separated value) format.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: SY5Y.csv.gz  (comma separated value file containing gene count matrix)
Supplementary_files_format_and_content: filtered_feature_bc_matrix.h5  (10X HDF5 Filtered Feature Barcode Matrix  also containing Hashtag Counts)
Supplementary_files_format_and_content: raw_feature_bc_matrix.h5  (10X HDF5 Raw Feature Barcode Matrix also Containing Hashtag Counts)
Supplementary_files_format_and_content: feature_reference.csv  (containing detailed information on the hashtags)

source_name: ATCC

growth_protocol: SH-SY5Y neuroblastoma cells were cultured in T-75 flasks (CytoONE®, Starlab #CC7682-4175, Milan, ITALY) using DMEM high glucose, GlutaMAX™, pyruvate medium (Gibco™, Thermo Fisher Scientific #10569010, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Gibco™, Thermo Fisher Scientific #10270106) and 1% Penicillin-Streptomycin (Gibco™, Thermo Fisher Scientific #15070063), and maintained at 37°C in a humidified atmosphere with 5% CO2. Medium was changed twice a week and cells were passaged for maintenance when 90% confluence was reached in the culture flask.

extract_protocol:
Untreated cells were splitted into 2 separate flasks, and left growing to reach about 80% confluence berfore harvesting and sequencing. Cell hashing was performed following manufacturer’s instructions (TotalSeq™-A Cell Hashing and TotalSeq™-A Antibodies Protocol for Simultaneous Proteomics and Transcriptomics with 10X Single Cell 3' Reagent Kit v2; BioLegend, San Diego, CA, USA). Briefly, after counting and viability assessment, single cells suspension samples were incubated 10 min on ice with Human TruStain FcX™ Fc Blocking reagent (BioLegend). Next, sample-specific TotalSeq A antibodies (TotalSeq-A0251 anti-human Hashtag 1 Antibody and TotalSeq-A0252 anti-human Hashtag 2 Antibody, BioLegend) were added with subsequent incubation on ice for 30 min. Cells were washed three times with Cell Staining Buffer (BioLegend, Cat# 420201) and finally resuspended in PBS. Cells were counted in an automatic cell counter (Cell counter Thermo Scientific) and samples pooled together. Primers to cDNA PCR (HTO PCR additive primer) were added to increase yield of Hashtag oligonucleotide (HTO, cDNA derived from the TotalSeq™ Hashtag antibodies). After cDNA amplification, HTO-derived cDNAs (180bp) and mRNA-derived cDNAs (>300bp) 2.0 Fluorometer (Invitrogen®, Waltham, MA, USA) and Agilent Bioanalyzer DNA assay (Agilent®, Santa Clara, CA, USA).
Libraries were prepared for sequencing following manufacturer’s instructions (Illumina®, San Diego, CA, USA)
scRNA-seq 10X Genomics

treatment_protocol: untreated

tag: treatment

value: untreated

value: Human neuroblastoma cell line SH-SY5Y

value: Neuroblastoma


title: Memory B cell +, B3_S8

value: Memory B cell +


title: HMC3-MINT-Seq

data_processing:
Library strategy: MINT-Seq
MINT-Seq, TT-Seq, MeRIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig


title: Perturb_CD4_stim_intra_D6_ADT

description: antibody oligos

data_processing:
Library strategy: CITE-Seq
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
The two sequencing lanes (C6 and D6) were combined using CellRanger-ATAC aggr
For ADT and HTO count libraries, tag abundances were quantified per barcode using the kallisto/kite framework. gRNA-based KOs were assigned based on a modified version of HTO Demux.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library

value: Selected cell surface markers


title: hNPC-RNA-Seq


title: Memory B cell -, C4_S13

value: Memory B cell -


title: SH-SY5Y untreated cells, HTO_library

description:
SH-SY5Y Split 1, tagged with Hashtag-1,A0251
SH-SY5Y Split 1, tagged with Hashtag-2,A0252
filtered_feature_bc_matrix.h5
raw_feature_bc_matrix.h5
feature_reference.csv


title: Perturb_CD4_stim_intra_C6_HTO

description: antibody oligos


title: Activated B cell, A5_S5

value: Activated B cell


title: Perturb_CD4_stim_intra_C6_ATAC


title: Perturb_CD4_stim_intra_C6_ADT

description: antibody oligos


title: Hela MeRIP-Seq siCTL

description: nuclear RNA

source_name: Hela cell

value: Human cervical cancer cells


title: HMC3-MeRIP-Seq


title: Hela RNA-Seq siCTL

description: nuclear RNA


title: E. faecalis ∆gdpP∆dhhP grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 1

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description: ∆gdpP∆dhhP 1

data_processing:
Read mapping was performed on a Galaxy server hosted by the University of Florida Research Computer
Map with Bowtie for Illumina was used to map the reads to the E. faecalis OG1RF genome (CP002621.1)
htseq-count was used to tabulate the reads per open reading frame
Degust was used to make final comparisons in counts between cells grown in the complete versus the metal-depleted media.
Genome_build: CP002621.1
Supplementary_files_format_and_content: The processed .csv data files indicate the number of reads obtained for each open reading frame (OG1RF_xxxxx) for each sample after each of four original raw data files (.fastq) were compiled and mapped against the E. faecalis OG1RF genome (CP002621.1) using Galaxy as described above.

organism: Enterococcus faecalis

growth_protocol: Cells were grown to OD600 of 0.35, then harvested by centrifugation.  Pellets were treated with RNA protect reagent, harvested by centrifugation, and stored at -80°C until use

extract_protocol:
Harvested cells were resuspended in 1mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA was isolated from homogenized E. faecalis cell lysates by acid-phenol:chloroform extractions.  The nucleic acid was subjected to DNase I digestion (Ambion).   The RNA was then purified using the Qiagen RNeasy colum purification kit, including an additional on-column DNase digest.  Total RNA was subjected to two rounds of mRNA enrichment using the MICROBExpress Bacterial mRNA Purification kit (ThermoFisher).
cDNA libraries with unique barcodes were generated from 100ng enriched mRNA using the NEB Next UltraII Directional RNA Library Prep kit for Illumina (New England Biolabs).
Pooled libraries were subjected to RNA deep sequencing at the University of Florida Interdisciplinary Center for Biotechnology Research using the Illumina NextSeq500 platform.

tag: genotype/variation

value: {delta}gdpP{delta}dhhP ({delta}OG1RF_11161; RS06025/{delta}OG1RF_10010; RS0060)


title: E. faecalis ∆gdpP∆dhhP grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 3

description: ∆gdpP∆dhhP 3


title: E. faecalis ∆gdpP∆dhhP grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 2

description: ∆gdpP∆dhhP 2


title: CD28_CD3_DIG_stim_Multiome_ADT

description: antibody oligos

data_processing:
Library strategy: CITE-seq
Fastqs were generated using CellRanger-ARC mkfastq v1.0.0
Sequencing reads were aligned using CellRanger-ARC for the hg38 reference genome
For ADT count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the singlecell QC metrics, barcoded accessible chromatin fragments per ATAC library, gene expression counts, and mRNA counts

source_name: Peripherial blood mononuclear cells

extract_protocol:
Control and stimulated PBMCs were stained with a TotalSeqA antibody panel (210 antibodies), sorted to remove dead cells and granulocytes, and permeabilised with two methods: 1) 0.1% PFA fixation followed by permeabilization with LLL buffer and 2) permeabilization with 0.1% digitonin . Cells were subsequently subjected to transposition and loaded into the 10x Multiome chip for the barcoding reaction.
ATAC and GEX libraries were constructed according to the 10x Genomics single cell Multiome protocol. Protein tags were captured via the polyT barcoded oligos and amplfied using tag-specific handles.
10x Genomics Multiome + CITE-seq antibody capture

treatment_protocol: Thawed cryopreserved PBMCs were resuspended to 1M/ml density in either complete medium supplemented with IL2 (unstimulated control) or complete medium supplemented with IL2 and ImmunoCult Human CD3/CD28 T cell Activator (stimulated sample) for 16 hours.

value: Peripherial blood mononuclear cells

value: 16hr incubation with IL2 and anti-CD3/CD28

tag: target molecule

value: Cell Surface Markers

tag: ab tags

value: 15 bases long (210 tags total)

tag: lysis buffer

value: DIG


title: hNPC-MeRIP-Seq

value: neural progenitor cells


title: CD28_CD3_DIG_stim_Multiome_RNA

description: cDNA

data_processing:
Fastqs were generated using CellRanger-ARC mkfastq v1.0.0
Sequencing reads were aligned using CellRanger-ARC for the hg38 reference genome
For ADT count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the singlecell QC metrics, barcoded accessible chromatin fragments per ATAC library, gene expression counts, and mRNA counts

value: polyA mRNA


title: Germinal Center B cell, A2_S2

value: lymph node

value: Germinal Center B cell


title: CD28_CD3_DIG_stim_Multiome_ATAC

description: tagmented gDNA

value: Accessible chromatin


title: E. faecalis ∆dhhP grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 3

description: ∆dhhP 3


title: Hela MINT-Seq siCTL

description: nuclear RNA


title: Follicular B cell, B1_S6

value: Follicular B cell


title: E. faecalis ∆dhhP grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 2

description: ∆dhhP 2


title: Follicular B cell, A1_S1


title: CD28_CD3_DIG_control_Multiome_ADT

description: antibody oligos

value: 16hr incubation with IL2


title: K562 MeRIP-Seq rep2

description: nuclear RNA

value: immortalized myelogenous leukemia cell line


title: R255K-8

first: Shan

last: Xiao

address: Southern Shatai Road

department: Developmental Biology

institute: Southern Medical University

data_processing:
Reads that mapped to rRNA fasta sequences from the UCSC gene annotation (mm10) using bowtie2 (v.2.2.6) 11 were discarded, and remaining reads were aligned to mm10 using hisat2-align-s (v.2.0.5) 12. Unique reads with high mapping quality were retained using Picard (http://broadinstitute.github.io/picard, v.2.16.0) and SAMtools (v.0.1.09)13.
For mRNA lifetime RNA-seq data analysis, FPKM of gene were calculated, and the lifetime was calculated.
Genome_build: mm10
Supplementary_files_format_and_content: txt

molecule: polyA RNA

source_name: E14Tg2a cells

growth_protocol: E14Tg2a murine embryonic stem cells (mESCs) were cultured in high-glucose DMEM (Invitrogen, 12430) supplemented with 15% fetal bovine serum (FBS, Biological Industries, 04-002-1A), 1% non-essential amino acid (Invitrogen, 11140050), 1 mM glutamine (Invitrogen, 35050061), 0.15 mM 1-thioglycerol (Sigma-Aldrich, M6145), 100 U/mL Penicillin/Streptomycin (Invitrogen,15140122) and 1000 U/mL LIF (Millipore, ESG1107) at 37 °C with 5% CO2. Cells were maintained in plates coated with 0.2% gelatin (Sigma-Aldrich, V900863).

extract_protocol:
RNA were havested by TRNZOL.
mRNA library was constructed using NEBNext Ultra RNA Library Prep Kit (NEB). Sequencing was carried out on the Illumina Hiseq Nova platform.

treatment_protocol: mESC Cells were treated with 5 μg/ml actinomycin D (JK chemical) for 0h, 4h or 8h.

value: E14Tg2a cells

tag: genotype

value: METTL14 R255K


title: Hela TT-Seq siCTL

description: nuclear RNA

value: Human cervical cancer cells


title: K562 RNA-Seq rep2

description: nuclear RNA


title: Memory B cell -, A4_S4

value: Memory B cell -


title: Memory B cell +, A3_S3

value: Memory B cell +


title: E. faecalis ∆dhhP grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 1

description: ∆dhhP 1


title: R255K-0


title: R255K-4


title: E. faecalis ∆cdaA grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 3

description: ∆cdaA 3


title: CD28_CD3_DIG_control_Multiome_ATAC

description: tagmented gDNA

value: Peripherial blood mononuclear cells


title: K562 MeRIP-Seq rep1

description: nuclear RNA


title: E14-8

value: WT


title: CD28_CD3_LLL_stim_Multiome_ADT

description: antibody oligos

value: 16hr incubation with IL2 and anti-CD3/CD28

value: Cell Surface Markers

value: 15 bases long (210 tags total)

value: LLL


title: CD28_CD3_LLL_stim_Multiome_RNA

description: cDNA

value: polyA mRNA


title: E. faecalis ∆cdaA grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 1

description: ∆cdaA 1


title: K562 RNA-Seq rep1

description: nuclear RNA


title: E14-4


title: K562 MINT-Seq rep2

description: nuclear RNA


title: CD28_CD3_LLL_stim_Multiome_ATAC

description: tagmented gDNA


title: E14-0


title: CD28_CD3_DIG_control_Multiome_RNA

description: cDNA

value: DIG


title: E. faecalis OG1RF grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 3

description: OG1RF WT 3

source_name: OG1RF wild type

value: OG1RF wild type


title: K562 TT-Seq rep2

description: nuclear RNA


title: E. faecalis OG1RF grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 1

description: OG1RF WT 1


title: CD28_CD3_LLL_control_Multiome_ADT

description: antibody oligos


title: PomcDsRed_P12

city: Ann Arbor

first: Malcolm

last: Low

state: MI

address: 1000 wall street

department: Molecular & Integrative Physiology

institute: University of Michigan

data_processing:
Cell ranger (v.2.2.0) was used to QC and generate filtered gene matrices for samples PomcDsRed_E115, PomcDsRed_E135, PomcDsRed_E155, and PomcDsRed_E175.
Cell ranger (v.3.0.0) was used to QC and generate filtered gene matrices for samples PomcDsRed_P5, and PomcDsRed_P12.
Seurat (v3.0) was used for downstream analysis. Cells with high mitochondrial contents, high hemoglobin subunit genes expression and low quality were removed.  Cells with Pomc UMI > 0 were filtered for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: txt file with the UMI count matrices of cells that meet the criteria

source_name: brain-hypothalamus

growth_protocol: Mice were housed in ventilated cages under controlled temperature and photoperiod (12-h light/12-h dark cycle, lights on from 6:00 AM to 6:00 PM), with free access to tap water and laboratory chow (5L0D, LabDiet).

extract_protocol:
Embryonic hypothalami were dissected at E11.5, E13.5, E15.5, and E17.5. Postnatal hypothalami were isolated from pups at postnatal day 6 (P6) and P12. In each dissection, hypothalami from at least 6 pups were pooled together to acquire enough cells for fluorescence-activated cell sorting (FACS). Pooled tissue samples were digested in papain solution supplemented with DNAse for 20 mins (E11.5 and E13.5), 30 mins (E15.5), 40 mins (E17.5) or 1hr (P6, and P12) with gentle agitation. After incubation, digested tissue were centrifuged at 300 x g for 5min at 4°C and resuspended with EBSS medium. Tissue were further triturated with series of fire-polished pasteur pipets, centrifuged at 300 x g for 5min, resuspended with PBS and filtered with 20μm strainer. The isolated cells were underwent FACS for red fluorescent protein.
The Chromium™ Single Cell 3’ v2 Protocol was applied to samples PomcDsRed_E115, PomcDsRed_E135, PomcDsRed_E155, and PomcDsRed_E175. The Chromium™ Single Cell 3’ v3 Protocol was applied to samples PomcDsRed_P5, and PomcDsRed_P12. Both are standard library construction protocols from 10x Genomics.

treatment_protocol: Adult male POMCDsRed/+ mice were bred with female POMCDsRed/+ mice and the day of copulation plug detection was counted as embryonic day 0.5 (E0.5).

value: brain-hypothalamus

value: FACS sorted Pomc-DsRed cells

tag: strain

tag: developmental stage


title: E. faecalis OG1RF grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 2

description: OG1RF WT 2


title: K562 TT-Seq rep1

description: nuclear RNA

source_name: K562 cell

value: immortalized myelogenous leukemia cell line


title: K562 MINT-Seq rep1

description: nuclear RNA


title: CD28_CD3_LLL_control_Multiome_RNA

description: cDNA

value: 16hr incubation with IL2


title: CD28_CD3_LLL_control_Multiome_ATAC

description: tagmented gDNA

value: Accessible chromatin


title: E. faecalis ∆cdaA grown in CDM medium supplemented with 20mM glucose to OD600 = 0.35.  Replicate 2

description: ∆cdaA 2


title: t93_Normal

status: Public on May 13 2021

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

data_processing:
3'UTR sequence data were processed and mapped to the genome using STAR.
A global polyadenylation atlas was obtained by considering the locus of the last nucleotide of each alignement at the 3' end and clustering the signal acorss samples.
Only loci that had any of the 18 characterized poly(A) sites [ -30…...-10] nt region relative to the detected cleavage site were considered in the analysis.
Genomic position that had more than 6 consecutive as or more than 8 sparse in any 10nt window in the region spanning the detected cleavage site were ecluded to filter out internal-priming events.
Data analysis was performed with expressRNA platform incorporating tools for read alignement, genome annotation and calling of diffrentially polyadenylated genes.
Genome_build: Hg38
Supplementary_files_format_and_content: excel file of analyzed data

source_name: Frozen Lung Tissue

extract_protocol:
Fresh lung tumor and matched adjacent non-involved tissues were obtained from patients directly after surgery, flash frozen and stored at -80*C. RNA was harvested using Tryzol reagent. 500ng of RNA were used for libraries construction.
Construction of RNA libraries was performed using the QuantSeq Rev 3’mRNA-Seq Library Prep Kit for Illumina (Lexogen, Vienna, Austria). Libraries were pooled and sequenced on the Illumina Hiseq 2500 with 100 bp single end reads.

tag: tissue

value: lung

tag: disease state

value: Normal

tag: patient diagnosis

value: non-small cell lung cancer

tag: race

value: AA


title: t95_Normal


title: t97_Normal


title: t92_Normal


title: t98_Normal

value: EA


title: t9_Normal


title: t94_Normal


title: t91_Normal


title: t88_Normal


title: t86_Normal


title: t87_Normal


title: t90_Normal


title: t83_Normal


title: t84_Normal


title: t85_Normal


title: PomcDsRed_P5

tag: cell type


title: t96_Normal


title: t8_Normal


title: t78_Normal


title: t76_Normal


title: t74_Normal


title: t75_Normal


title: Boiler Bay mid zone, plot 3, Pooled RNA from gill sample A-E

city: Columbia

first: Sean

middle: P

last: Place

state: SC

address: 715 Sumter St.

department: Biological Sciences

institute: University of South Carolina

description: Biological replicate 3 of 5:Boiler Bay Mid zone vs. Pooled Reference RNA

hyb_protocol: Samples were brought to a final volume of 45 µl in 25 mM Hepes, 0.75 mg/ml tRNA (Sigma, St. Louis MO, USA), 3X SSC, and 0.2% SDS. Samples were boiled for 1 min, allowed to cool to room temperature, and then applied to microarray slides. Hybridizations were conducted overnight at 65°C in hybridization chambers (Genetix, Boston, MA, USA).

scan_protocol: Scanned on a AXON GenePix 4000B scanner. The ratio of Cy5 to Cy3 fluorescence was quantified using GenePix Pro 4.0 software

data_processing: background subtracted, LOWESS normalized data obtained from median log2 ratio of processed 635 signal /532 signal

organism: Mytilus californianus

source_name: Total RNA pooled from gill tissue isolated from 30 lab acclimated mussels

label_protocol: 10 µg of total RNA was reverse transcribed to cDNA using anchored oligo(dT15) primers and amino-allyl dUTP. Single stranded cDNA was labeled by indirect coupling of the aa-dUTP substituded cDNA with 5 ul cyanine monoreactive dye (GE Healthcare)

extract_protocol: Total RNA extracted from 100 mg of gill tissue using Trizol (Invitrogen) following manufacturer's instructions. Total RNA was further cleaned using spin columns (Ambion) as described in Place et al., 2008

treatment_protocol: Gill tissue was sampled from individuals and immediately frozen on dry ice.

tag: sample type

value: gill

source_name: Field collected gill tissue, Boiler Bay, OR population

tag: origin


title: t82_Normal


title: t72_Normal


title: t81_Normal


title: t66_Normal


title: t64_Normal


title: t70_Normal


title: t79_Normal


title: t77_Normal


title: t59_Normal


title: t73_Normal


title: t89_Normal


title: t6_Normal


title: t53_Normal


title: t69_Normal


title: t71_Normal


title: t68_Normal


title: t52_Normal


title: t67_Normal


title: t7_Normal


title: t80_Normal


title: t63_Normal


title: t61_Normal


title: t58_Normal


title: t62_Normal


title: t5_Normal


title: t57_Normal


title: fused SUM-159 replicate 2

city: Ashburn

first: Daniel

last: Feliciano

state: VA

address: 19700 Helix Dr

institute: Janelia, HHMI

data_processing:
Sequencing reads were trimmed to remove TruSeq adapters using Cutadapt v1.16, then were aligned to the human genome (Hg38) using STAR v2.5.3a.
Gene expression estimates were made using the built-in htseq-count feature in STAR.
Differential expression analysis was performed using edgeR v3.6 with FDR = 0.05.  Gene enrichment analyses were performed using DAVID Bioinformatics Resources.
We used ToppCluster and Cytoscape to construct the subcategory network.
Genome_build: Hg38
Supplementary_files_format_and_content: gene_counts_matrix.txt = text file containing un-normalized htseq counts

source_name: cultured SUM-159 cells

growth_protocol: SUM-159 cells were grown in a 37C, 5% CO2 tissue culture incubator on tissue culture treated dishes.  Cells were cultured in DMEM + 10% FBS, L-glutamine, and antibiotics.

extract_protocol:
Media was removed and cells were lysed with Trizol (Thermo) according to manufacturer's instructions.  A second CHCl3 extraction was performed to increase purity.  Total RNA was quantified by Nanodrop.
RNA-seq libraries were made from 5 ng total RNA spiked with 1e-5 final dilution of ERCC Mix 1 (Thermo) using Ovation RNA-seq v2 kit (NuGEN) to make cDNA and Ovation Rapid DR Multiplex System (NuGEN) to make libraries according to manufacturer's instructions.

treatment_protocol: Cells were transfected with VSV-G using Lipofectamine 3000 (Thermo) according to manufacturer's instructions.

tag: transfection treatment

value: fused

tag: fusion buffer

value: 125mM NaCl, 5mM KCl, 20mM NaOAc, pH 5.5-6.0


title: fused SUM-159 replicate 3


title: t55_Normal


title: t54_Normal


title: t44_Normal


title: t51_Normal


title: t50_Normal


title: t56_Normal


title: t47_Normal


title: t48_Normal


title: t46_Normal


title: t45_Normal


title: t60_Normal


title: t42_Normal


title: SUM-159 control replicate 3

value: control


title: t49_Normal


title: SUM-159 control replicate 2


title: SUM-159 control replicate 1


title: t4_Normal


title: fused SUM-159 replicate 4


title: t43_Normal


title: SUM-159 control replicate 4


title: t41_Normal


title: t40_Normal


title: fused SUM-159 replicate 1


title: t37_Normal


title: t35_Normal


title: CMS16-BMDM-6h-IP

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

institute: Chiba University

data_processing:
Library strategy: CMS-Seq
Reads were mapped to mouse genome mm9 using the BSMAP mapping tool.
Enriched regions relative to input DNA were detected using the “findPeaks” routine in HOMER with the “histone” mode and default parameter values.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: BMDMs

growth_protocol: 10 million bone marrow cells were seeded per 10 cm non-tissue culture plates in DMEM high glucose (50%) with 20% FBS, 30% L929-cell conditioned laboratory-made media (as source of M-CSF), and 100 U/ml penicillin/streptomycin+L-glutamine (GIBCO). After 4 days of differentiation, 20 ng/ml mouse M-CSF (Shenandoah Biotechnology) was added to the media. After an additional 2 days of culture, non-adherent cells were washed off with room temperature DMEM and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated Petri dishes overnight in DMEM containing 20% FBS, 30% L929-cell conditioned laboratory-made media, and 100 U/ml penicillin/streptomycin+L-glutamine.

extract_protocol:
DNA (5 to 10 μg in 130 μl tris-EDTA buffer) was sheared with a Covaris E220 using microTUBE for 4 min. DNA was cleaned up with Ampure XP beads, processed with NEBNext End Repair and A-tail Modules (NEB, Ipswich, MA, USA), and ligated to methylated Illumina adaptors (NEB). DNA was then bisulfite-treated (MethylCode, Thermo Fisher Scientific), denatured, and immunoprecipitated with anti-CMS serum (in-house) and a mixture of protein A and G Dynabeads (Thermo Fisher Scientific).
Libraries for immunoprecipitated DNA were generated by PCR with barcoded primers (NEBNext Multiplex Oligos for Illumina; NEB) for 15 cycles using KAPA HiFi HotStart Uracil+ ReadyMix (Roche), followed by a cleanup with Ampure XP beads (Beckman Coulter), and sequenced with a HiSeq 2500 (Illumina, San Diego, CA, USA) with paired-end 50-bp reads.

value: wild type

tag: treatment

value: bone marrow derived macrophages

tag: ip antibody

value: anti-CMS serum (in-house)


title: CMS15-BMDM-4h-IP


title: t36_Normal


title: CMS14-BMDM-2h-IP


title: t34_Normal


title: CMS11-BMDM-0h-IP


title: CMS12-BMDM-0.5h-IP


title: CMS17-BMDM-Input


title: t33_Normal


title: t32_Normal


title: CMS13-BMDM-1h-IP


title: t39_Normal


title: t38_Normal


title: t31_Normal


title: CMS6-Naïve-Input

source_name: Naïve CD4 T-cells

growth_protocol: Total CD4+ T cells were isolated with the EasySep Mouse CD4+ T cell isolation kit (STEMCELL Technologies, Canada) from the spleen and lymph nodes. Then, CD4+CD25−CD62LhiCD44lo naive CD4+ T cells were FACS sorted.

value: T-cells from the spleen and lymphnodes


title: CMS4-iTerg-Input

source_name: iTregs

growth_protocol: For iTreg differentiation, with plate-bound anti-CD3 (clone 2C11) and anti-CD28 (clone 37.51) antibodies at 1 μg/ml in the presence of 10 ng/ ml recombinant human TGF-β (PeproTech) and 100 U/ml recombinant human IL-2 (rhIL-2). On day 3 of culture, cells were removed from TCR/CD28 costimulation conditions and expanded in the presence of 100 U/mL IL-2 for 3 days.


title: CMS5-Naïve-IP


title: CMS3-Th2-Input

source_name: Th2 cells

growth_protocol: For Th2 polarization naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (clone 2C11) and anti-CD28 (clone 37.51) antibodies at 1 μg/ml in the presence of 1000 U/ ml IL-4, 1 μg/ml anti-IFN-γ, for 2 days. On day 3 of culture, cells were removed from TCR/CD28 costimulation conditions and expanded in the presence of 20 U/mL IL-2 for 3 days.


title: CMS2-iTerg-IP


title: t29_Normal


title: CMS1-Th2-IP


title: t3_Normal


title: t28_Normal


title: t27_Normal


title: t26_Normal


title: t24_Normal

value: H


title: iBMDM_sh.Stat1_Stat1_TAmut_IFNγ_4h_rep2_RNA-seq [dataset 9]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: RNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 TA mutante overexpression

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to "wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using the custom R scripts.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

growth_protocol: iBMDM cells were cultured in DMEM supplemented with 10% FBS. The cells transduced with non-specfic shRNA or Sta1 sh RNA along with Doxycycline-inducible overexpression of GFP,  Stat1 wildtype, DBD mutant or TA mutant.

extract_protocol:
Two replicates for the each of the different sets of iBMDM cells were seeded at ~7.5 × 105 cells per well in 6-well plates and treated as described above.  The cells were collected and total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions.  The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen, 61002)
The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011).  The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of the final library DNA fragments) and sequenced using an Illumina HiSeq 2500 and NextSeq 500

treatment_protocol: iBMDM cells were seeded in 6 well plates and treated with Doxycycline (1 µg/mL) for 24 hours followed by IFNγ (100 ng/mL) for 1 hour.

value: immortalized bone marrow derived macrophages (iBMDM)

tag: genotype/variation

value: IFNγ


title: t30_Normal


title: t25_Normal


title: t22_Normal


title: t21_Normal


title: t23_Normal


title: t20_Normal


title: Exo3-26_89

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

data_processing:
Standard Illumina base-calling (HiSeq 2500)
Adapter trimming, allignment and annotation on rnaworld (PMID: 22836126)
Genome_build: hg19
Supplementary_files_format_and_content: Excel files showing miRNA read counts and sample metadata

source_name: RNase treated exosomes from the medium of RAW 264.7 murine macrophages

extract_protocol:
Total RNA extraction from serum, plasma or pulled exosomes using miRNeasy Serum/Plasma kit (Qiagen, # 217184)
In-house small RNA library preparation (as described in PMID 28335433)

tag: disease severity

tag: library preparation

value: In-house

tag: 3' adapter sequence

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: Exo3-26_77

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: iBMDM_sh.Stat1_Stat1_TAmut_IFNγ_4h_rep1_RNA-seq [dataset 9]

description: RNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 TA mutant overexpression


title: t2_Normal

value: lung

value: Normal

value: non-small cell lung cancer


title: iBMDM_sh.Stat1_Stat1_TAmut_Control_rep2_RNA-seq [dataset 9]

description: RNA from untreated iBMDM with Stat1 shRNA and Stat1 TA mutant overexpression

value: Untreated


title: iBMDM_sh.Stat1_Stat1_DBDmut_IFNγ_4h_rep2_RNA-seq [dataset 9]

description: RNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 DBD mutante overexpression


title: t19_Normal

value: EA


title: iBMDM_sh.Stat1_Stat1_DBDmut_IFNγ_4h_rep1_RNA-seq [dataset 9]

description: RNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 DBD mutant overexpression


title: iBMDM_sh.Stat1_Stat1_TAmut_Control_rep1_RNA-seq [dataset 9]

value: Stat1 shRNA and Stat1 TA mutant overexpression


title: iBMDM_sh.Stat1_Stat1_TAmut_IFNγ_1h_rep1_RNA-seq [dataset 9]


title: iBMDM_sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep1_RNA-seq [dataset 9]

value: Stat1 shRNA and Stat1 DBD mutant overexpression


title: t17_Normal


title: iBMDM_sh.Stat1_Stat1_DBDmut_Control_rep2_RNA-seq [dataset 9]

description: RNA from untreated iBMDM with Stat1 shRNA and Stat1 DBD mutant overexpression


title: iBMDM_sh.Stat1_Stat1_DBDmut_Control_rep1_RNA-seq [dataset 9]


title: iBMDM_sh.Stat1_Stat1_TAmut_IFNγ_1h_rep2_RNA-seq [dataset 9]

value: Stat1 shRNA and Stat1 TA mutante overexpression


title: iBMDM_sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep2_RNA-seq [dataset 9]

value: Stat1 shRNA and Stat1 DBD mutante overexpression


title: t16_Normal


title: t15_Normal


title: t18_Normal

value: AA


title: t14_Normal


title: t13_Normal


title: t12_Normal


title: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_4h_rep2_RNA-seq [dataset 9]

description: RNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 Wildtype overexpression


title: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_4h_rep1_RNA-seq [dataset 9]

value: Stat1 shRNA and Stat1 Wildtype overexpression


title: t1_Normal


title: iBMDM_sh.Stat1_Stat1_Wt_Control_rep2_RNA-seq [dataset 9]

description: RNA from untreated iBMDM with Stat1 shRNA and Stat1 Wildtype overexpression


title: iBMDM_sh.Stat1_GFP_IFNγ_4h_rep2_RNA-seq [dataset 9]

description: RNA from  IFNγ treated iBMDM with Stat1 shRNA and GFP overexpression

value: Stat1 shRNA and GFP overexpression


title: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_1h_rep2_RNA-seq [dataset 9]

value: immortalized bone marrow derived macrophages (iBMDM)


title: t11_Normal


title: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_1h_rep1_RNA-seq [dataset 9]

value: IFNγ


title: c97_Tumor

value: Tumor


title: t10_Normal


title: iBMDM_sh.Stat1_Stat1_Wt_Control_rep1_RNA-seq [dataset 9]


title: iBMDM_sh.Stat1_GFP_IFNγ_1h_rep1_RNA-seq [dataset 9]


title: iBMDM_sh.Stat1_GFP_IFNγ_4h_rep1_RNA-seq [dataset 9]


title: iBMDM_sh.Stat1_GFP_Control_rep2_RNA-seq [dataset 9]

description: RNA from untreated iBMDM with Stat1 shRNA and GFP overexpression


title: iBMDM_sh.Stat1_GFP_IFNγ_1h_rep2_RNA-seq [dataset 9]


title: iBMDM_sh.Stat1_GFP_Control_rep1_RNA-seq [dataset 9]


title: c94_Tumor


title: iBMDM_sh.ns_GFP_IFNγ_4h_rep2_RNA-seq [dataset 9]

description: RNA from  IFNγ treated iBMDM with non-specific shRNA and GFP overexpression


title: c92_Tumor


title: c91_Tumor


title: iBMDM_sh.ns_GFP_IFNγ_1h_rep2_RNA-seq [dataset 9]

value: non-specific shRNA and GFP overexpression


title: iBMDM_sh.ns_GFP_IFNγ_4h_rep1_RNA-seq [dataset 9]


title: c90_Tumor


title: c89_Tumor


title: iBMDM_sh.ns_GFP_Control_rep2_RNA-seq [dataset 9]

description: RNA from untreated iBMDM with non-specific shRNA and GFP overexpression


title: iBMDM_sh.ns_GFP_IFNγ_1h_rep1_RNA-seq [dataset 9]


title: c98_Tumor


title: c9_Tumor


title: c95_Tumor


title: c96_Tumor


title: iBMDM_sh.Parp1_IFNγ_4h_rep2_RNA-seq [dataset 8]

description: RNA from iBMDM expressing Parp1 shRNA

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using the Bosh.nsie software package (Langmead et al, 2009) .
Mapped reads were further converted to “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using custom R scripts.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig

growth_protocol: iBMDM cells were cultured in DMEM supplemented with 10% FBS. The cells expressing non-specfic shRNA or Parp1 targeting shRNA.

treatment_protocol: iBMDM cells were seeded in 6 well plates and treated with IFNγ (100 ng/mL)  for indicated times.

tag: genotype

value: Parp1 shRNA


title: c87_Tumor

value: lung


title: iBMDM_sh.ns_GFP_Control_rep1_RNA-seq [dataset 9]


title: c88_Tumor


title: iBMDM_sh.Parp1_IFNγ_4h_rep1_RNA-seq [dataset 8]

description: RNA from iBMDM expressing Parp1 shRNA


title: c85_Tumor


title: iBMDM_sh.Parp1_IFNγ_1h_rep2_RNA-seq [dataset 8]

description: RNA from iBMDM expressing Parp1 shRNA


title: c83_Tumor


title: t65_Normal

value: Normal


title: c86_Tumor

value: non-small cell lung cancer


title: iBMDM_sh.Parp1_IFNγ_1h_rep1_RNA-seq [dataset 8]

description: RNA from iBMDM expressing Parp1 shRNA


title: c84_Tumor


title: iBMDM_sh.Parp1_IFNγ_2h_rep1_RNA-seq [dataset 8]

description: RNA from iBMDM expressing Parp1 shRNA


title: c93_Tumor


title: c82_Tumor


title: c81_Tumor


title: iBMDM_sh.Parp1_Control_rep1_RNA-seq [dataset 8]

description: RNA from iBMDM expressing Parp1 shRNA

value: Untreated


title: iBMDM_sh.Parp1_Control_rep2_RNA-seq [dataset 8]

description: RNA from iBMDM expressing Parp1 shRNA


title: c80_Tumor

value: EA


title: c8_Tumor


title: c79_Tumor


title: iBMDM_sh.ns_IFNγ_4h_rep1_RNA-seq [dataset 8]

description: RNA from iBMDM expressing non-speciifc shRNA

value: non-specific shRNA


title: iBMDM_sh.ns_IFNγ_1h_rep2_RNA-seq [dataset 8]


title: c78_Tumor


title: iBMDM_sh.ns_IFNγ_2h_rep2_RNA-seq [dataset 8]


title: c77_Tumor


title: iBMDM_sh.Parp1_IFNγ_2h_rep2_RNA-seq [dataset 8]

description: RNA from iBMDM expressing Parp1 shRNA


title: c76_Tumor


title: c75_Tumor


title: iBMDM_sh.ns_Control_rep1_RNA-seq [dataset 8]


title: iBMDM_sh.ns_Control_rep2_RNA-seq [dataset 8]


title: iBMDM_IFNγ_4h+PJ34_rep2_RNA-seq [dataset 7]

description: RNA from  IFNγ + PJ34 treated iBMDM

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using custom R scripts.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

source_name: iBMDM_IFNγ_4h + PJ34

growth_protocol: iBMDM cells were cultured in DMEM supplemented with 10% FBS. The cells transduced with non-specfic shRNA or Parp1 targeting shRNA.

treatment_protocol: iBMDM were seeded in 6 well plates and treated with IFNγ (100 ng/mL) for indicated times. For PARP inhibitor treatment condition, PJ34 (20 µM) was added 2 hours prior to the IFNγ treatment.

value: IFNγ + PJ34


title: iBMDM_sh.ns_IFNγ_2h_rep1_RNA-seq [dataset 8]


title: c72_Tumor


title: c70_Tumor


title: iBMDM_IFNγ_1h+PJ34_rep2_RNA-seq [dataset 7]

description: RNA from  IFNγ + PJ34 treated iBMDM

source_name: iBMDM_IFNγ_1h + PJ34


title: iBMDM_IFNγ_2h+PJ34_rep1_RNA-seq [dataset 7]

description: RNA from  IFNγ + PJ34 treated iBMDM

source_name: iBMDM_IFNγ_2h + PJ34


title: iBMDM_sh.ns_IFNγ_1h_rep1_RNA-seq [dataset 8]


title: c74_Tumor


title: iBMDM_IFNγ_2h+PJ34_rep2_RNA-seq [dataset 7]

description: RNA from  IFNγ + PJ34 treated iBMDM


title: c69_Tumor


title: c7_Tumor


title: iBMDM_sh.ns_IFNγ_4h_rep2_RNA-seq [dataset 8]


title: iBMDM_IFNγ_1h+PJ34_rep1_RNA-seq [dataset 7]

description: RNA from  IFNγ + PJ34 treated iBMDM


title: c68_Tumor


title: iBMDM_PJ34_rep2_RNA-seq [dataset 7]

description: RNA from PJ34 treated iBMDM


title: c67_Tumor


title: c65_Tumor


title: c66_Tumor


title: iBMDM_PJ34_rep1_RNA-seq [dataset 7]

description: RNA from PJ34 treated iBMDM


title: iBMDM_IFNγ_4h_rep2_RNA-seq [dataset 7]

description: RNA from IFNγ treated iBMDM


title: c64_Tumor


title: iBMDM_IFNγ_4h+PJ34_rep1_RNA-seq [dataset 7]

description: RNA from  IFNγ + PJ34 treated iBMDM


title: c63_Tumor


title: c73_Tumor


title: iBMDM_IFNγ_2h_rep2_RNA-seq [dataset 7]

description: RNA from IFNγ treated iBMDM


title: c71_Tumor


title: iBMDM_IFNγ_2h_rep1_RNA-seq [dataset 7]

description: RNA from IFNγ treated iBMDM


title: iBMDM_IFNγ_1h_rep1_RNA-seq [dataset 7]

description: RNA from IFNγ treated iBMDM


title: c62_Tumor


title: c60_Tumor


title: iBMDM_IFNγ_1h_rep2_RNA-seq [dataset 7]

description: RNA from IFNγ treated iBMDM


title: c6_Tumor


title: iBMDM_Control_rep1_RNA-seq [dataset 7]

description: RNA from untreated iBMDM

source_name: iBMDM_Untreated control


title: iBMDM_Control_rep2_RNA-seq [dataset 7]

description: RNA from untreated iBMDM


title: c59_Tumor


title: c58_Tumor


title: c57_Tumor


title: sh.Stat1_Stat1_TAmut_IFNγ_1h_rep2_H3K27ac [dataset4]

description: ChIPed DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 TA mutante overexpression

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bed” files for later Metagene and read-density analyses by using the BEDTools software package  (Quinlan et al, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: Bed

extract_protocol:
iBMDM cells were cultured and treated as described above. Briefly, the cells were cross-linked with 1% formaldehyde in PBS for 10 minutes at 37°C and quenched in 125 mM glycine in PBS for 5 minutes at 4°C.  Cross-linked cells were then collected by centrifugation and lysed in Farnham Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail).  A crude nuclear pellet was collected by centrifugation, resuspended in Sonication Buffer (50 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), and sonicated to generate chromatin fragments of ~300 bp in length.  The soluble chromatin was clarified by centrifugation, diluted 1:10 with ChIP Dilution Buffer (20 mM Tris-HCl pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail) and pre-cleared with protein A Dynabeads (Thermo Fischer, 1002D).The pre-cleared samples were used in immunoprecipitation reactions with antibodies against STAT1 with incubation overnight at 4°C with gently mixing.  The samples were washed with (1) Low Salt Wash Buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), (2) High Salt Wash Buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), (3) LiCl Wash Buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, , 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), and (4) 1x Tris-EDTA (TE).  The immunoprecipitated genomic DNA was eluted in Elution Buffer (100 mM NaHCO3, 1% SDS), digested with proteinase K and RNase H to remove protein and RNA, respectively, extracted with phenol:chloroform:isoamyl alcohol, and precipitated with ethanol.  The precipitated ChIPed DNA was collected by centrifugation, air dried, and dissolved in DEPC- treated, nuclease-free  water.
ChIP-seq libraries were generated from two biological replicates for each condition.  A total of 10 ng of ChIPed DNA, or equivalent amounts input DNA, were used to generate libraries for sequencing.  ChIP-seq libraries were generated and analyzed as described previously (Franco et al., 2015) and sequenced using a Illumina HiSeq 2500.

treatment_protocol: iBMDM were seeded in15 cm plates and treated with Doxycycline (1 µg/mL) for 24 hours followed by IFNγ (100 ng/mL) for 1 hour.

tag: chip antibody

value: Histone H3 (acetyl K27) (Abcam, ab4729) rabbit polyclonal antibodies


title: sh.Stat1_Stat1_TAmut_IFNγ_1h_rep1_H3K27ac [dataset4]

description: ChIPed DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 TA mutant overexpression


title: iBMDM_IFNγ_4h_rep1_RNA-seq [dataset 7]

description: RNA from IFNγ treated iBMDM


title: c61_Tumor

tag: tissue


title: c55_Tumor

tag: disease state


title: sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep2_H3K27ac [dataset4]

description: ChIPed DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 DBD mutante overexpression


title: sh.Stat1_Stat1_TAmut_Control_rep2_H3K27ac [dataset4]

description: ChIPed DNA from untreated iBMDM with Stat1 shRNA and Stat1 TA mutant overexpression


title: c56_Tumor

tag: patient diagnosis


title: sh.Stat1_Stat1_DBDmut_Control_rep2_H3K27ac [dataset4]

description: ChIPed DNA from untreated iBMDM with Stat1 shRNA and Stat1 DBD mutant overexpression


title: sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep1_H3K27ac [dataset4]

description: ChIPed DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 DBD mutant overexpression


title: c54_Tumor

tag: race


title: c52_Tumor


title: sh.Stat1_Stat1_TAmut_Control_rep1_H3K27ac [dataset4]

tag: cell type

value: Stat1 shRNA and Stat1 TA mutant overexpression


title: c51_Tumor

value: AA


title: sh.Stat1_Stat1_Wt_IFNγ_1h_rep2_H3K27ac [dataset4]

description: ChIPed DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 Wildtype overexpression


title: sh.Stat1_Stat1_DBDmut_Control_rep1_H3K27ac [dataset4]

value: Stat1 shRNA and Stat1 DBD mutant overexpression


title: sh.Stat1_Stat1_Wt_IFNγ_1h_rep1_H3K27ac [dataset4]

source_name: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_1h _ChIP

value: Stat1 shRNA and Stat1 Wildtype overexpression


title: c50_Tumor


title: c5_Tumor


title: sh.Stat1_Stat1_Wt_Control_rep2_H3K27ac [dataset4]

description: ChIPed DNA from untreated iBMDM with Stat1 shRNA and Stat1 Wildtype overexpression

value: immortalized bone marrow derived macrophages (iBMDM)


title: sh.Stat1_Stat1_TAmut_IFNγ_1h_rep2_Input [dataset4]

description: Input DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 TA mutante overexpression

value: IFNγ

value: Input


title: c48_Tumor

value: Tumor


title: c46_Tumor


title: sh.Stat1_Stat1_Wt_Control_rep1_H3K27ac [dataset4]


title: c45_Tumor


title: c43_Tumor


title: sh.Stat1_Stat1_TAmut_IFNγ_1h_rep1_Input [dataset4]

description: Input DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 TA mutant overexpression


title: sh.Stat1_Stat1_TAmut_Control_rep1_Input [dataset4]

description: Input DNA from untreated iBMDM with Stat1 shRNA and Stat1 TA mutant overexpression


title: sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep2_Input [dataset4]

description: Input DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 DBD mutante overexpression


title: c44_Tumor


title: c42_Tumor


title: c41_Tumor


title: sh.Stat1_Stat1_DBDmut_Control_rep2_Input [dataset4]

description: Input DNA from untreated iBMDM with Stat1 shRNA and Stat1 DBD mutant overexpression


title: c40_Tumor


title: c53_Tumor


title: c4_Tumor


title: sh.Stat1_Stat1_DBDmut_Control_rep1_Input [dataset4]


title: sh.Stat1_Stat1_Wt_IFNγ_1h_rep2_Input [dataset4]

description: Input DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 Wildtype overexpression

source_name: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_1h_ Input


title: c39_Tumor


title: c38_Tumor


title: c37_Tumor


title: c49_Tumor


title: sh.Stat1_Stat1_Wt_Control_rep2_Input [dataset4]

description: Input DNA from untreated iBMDM with Stat1 shRNA and Stat1 Wildtype overexpression


title: c36_Tumor


title: sh.Stat1_Stat1_Wt_Control_rep1_Input [dataset4]


title: iBMDM_sh.Stat1_Stat1_TAmut_IFNγ_1h_rep2_STAT1 [dataset 3]

value: Stat1 shRNA and Stat1 TA mutante overexpression

value: STAT1 (Santa Cruz Biotech, sc-592)


title: c47_Tumor

value: lung


title: sh.Stat1_Stat1_TAmut_Control_rep2_Input [dataset4]


title: sh.Stat1_Stat1_Wt_IFNγ_1h_rep1_Input [dataset4]


title: sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep1_Input [dataset4]

description: Input DNA from  IFNγ treated iBMDM with Stat1 shRNA and Stat1 DBD mutant overexpression


title: c34_Tumor

value: non-small cell lung cancer


title: c35_Tumor


title: c33_Tumor


title: iBMDM_sh.Stat1_Stat1_TAmut_Control_rep2_STAT1 [dataset 3]

value: Untreated


title: iBMDM_sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep2_STAT1 [dataset 3]

value: Stat1 shRNA and Stat1 DBD mutante overexpression


title: iBMDM_sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep1_STAT1 [dataset 3]


title: iBMDM_sh.Stat1_Stat1_TAmut_Control_rep1_STAT1 [dataset 3]


title: iBMDM_sh.Stat1_Stat1_TAmut_IFNγ_1h_rep1_STAT1 [dataset 3]


title: c31_Tumor


title: iBMDM_sh.Stat1_Stat1_DBDmut_Control_rep1_STAT1 [dataset 3]


title: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_1h_rep2_STAT1 [dataset 3]


title: c28_Tumor


title: c29_Tumor


title: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_1h_rep1_STAT1 [dataset 3]


title: iBMDM_sh.Stat1_Stat1_Wt_Control_rep2_STAT1 [dataset 3]


title: c27_Tumor

value: EA


title: c26_Tumor


title: iBMDM_sh.Stat1_Stat1_Wt_Control_rep1_STAT1 [dataset 3]


title: c25_Tumor


title: iBMDM_sh.ns_GFP_IFNγ_1h_rep2_STAT1 [dataset 3]

description: ChIPed DNA from  IFNγ treated iBMDM with non-specific shRNA and GFP overexpression


title: iBMDM_sh.ns_GFP_Control_rep2_STAT1 [dataset 3]

description: ChIPed DNA from untreated iBMDM with non-specific shRNA and GFP overexpression

source_name: iBMDM_sh.ns_GFP_untreated control_ChIP


title: iBMDM_sh.ns_GFP_IFNγ_1h_rep1_STAT1 [dataset 3]

value: non-specific shRNA and GFP overexpression


title: c23_Tumor

value: Hispanic (H) excluded from population differences analysis


title: c24_Tumor


title: c22_Tumor


title: iBMDM_sh.Stat1_Stat1_TAmut_IFNγ_1h_rep2_Input [dataset 3]

value: none; Input


title: c21_Tumor

value: AA


title: iBMDM_sh.Stat1_Stat1_TAmut_IFNγ_1h_rep1_Input [dataset 3]

value: Stat1 shRNA and Stat1 TA mutant overexpression


title: c32_Tumor


title: c30_Tumor


title: c20_Tumor


title: iBMDM_sh.Stat1_Stat1_DBDmut_Control_rep2_STAT1 [dataset 3]

value: Stat1 shRNA and Stat1 DBD mutant overexpression


title: c19_Tumor


title: c3_Tumor


title: iBMDM_sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep2_Input [dataset 3]

value: immortalized bone marrow derived macrophages (iBMDM)


title: iBMDM_sh.Stat1_Stat1_TAmut_Control_rep1_Input [dataset 3]


title: c2_Tumor


title: c18_Tumor


title: iBMDM_sh.Stat1_Stat1_DBDmut_IFNγ_1h_rep1_Input [dataset 3]

value: IFNγ


title: c17_Tumor


title: c16_Tumor


title: c15_Tumor


title: iBMDM_sh.Stat1_Stat1_DBDmut_Control_rep1_Input [dataset 3]


title: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_1h_rep2_Input [dataset 3]

value: Stat1 shRNA and Stat1 Wildtype overexpression


title: iBMDM_sh.ns_GFP_Control_rep1_STAT1 [dataset 3]


title: c14_Tumor

value: Tumor


title: c13_Tumor


title: c11_Tumor


title: c12_Tumor


title: iBMDM_sh.Stat1_Stat1_Wt_IFNγ_1h_rep1_Input [dataset 3]


title: iBMDM_sh.Stat1_Stat1_TAmut_Control_rep2_Input [dataset 3]


title: iBMDM_sh.Stat1_Stat1_Wt_Control_rep2_Input [dataset 3]


title: iBMDM_sh.ns_GFP_IFNγ_1h_rep2_Input [dataset 3]

description: Input DNA from  IFNγ treated iBMDM with non-specific shRNA and GFP overexpression

source_name: iBMDM_sh.ns_GFP_IFNγ_1h_ Input


title: iBMDM_sh.Stat1_Stat1_Wt_Control_rep1_Input [dataset 3]


title: iBMDM_sh.ns_GFP_IFNγ_1h_rep1_Input [dataset 3]


title: iBMDM_sh.ns_GFP_Control_rep2_Input [dataset 3]

description: Input DNA from untreated iBMDM with non-specific shRNA and GFP overexpression

source_name: iBMDM_sh.ns_GFP_untreated control_Input


title: BMDM_IFNγ_1h+PJ34_rep1_H3K27ac_ChIP [dataset 2]

description: ChIP-enriched  DNA from  IFNγ + PJ34 treated BMDM

source_name: BMDM_IFNγ_1h + PJ34_H3K27ac_ChIP

growth_protocol: Bone marrow was harvested from 8-12 weeks old C57Bl6 mice and macrophages were differentiated in culture in DMEM supplemented with 20% FBS and LCCM.

extract_protocol:
BMDM cells were cultured and treated as described above. Briefly, the cells were cross-linked with 1% formaldehyde in PBS for 10 minutes at 37°C and quenched in 125 mM glycine in PBS for 5 minutes at 4°C.  Cross-linked cells were then collected by centrifugation and lysed in Farnham Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail).  A crude nuclear pellet was collected by centrifugation, resuspended in Sonication Buffer (50 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), and sonicated to generate chromatin fragments of ~300 bp in length.  The soluble chromatin was clarified by centrifugation, diluted 1:10 with ChIP Dilution Buffer (20 mM Tris-HCl pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail) and pre-cleared with protein A Dynabeads (Thermo Fischer, 1002D).The pre-cleared samples were used in immunoprecipitation reactions with antibody against H3K27ac with incubation overnight at 4°C with gently mixing.  The samples were washed with (1) Low Salt Wash Buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), (2) High Salt Wash Buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), (3) LiCl Wash Buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, , 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), and (4) 1x Tris-EDTA (TE).  The immunoprecipitated genomic DNA was eluted in Elution Buffer (100 mM NaHCO3, 1% SDS), digested with proteinase K and RNase H to remove protein and RNA, respectively, extracted with phenol:chloroform:isoamyl alcohol, and precipitated with ethanol.  The precipitated ChIPed DNA was collected by centrifugation, air dried, and dissolved in DEPC- treated, nuclease-free  water.
ChIP-seq libraries were generated from two biological replicates for each condition.  A total of 10 ng of ChIPed DNA, or equivalent amounts input DNA, were used to generate libraries for sequencing.  ChIP-seq libraries were generated and analyzed as described previously (Franco et al., 2015) and sequenced using a Illumina HiSeq 2500.

treatment_protocol: BMDM were seeded in15 cm plates and treated with IFNγ (100 ng/mL) for indicated times. For PARP inhibitor treatment condition, PJ34 (20 µM) was added 1 hour prior to the IFNγ treatment.

value: bone marrow derived macrophages (BMDM)

value: IFNγ + PJ34

value: Histone H3 (acetyl K27) (Abcam, ab4729) rabbit polyclonal antibodies


title: BMDM_PJ34_rep2_H3K27ac_ChIP [dataset 2]

description: ChIP-enriched DNA from PJ34 treated BMDM


title: Exo3-26_85

source_name: ultracentrifuged and RNase-treated whole plasma

value: In-house

value: TTAAGTCGTATGCCGTCTTCTGCTTG


title: iBMDM_sh.ns_GFP_Control_rep1_Input [dataset 3]

value: Untreated


title: Exo3-26_84

source_name: whole plasma

value: TCTGATCGTATGCCGTCTTCTGCTTG


title: BMDM_PJ34_rep1_H3K27ac_ChIP [dataset 2]


title: iBMDM_sh.Stat1_Stat1_DBDmut_Control_rep2_Input [dataset 3]


title: BMDM_IFNγ_1h_rep2_H3K27ac_ChIP [dataset 2]

description: ChIP-enriched DNA from IFNγ treated BMDM


title: Exo3-26_76

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: BMDM_IFNγ_1h_rep1_H3K27ac_ChIP [dataset 2]


title: Exo5B-26_80

source_name: whole serum

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: BMDM_Control_rep2_H3K27ac_ChIP [dataset 2]

description: ChIP-enriched DNA from untreated BMDM

source_name: BMDM_Untreated control_H3K27ac_ChIP


title: Exo5B-26_79

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: BMDM_IFNγ_1h+PJ34_rep2_Input [dataset 2]

description: Input DNA from  IFNγ + PJ34 treated BMDM

source_name: BMDM_IFNγ_1h + PJ34_Input

value: none; Input


title: BMDM_Control_rep1_H3K27ac_ChIP [dataset 2]

description: ChIP-enriched DNA from untreated BMDM


title: Exo5B-26_77

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: BMDM_IFNγ_1h+PJ34_rep1_Input [dataset 2]


title: BMDM_PJ34_rep2_Input [dataset 2]

description: Input DNA from PJ34 treated BMDM


title: Exo5B-26_78

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: c10_Tumor

source_name: Frozen Lung Tissue

value: lung

value: non-small cell lung cancer

value: EA


title: c1_Tumor

value: Tumor

value: AA


title: BMDM_IFNγ_1h+PJ34_rep2_H3K27ac_ChIP [dataset 2]

value: bone marrow derived macrophages (BMDM)

value: IFNγ + PJ34


title: Exo5B-26_76

value: In-house


title: Exo5B-26_75

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: BMDM_PJ34_rep1_Input [dataset 2]

description: Input DNA from PJ34 treated BMDM


title: BMDM_IFNγ_1h_rep2_Input [dataset 2]

description: Input DNA from IFNγ treated BMDM

value: IFNγ


title: Covid-19-Whole_2-26_94

value: Death

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_2-26_92

value: Severe

value: TAGGATCGTATGCCGTCTTCTGCTTG


title: BMDM_IFNγ_1h_rep1_Input [dataset 2]

description: Input DNA from IFNγ treated BMDM

source_name: BMDM_IFNγ_1h _Input

value: none; Input


title: BMDM_Control_rep2_Input [dataset 2]

description: Input DNA from untreated BMDM

source_name: BMDM_Untreated control_Input

value: Untreated


title: Covid-19-Whole_2-26_90

value: TAATATCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_2-26_89

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: IFNγ_1h+PJ34_rep2_STAT1_ChIP [dataset1]

source_name: BMDM_IFNγ_1h + PJ34_STAT1_ChIP

extract_protocol:
BMDM cells were cultured and treated as described above. Briefly, the cells were cross-linked with 1% formaldehyde in PBS for 10 minutes at 37°C and quenched in 125 mM glycine in PBS for 5 minutes at 4°C.  Cross-linked cells were then collected by centrifugation and lysed in Farnham Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail).  A crude nuclear pellet was collected by centrifugation, resuspended in Sonication Buffer (50 mM Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), and sonicated to generate chromatin fragments of ~300 bp in length.  The soluble chromatin was clarified by centrifugation, diluted 1:10 with ChIP Dilution Buffer (20 mM Tris-HCl pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail) and pre-cleared with protein A Dynabeads (Thermo Fischer, 1002D).The pre-cleared samples were used in immunoprecipitation reactions with antibodies against STAT1 with incubation overnight at 4°C with gently mixing.  The samples were washed with (1) Low Salt Wash Buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), (2) High Salt Wash Buffer (20 mM Tris-HCl pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), (3) LiCl Wash Buffer (10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, , 1 mM sodium orthovanadate, 10 mM sodium butyrate, and 1x complete protease inhibitor cocktail), and (4) 1x Tris-EDTA (TE).  The immunoprecipitated genomic DNA was eluted in Elution Buffer (100 mM NaHCO3, 1% SDS), digested with proteinase K and RNase H to remove protein and RNA, respectively, extracted with phenol:chloroform:isoamyl alcohol, and precipitated with ethanol.  The precipitated ChIPed DNA was collected by centrifugation, air dried, and dissolved in DEPC- treated, nuclease-free  water.
ChIP-seq libraries were generated from two biological replicates for each condition.  A total of 5 ng (For STAT1) of ChIPed DNA, or equivalent amounts input DNA, were used to generate libraries for sequencing.  ChIP-seq libraries were generated and analyzed as described previously (Franco et al., 2015) and sequenced using a Illumina HiSeq 2500.

treatment_protocol: BMDM were seeded in 15 cm plates and treated with IFNγ (100 ng/mL) for indicated times. For PARP inhibitor treatment condition, PJ34 (20 µM) was added 1 hour prior to the IFNγ treatment.

value: STAT1 (Santa Cruz Biotech, sc-592)


title: BMDM_Control_rep1_Input [dataset 2]

description: Input DNA from untreated BMDM


title: Exo3-26_75


title: PJ34_rep2_STAT1_ChIP [dataset1]


title: Covid-19-Whole_2-26_83

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: IFNγ_1h+PJ34_rep1_STAT1_ChIP [dataset1]


title: Covid-19-Whole_2-26_82

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: IFNγ_1h_rep2_STAT1_ChIP [dataset1]


title: PJ34_rep1_STAT1_ChIP [dataset1]


title: Covid-19-Whole_2-26_81

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: IFNγ_1h_rep1_STAT1_ChIP [dataset1]

value: bone marrow derived macrophages (BMDM)


title: Control_rep2_STAT1_ChIP [dataset1]

description: ChIP-enriched DNA from untreated BMDM

source_name: BMDM_Untreated control_STAT1_ChIP


title: Covid-19-Whole_2-26_78

value: Mild

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_2-26_79

value: In-house

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_2-26_80

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_2-26_77

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_2-26_76

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: IFNγ_1h+PJ34_rep2_Input [dataset1]

value: IFNγ + PJ34


title: Control_rep1_STAT1_ChIP [dataset1]

description: ChIP-enriched DNA from untreated BMDM


title: Covid-19-Whole_2-26_91

value: Severe

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: PJ34_rep2_Input [dataset1]

description: Input DNA from PJ34 treated BMDM

value: none; Input


title: IFNγ_1h+PJ34_rep1_Input [dataset1]


title: Covid-19-Whole_2-26_75

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: PJ34_rep1_Input [dataset1]

description: Input DNA from PJ34 treated BMDM


title: Covid-19-Whole_1-26_94

value: Death

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_1-26_92

value: TAGGATCGTATGCCGTCTTCTGCTTG


title: IFNγ_1h_rep1_Input [dataset1]

description: Input DNA from IFNγ treated BMDM

value: IFNγ


title: Covid-19-Whole_2-26_84

value: TCTGATCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_1-26_91


title: Covid-19-Whole_1-26_89

value: TAACGTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_1-26_90

value: TAATATCGTATGCCGTCTTCTGCTTG


title: Control_rep1_Input [dataset1]

description: Input DNA from untreated BMDM

value: bone marrow derived macrophages (BMDM)

value: Untreated


title: Control_rep2_Input [dataset1]

description: Input DNA from untreated BMDM


title: Covid-19-Whole_1-26_84

value: In-house


title: Covid-19-Whole_1-26_83

value: TCTCCTCGTATGCCGTCTTCTGCTTG


title: Rnmt cKO 4 mock

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

country: United Kingdom

institute: Beatson CRUK

data_processing:
Libraries from the first experiment comparing antibodies were sequenced on a MiSeq with a v3 150 cycle kit in paired-end mode. Libaries from the Rnmt cKO vs control CD4 T cell libraries were sequenced on a  NextSeq 500 with a mid output v2.5 kit (150 cycles) in single end mode.
First the 10nt randomer barcode was extracted using umi_tools, then adapter sequences were trimmed from the reads using cutadapt (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA). For paired end libaries only read one was used since reads were too short for the second read to be advantageous.
Reads were aligned to mm10 with gencode vM12 basic annotation using STAR 2.5.2b, then demultiplexed using umi_tools to remove PCR duplicates.
Secondary alignments and alignments with a MAPQ <20 were removed using samtools.
Bedgraph files were generated using deeptools, options -bs 1 --Offset 1 1  -of bedgraph
Genome_build: Supplementary_Data_1.fa from GSE128947
Supplementary_files_format_and_content: Bed files have the counts of reads starting within the 1bp windows

source_name: 20 hour activated CD4 T cells

growth_protocol: CD4 T cells were sorted from lymph nodes using an EasySep mouse naive CD4 T cell isolation kit.

extract_protocol:
Total RNA was extracted using trizol.
Libraries were made following the pseudoruridine sequencing protocol published by Schwartz, S. et al 2014. 300ng of total RNA from each replicate was made up in BEU buffer (50mM bicine pH 8.3, 4mM EDTA, 7M urea) for the mock treated sample or BEU buffer plus 0.17M CMC (N-Cyclohexyl-N′-(2-morpholinoethyl)carbodiimide methyl-p-toluenesulfonate) (Sigma). Samples were heated to 37°C for 20 mins, then RNA precipitated by adding 100ul buffer A (0.3M NaOAc, 0.1mM EDTA), 1 ul glycogen and 700ul ethanol and washed 1X in 75% EtOH. Samples were resuspended in buffer A, then precipitated as before with ethanol to remove any remaining CMC. RNA was made up in 50mM sodium bicarbonate pH10.4 and heated to 37°C for 3 hours (this removes unwanted CMC adducts). RNA was precipitated with 100ul buffer A, 1ul glycogen, 700ul Ethanol, and washed in 75% ethanol. RNA was made up in 50mM sodium bicarbonate pH9.2 and heated to 95C for 8 mins to fragment, then onto ice. RNA was precipitated with 200ul buffer A, 1 ul glycogen, 500ul ethanol, and washed in 75% ethanol. RNA was dephosphorylated with FastAP (thermo), and linker ligated with high concentration T4 ligase (NEB). Products were reverse transcribed, then the second linker ligated using the high concentration T4 ligase (NEB). Clean ups between these steps were conducted using myOne silane beads. The libraries were PCR amplified and gel purified, then sequenced with a Nextseq High Output v2.5 kit (75 cycles, single end).

treatment_protocol: CD4 T cells were cultured for 20 hours in T cell culture medium (RPMI + 10% heat inactivated FCS + pen/strep + 50µM 2ME) on anti-CD3/CD28 coated plates prepared by incubating the plates with PBS with 5ug/ml anti-CD3 and 1ug/ml anti-CD28 at 37C for three hours.

value: Rnmt fl/fl CD4cre +

tag: Sex

value: Female

value: mock

value: CD4 T cells


title: Rnmt cKO 4 CMC

value: CMC


title: Covid-19-Whole_1-26_82

value: Severe

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: Rnmt cKO 3 mock


title: Rnmt cKO 3 CMC


title: Covid-19-Whole_1-26_81

value: Mild

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_1-26_80

value: TCGATTCGTATGCCGTCTTCTGCTTG


title: Rnmt cKO 2 mock


title: Rnmt cKO 1 mock


title: Covid-19-Whole_1-26_79

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_1-26_78

value: TCCGTTCGTATGCCGTCTTCTGCTTG


title: Rnmt cKO 1 CMC


title: IFNγ_1h_rep2_Input [dataset1]

description: Input DNA from IFNγ treated BMDM

value: IFNγ

value: none; Input


title: Covid-19-Whole_1-26_76

value: TCATCTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_1-26_77

value: In-house

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Whole_1-26_75

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: Control 4 CMC

value: Rnmt fl/fl CD4cre -

value: Female


title: Control 4 mock

value: mock

value: CD4 T cells


title: Control 3 mock


title: Control 3 CMC

value: CMC


title: Covid-19-Exo_4-26_92

source_name: exosomes immunopurified from serum (exo-CATCHER protocol)

value: Severe

value: TAGGATCGTATGCCGTCTTCTGCTTG


title: Covid-19-Exo_4-26_94

value: Death

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Exo_4-26_91

value: TAGAGTCGTATGCCGTCTTCTGCTTG


title: Covid-19-Exo_4-26_90

value: TAATATCGTATGCCGTCTTCTGCTTG


title: Control 2 CMC