title: Exp0_KGN_Control_IgG_ChIP

data_processing:
Chip-seq data processing: Fastq datasets were concatenated using the "concatenate” tool (Galaxy tool ID: Cat1, version1.0.0) and trimmed with Trimmomatic version 0.36.0 (with  illuminaclip step, Truseq3 (single ended, Mi and Hiseq), max mismatch=2, sliding window, average quality 20). Mapped with Bowtie2 against hg38 using preset settings. Duplicates removed with rmdup.Peak calling with Easeq software: Adaptive Local Thresholding (default settings)  with respective knocout samples as negative controls.
RNA-seq data processing: Fastq datasets were concatenated using the "concatenate” tool (Galaxy tool ID: Cat1, version1.0.0) and trimmed with Trimmomatic version 0.36.0 (with  illuminaclip step, Truseq3 (single ended, Mi and Hiseq), max mismatch=2, sliding window, average quality 20). Sequencing data was aligned via RNAstar (version2.4.0d-2, single-end reads) using  hg38 (Canonical) as refgene and reads were counted using Htseq-count (version 0.6.1, galaxy1 using Union mode and Stranded with a minimum alignment quality of 10). Differential expression was analysed using Deseq2. Genes were called as differentially expressed for expression changes larger than 2-fold and an FDR ≤0.01. A minimum of three biological replicates of each sample were used.
Genome_build: hg38
Supplementary_files_format_and_content: GZIPped WIG file containing ChIP-Seq peaks and output txt files from Deseq2 analysis of RNA seq data. Collumns in Deseq2 data provide the following:  Collumn 1: Gene; Collumn 2: Total Counts; Collumn 3: log2 fold difference; Collumn 4: Standard deviation; Collumn 5: Wald Stats; Collumn 6: Wald P value; Collumn 7: Benjamini-Hochberg  P value

value: Normal Goat IgG Control (R&D Systems AB-108-C)


title: Exp0_KGN_FOXL2_mAb1_ChIP

status: Public on Jul 01 2020

type: SRA

city: Copenhagen

first: Paul

middle: Andreas Compare

last: Cloos

address: Ole Maaløesvej5

department: Biotech Research Innovation Centre

country: Denmark

institute: Copenhagen University

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: KGN cell-line

growth_protocol: Cells grown in Ham medium with 10% FCS

extract_protocol:
Confluent cell plates of KGN or HGrC1 cells were washed in PBS and cells were released by treatment with trypsin. Cells were collected by centrifugation (300g, 5 minutes), washed with PBS and centrifuged again. Cells were cross-linked with 0.2-mM DSG for 30 min. at room-temperature followed by cross-linking with 1% formaldehyde for 5 min at room temperature. Glycine was added at a final concentration of 125mM to quench the formaldehyde. Cells was washed twice with ice cold PBS and harvested in SDS buffer (50mM TrisHCl pH 8.1, 100mM NaCl, 5mM EDTA pH 8.0, 0,2% NaN3, 0.5% SDS). Cells were spun down, resuspended in Triton X-IP buffer (100mM Tris pH 8.6, 0.3% SDS, 1.7% Triton X-100 and 5mM EDTA) and the chromatin was sonicated to get DNA fragments of <600bp (with average DNA fragment size of 300bp) and then cleared by centrifugation. 1mg (transcription factors) or 100  g of chromatin (histone modifications) was precleared with Protein G coupled Sepharose beads (GE Healthcare) for 3hrs and incubated with 0,5-10  g antibody overnight at 4  C. The next day, Protein G coupled sepharose beads were added and samples were incubated end-over-end for 4hrs at 4  C. Beads were washed for a total of five times in low salt buffer (20mM Tris-HCl pH 8.0, 1% Triton X-100, 0.1% SDS, 150mM NaCl, 2mM EDTA pH 8.0), two times in RIPA buffer (50mM Tris-HCl pH 7.5, 150mM NaCl, 1% NP40, 0.1% SDS, 0.5% DOC, 1mM EDTA), and one time with high salt buffer (20mM Tris-HCl pH 8.0, 1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA pH 8.0). Beads were incubated with elution buffer (1% SDS, 0.1M sodium bicarbonate) at 65  C overnight to de-crosslink. The DNA was isolated using QIAquick PCR Purification kit (Qiagen) and eluted in 50  l EB buffer.)
ChIP sequencing libraries were prepared for sequencing using standard Illumina protocols
RNA and ChIP sequencing libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: KGN

tag: chip antibody

value: Custom-made monoclonal mouse antibody to human FOXL2 Produced by Paul Cloos (Clone 1512)

tag: genotype/variation

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation


title: Exp0_KGN_Input

value: No antibody


title: 45_38month_array

type: RNA

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

country: USA

institute: Dartmouth Medical School

description:
45_38month_252800422219_1_1.txt
disease

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Agilent scanner

data_processing:
Images were quantified using Feature Extraction Software, log10 Green over Red.  Raw, individual array files need log2 adjusted and reversed for Red over Green.
Log(base2) of R/G Lowess Normalized Ratio (Mean), NONmedian centered data were multiplied by -3.321928 to convert to Log2(Cy3/Cy5) ratios, probes with > 20% data were removed

molecule: total RNA

source_name: Sample: Human PBMC

label_protocol: 50ng of total RNA was reversed transcribed using Agilent Low Input Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted from PBMC following manufacturer's protocol. UHR is Stratagene, Universal Human Reference RNA Catalog #740000

treatment_protocol: Collection of PBMC in PAXgene

tag: diagnosis

value: SSc

tag: treatment

value: Transplant

tag: timepoint

value: post

tag: response

value: Responder

tag: tissue

value: PMBC

source_name: Universal Human Reference

tag: sample type

value: Universal Human Reference (UHR)


title: 44_base_array

description:
44_base_252800420363_1_1.txt
disease

value: base


title: 44_38month_array

description:
44_38month_252800422213_1_1.txt
disease


title: 44_54month_array

description:
44_54month_252800422213_1_3.txt
disease


title: TTC_SC_446

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Single-cell RNA sequence reads were evaluated by AfterQC. Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than.
The reads were mapped to the mouse genome(mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts. Gene expression was represented by CPM (tags per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

organism: Mus musculus

source_name: KO

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

treatment_protocol: Tail tendons from 4-wk-old wild-type or Mkx-/- mice  was minced into desired pieces and digested in 0.2% collagenase I diluted in low-glucose Dulbecco’s modified Eagle’s medium solution at 37°C for 2 hours. Then the cell suspension was filtered using 40 μm strainer to remove the incompletely digested clumps and adjusted to a concentration of 4×10^5 cells/ml.

tag: strain

value: tail tendon

tag: genotype

value: Mkx-/-

tag: age


title: PROseq2_WT7_B

city: Hong Kong

first: Ming

middle: Kui

last: Chan

address: Tat Chee Avenue

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description: nascent RNA

data_processing:
Library strategy: PRO-seq
For RNAseq data, reads were mapped to the human genome hg19 and counted by STAR 2.6.1a with default parameters. R package DESeq2 was used to perform differential expression analysis (P value <0.05 and |log2 fold change| > 0.25). bamCoverage in deepTools was used to generate bigwig files for IGV visualization using the traditional normalization method: Reads Per Kilobase per Million mapped reads (RPKM)
For PROseq data, adapter cutting, reads aligning and coverage files generating follows the pipeline illustrated by Dig et. al. Counts data was gotten from the bigwig files using R package bigwig. R package DESeq2 was used to perform differential expression analysis (P value < 0.05 and |log2 fold change| > 0.25).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: pancreatic cancer cell line; adenocarcinoma derived

growth_protocol: S2VP10 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Briefly, cells were rinsed with ice-cold 1X PBS followed by wash buffer (10mM Tris-Cl, pH 7.4, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, 0.5mM DTT, 1X Protease Inhibitor Tablets (Roche), 40 units RNase inhibitor/ 10ml (added immediately before use) (AmbionTM; Cat#AM2682) dissolved in nuclease-free water once. Cells were lysed by incubating in lysis buffer (10mM Tris-Cl, pH 7.4, 10mM KCl, 250mM sucrose, 5mM MgCl2, 1mM EGTA, 0.05% Tween-20, 0.5mM DTT, 0.2% NP40 1X Protease Inhibitor Tablets (Roche), 40 units RNase inhibitor/ 10ml (AmbionTM; Cat#AM2682) for 5 minutes. The permeabilized cells were collected (1,000g for 5 minutes at 4°C) after two washes with wash buffer and flash frozen in 100L storage buffer (50mM Tris-CL pH 8.0, 40% glycerol, 5mM MgCl2, 0.1mM EDTA, 0.5mM DTT). Permeabilized cells in 100L storage buffer were mixed with 100L pre-warmed 2 nuclear run-on reaction mix (10mM Tris-Cl, pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 37.5M biotin-11-ATP (Perkin Elmer; Cat# NEL544001EA), 37.5M biotin-11-CTP (Perkin Elmer; Cat# NEL542001EA), 37.5M biotin-11-GTP (Perkin Elmer; Cat# NEL545001EA), 37.5M biotin-11-UTP (Perkin Elmer; Cat#NEL543001EA), 0.8 units/L RNase Inhibitor (Ambion™; Cat#AM2682), 1% Sarkosyl (Sigma-Aldrich; Cat# L5125) and incubated at 37°C for 5 minutes. The run-on reaction was terminated by adding Trizol LS (Invitrogen™; Cat# 10296010) and pelleted by ethanol precipitation. RNA pellets were re-dissolved in nuclease-free water and briefly denatured at 65°C followed by base hydrolysis with NaOH to produce 100-150 nt fragments. The biotinylated nascent transcripts were purified three times using Dynabeads™ M-280 Streptavidin (Invitrogen™; Cat#11206D), each round followed by Trizol (Invitrogen™; Cat# 15596026) extraction and ethanol precipitation. The 5’ cap of transcripts were removed with RNA 5' Pyrophosphohydrolase (NEB; Cat# M0356S) and the 5’ hydroxyl group repaired with T4 polynucleotide kinase (NEB; Cat# M0201).
The libraries were  generated using TruSeq small RNA adapters and size-selected to a range of 140-350bp through Solid Phase Reversible Immobilisation beads
PRO-seq libraries were sequenced with 75 bp paired end sequencing on NextSeq 500 (Illumina).

tag: cell type

value: pancreatic cancer cell line

value: WT

tag: batch


title: TTC_SC_444


title: 44_8month_array

description:
44_8month_252800420363_2_4.txt
disease


title: PROseq2_WT7_A

description: nascent RNA


title: PROseq2_WT16

description: nascent RNA


title: TTC_SC_443


title: 44_14month_array

description:
44_14month_252800421275_2_2.txt
disease


title: Tumor_wt_d12_rep2

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description:
Tumor_wt_d12_rep2
GL261_S1

data_processing:
RNA sequencing reads were aligned to GRCm38/mm10 build of Mus musculus genome using STAR-2.5.2a
The Unique mapped reads were normalized using PORT (https://github.com/itmat/normalization/wiki) and counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression
P values from Bayes moderated t tests were adjusted to control the global false discovery rate (FDR). Genes were called differentially expressed if they achieved an FDR of 0.05 or less
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts

source_name: Tumor

growth_protocol: Nrp1+/+ (CD45.2+Thy1.1+Thy1.2+) or Nrp1–/– (CD45.2+Thy1.2+) pMel-T cells were recovered from tumor, as well as the matched draining and non-draining lymph nodes of the CD45.1 recipient at the designated day(s) post B16-gp100 tumor challenge

extract_protocol:
The plate was spun down at 2000g for 2 minutes and immediately proceeded with reverse transcription (RT). A mixture (2 microliter) of RT primers and dNTP (1 mM) was added to each well followed by incubation at 70 ºC for 3 minutes,Denatured templates and RT primers were quickly spun down and added with 6 microl RT master mix containing MgCl2 (9mM), first-strand buffer (5x), Superscript II reverse transcriptase (10 U/microl), DTT (5 mM), Betaine (1M), RNase inhibitors (1 U/microl) and TSO (template switch oligo) (1 microM) followed by the RT reaction on a PCR cycler (42 ºC for 90 min, 10 cycles of 50ºC/42ºC and 70ºC for 15 min, hold at 4ºC). An addition of 15 cycle cDNA amplification was performed following cDNA synthesis by the KAPA Hot Start II High-Fidelity DNA Polymerase. The amplified cDNA was purified using Ampure XP beads (@ 0.6:1 bead to cDNA ratio) and eluted with 17.5 microl elution buffer. cDNA size (peak at 1.5~2kb) was verified with TapeStation5000 and quantified by the Qbit
Sequencing libraries were prepared from 1ng cDNA using the Nextera XT DNA Library Prep kit (Illumina FC-131-1096), following the manufacture’s instruction. cDNA Libraries were quantified by the KAPA library quantification kit (KAPA KK4854) and size (peak at ~ 400bp) verified on TapeStation1000. Ten diluted libraries (2nM) were pooled and sequenced with the NextSeq 500/550 High Output v2 kit using 75bp single read

treatment_protocol: Five hundred cells from either genotype were double-sorted (purity> 99.5%) directly to individual well of a 96-well plate containing 2 microliter lysis buffer (0.2% Triton X-100 with RNase inhibitor at 2 U/microliter).

tag: background strain

value: Tumor

value: pMel-T cells

tag: time


title: Tumor_wt_d21_rep2

description:
Tumor_wt_d21_rep2
GL271_S1


title: Tumor_wt_d21_rep3

description:
Tumor_wt_d21_rep3
GL281_S1


title: 43_Base_R_array

description:
43_Base_R_252800422020_2_2.txt
disease

value: Cyclophosphamide

value: Non-responder


title: TTC_SC_442


title: Tumor_wt_d12_rep1

description:
Tumor_wt_d12_rep1
GL122_S1


title: PROseq2_Mut3

description: nascent RNA


title: TTC_SC_441


title: PROseq2_Mut32

description: nascent RNA


title: Tumor_ko_d21_rep3

description:
Tumor_ko_d21_rep3
GL282_S2

value: NRP1 KO


title: TTC_SC_445


title: Tumor_ko_d21_rep1

description:
Tumor_ko_d21_rep1
GL196_S4


title: PROseq1_WT16

description: nascent RNA


title: Tumor_ko_d21_rep2

description:
Tumor_ko_d21_rep2
GL272_S2


title: TTC_SC_439


title: Tumor_wt_d21_rep1

description:
Tumor_wt_d21_rep1
GL195_S3


title: 43_26month_array

description:
43_26month_252800421275_2_3.txt
disease


title: 43_38month_array

description:
43_38month_252800422212_2_2.txt
disease


title: 44_26month_array

description:
44_26month_252800420363_2_3.txt
disease


title: 43_14month_array

description:
43_14month_252800420364_2_3.txt
disease


title: Tumor_ko_d12_rep2

description:
Tumor_ko_d12_rep2
GL262_S2


title: 43_8month_array

description:
43_8month_252800420363_2_1.txt
disease


title: 42_base_array

description:
42_base_252800422380_1_4.txt
disease


title: Tumor_ko_d12_rep1

description:
Tumor_ko_d12_rep1
GL123_S2


title: Melanoma, Sondel_RNA_W

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: exome captured

data_processing:
[Mapping]  STAR 2.4.0k
[Variant calling]  GATK 3.4-0
[Fusion detection]  Tophat-Fusion 2.0.13; FusionCatcher 0.99.5a; Defuse 0.7.0
[Gene expression]  Rsubread 1.34 to get raw read count and EdgeR 3.7 to get the normalized expression of genes
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: RPKM file is tab delimited text file for each sample

extract_protocol:
RNA was extracted using Qiagen RNeasy FFPE kits from FFPE tumor blocks
Illumina TruSeq RNA Exome kits

value: melanoma

tag: tissue type

value: tumor

tag: study group

value: A

tag: death

tag: overall survival time (os in months)

tag: event

tag: recurrence free survival time (rfs in months)


title: TTC_SC_438


title: TTC_SC_437


title: Melanoma, Sondel_RNA_V

description: exome captured

tag: diagnosis

tag: treatment


title: TTC_SC_436

tag: tissue


title: NDLN_wt_d63_rep1

description:
NDLN_wt_d63_rep1
GL279_S9

source_name: Non Draining lymph node

value: Non Draining lymph node


title: TTC_SC_440


title: NDLN_wt_d63_rep2

description:
NDLN_wt_d63_rep2
GL289_S9


title: TTC_SC_435


title: 41_base_array

description:
41_base_252800420325_1_3.txt
disease

value: SSc

tag: timepoint

tag: response

value: Responder

tag: sample type


title: Melanoma, Sondel_RNA_U

description: exome captured


title: Melanoma, Sondel_RNA_T

description: exome captured


title: PROseq1_Mut3

description: nascent RNA

tag: cell line

tag: genotype


title: TTC_SC_434

tag: strain

tag: age


title: PROseq1_Mut32

description: nascent RNA

tag: cell type

tag: batch


title: NDLN_wt_d35_rep2

description:
NDLN_wt_d35_rep2
GL269_S9

tag: background strain

tag: time


title: NDLN_wt_d35_rep1

description:
NDLN_wt_d35_rep1
GL267_S7


title: TTC_SC_433


title: 41_54month_array

description:
41_54month_252800422041_1_4.txt
disease

value: post

value: PMBC

value: Universal Human Reference (UHR)


title: 41_8month_array

description:
41_8month_252800420363_2_2.txt
disease


title: 41_38month_array

description:
41_38month_252800422041_2_1.txt
disease


title: 39_base_array

description:
39_base_252800422038_1_2.txt
disease

value: base


title: 41_14month_array

description:
41_14month_252800420325_2_4.txt
disease


title: 41_26month_array

description:
41_26month_252800420326_1_3.txt
disease


title: TTC_SC_432

value: tail tendon

value: Mkx-/-


title: Melanoma, Sondel_RNA_R

description: exome captured

tag: tissue type

tag: study group

value: B

tag: death

tag: overall survival time (os in months)


title: TTC_SC_431


title: Melanoma, Sondel_RNA_Q

description: exome captured

tag: diagnosis

tag: treatment

tag: event

tag: recurrence free survival time (rfs in months)


title: Melanoma, Sondel_RNA_S

description: exome captured


title: NDLN_wt_d21_rep2

description:
NDLN_wt_d21_rep2
GL277_S7

tag: tissue

value: pMel-T cells

value: WT


title: NDLN_wt_d21_rep1

description:
NDLN_wt_d21_rep1
GL199_S7


title: Melanoma, Sondel_RNA_P

description: exome captured

value: Never Treated


title: NDLN_wt_d12_rep1

description:
NDLN_wt_d12_rep1
GL130_S9


title: Melanoma, Sondel_RNA_O

description: exome captured


title: TTC_SC_429


title: TTC_SC_430


title: TTC_SC_428


title: Melanoma, Sondel_RNA_N

description: exome captured


title: 39_14month_array

description:
39_14month_252800422040_1_4.txt
disease

value: Cyclophosphamide

tag: timepoint

tag: response

value: Non-responder

tag: sample type


title: 39_8month_array

description:
39_8month_252800422040_1_1.txt
disease


title: NDLN_ko_d63_rep2

description:
NDLN_ko_d63_rep2
GL290_S10

tag: genotype

value: NRP1 KO


title: 37_base_array

description:
37_base_252800422040_2_3.txt
disease

value: Transplant


title: Melanoma, Sondel_RNA_M

description: exome captured

value: melanoma

value: tumor

value: A


title: NDLN_ko_d63_rep1

description:
NDLN_ko_d63_rep1
GL280_S10

value: Non Draining lymph node

tag: cell type


title: TTC_SC_427

tag: strain

tag: age


title: 38_base_array

description:
38_base_252800422379_2_2.txt
disease

value: SSc

value: PMBC


title: TTC_SC_426


title: NDLN_wt_d12_rep2

description:
NDLN_wt_d12_rep2
GL265_S5

tag: background strain

tag: time


title: Melanoma, Sondel_RNA_L

description: exome captured

tag: tissue type

tag: study group


title: TTC_SC_425


title: NDLN_ko_d35_rep2

description:
NDLN_ko_d35_rep2
GL270_S10


title: Melanoma, Sondel_RNA_K

description: exome captured

tag: death

tag: overall survival time (os in months)


title: 37_14month_array

description:
37_14month_252800422040_2_2.txt
disease

tag: diagnosis

tag: treatment

value: post

value: Universal Human Reference (UHR)


title: NDLN_ko_d35_rep1

description:
NDLN_ko_d35_rep1
GL268_S8


title: 37_8month_array

description:
37_8month_252800422040_1_3.txt
disease


title: TTC_SC_424

value: tail tendon

value: Mkx-/-


title: NDLN_ko_d21_rep2

description:
NDLN_ko_d21_rep2
GL278_S8

value: pMel-T cells


title: Melanoma, Sondel_RNA_J

description: exome captured

tag: event

tag: recurrence free survival time (rfs in months)


title: TTC_SC_423

tag: tissue


title: Melanoma, Sondel_RNA_I

description: exome captured

value: B


title: Melanoma, Sondel_RNA_H

description: exome captured


title: 35_8month_array

description:
35_8month_252800422022_2_4.txt
disease

tag: timepoint

tag: response

value: Responder


title: 35_base_array

description:
35_base_252800422033_2_1.txt
disease

value: Cyclophosphamide

value: base

tag: sample type


title: 35_54month_array

description:
35_54month_252800422041_1_3.txt
disease


title: TTC_SC_422

tag: genotype


title: TTC_SC_421

tag: strain


title: 35_38month_array

description:
35_38month_252800422041_2_3.txt
disease


title: Melanoma, Sondel_RNA_G

description: exome captured


title: DLN_wt_d63_rep1

description:
DLN_wt_d63_rep1
GL275_S5

source_name: Draining lymph node

value: Draining lymph node

tag: cell type

value: WT


title: NDLN_ko_d12_rep1

description:
NDLN_ko_d12_rep1
GL131_S10

tag: background strain

value: NRP1 KO


title: 35_20month_array

description:
35_20month_252800422023_2_2.txt
disease


title: Melanoma, Sondel_RNA_F

description: exome captured

value: melanoma

value: tumor


title: DLN_wt_d21_rep2

description:
DLN_wt_d21_rep2
GL273_S3

tag: time


title: 35_14month_array

description:
35_14month_252800422023_2_4.txt
disease


title: Melanoma, Sondel_RNA_E

description: exome captured

tag: tissue type

value: A


title: TTC_SC_419

tag: age


title: NDLN_ko_d21_rep1

description:
NDLN_ko_d21_rep1
GL200_S8

value: Non Draining lymph node


title: DLN_wt_d21_rep1

description:
DLN_wt_d21_rep1
GL197_S5


title: Melanoma, Sondel_RNA_D

description: exome captured

tag: study group

tag: death


title: DLN_wt_d12_rep2

description:
DLN_wt_d12_rep2
GL263_S3


title: TTC_SC_418


title: TTC_SC_417


title: Melanoma, Sondel_RNA_C

description: exome captured

tag: diagnosis

value: Never Treated

tag: overall survival time (os in months)


title: NDLN_ko_d12_rep2

description:
NDLN_ko_d12_rep2
GL266_S6


title: 34_base_array

description:
34_base_252800422379_2_4.txt
disease

value: SSc

tag: treatment

value: Transplant

value: PMBC


title: 33_base_array

description:
33_base_252800422381_1_1.txt
disease

value: Universal Human Reference (UHR)


title: DLN_wt_d12_rep1

description:
DLN_wt_d12_rep1
GL128_S7

value: pMel-T cells


title: TTC_SC_416

value: tail tendon

value: Mkx-/-


title: 32_base_array

description:
32_base_252800422041_1_1.txt
disease

value: Non-responder


title: DLN_ko_d63_rep1

description:
DLN_ko_d63_rep1
GL276_S6


title: Melanoma, Sondel_RNA_B

description: exome captured

value: B

tag: event

tag: recurrence free survival time (rfs in months)


title: TTC_SC_420

tag: tissue


title: 32_8month_array

description:
32_8month_252800422041_2_4.txt
disease

tag: timepoint

value: post

tag: response


title: Melanoma, Sondel_RNA_A

description: exome captured


title: 32_26month_array

description:
32_26month_252800422041_2_2.txt
disease

tag: sample type


title: DLN_ko_d21_rep1

description:
DLN_ko_d21_rep1
GL198_S6

value: Draining lymph node

tag: genotype


title: DLN_ko_d21_rep2

description:
DLN_ko_d21_rep2
GL274_S4

tag: cell type

value: NRP1 KO


title: TTC_SC_413

tag: strain


title: TTC_SC_414


title: DLN_ko_d12_rep2

description:
DLN_ko_d12_rep2
GL264_S4

tag: background strain

tag: time


title: 32_14month_array

description:
32_14month_252800422041_1_2.txt
disease


title: TTC_SC_412

tag: age


title: TTC_SC_411


title: DLN_ko_d12_rep1

description:
DLN_ko_d12_rep1
GL129_S8


title: 86422 HiC-Seq Mature B cells WT

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: HiC-Seq Mature B cells WT

data_processing:
ChIP-Seq: Sequence reads were uniquely aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 1.0.  CTCF peaks were called by MACS 2.0.  Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously. Differential gene expression between ex vivo sorted Wapl+/+ and Wapl_delta_P1,2/_delta_P1,2 pro-B cells was analyzed using R version 3.3.3. and DESeq2 version 2.1.14.1. Regularized log transformations were computed with the blind option set to ‘FALSE’. Genes with an adjusted P value < 0.05, TPM (averaged for each genotype) > 5 at least in of the two genotypes, and a fold-change of > 2 were called as significantly expressed. All transcripts of the V, D and J gene segments at the Igh, Igk and Igl loci were eliminated from the list of significantly regulated genes, although the immunoglobulin and T cell receptor transcripts were included in all TPM calculations. Differential gene expression between ex vivo sorted control and Rag1Cre/+ Eedfl/fl pro-B cells was analyzed as described above, except that only genes with an expression difference of > 3-fold were considered. The control samples consisted of 3 independent experiments performed with Rag1Cre/+ Eedfl/+ pro-B cells and 1 experiment performed with Eedfl/fl pro-B cells.
ATAC-Seq: Read have been aligned using 'bowtie' version 2.1.0. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM), using 'bedtools' and 'kent source utilities'.
Hi-C Seq:  The HiCUP pipeline version 0.5.10 with the scorediff parameter set to "10" was used to truncate, align and filter the reads by applying the following software versions: R 3.4.1, Bowtie 2.2.9 (26) and SAMtools 1.4 (37). Contact matrix files have  been produced with Juicer tools 1.8.9.
3C-Seq: We analyzed the 3C-seq data with the captureC 2.0 program, using cutadapt 1.16 and trim_galore 0.4.2. The 3C-seq data were further analyzed with r3Cseq 1.32 with minor modifications to adjust for a larger viewing range required for the Igh locus and for the insertion of the CBE array by generating a modified genome version.
Genome_build: mm9 (RNA-Seq, ChIP-Seq, Hi-C-Seq, 3C-Seq); mm10 (VDJ-Seq)
Supplementary_files_format_and_content: bed = MACS peak coordinates in BED format; bigwig = read coverage (reads per million) in bigWIG format; density bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs; bedGraph = bedGraph track of read density coverage, normalized (RPM) and scaled to track with lowest counts; txt = normalized count values, such as TPMs or VDJ-Seq normalized counts, in ASCII text format tab delimited; hic = binary output format provided by the 'HiCUP' pipeline

source_name: Mature B cells

extract_protocol: Hi-C libraries were prepared as described in Rao et al., 2014

value: WT

tag: cell preparation

value: Ex-vivo MACS-sorted, CD43- CD4- Ter119-


title: 31_base_array

description:
31_base_252800422038_2_4.txt
disease

value: Cyclophosphamide

value: base


title: 86421 HiC-Seq Progenitors Pax5(fl/fl) Vav-Cre

description: HiC-Seq Progenitors Pax5(fl/fl) Vav-Cre

source_name: Progenitors

value: Pax5(fl/fl) Vav-Cre

value: 12-days in-vitro expansion, MACS-sorted, B220+


title: TTC_SC_410


title: TTC_SC_415


title: 31_8month_array

description:
31_8month_252800422038_2_2.txt
disease

value: SSc


title: 30_base_array

description:
30_base_252800422212_2_4.txt
disease

value: PMBC


title: TTC_SC_409


title: 85436 HiC-Seq Progenitors Pax5(fl/fl) Vav-Cre

description: HiC-Seq Progenitors Pax5(fl/fl) Vav-Cre


title: 31_14month_array

description:
31_14month_252800422038_2_1.txt
disease

value: Universal Human Reference (UHR)


title: TTC_SC_407


title: 79197 HiC-Seq Pro-B cells Wapl(+/+)

description: HiC-Seq Pro-B cells Wapl(+/+)

source_name: Pro-B cells

value: 5-days in-vitro expansion, MACS-sorted, CD19+ IgM-


title: 30_8month_array

description:
30_8month_252800422212_1_4.txt
disease


title: TTC_SC_408

value: tail tendon


title: 30_20month_array

description:
30_20month_252800422212_1_2.txt
disease


title: TTC_SC_406

value: Mkx-/-


title: 78382 HiC-Seq Pro-B cells Wapl(+/+)

description: HiC-Seq Pro-B cells Wapl(+/+)


title: TTC_SC_405


title: 30_14month_array

description:
30_14month_252800422212_2_1.txt
disease

value: Non-responder


title: TTC_SC_404


title: 75860 HiC-Seq Pro-B cells Wapl(∆P1,2/∆P1,2)

description: HiC-Seq Pro-B cells Wapl(∆P1,2/∆P1,2)

value: 4-days in-vitro expansion, FACS-sorted


title: 29_base_array

description:
29_base_252800422218_1_3.txt
disease


title: ALPL_scRNAseq

city: Palo Alto

first: Andrew

last: Yang

address: 3801 Miranda Ave

institute: Stanford University

data_processing:
The Cellranger toolkit (v3.0.0) was used to de-multiplex and align reads to the mm10 genome
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx matrices from Cellranger

source_name: Aged brain endothelial cells

extract_protocol:
Flow cytometry of brains prepared with a Neural Dissociation Kit (Miltenyi); each sample is a pool of 4 mice
10x Genomics v3; single-cell transcriptomics

value: 22 months old

tag: brain region

value: Cortex & hippocampus

value: Aged brain endothelial cells


title: 29_26month_array

description:
29_26month_252800422218_1_1.txt
disease

tag: diagnosis

value: post


title: 29_14month_array

description:
29_14month_252800422218_2_2.txt
disease


title: Vehicle_scRNAseq


title: TTC_SC_403


title: TTC_SC_402


title: TTC_SC_401


title: 28_8month_array

description:
28_8month_252800422022_2_1.txt
disease

value: Transplant

value: Responder


title: 79196 HiC-Seq Pro-B cells Wapl(∆P1,2/∆P1,2)

description: HiC-Seq Pro-B cells Wapl(∆P1,2/∆P1,2)

value: 4-days in-vitro expansion, MACS-sorted, CD19+ IgM-


title: 28_base_array

description:
28_base_252800422034_2_3.txt
disease

value: base


title: Zymosan_SeV_rep3

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

data_processing:
Reads were aligned with BWA aln version 0.7.15 with -l 24
Alignments were demultiplexed with a custom script
UMIs were used to collapse reads and make a count table using a custom script
Genome_build: mm10

source_name: Bone marrow

growth_protocol: Bone marrow-derived dendritic cells (BMDCs) were generated from 6- to 8-week old female C57BL/6J mice. Bone marrow cells were collected from femora and tibiae and plated at 2X10^6 cells in 10-cm non-tissue culture treated petri dishes (Corning 351029) in 10 mL of complete RPMI medium containing RPMI-1640 medium (ThermoFisher Scientific 11875119) supplemented with 10% volume/volume (v/v) heat-inactivated fetal bovine serum (Seradigm 1400-500), L-glutamine (2 mM, Corning 25005CI), penicillin/streptomycin (100 U/mL/100g/mL, Lonza Biowhittaker 17602E), MEM non-essential amino acids (0.5X, Corning 25025CI), HEPES (10 mM, Corning 25-060-CI), sodium pyruvate (1 mM, Corning 25000CI), -mercaptoethanol (55M, Fisher Scientific 21-985-023), and recombinant murine GM-CSF (15 ng/mL; Peprotech 315-03-100g). Cells were fed at day 2, 5 and 7 with 3 mL of complete RPMI medium supplemented with GM-CSF as described.

extract_protocol:
Stimulated BMDCs were lysed with 30 µL of RLT buffer (Qiagen 79216) containing 1% (v/v) b-mercaptoethanol (VWR 97604-848). Total RNA was isolated using Dynabeads MyOne Silane (Thermo Fisher Scientific 37002D) and RLT buffer. Remaining genomic DNA was removed by on-bead DNase I (Thermo Fisher Scientific AM2239) treatment at 37oC for 20 min. After washing two times with 80% ethanol, total RNA was eluted from beads in nuclease-free water.
Total RNA samples obtained from 1x10^5 mouse BMDCs were reverse transcribed to cDNA by denaturing 10-µL RNA samples with 1 µL containing 2 pmoles of a custom RT primer at 72oC for 2 min and snap cooled on ice. A 9-µL RT mix containing 4 µL of 5X RT buffer, 1 µL of 10 mM dNTPs, 2 pmoles of template switching oligo, 0.5 µL Maxima H Minus Reverse Transcriptase (ThermoFisher Scientific EP0753) and 3.5 µL of nuclease-free water was added to the denatured RNA samples, and plates were incubated at 42oC for 120 min. Double-stranded cDNA samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research D4013), and residual RT primers were removed using exonuclease I (New England Biolabs M0293).  Pooled full-length cDNA was amplified with 4-6 cycles of single-primer PCR with the Advantage 2 PCR Kit (Clontech 639206) in a 50-µL reaction volume. Amplified cDNAs were cleaned up with magnetic beads Agencourt AMPure XP (Beckman Coulter A63880) and quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851). 1 ng of cDNA was tagmented and amplified by PCR using Nextera XT Kit (Illumina). Libraries were gel purified using E-Gel EX Agarose Gels, 2% (ThermoFisher Scientific G402002), quantified with the Qubit dsDNA High Sensitivity Assay Kit, and sequenced on the NextSeq550 platform (Illumina).

treatment_protocol: 100,000 BMDCs were plated in 100 µL of medium in non-tissue culture treated 96-well flat bottom plates (ThermoFisher Scientific 260860) and incubated overnight prior to stimulations as indicated. Cells were stimulated with ligands and their combinations for 6 hours.

value: Bone marrow derived dendritic cells

tag: ligands

value: Zymosan depleted, SeV


title: Zymosan_SeV_rep1


title: 28_54month_array

description:
28_54month_252800422214_1_2.txt
disease

value: SSc

tag: treatment

value: PMBC


title: Zymosan_SeV_rep2


title: Zymosan_SeV_CpGB_rep3

value: Zymosan depleted, SeV, CpGB


title: TTC_SC_400

value: tail tendon


title: 28_38month_array

description:
28_38month_252800422214_2_1.txt
disease

value: Universal Human Reference (UHR)


title: TTC_SC_398

value: Mkx-/-


title: Zymosan_SeV_CpGB_rep2


title: Zymosan_SeV_CpGB_rep1


title: Zymosan_SeV_cGAMP_rep3

value: Zymosan depleted, SeV, 3',3'-cGAMP


title: TTC_SC_396


title: TTC_SC_397


title: 9158 Streptavidin (Pax5) ChIP-Seq Pax5(Bio/Bio) IRES-BirA

source_name: Stimulated B cells

extract_protocol: ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: Pax5(Bio/Bio) IRES-BirA

value: 4-days in-vitro stimulation with IL-4 and anti-CD40

tag: chip antibody

value: Streptavidin


title: 9591 H3K4me3 ChIP-Seq Rag2(-/-)

description: H3K4me3 ChIP-Seq Rag2(-/-)

value: 5-days in-vitro expansion

value: anti-H3K4me3 (rabbit polyclonal Ab, pAb-003-050; Diagenode)


title: TTC_SC_395


title: 26_base_array

description:
26_base_252800422381_2_2.txt
disease

value: Cyclophosphamide

value: Non-responder


title: TTC_SC_394


title: 25_base_array

description:
25_base_252800422219_2_2.txt
disease

value: base

value: Responder


title: 10192 H3K4me3 ChIP-Seq Pax5(-/-) Rag2(-/-)

description: H3K4me3 ChIP-Seq Pax5(-/-) Rag2(-/-)

value: in-vitro expansion


title: TTC_SC_399


title: 25_8month_array

description:
25_8month_252800422221_2_1.txt
disease

value: SSc

value: post


title: 28_20month_array

description:
28_20month_252800422022_1_2.txt
disease

value: Transplant

value: PMBC


title: TTC_SC_393

value: tail tendon


title: 25_54month_array

description:
25_54month_252800422219_1_4.txt
disease

value: Universal Human Reference (UHR)


title: Zymosan_SeV_cGAMP_rep1

value: Bone marrow derived dendritic cells

value: Zymosan depleted, SeV, 3',3'-cGAMP


title: 28_14month_array

description:
28_14month_252800422022_1_4.txt
disease


title: TTC_SC_392

value: Mkx-/-


title: TTC_SC_391


title: Zymosan_rep3

value: Zymosan depleted


title: Zymosan_rep2


title: Input RNAi dH1

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

data_processing:
Encoding is Sanger/Illumina 1.9
Quality control of FastQ sequences was assessed using the FastQC software version 0.10.1.
Reads were aligned against the dm3 UCSC genome 2012 release using Bowtie 0.12.5, allowing 2 mismatches in the read seed and considering all possible alignment sites for each read in both Immunoprecipitated and control Input samples (setting an upper limit of 10.000 to limit output file size), in order to compare enrichment proportion for genomic features with multiple copies across the genome (i.e. transposons).
Identification and removal of potential PCR-amplification artifacts was performed with sambamba v0.5.1 using the markdup option and default settings. Coverage TDF tracks were generated with the IGV software version 2.1.16.
Peak calling between IP and their respective Input control and between γH2Av  and wild type immunoprecipitated samples was performed with the PeakRanger CCAT software (Xu et al., 2010) version 1.16 using a False Discovery Rate of 0.1, a fold-change threshold of 3 and specifying 50bp as read length, leaving the other options as default.
Genome_build: dm3
Supplementary_files_format_and_content: BED files are in CCAT details output format and include chromosome, start, end, nearby gene, regionID, region summits, False Discovery Rate, strand and quantitative columns with 'Treated' (region_treads) and 'Control' (region_creads) coverage for the identified regions in the Drosophila melanogaster dm3 genome.

organism: Drosophila melanogaster

source_name: Input for gammaH2AvD RNAi dH1

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Sigma) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αgH2Av antibodies (3mL). Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 15 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

treatment_protocol: Drosophila S2 cells were grown to 5x105 cell/ml and incubated for 8 days with 100μg of dsRNA against dH1 added to the culture at days 1, 4 and 7.

value: S2 cells

tag: genotype/variation

value: dH1 depletion


title: gammaH2AvD WT

source_name: gammaH2AvD IP, WT

value: WT

value: rabbit gammaHAvD


title: Zymosan_SeV_cGAMP_rep2


title: Input WT

source_name: Input for gammaH2AvD WT


title: Zymosan_rep1


title: Zymosan_CpGB_rep3

value: Zymosan depleted, CpGB


title: 25_38month_array

description:
25_38month_252800422219_1_2.txt
disease

value: Cyclophosphamide

value: Responder

tag: tissue


title: TTC_SC_390


title: TTC_SC_389


title: gammaH2AvD RNAi dH1

source_name: gammaH2AvD IP,  RNAi dH1


title: 24_8month_array

description:
24_8month_252800420320_2_2.txt
disease

source_name: Sample: Human PBMC

value: SSc

tag: timepoint


title: 24_base_array

description:
24_base_252800421274_1_3.txt
disease

value: base

tag: response

source_name: Universal Human Reference


title: MNCs incubated with high Day 100 serum VDBP

city: Cincinnati

first: Stella

last: Davies

state: OH

address: 3333 Burnet Ave

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

description: countsTable.xls (SDNL2)

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: MNC RNA

extract_protocol:
Total RNA was extracted from mononuclear cells using a standard TRIzol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cultured MNCs

tag: type

value: High VDBP levels (1314 ug/mL)

value: blood


title: Zymosan_CpGB_rep2


title: 27_base_array

description:
27_base_252800422381_1_4.txt
disease

value: Transplant

value: PMBC

tag: sample type

value: Universal Human Reference (UHR)


title: MNCs incubated with low Day 100 serum VDBP

description: countsTable.xls (SDNL1)

tag: cell type

value: Low VDBP levels (164 ug/mL)


title: TTC_SC_388

source_name: KO

tag: strain

value: tail tendon

tag: genotype

value: Mkx-/-


title: Zymosan_CpGB_rep1

value: Bone marrow derived dendritic cells


title: 24_54month_array

description:
24_54month_252800422218_2_4.txt
disease

value: post


title: Zymosan_cGAMP_rep3

value: Zymosan depleted, 3',3'-cGAMP


title: TTC_SC_386


title: 24_38month_array

description:
24_38month_252800422218_1_4.txt
disease


title: Zymosan_cGAMP_rep2


title: TTC_SC_385


title: Zymosan_cGAMP_rep1


title: 25_26month_array

description:
25_26month_252800422219_2_1.txt
disease


title: TTC_SC_383


title: TTC_SC_387


title: Zymosan_cGAMP_CpGB_rep2

value: Zymosan depleted, 3',3'-cGAMP, CpGB


title: TTC_SC_381


title: TTC_SC_382


title: Zymosan_cGAMP_CpGB_rep1


title: TTC_SC_380


title: SeV_rep3

value: SeV


title: 24_14month_array

description:
24_14month_252800420364_1_1.txt
disease

value: Responder


title: SeV_rep2


title: TTC_SC_384


title: 24_26month_array

description:
24_26month_252800421275_1_4.txt
disease

value: SSc


title: LPS treated wild type BMDMs, replicate B

city: St. Louis

first: MALAY

last: HALDAR

state: MO

address: 7751 charing square lane

department: Pathology and Immunology

institute: Washington University in St. Louis

description:
LPS-WT-B
Gene expression data from LPS treated wild type BMDMs.
Cultured cells.

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Arrays using the GeneChip Hybridization oven 645.

scan_protocol: GeneChip 3000 7G scanner was used to collect fluorescence signal. Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Expression values were analyzed after RMA quantile normalization using ArrayStar software (DNASTAR).

label: Biotin

source_name: Cultured mouse BMDM treated with LPS.

label_protocol: Fragmented cDNA biotinylated by terminal transferase end labeling.

growth_protocol: Total bone marrow (BM) cells were harvested from wild type and Spic knockout mice. BM cells were cultured with M-CSF (20 nanograms per ml) for seven days to generate bone marrow derived macrophages (BMDMs).

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

treatment_protocol: BMDMs were treated with either LPS (100 nanograms per ml of PBS) or PBS (control). RNA was extracted 24 hours later.

value: WT

value: LPS

value: bone marrow derived macrophages (BMDM)


title: 23_8month_array

description:
23_8month_252800422032_1_4.txt
disease

value: Cyclophosphamide


title: LPS treated Spic-deficient BMDMs, replicate B

description:
LPS-KO-B
Gene expression data from LPS treated Spic-deficient BMDMs.
Cultured cells.

value: Spic KO


title: 23_20month_array

description:
23_20month_252800422022_1_1.txt
disease

value: PMBC


title: Zymosan_cGAMP_CpGB_rep3


title: TTC_SC_379


title: Circulating Ly6C-low monocytes from LPS treated Spic-knockout mice, replicate 2

description:
KO-LPS-2
Gene expression data from circulating patrolling monocytes.
Circulating leukocyte

source_name: Ly6C-low monocytes from murine peripheral blood

growth_protocol: Circulating Ly6C-low monocytes were isolated from peripheral blood by fluorescence assisted cell sorting (FACS) and immediately lysed to extract RNA.

treatment_protocol: Not applicable.

value: Ly6C-low monocytes


title: LPS treated wild type BMDMs, replicate A

description:
LPS-WT-A
Gene expression data from LPS treated wild type BMDMs.
Cultured cells.


title: 23_38month_array

description:
23_38month_252800422218_2_1.txt
disease

value: Universal Human Reference (UHR)


title: 23_base_array

description:
23_base_252800422021_2_4.txt
disease

value: base


title: Circulating Ly6C-low monocytes from LPS treated Spic-knockout mice, replicate 1

description:
KO-LPS-1
Gene expression data from circulating patrolling monocytes.
Circulating leukocyte


title: 23_14month_array

description:
23_14month_252800422033_1_4.txt
disease


title: Circulating Ly6C-low monocytes from LPS treated Spic-heterozygous mice, replicate 1

description:
Het-LPS-1
Gene expression data from circulating patrolling monocytes.
Circulating leukocyte

value: Spic-heterozygous


title: 21_base_array

description:
21_base_252800422380_1_2.txt
disease

value: Transplant


title: 23_54month_array

description:
23_54month_252800422218_1_2.txt
disease

value: post


title: SeV_rep1

value: Bone marrow derived dendritic cells


title: SeV_CpGB_rep3

value: SeV, CpGB


title: TTC_SC_378

value: tail tendon

value: Mkx-/-


title: TTC_SC_377


title: LPS treated Spic-deficient BMDMs, replicate A

description:
LPS-KO-A
Gene expression data from LPS treated Spic-deficient BMDMs.
Cultured cells.


title: Circulating Ly6C-low monocytes from LPS treated Spic-heterozygous mice, replicate 2

description:
HET-LPS-2
Gene expression data from circulating patrolling monocytes.
Circulating leukocyte


title: SeV_CpGB_rep2


title: TTC_SC_376


title: TTC_SC_375


title: 20_20month_array

description:
20_20month_252800422214_1_3.txt
disease

value: SSc

value: Non-responder


title: 20_8month_array

description:
20_8month_252800422214_2_3.txt
disease


title: 95737 3C-Seq 3' VP HS5 Rag2(-/-)

description: 3C-Seq 3' VP HS5 Rag2(-/-)

data_processing:
Library strategy: 3C-seq
ChIP-Seq: Sequence reads were uniquely aligned to the mouse genome assembly version of July 2007 (NCBI37/mm9) using the Bowtie program version 1.0.  CTCF peaks were called by MACS 2.0.  Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously. Differential gene expression between ex vivo sorted Wapl+/+ and Wapl_delta_P1,2/_delta_P1,2 pro-B cells was analyzed using R version 3.3.3. and DESeq2 version 2.1.14.1. Regularized log transformations were computed with the blind option set to ‘FALSE’. Genes with an adjusted P value < 0.05, TPM (averaged for each genotype) > 5 at least in of the two genotypes, and a fold-change of > 2 were called as significantly expressed. All transcripts of the V, D and J gene segments at the Igh, Igk and Igl loci were eliminated from the list of significantly regulated genes, although the immunoglobulin and T cell receptor transcripts were included in all TPM calculations. Differential gene expression between ex vivo sorted control and Rag1Cre/+ Eedfl/fl pro-B cells was analyzed as described above, except that only genes with an expression difference of > 3-fold were considered. The control samples consisted of 3 independent experiments performed with Rag1Cre/+ Eedfl/+ pro-B cells and 1 experiment performed with Eedfl/fl pro-B cells.
ATAC-Seq: Read have been aligned using 'bowtie' version 2.1.0. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM), using 'bedtools' and 'kent source utilities'.
Hi-C Seq:  The HiCUP pipeline version 0.5.10 with the scorediff parameter set to "10" was used to truncate, align and filter the reads by applying the following software versions: R 3.4.1, Bowtie 2.2.9 (26) and SAMtools 1.4 (37). Contact matrix files have  been produced with Juicer tools 1.8.9.
3C-Seq: We analyzed the 3C-seq data with the captureC 2.0 program, using cutadapt 1.16 and trim_galore 0.4.2. The 3C-seq data were further analyzed with r3Cseq 1.32 with minor modifications to adjust for a larger viewing range required for the Igh locus and for the insertion of the CBE array by generating a modified genome version.
Genome_build: mm9 (RNA-Seq, ChIP-Seq, Hi-C-Seq, 3C-Seq); mm10 (VDJ-Seq)
Supplementary_files_format_and_content: bed = MACS peak coordinates in BED format; bigwig = read coverage (reads per million) in bigWIG format; density bigwig = bigWig Track format of read density coverage in reads per million after extension to 150 base pairs; bedGraph = bedGraph track of read density coverage, normalized (RPM) and scaled to track with lowest counts; txt = normalized count values, such as TPMs or VDJ-Seq normalized counts, in ASCII text format tab delimited; hic = binary output format provided by the 'HiCUP' pipeline

source_name: in vitro pro-B cell

extract_protocol: 3C-template DNA was sheared using the Bioruptor sonicator (Diagenode) and subjected to end-repair and A-tailing, followed by ligation of adapters containing 12 UMI sequences using the NEBNext Ultra II DNA library prep kit for Illumina (NEB). A primer extension step with biotinylated viewpoint-specific primers generated the single-stranded DNA products that were captured using Dynabeads MyOne streptavidin T1 beads (Thermo Fisher Scientific) and PCR-amplified with nested viewpoint-specific and adapter-binding primers. The llumina sequencing adapter primers including the indexes for multiplexing of libraries were added to the PCR products in a final PCR amplification step.

value: Wapl(deltaP1,2/deltaP1,2) Rag2(-/-)

value: 4-days in-vitro expansion


title: SeV_cGAMP_rep2

value: SeV, 3',3'-cGAMP


title: SeV_cGAMP_rep3


title: PreRPMs isolated from wild type spleen, replicate 1

description:
PreRPM WT1
Gene expression data from splenic PreRPM.
Splenocytes

source_name: Murine Pre-red pulp macrophages (PreRPM)

growth_protocol: PreRPMs were isolated from spleen by fluorescence assisted cell sorting (FACS) and immediately lysed to extract RNA.

treatment_protocol: Not applicable

value: WT

value: pre-Red Pulp Macrophages (PreRPM)


title: PreRPMs isolated from wild type spleen, replicate 2

description:
PrePRM WT2
Gene expression data from splenic PreRPM.
Splenocytes


title: PreRPMs isolated from Spic deficient spleen, replicate 2

description:
PreRPM KO2
Gene expression data from splenic PreRPM.
Splenocytes

value: Spic KO


title: SeV_CpGB_rep1


title: 95735 3C-Seq 3' VP HS5 Igh(CBE-inv/CBE-inv)

description: 3C-Seq 3' VP HS5 Igh(CBE-inv/CBE-inv)

value: 5-days in-vitro expansion


title: TTC_SC_373


title: SeV_cGAMP_rep1


title: SeV_cGAMP_CpGB_rep3

value: SeV, 3',3'-cGAMP, CpGB


title: 95734 3C-Seq 3' VP HS5 Igh(CBE-inv/CBE-inv)

description: 3C-Seq 3' VP HS5 Igh(CBE-inv/CBE-inv)


title: TTC_SC_371


title: 95733 3C-Seq 3' VP HS5 Igh(CBE/CBE)

description: 3C-Seq 3' VP HS5 Igh(CBE/CBE)


title: TTC_SC_374


title: 19_base_array

description:
19_base_252800420320_1_4.txt
disease

value: Cyclophosphamide

value: base

value: PMBC

value: Universal Human Reference (UHR)


title: 19_54month_array

description:
19_54month_252800422214_2_2.txt
disease

value: post


title: 19_8month_array

description:
19_8month_252800421275_1_1.txt
disease


title: PreRPMs isolated from Spic deficient spleen, replicate 1

description:
PreRPM KO1
Gene expression data from splenic PreRPM.
Splenocytes


title: 95736 3C-Seq 3' VP HS5 Rag2(-/-)

description: 3C-Seq 3' VP HS5 Rag2(-/-)


title: 20_14month_array

description:
20_14month_252800422214_1_1.txt
disease

value: Transplant


title: SeV_cGAMP_CpGB_rep2

value: Bone marrow derived dendritic cells


title: TTC_SC_372

value: tail tendon

value: Mkx-/-


title: TTC_SC_370


title: 95732 3C-Seq 3' VP HS5 Igh(CBE/CBE)

description: 3C-Seq 3' VP HS5 Igh(CBE/CBE)

value: Wapl(deltaP1,2/deltaP1,2) Rag2(-/-)


title: TTC_SC_369


title: SeV_cGAMP_CpGB_rep1


title: 19_26month_array

description:
19_26month_252800420320_2_4.txt
disease

value: SSc

value: Non-responder


title: 19_14month_array

description:
19_14month_252800420363_1_3.txt
disease


title: 95731 3C-Seq 3' VP HS5 Igh(+/+)

description: 3C-Seq 3' VP HS5 Igh(+/+)


title: PAM_Zymosan_SeV_rep3

value: PAM, Zymosan depleted, SeV


title: TTC_SC_368


title: 95730 3C-Seq 3' VP HS5 Igh(+/+)

description: 3C-Seq 3' VP HS5 Igh(+/+)


title: TTC_SC_367


title: 97752 3C-Seq VP1-83/81 Wapl(∆P1,2/∆P1,2) Rag2(-/-)

value: Igh(CBE-inv/CBE-inv)

value: 4-days in-vitro expansion


title: 18_base_array

description:
18_base_252800422381_2_1.txt
disease


title: PAM_Zymosan_SeV_rep1


title: PAM_Zymosan_SeV_rep2


title: 19_38month_array

description:
19_38month_252800422214_2_4.txt
disease


title: 97751 3C-Seq VP1-83/81 Wapl(∆P1,2/∆P1,2) Rag2(-/-)


title: 97750 3C-Seq VP1-83/81 Rag2(-/-)

description: 3C-Seq VP1-83/81 Rag2(-/-)

value: Igh(CBE/CBE)


title: PAM_Zymosan_rep3

value: PAM, Zymosan depleted


title: TTC_SC_365


title: PAM_Zymosan_rep2


title: TTC_SC_366


title: 15_8month_array

description:
15_8month_252800422024_2_1.txt
disease

value: Responder


title: PAM_Zymosan_rep1


title: TTC_SC_363


title: 97748 3C-Seq 3' VP HS5 Wapl(∆P1,2/∆P1,2) Rag2(-/-)


title: TTC_SC_362


title: 97747 3C-Seq 3' VP HS5 Wapl(∆P1,2/∆P1,2) Rag2(-/-)


title: PAM_Zymosan_CpGB_rep2

value: PAM, Zymosan depleted, CpGB


title: TTC_SC_361


title: 15_38month_array

description:
15_38month_252800422216_1_3.txt
disease

value: PMBC


title: PAM_Zymosan_CpGB_rep3


title: 108698 3C-Seq 5' VP VH1-86 in vitro pro-B cell Igh(890-inv/890-inv) Rag2(-/-)

value: 5-days in-vitro expansion


title: TTC_SC_360


title: TTC_SC_364


title: 108697 3C-Seq 5' VP VH1-86 in vitro pro-B cell Igh(890-inv/890-inv) Rag2(-/-)


title: 15_base_array

description:
15_base_252800422025_1_4.txt
disease

value: base

value: Universal Human Reference (UHR)


title: 14_base_array

description:
14_base_252800422033_2_3.txt
disease

value: Cyclophosphamide


title: 15_26month_array

description:
15_26month_252800422024_2_4.txt
disease

value: Transplant

value: post


title: 15_14month_array

description:
15_14month_252800422024_1_1.txt
disease


title: 15_54month_array

description:
15_54month_252800422216_2_3.txt
disease


title: 14_8month_array

description:
14_8month_252800422023_1_4.txt
disease


title: 97749 3C-Seq VP1-83/81 Rag2(-/-)

description: 3C-Seq VP1-83/81 Rag2(-/-)


title: PAM_Zymosan_cGAMP_rep3

value: Bone marrow derived dendritic cells

value: PAM, Zymosan depleted, 3',3'-cGAMP


title: 108695 3C-Seq 5' VP VH1-86 in vitro pro-B cell Igh(+/+) Rag2(-/-)


title: PAM_Zymosan_cGAMP_rep2


title: 14_54month_array

description:
14_54month_252800422217_2_3.txt
disease

value: SSc


title: TTC_SC_358

value: tail tendon

value: Mkx-/-


title: 108696 3C-Seq 5' VP VH1-86 in vitro pro-B cell Igh(+/+) Rag2(-/-)


title: TTC_SC_357


title: 112070 3C-Seq 5' VP CBE in vitro pro-B cell Igh(CBE-inv/CBE-inv)

value: Igh(CBE-inv/CBE-inv)


title: 14_20month_array

description:
14_20month_252800422032_2_2.txt
disease


title: PAM_Zymosan_CpGB_rep1


title: PAM_SeV_rep3

value: PAM, SeV


title: 112069 3C-Seq 5' VP CBE in vitro pro-B cell Igh(CBE-inv/CBE-inv)


title: 14_14month_array

description:
14_14month_252800422034_1_1.txt
disease


title: PAM_SeV_rep2


title: 112068 3C-Seq 5' VP CBE in vitro pro-B cell Igh(CBE/CBE)

value: Igh(CBE/CBE)


title: TTC_SC_355


title: TTC_SC_356


title: 13_base_array

description:
13_base_252800421274_2_3.txt
disease

value: Responder


title: 112067 3C-Seq 5' VP CBE in vitro pro-B cell Igh(CBE/CBE)


title: PAM_Zymosan_cGAMP_rep1


title: PAM_SeV_rep1


title: PAM_SeV_CpGB_rep3

value: PAM, SeV, CpGB


title: TTC_SC_353


title: 112066 3C-Seq 5' VP CBE in vitro pro-B cell Igh(+/+)


title: 14_38month_array

description:
14_38month_252800422217_1_3.txt
disease

value: PMBC


title: TTC_SC_352


title: 13_26month_array

description:
13_26month_252800420363_1_2.txt
disease


title: 13_8month_array

description:
13_8month_252800421274_1_1.txt
disease


title: PAM_SeV_CpGB_rep2


title: 13_38month_array

description:
13_38month_252800422213_2_4.txt
disease


title: 108694 3C-Seq 3' VP HS5 in vitro pro-B cell Igh(890-inv/890-inv) Rag2(-/-)

value: 5-days in-vitro expansion


title: PAM_SeV_cGAMP_rep3

value: PAM, SeV, 3',3'-cGAMP


title: 108693 3C-Seq 3' VP HS5 in vitro pro-B cell Igh(890-inv/890-inv) Rag2(-/-)


title: TTC_SC_350


title: 112065 3C-Seq 5' VP CBE in vitro pro-B cell Igh(+/+)


title: 108691 3C-Seq 3' VP HS5 in vitro pro-B cell Igh(+/+) Rag2(-/-)


title: TTC_SC_349


title: PAM_SeV_cGAMP_rep2


title: TTC_SC_347


title: TTC_SC_348


title: 97760_Igh VDJ-Seq Pro-B cell Eed(fl/fl) Rag1(Cre/+)

data_processing:
Library strategy: VDJ-seq
The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline:
preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline)
deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline)
assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline)
The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
Genome_build: MM10
Supplementary_files_format_and_content: txt (ascii text)

source_name: Pro-B cell

extract_protocol:
Ex-vivo FACS sorted from bone marrow
DNA was sheared using the Bioruptor sonicator (Diagenode) and subjected to end-repair and A-tailing, followed by ligation of adapters containing 12 UMI sequences using the NEBNext Ultra II DNA library prep kit for Illumina (NEB). A primer extension step with biotinylated JH-specific primers generated the single-stranded DNA products that were captured using Dynabeads MyOne streptavidin T1 beads (Thermo Fisher Scientific) and PCR-amplified with nested JH-specific and adapter-binding primers. The llumina sequencing adapter primers including the indexes for multiplexing of libraries were added to the PCR products in a final PCR amplification step.

value: Pro-B cell

value: Eed(fl/fl) Rag1(Cre/+)


title: PAM_SeV_CpGB_rep1


title: PAM_rep3

value: PAM


title: 12_20month_array

description:
12_20month_252800422213_1_2.txt
disease

value: Cyclophosphamide

value: post

value: Non-responder

value: Universal Human Reference (UHR)


title: 13_54month_array

description:
13_54month_252800422213_2_2.txt
disease

value: SSc

value: Transplant


title: 12_14month_array

description:
12_14month_252800422213_2_1.txt
disease


title: PAM_SeV_cGAMP_rep1

value: Bone marrow derived dendritic cells


title: 13_14month_array

description:
13_14month_252800420325_1_2.txt
disease


title: 12_base_array

description:
12_base_252800422213_1_4.txt
disease

value: base


title: TTC_SC_351

value: tail tendon

value: Mkx-/-


title: 108692 3C-Seq 3' VP HS5 in vitro pro-B cell Igh(+/+) Rag2(-/-)


title: TTC_SC_346


title: PAM_rep2


title: TTC_SC_345


title: PAM_rep1


title: 97759_Igh VDJ-Seq Pro-B cell Eed(fl/fl) Rag1(Cre/+)


title: 11_base_array

description:
11_base_252800422379_1_3.txt
disease

value: Responder


title: TTC_SC_344


title: 97757_Igh VDJ-Seq Pro-B cell Eed(fl/fl) Rag1(Cre/+)


title: 97758_Igh VDJ-Seq Pro-B cell Eed(fl/fl) Rag1(Cre/+)


title: PAM_LPS_Zymosan_rep3

value: PAM, LPS, Zymosan depleted


title: 10_base_array

description:
10_base_252800422216_2_2.txt
disease

value: PMBC


title: 10_8month_array

description:
10_8month_252800422216_1_1.txt
disease


title: PAM_LPS_Zymosan_rep2


title: TTC_SC_343


title: 97756_Igh VDJ-Seq Pro-B cell Eed(fl/+) Rag1(+/+)


title: TTC_SC_341


title: 97755_Igh VDJ-Seq Pro-B cell WT

description: Igh VDJ-Seq Pro-B cell WT

value: WT


title: PAM_LPS_Zymosan_rep1


title: PAM_LPS_SeV_rep2

value: PAM, LPS, SeV


title: 10_54month_array

description:
10_54month_252800422216_2_4.txt
disease


title: 86494_Igh VDJ-Seq Pro-B cell Wapl(∆P1/∆P1)

description: Igh VDJ-Seq Pro-B cell Wapl(∆P1/∆P1)

value: Pro-B cell


title: 10_38month_array

description:
10_38month_252800422216_1_4.txt
disease


title: PAM_LPS_SeV_rep3


title: TTC_SC_340


title: PAM_LPS_SeV_rep1


title: TTC_SC_339


title: 86493_Igh VDJ-Seq Pro-B cell Wapl(∆P1/∆P1)

description: Igh VDJ-Seq Pro-B cell Wapl(∆P1/∆P1)


title: TTC_SC_342


title: TTC_SC_338


title: PAM_LPS_rep2

value: PAM, LPS


title: 10_26month_array

description:
10_26month_252800422216_1_2.txt
disease

value: Cyclophosphamide


title: 09_54month_array

description:
09_54month_252800422217_2_4.txt
disease

value: post


title: 86491_Igh VDJ-Seq Pro-B cell Wapl(+/+)

description: Igh VDJ-Seq Pro-B cell Wapl(+/+)


title: TTC_SC_337


title: 09_38month_array

description:
09_38month_252800422217_1_4.txt
disease


title: 86495_Igh VDJ-Seq Pro-B cell Wapl(∆P1/∆P1)

description: Igh VDJ-Seq Pro-B cell Wapl(∆P1/∆P1)


title: PAM_LPS_rep1


title: 86490_Igh VDJ-Seq Pro-B cell Wapl(+/+)

description: Igh VDJ-Seq Pro-B cell Wapl(+/+)


title: 04_base_array

description:
04_base_252800422032_2_1.txt
disease


title: TTC_SC_336


title: 04_8month_array

description:
04_8month_252800422022_2_2.txt
disease


title: 10_14month_array

description:
10_14month_252800422216_2_1.txt
disease


title: PAM_LPS_HMW_rep2

value: PAM, LPS, HMW


title: 82668_Igh VDJ-Seq Pro-B cell Igh(CBE-inv/CBE-inv)

value: Igh(CBE-inv/CBE-inv)


title: TTC_SC_335


title: 82667_Igh VDJ-Seq Pro-B cell Igh(CBE-inv/CBE-inv)


title: TTC_SC_334


title: PAM_LPS_rep3


title: PAM_LPS_HMW_rep3


title: TTC_SC_333


title: 82666_Igh VDJ-Seq Pro-B cell Igh(CBE-inv/CBE-inv)


title: PAM_LPS_HMW_rep1


title: PAM_LPS_CpGB_rep3

value: PAM, LPS, CpGB


title: PAM_LPS_CpGB_rep2


title: 02_48month_array

description:
02_48month_252800422217_1_2.txt
disease

value: SSc

value: Transplant

value: Universal Human Reference (UHR)


title: 02_8month_array

description:
02_8month_252800420326_2_1.txt
disease


title: TTC_SC_331

value: tail tendon


title: 04_14month_array

description:
04_14month_252800422022_1_3.txt
disease


title: PAM_LPS_CpGB_rep1

value: Bone marrow derived dendritic cells


title: 82665_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: 82664_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: TTC_SC_329

value: Mkx-/-


title: 02_38month_array

description:
02_38month_252800422217_2_1.txt
disease

value: Responder


title: Kp_MS6671 in PBT2 + Colistin

city: Brisbane

first: David

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

description: Transcriptional response to PBT2 + colistin

data_processing:
NovaSeq ultra-high-throughput sequencing system was used for base-calling
Samples were trimmed and mapped to the reference genome (K. pneumoniae MS6671 accession number: LN824133) using bowtie2 with --very-sensitive-local settings
Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR/limma-voom
Genome_build: LN824133
Supplementary_files_format_and_content: counts

organism: Klebsiella pneumoniae

source_name: Bacteria

growth_protocol: Bacteria were grown in cation-adjusted Mueller-Hinton broth (CA-MHB) as per CLSI guidelines at 37°C under aerobic conditions.

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to OD600 of 0.5 in CA-MHB in the presence or absence of PBT2. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions. To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNASeq analysis was performed at the Australian Genome Research Facility. The cDNA library was prepared using a Ribo-zero stranded protocol. In brief, rRNA was depleted with Ribo Zero, RNA was fragmented (heat and divalent cations) and 1st strand cDNA synthesis was done with SuperScript II Reverse Transcriptase (Invitrogen). For the 2nd strand cDNA synthesis, the strand was “marked” with dUTP.  A 3’ adenylation of DNA fragments was performed followed by sequencing adapter ligation (utilizing T-A pairing of adapter and DNA fragments). The library was amplified by PCR (amplification of “unmarked” 1st strand only). Libraries were assessed using either Agilent’s Bioanalyzer DNA 1000 chip or TapeStation D1K TapeScreen system. qPCR was used to quantify individual libraries before normalizing (2 nM) and pooling. Libraries were pooled and clustered through the Illumina cBot system using TruSeq PE Cluster Kit v3 reagents followed by sequencing on the Illumina HiSeq 2500 system with TruSeq SBS Kit v3 reagents with 110 (101 read 1, 9 cycles index read). Libraries were sequenced with a HiSeq 2500 ultra-high-throughput sequencing system (Illumina) to produce 50-base-single end reads. An average of 30 million reads per sample were generated, uploaded to the Galaxy web platform (public server at usegalaxy.org), and mapped to the reference genome (K. pneumoniae MS6671 accession number: LN824133) using bowtie2 with default parameters. Read counts were determined using featureCounts and differential gene expression was analyzed with edgeR with the CPM threshold set at 2.0. Figures were generated using ggplot2 and ggpubr packages in R-studio

treatment_protocol: Bacteria were grown to  OD600 of 0.5 in CA-MHB in the presence or absence of combinations of PBT2 (64 µM) and colistin (0.25 µg/mL).


title: TTC_SC_328


title: TTC_SC_330


title: PAM_LPS_cGAMP_rep2

value: PAM, LPS, 3',3'-cGAMP


title: 82661_Igh VDJ-Seq Pro-B cell Igh(CBE/CBE)

description: Igh VDJ-Seq Pro-B cell Igh(CBE/CBE)

value: Igh(CBE/CBE)


title: 82663_Igh VDJ-Seq Pro-B cell Igh(CBE/CBE)

description: Igh VDJ-Seq Pro-B cell Igh(CBE/CBE)


title: TTC_SC_327


title: 82662_Igh VDJ-Seq Pro-B cell Igh(CBE/CBE)

description: Igh VDJ-Seq Pro-B cell Igh(CBE/CBE)


title: 82660_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: 02_26month_array

description:
02_26month_252800421275_1_2.txt
disease

value: PMBC


title: Kp_MS6671 in Colistin

description: Transcriptional response to colistin


title: TTC_SC_332


title: PAM_LPS_cGAMP_rep3


title: PAM_HMW_Zymosan_rep3

value: PAM, HMW, Zymosan depleted


title: 02_14month_array

description:
02_14month_252800420325_1_4.txt
disease


title: PAM_LPS_cGAMP_rep1


title: TTC_SC_359


title: 82659_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)

value: Pro-B cell


title: PAM_HMW_Zymosan_rep2


title: Kp_MS6671 in PBT2

description: Transcriptional response to PBT2


title: TTC_SC_325


title: TTC_SC_326


title: Kp_MS6671 in MHB

description: Transcriptional response to MHB


title: m6A_shGFP_Input2

city: wuhan

first: linjian

last: xia

address: wuhan

institute: wuhan University

data_processing:
Quality control of MeRIP-Seq data was performed using FastQC. Low quality bases and adaptor contamination were deleted by Trimmomatic (v. 0.33.0) 8 . Raw Sequencing reads were aligned using Hisat2 (v. 2.1.0) 9 with default parameters to the hg38 or mm10 reference genome. The mapped reads were filtered with Picard (http://broadinstitute.github.io/picard, v. 2.16.0) to remove PCR duplicates and SAMtools (v. 1.7) 10 to remove the reads with mapping quality below 30. MACS2 (v. 2.1.1) 11 was used to identify peaks (p-value of 1e-4).
For ChIP-seq, raw sequencing reads were aligned using Bowtie (v. 2.3.4.1) 15 with default parameters to the mm10 reference genome. The mapped reads were filtered with Picard (http://broadinstitute.github.io/picard, v. 2.16.0) to remove PCR duplicates and SAMtools10 to remove the reads with mapping quality below 30. MACS2 11 was used to identify peaks (p-value of 1e-4).
For RNA-seq, reads mapping and processing were performed as described for MeRIP-seq data above. FeatureCounts (v. 1.6.3) 5 was used to calculate the number of reads mapped to each gene. EdgeR (v.3.22.5) 19 was used for differential expression analysis.
Genome_build: hg38/mm10

growth_protocol: HEK293T cells were grown in DMEM medium (Invitrogen) containing 10% FBS, and 1% penicillin-streptomycin. Mouse embryonic stem cell (mESC) E14TG2a was cultured with N2B27 base medium supplemented with 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.15 mM 1-thioglycerol (Sigma), 100 U/mL penicillin-streptomycin (Invitrogen), 25 μg/ml BSA (Sigma), 1μM MEK inhibitor PD0325901 (Selleck Chemicals), 3μM GSK3β inhibitor CHIR99021 (Selleck Chemicals), 2% KOSR (Thermofisher) and 1000 U/ml ESGRO leukemia inhibitory factor LIF (Millipore) on plates coated with 0.2% gelatin.

extract_protocol:
For RNA-seq, RNA was isolated using TRNzol reagent. After DNase I treatment, rRNA was removed using QIAseq FastSelect RNA Removal Kit (QIAGEN). For RIP-seq, chromatin RNA was extracted, then fragmented to about 100-300 nt-long, and incubated with anti-m6A antibody (Millipore). Then the mixture was subjected to Dynabeads protein G binding. After washing, the bound RNA was eluted by RLT and retrieved by RNeasy Plus Micro Kit (Qiagen). H3K9me2 ChIP-seq was performed using the iDeal ChIP-seq Kit for Histones (Diagenode). For KDM3B, METTL3 and Pol II ChIP-seq, cells were crosslinked, sonicated, and subjected to ChIP.
RNA-seq libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). RIP-seq libraries were generated using  SMARTer Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian (Takara) following the manual. ChIP-seq libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina.
RNA-seq, RIP-seq and ChIP-seq

treatment_protocol: GFP/FTO/ALKBH5/YTHDC1 shRNA knockdown cells were generated by lentiviral infection and puromycin selection.

tag: cell line

value: shGFP

tag: protocol

value: RIP


title: m6A_shGFP_Input1


title: TTC_SC_324

tag: age


title: 81585_Igh VDJ-Seq Pro-B cell Igh(V8-8/V8-8)

description: Igh VDJ-Seq Pro-B cell Igh(V8-8/V8-8)


title: PAM_HMW_SeV_rep3

value: PAM, HMW, SeV


title: m6A_shGFP_IP2


title: PAM_HMW_SeV_rep2


title: 81584_Igh VDJ-Seq Pro-B cell Igh(V8-8/V8-8)

description: Igh VDJ-Seq Pro-B cell Igh(V8-8/V8-8)


title: TTC_SC_323


title: PAM_HMW_SeV_rep1


title: TTC_SC_322


title: m6A_shGFP_IP1


title: m6A_shFTO_Input2

value: shFTO


title: 81582_Igh VDJ-Seq Pro-B cell Igh(V8-8-inv/V8-8-inv)


title: TTC_SC_321


title: m6A_shFTO_Input1


title: 81586_Igh VDJ-Seq Pro-B cell Igh(V8-8-inv/V8-8-inv)


title: PAM_HMW_rep3

value: PAM, HMW


title: 81580_Igh VDJ-Seq Pro-B cell Igh(V8-8-inv/V8-8-inv)


title: 81581_Igh VDJ-Seq Pro-B cell Igh(V8-8-inv/V8-8-inv)

value: Igh(V8-8-inv/V8-8-inv), the insertion of a CTCF binding array (Igh(CBE/CBE),Igh(CBE-inv/CBE-inv)),


title: TTC_SC_319


title: PAM_HMW_Zymosan_rep1


title: TTC_SC_320


title: m6A_shFTO_IP1


title: PAM_HMW_rep2


title: 81583_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: PAM_HMW_rep1


title: m6A_shFTO_IP2


title: PAM_HMW_CpGB_rep3

value: PAM, HMW, CpGB


title: TTC_SC_318


title: TTC_SC_317


title: 81578_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: m6A_shALKBH5_Input2


title: m6A_shALKBH5_Input1


title: PAM_HMW_CpGB_rep1


title: PAM_HMW_CpGB_rep2


title: TTC_SC_314


title: TTC_SC_315


title: 81577_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: 81576_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: m6A_shALKBH5_IP1


title: TTC_SC_316


title: TTC_SC_313


title: TTC_SC_354


title: m6A_shALKBH5_IP2


title: 79224_Igh VDJ-Seq Pro-B cell Wapl(∆P2/∆P2)

description: Igh VDJ-Seq Pro-B cell Wapl(∆P2/∆P2)


title: PAM_HMW_cGAMP_rep2

value: PAM, HMW, 3',3'-cGAMP


title: 81575_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: 81579_Igh VDJ-Seq Pro-B cell Igh(V8-8/V8-8)

description: Igh VDJ-Seq Pro-B cell Igh(V8-8/V8-8)


title: H3K9me2_shGFP_Input

value: ChIP


title: PAM_HMW_cGAMP_rep1

value: Bone marrow derived dendritic cells


title: PAM_CpGB_rep3

value: PAM, CpGB


title: 86492_Igh VDJ-Seq Pro-B cell Wapl(+/+)

description: Igh VDJ-Seq Pro-B cell Wapl(+/+)


title: TTC_SC_312

value: tail tendon

value: Mkx-/-


title: 79223_Igh VDJ-Seq Pro-B cell Wapl(∆P2/∆P2)

description: Igh VDJ-Seq Pro-B cell Wapl(∆P2/∆P2)


title: H3K9me2_shGFP_IP


title: 79222_Igh VDJ-Seq Pro-B cell Wapl(∆P2/∆P2)

description: Igh VDJ-Seq Pro-B cell Wapl(∆P2/∆P2)


title: TTC_SC_310


title: PAM_HMW_cGAMP_rep3


title: PAM_CpGB_rep1


title: PAM_CpGB_rep2


title: 02_base_array

description:
02_base_252800420364_2_2.txt
disease

value: SSc

value: Transplant

value: base

value: Responder

value: Universal Human Reference (UHR)


title: TTC_SC_309


title: H3K9me2_shFTO_IP2


title: PAM_cGAMP_rep3

value: PAM, 3',3'-cGAMP


title: TTC_SC_307


title: PAM_cGAMP_rep2


title: TTC_SC_308


title: H3K9me2_shFTO_IP1


title: 69954_Igh VDJ-Seq Pro-B cell Pax5(+/+)

description: Igh VDJ-Seq Pro-B cell Pax5(+/+)

value: Pro-B cell


title: H3K9me2_shALKBH5_Input2


title: TTC_SC_306


title: H3K9me2_shFTO_Input2

value: shFTO


title: TTC_SC_311


title: H3K9me2_shALKBH5_Input1


title: 69953_Igh VDJ-Seq Pro-B cell Pax5(fl/fl) Rag2(+/+) Vav-Cre

value: Pax5(fl/fl) Rag2(+/+) Vav-Cre


title: TTC_SC_305


title: PAM_cGAMP_CpGB_rep3

value: PAM, 3',3'-cGAMP, CpGB


title: 79221_Igh VDJ-Seq Pro-B cell Wapl(+/+)

description: Igh VDJ-Seq Pro-B cell Wapl(+/+)


title: 69952_Igh VDJ-Seq Pro-B cell Pax5(fl/fl) Rag2(+/+) Vav-Cre


title: PAM_cGAMP_CpGB_rep2


title: H3K9me2_shALKBH5_IP2


title: 69951_Igh VDJ-Seq Pro-B cell Pax5(fl/fl) Rag2(+/-) Vav-Cre

value: Pax5(fl/fl) Rag2(+/-) Vav-Cre


title: H3K9me2_shFTO_Input1


title: H3K9me2_shALKBH5_IP1


title: 79220_Igh VDJ-Seq Pro-B cell Wapl(+/+)

description: Igh VDJ-Seq Pro-B cell Wapl(+/+)


title: PAM_cGAMP_CpGB_rep1


title: PAM_cGAMP_rep1


title: 69950_Igh VDJ-Seq Pro-B cell Igh(890-inv/890-inv)


title: Patient 30 week12

first: Antonio

last: Julià

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

institute: Vall d'Hebron Hospital Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
FASTQ files were aligned to the GRCh37 human reference genome assembly using STAR. After alignment, we performed deduplication of the PCR duplicates using UMItools  to mark and after removing with samtools.
Gene-level read counts of the deduplicated bam files were obtained with featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole Blood

extract_protocol:
Whole blood samples were obtained at the start of the therapy with abatacept and at week 12. Blood was collected using RNA-stabilizing PaxGene tubes (PreAnalytiX, Switzerland), which preserve total RNA from the time of venipuncture. Total RNA was extracted using the PaxGene blood isolation kit (Qiagen). All samples had a RIN index > 7 and were included for RNA-seq analysis
RNA-seq libraries were performed using with the KAPA RNA HyperPrep Kit, with RiboErase (HMR) Globin (globin and rRNA depletion protocol) for Illumina sequencing platforms and with the addition of Unique Molecule Identifiers (UMIs). Sequencing was performed using the NovaSeq platform (Illumina) at average of 250 paired-end reads

tag: gender

value: M

value: abatacept

tag: time

value: 12 weeks

tag: individual id

value: Whole Blood


title: LPS_Zymosan_SeV_rep3

source_name: Bone marrow

value: Bone marrow derived dendritic cells

tag: ligands

value: LPS, Zymosan depleted, SeV


title: 79219_Igh VDJ-Seq Pro-B cell Wapl(+/+)

description: Igh VDJ-Seq Pro-B cell Wapl(+/+)


title: TTC_SC_304

value: tail tendon

value: Mkx-/-


title: Patient 30 week0

tag: treatment

value: control

value: 0 week


title: LPS_Zymosan_SeV_rep2


title: TTC_SC_303


title: TTC_SC_302


title: 69948_Igh VDJ-Seq Pro-B cell Igh(890-inv/890-inv)


title: TTC_SC_301


title: 69949_Igh VDJ-Seq Pro-B cell Igh(890-inv/890-inv)


title: Patient 11 week12

value: F


title: TTC_SC_300


title: LPS_Zymosan_SeV_rep1


title: Patient 11 week0


title: LPS_Zymosan_rep3

value: LPS, Zymosan depleted


title: TTC_SC_299


title: 69947_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)

value: Pro-B cell


title: Patient 33 week0


title: LPS_Zymosan_rep2


title: TTC_SC_298


title: 69945_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: Patient 33 week12


title: TTC_SC_297


title: LPS_Zymosan_rep1


title: 66825_Igh VDJ-Seq Pro-B cell Wapl(∆P1,2/+)

description: Igh VDJ-Seq Pro-B cell Wapl(∆P1,2/+)


title: TTC_SC_296


title: LPS_Zymosan_CpGB_rep3

value: LPS, Zymosan depleted, CpGB


title: Patient 7 week12


title: LPS_Zymosan_CpGB_rep2


title: Patient 7 week0


title: 66824_Igh VDJ-Seq Pro-B cell Wapl(∆P1,2/+)

description: Igh VDJ-Seq Pro-B cell Wapl(∆P1,2/+)


title: TTC_SC_295


title: Patient 32 week12


title: LPS_Zymosan_CpGB_rep1


title: 66822_Igh VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)


title: TTC_SC_294


title: LPS_Zymosan_cGAMP_rep3

value: LPS, Zymosan depleted, 3',3'-cGAMP


title: 69946_Igh VDJ-Seq Pro-B cell Igh(+/+)

description: Igh VDJ-Seq Pro-B cell Igh(+/+)


title: TTC_SC_293


title: 66821_Igh VDJ-Seq Pro-B cell Wapl(+/+)

description: Igh VDJ-Seq Pro-B cell Wapl(+/+)


title: Patient 32 week0


title: LPS_Zymosan_cGAMP_rep2


title: Patient 9 week0


title: TTC_SC_290


title: 66820_Igh VDJ-Seq Pro-B cell Wapl(+/+)

description: Igh VDJ-Seq Pro-B cell Wapl(+/+)


title: Patient 9 week12


title: Patient 36 week0


title: LPS_SeV_rep2

value: LPS, SeV


title: Patient 36 week12


title: TTC_SC_288


title: TTC_SC_291


title: TTC_SC_289


title: LPS_SeV_rep1


title: TTC_SC_292


title: LPS_SeV_rep3


title: LPS_SeV_CpGB_rep3

value: LPS, SeV, CpGB


title: Patient 6 week0


title: Patient 6 week12


title: Patient 37 week12

value: M


title: 66823_Igh VDJ-Seq Pro-B cell Wapl(∆P1,2/∆P1,2)


title: TTC_SC_287


title: TTC_SC_286


title: Patient 37 week0


title: LPS_SeV_CpGB_rep1


title: TTC_SC_285


title: LPS_Zymosan_cGAMP_rep1


title: TTC_SC_284


title: Patient 29 week12

value: abatacept


title: LPS_SeV_cGAMP_rep3

value: LPS, SeV, 3',3'-cGAMP


title: TTC_SC_283


title: Patient 10 week12

value: 12 weeks

value: Whole Blood


title: TTC_SC_282


title: LPS_SeV_cGAMP_rep1

value: Bone marrow derived dendritic cells


title: Patient 10 week0


title: LPS_rep3

value: LPS


title: TTC_SC_281

value: tail tendon

value: Mkx-/-


title: TTC_SC_280


title: LPS_rep2


title: Patient 38 week12


title: TTC_SC_279


title: Patient 38 week0

value: control

value: 0 week


title: LPS_SeV_CpGB_rep2


title: LPS_HMW_Zymosan_rep3

value: LPS, HMW, Zymosan depleted


title: ATAC_GSdelta44_R2

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

description: ATAC-seq experiment

data_processing:
ChIP-seq analysis: Sequence of the reads were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles were normalized by the total number of fly reads of each sample.
ATAC-seq analysis: Sequence reads of the samples were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the options -m 1, --chunkmbs 2000 and -X 2000.
ATAC-seq analysis: after mapping, we gathered the two replicates of each condition into a single pool. Both pools were down-sampled to 84 million reads.
ATAC-seq analysis: Peak detection at each pool (WT and GSdelta44) was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ATAC-seq genome-wide profiles of the pools were normalized by the total number of reads of each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/ATAC-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq/ATAC-seq signal enriched regions)

source_name: GSΔ44 donor myoblasts

growth_protocol: WT and GSΔ44 myoblasts were cultured in Human skeletal muscle growth medium (PromoCell) and grown in a humidified incubator, at 5% CO2 and 37 °C.

extract_protocol:
ChIP-seq libraries were prepared starting with 20 million cells (Pubmed ID 27863225)
Libraries were prepared according to Illumina instructions.

treatment_protocol: Cells were treated with formaldehyde to a final concentration of 1% at room temperature (RT) for 10 min.

tag: disease state

value: myoblasts

tag: chip antibody


title: Patient 5 week12

value: F

tag: tissue


title: TTC_SC_278

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.


title: LPS_HMW_Zymosan_rep2


title: Patient 5 week0


title: ATAC_WT_R2

description: ATAC-seq experiment

source_name: healthy donor myoblasts

value: healthy


title: Patient 29 week0


title: ATAC_GSdelta44_R1

description: ATAC-seq experiment


title: TTC_SC_277


title: LPS_HMW_Zymosan_rep1


title: LPS_SeV_cGAMP_rep2


title: Patient 8 week12


title: TTC_SC_275


title: ATAC_WT_R1

description: ATAC-seq experiment


title: TTC_SC_276


title: Patient 8 week0


title: Patient 12 week12


title: LPS_HMW_SeV_rep3

value: LPS, HMW, SeV


title: ChIP_H3K27me3_GSdelta44

description: ChIP-seq experiment

value: H3K27me3 rabbit Millipore 07-449


title: LPS_HMW_SeV_rep2


title: TTC_SC_274


title: ChIP_H3K27me3_WT

description: ChIP-seq experiment


title: Patient 12 week0


title: LPS_rep1


title: LPS_HMW_SeV_rep1


title: Patient 28 week12


title: ChIP_H3K4me3_GSdelta44

description: ChIP-seq experiment

value: H3K4me3 rabbit Diagenode p-Ab-003-050


title: TTC_SC_273


title: LPS_HMW_rep3

value: LPS, HMW


title: TTC_SC_272


title: Patient 28 week0


title: ChIP_H3K27ac_GSdelta44

description: ChIP-seq experiment

value: H3K27ac mouse active motif 39685


title: LPS_HMW_rep2


title: TTC_SC_270


title: TTC_SC_271


title: ChIP_H3_GSdelta44

description: ChIP-seq experiment

value: H3 rabbit pAb Abcam ab1791


title: LPS_HMW_rep1


title: Patient 35 week12

value: abatacept

value: 12 weeks

value: Whole Blood


title: LPS_HMW_CpGB_rep1

value: Bone marrow derived dendritic cells

value: LPS, HMW, CpGB


title: Patient 35 week0

value: control


title: ChIP_H3_WT

description: ChIP-seq experiment


title: Patient 4 week0

value: 0 week


title: TTC_SC_269

value: tail tendon

value: Mkx-/-


title: ChIP_H3K27ac_WT

description: ChIP-seq experiment

value: myoblasts


title: LPS_HMW_CpGB_rep3


title: Patient 4 week12

value: F


title: LPS_HMW_CpGB_rep2


title: ChIP_H3K4me3_WT

description: ChIP-seq experiment

value: healthy


title: LPS_HMW_cGAMP_rep3

value: LPS, HMW, 3',3'-cGAMP


title: TTC_SC_265


title: shp65_RNAseq_IL1_4h_rep1

city: Cleveland

first: George

last: Stark

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

data_processing:
For ChIP-seq analysis: The FASTQ reads were aligned to human genome hg19 using bowtie2. The sam/bam files from each duplicate were then merged using samtools.
For ChIP-seq analysis: Peak calling of the merged bam files were performed with MACS2 (callpeak -B -t ChIPFilename.bam -c InputFilename.bam -f BAM -g hs -n OutputFilename -q 0.05). The resulting ChIP-seq peaks/regions were then subdivided into discrete signal peaks by inputting the .narrowPeak and bedGraph files into PeakSplitter 1.0.
For ChIP-seq analysis: Differentially induced peaks between treated and untreated samples were determined by inputting the EGF or IL1 and the UT .bam and .bed files into Manorm.
For RNA-seq analysis: The FASTQ reads were aligned to human genome hg19 using TopHat2. Counts for coding genes were generated from the resulting sam/bam files using HTSeq-count.
For RNA-seq analysis: Differential gene expression analysis looking at the interaction between treatment versus p65 knockdown status to determine p65-dependent genes up- or down-regulated by EGF or IL-1 was performed by inputting the count files into edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files were converted into bigWig formats using the UCSC bedGraphToBigWig tool.

source_name: Human mammary epithelial cells (HMEC)

growth_protocol: HMECs immortalized with human telomerase reverse transcriptase (Clontech) were grown in Medium 171 with mammary epithelial growth supplement (Invitrogen). All cultures were kept in 5% CO2 at 37°C.

extract_protocol:
For ChIP-seq: Cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 45 min and then 1% formaldehyde for 15 min at room temperature. Following cell lysis, chromatin was sheared using a Misonix 3000 probe sonicator (30 x 30 sec, 30 sec off). p65-bound chromatin was then immunoprecipitated using 8 micrograms anti-p65 (sc-372/C-20X) antibody. Following washing and reverse crosslinking, chromatin was purified using phenol-chloroform extraction. For RNA-seq: total mRNA was isolated using RNeasy Kit (Qiagen).
DNA and mRNA libraries were created following standard Illumina protocols with PolyA capture for mRNA.
ChIP-seq and RNA-seq; 2-lane flow cell (single-end 50 bp sequencing)

treatment_protocol: For ChIP-seq: HME (80-100 million) cells deprived of EGF-containing supplements overnight were treated with or without 100 ng/mL EGF (Millipore) or 10 ng/mL IL-1β (Peprotech) for 1 h. For RNA-seq: One million HME cells stably transduced with non-targeting (“shctrl”) or shRNA against p65 (“shp65”) (Sigma, TRCN0000014687) were deprived of EGF-containing supplements overnight and were treated or not with 100 ng/mL EGF or 10 ng/mL IL-1β for 4 h.

value: 10 ng/mL IL-1 for 4 h

tag: shRNA

value: HMEC


title: TTC_SC_267

data_processing:
Single-cell RNA sequence reads were evaluated by AfterQC. Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than.
The reads were mapped to the mouse genome(mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts. Gene expression was represented by CPM (tags per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample


title: Patient 17 week12


title: shp65_RNAseq_IL1_4h_rep2


title: TTC_SC_266


title: LPS_HMW_cGAMP_rep2


title: Patient 19 week12


title: shp65_RNAseq_EGF_4h_rep1

value: 100 ng/mL EGF for 4 h


title: Patient 19 week0


title: Patient 17 week0


title: shp65_RNAseq_EGF_4h_rep2


title: LPS_HMW_cGAMP_rep1


title: TTC_SC_264


title: TTC_SC_262


title: TTC_SC_268


title: TTC_SC_261


title: LPS_CpGB_rep1

value: LPS, CpGB


title: LPS_CpGB_rep3


title: TTC_SC_260


title: TTC_SC_263


title: shctrl_RNAseq_IL1_4h_rep1

value: non-targeting shRNA (Sigma)


title: LPS_cGAMP_rep2

value: LPS, 3',3'-cGAMP


title: shp65_RNAseq_UT_rep1

value: untreated


title: shp65_RNAseq_UT_rep2


title: LPS_CpGB_rep2

value: Bone marrow derived dendritic cells


title: Patient 14 week0

value: Whole Blood


title: shctrl_RNAseq_IL1_4h_rep2


title: shctrl_RNAseq_EGF_4h_rep2


title: LPS_cGAMP_rep1


title: TTC_SC_258


title: LPS_cGAMP_rep3


title: TTC_SC_259


title: Patient 34 week12

value: abatacept

value: 12 weeks


title: Patient 20 week12


title: Patient 20 week0

value: control

value: 0 week


title: TTC_SC_256

value: tail tendon

value: Mkx-/-


title: Patient 27 week0

value: F


title: LPS_cGAMP_CpGB_rep3

value: LPS, 3',3'-cGAMP, CpGB


title: TTC_SC_257


title: Patient 27 week12


title: shctrl_RNAseq_UT_rep2


title: Patient 14 week12


title: shctrl_RNAseq_UT_rep1


title: LPS_cGAMP_CpGB_rep2


title: TTC_SC_255


title: LPS_cGAMP_CpGB_rep1


title: TTC_SC_253


title: Patient 34 week0


title: HMW_Zymosan_SeV_rep3

value: HMW, Zymosan depleted, SeV


title: shctrl_RNAseq_EGF_4h_rep1

value: HMEC


title: HMW_Zymosan_SeV_rep2


title: Input_DNA_rep2


title: Patient 26 week0


title: HMW_Zymosan_SeV_rep1


title: Patient 26 week12


title: Patient 25 week0

value: M


title: p65_ChIPSeq_IL1_1h_rep2

description:
IL1-2_peaks.narrowPeak.bed
IL1_merge_peaks.narrowPeak.bed
IL1_merge_peaks.subpeaks.narrowPeak.bed
IL1_merge_BigWig.bw
IL1_merge_peaks.subpeaks.narrowPeak.bw
IL1_merge_peaks.subpeaks.narrowPeak.SortedUniq.bdg

value: 10 ng/mL IL-1 for 1 h


title: HMW_Zymosan_rep3

value: HMW, Zymosan depleted


title: TTC_SC_250


title: p65_ChIPSeq_IL1_1h_rep1

description:
IL1-1_peaks.narrowPeak.bed
IL1_merge_peaks.narrowPeak.bed
IL1_merge_peaks.subpeaks.narrowPeak.bed
IL1_merge_BigWig.bw
IL1_merge_peaks.subpeaks.narrowPeak.bw
IL1_merge_peaks.subpeaks.narrowPeak.SortedUniq.bdg


title: Patient 25 week12


title: TTC_SC_252


title: p65_ChIPSeq_EGF_1h_rep1

description:
EGF-1_peaks.narrowPeak.bed
EGF_merge_peaks.narrowPeak.bed
EGF_merge_peaks.subpeaks.narrowPeak.bed
EGF_merge_BigWig.bw
EGF_merge_peaks.subpeaks.narrowPeak.bw
EGF_merge_peaks.subpeaks.narrowPeak.SortedUniq.bdg

value: 100 ng/mL EGF for 1 h


title: HMW_Zymosan_rep2


title: TTC_SC_251


title: Patient 21 week12


title: Patient 21 week0


title: Input_DNA_rep1

value: untreated


title: HMW_Zymosan_rep1

value: Bone marrow derived dendritic cells


title: p65_ChIPSeq_EGF_1h_rep2

description:
EGF-2_peaks.narrowPeak.bed
EGF_merge_peaks.narrowPeak.bed
EGF_merge_peaks.subpeaks.narrowPeak.bed
EGF_merge_BigWig.bw
EGF_merge_peaks.subpeaks.narrowPeak.bw
EGF_merge_peaks.subpeaks.narrowPeak.SortedUniq.bdg


title: TTC_SC_249


title: Patient 23 week12

value: Whole Blood


title: HMW_Zymosan_CpGB_rep3

value: HMW, Zymosan depleted, CpGB


title: p65_ChIPSeq_UT_rep2

description:
UT-2_peaks.narrowPeak.bed
UT_merge_peaks.narrowPeak.bed
UT_merge_peaks.subpeaks.narrowPeak.bed
UT_merge_BigWig.bw
UT_merge_peaks.subpeaks.narrowPeak.bw
UT_merge_peaks.subpeaks.narrowPeak.SortedUniq.bdg


title: HMW_Zymosan_CpGB_rep2


title: Patient 18 week12

value: abatacept

value: 12 weeks


title: 10x juvenile S. Lacustris whole-body bulk RNAseq sample 1

city: Heidelberg

first: Jacob

last: Musser

address: Meyerhofstrasse 1

country: Germany

institute: European Molecular Biology Laboratory

data_processing:
Bulk-RNAseq was used to generate a de novo-transcriptome using Trinity with digital normalization select and other parameters as default
The Trinity de-novo transcriptome was annotated by constructing gene trees for all genes using an automated phylomics pipeline.
Fastq files for 10x data were generated with Cell Ranger Makefastq 2.1.1 with default settings
A count matrix for each 10x sample was generated by mapping 10x fastq files against the de-novo transcriptome using Cell Ranger Count 2.1.1 with default settings
The final 10x count matrix containing all cells was assemble dusing Cell Ranger Aggregate 2.1.1 with default settings
Genome_build: De-novo transcritpome assembled in house
Supplementary_files_format_and_content: spongilla_lacustris_Trinity.fasta: fasta file containing all Trinity constructed transcripts, and was used as the mapping reference for 10x data. spongilla_10x_count_matrix.txt: Final count matrix saved as tab-delimited file.

molecule: polyA RNA

organism: Spongilla lacustris

source_name: whole-body

growth_protocol: Sponge juveniles were grown from gemmules placed at room temperature in M-medium (1 mM CaCl2·6H2O, 0.5 mM MgSO4·7H2O, 0.5 mM NaHCO3, 0.05 mM KCl, 0.25 mM Na2SiO3).

extract_protocol:
Trizol extraction
strand-specific mRNAseq

tag: Stage

value: juvenile sponge


title: TTC_SC_254

value: tail tendon


title: TTC_SC_247

value: Mkx-/-


title: p65_ChIPSeq_UT_rep1

description:
UT-1_peaks.narrowPeak.bed
UT_merge_peaks.narrowPeak.bed
UT_merge_peaks.subpeaks.narrowPeak.bed
UT_merge_BigWig.bw
UT_merge_peaks.subpeaks.narrowPeak.bw
UT_merge_peaks.subpeaks.narrowPeak.SortedUniq.bdg


title: Patient 23 week0

value: F

value: control

value: 0 week


title: HMW_Zymosan_CpGB_rep1


title: TTC_SC_246


title: 10x juvenile S. Lacustris single-cell RNAseq sample 4

description: 10x makefastq sample name: "Spongilla_lacinulosa-4_8Day"

source_name: dissociated cells from whole-body

extract_protocol:
10x droplet capture
10x 3' single cell RNAseq version 2 kit

value: 8-day old juvenile sponge


title: Patient 18 week0


title: HMW_Zymosan_cGAMP_rep3

value: HMW, Zymosan depleted, 3',3'-cGAMP


title: TTC_SC_245


title: 10x juvenile S. Lacustris single-cell RNAseq sample 3

description: 10x makefastq sample name: "Spongilla_lacinulosa-3_8Day"


title: Patient 3 week12


title: 10x juvenile S. Lacustris single-cell RNAseq sample 2

description: 10x makefastq sample name: "Spongilla_lacinulosa-2_8Day"


title: TTC_SC_244


title: HMW_Zymosan_cGAMP_rep1


title: TTC_SC_243


title: HMW_SeV_rep3

value: HMW, SeV


title: TTC_SC_248


title: HMW_SeV_rep2


title: Patient 31 week12

value: M


title: TTC_SC_241


title: 10x juvenile S. Lacustris single-cell RNAseq sample 1

description: 10x makefastq sample name: "Spongilla_lacinulosa-1_8Day"


title: 12iF2_RNA: Foot regeneration RNA-seq, 12 hours post amputation, replicate 2, iCRT14 treated

city: Davis

first: Jack

last: Cazet

state: CA

address: 1 Shields Ave.

department: MCB

institute: University of California, Davis

data_processing:
Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: SE -threads 16  -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Trimmed reads were then mapped to the Hydra vulgaris 2.0 genome and read counts were calculated using rsem (V. 1.2.31) using the following settings: --no-bam-output --bowtie2.
processed data files format and content: Read count matrix for gene models from the Hydra vulgaris 2.0 genome for all RNA-seq samples. Generated using rsem.
Genome_build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)

organism: Hydra vulgaris

source_name: Mid-Body Column Tissue

growth_protocol: Hydra vulgaris strain 105 polyps were cultured according to standard protocol (Lenhoff, 1983)  at 18˚C and fed 1-2 times weekly with Artemia nauplii.

extract_protocol:
Total RNA was extracted from 30 regenerating tissue pieces using a standard trizol extraction. DNA was then removed using a DNaseI digest. A final purification step was then performed using a Zymogen RNA Clean & Concentrator kit.
KAPA Biosystems Stranded RNA-seq

treatment_protocol: For iCRT14 treatment, Hydra were pre-incubated in 5uM iCRT14 for two hours prior to amputation. Following amputation, iCRT14 treatment continued until tissue was collected for library preparation.

value: Mid-Body Column

tag: timepoint

value: 12 hours post amputation

tag: regeneration type

value: Foot Regeneration

value: treated with  5uM iCRT14 for 14 hours


title: 12iF3_RNA: Foot regeneration RNA-seq, 12 hours post amputation, replicate 3, iCRT14 treated

tag: strain


title: Patient 22 week12

value: Whole Blood


title: TTC_SC_242

first: HONGWEI

last: OUYANG

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

institute: Zhejiang University

tag: genotype


title: HMW_SeV_CpGB_rep3

tag: cell type

value: Bone marrow derived dendritic cells

value: HMW, SeV, CpGB


title: HMW_SeV_rep1


title: 12iF1_RNA: Foot regeneration RNA-seq, 12 hours post amputation, replicate 1, iCRT14 treated


title: TTC_SC_240


title: Patient 22 week0


title: 12iH3_RNA: Head regeneration RNA-seq, 12 hours post amputation, replicate 3, iCRT14 treated

value: Head Regeneration


title: HMW_Zymosan_cGAMP_rep2


title: Patient 13 week12

value: abatacept

value: 12 weeks


title: HMW_SeV_CpGB_rep2


title: TTC_SC_239

value: tail tendon

value: Mkx-/-


title: HMW_SeV_CpGB_rep1


title: 12iH2_RNA: Head regeneration RNA-seq, 12 hours post amputation, replicate 2, iCRT14 treated


title: TTC_SC_238


title: TTC_SC_237


title: Patient 3 week0

value: F

value: control

value: 0 week


title: Patient 31 week0


title: Patient 16 week12


title: Patient 13 week0


title: TTC_SC_236


title: HMW_SeV_cGAMP_rep3

value: HMW, SeV, 3',3'-cGAMP


title: HMW_SeV_cGAMP_rep2


title: TTC_SC_235


title: Patient 16 week0


title: 8iF2_RNA: Foot regeneration RNA-seq, 8 hours post amputation, replicate 2, iCRT14 treated

value: 8 hours post amputation

value: treated with  5uM iCRT14 for 10 hours


title: Patient 24 week12

value: M


title: 8iF3_RNA: Foot regeneration RNA-seq, 8 hours post amputation, replicate 3, iCRT14 treated

value: Mid-Body Column

value: Foot Regeneration


title: TTC_SC_234


title: 8iF1_RNA: Foot regeneration RNA-seq, 8 hours post amputation, replicate 1, iCRT14 treated