title: Diagenode, Input, Set1


title: Diagenode, H3K4me3, Set2, 5ng

status: Public on Jun 23 2023

type: SRA

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

country: USA

institute: The University of Texas MD Anderson Cancer Center

library_source: genomic

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
All ChIP-Seq reads were trimmed to 36 bp and mapped to the human genome (hg19). Mapping was performed using Bowtie (version 1.1.2), allowing for no more than two mismatches and retaining only reads that were mapped to unique positions. To avoid PCR bias, when multiple reads were mapped to the same genomic position, only one read was retained for analysis.
H3K4me3 and CTCF peaks were detected using MACS (version 1.4.2, p-value cutoff 1e-5 and window size 300 bp). Peaks that overlapped ENCODE blacklisted regions were removed. H3K4me3 peak calling was performed without a control library reference. CTCF peaks in each library were called by taking the corresponding total input library as a control.
The H3K27me3 enriched domains were initially identified using the enriched domain detector (EDD version 1.1.16), without any significance threshold (i.e. the FDR cutoff for EDD was set to be larger than 1). The EDD gap penalty and bin size were set to 10 and 20 kb, respectively. After peak calling with EDD, for each 20 kb bin, the z-score was calculated as: (p0-p)/σ, where p0=Number of ChIP reads/(Number of ChIP reads+Number of total H3 reads), p=0.5 and σ=sqrt(p×(1-p)/Number of ChIP reads+Number of total H3 reads).   The p-value for each candidate domain was calculated using Stouffer's Z-score method by combining all the bins within the putative domain. The p-values were corrected using the method of Benjamini & Hochberg (BH). The domains with FDR ≤ 0.05 were called as significantly enriched with H3K27me3. To minimize the effect of total H3 library quality, a combined total H3 was used as a control for the detection of H3K27me3 enriched domains with 15M reads from the total H3 library prepared by each protocol at the 10 ng level.
Genome_build: hg19
Supplementary_files_format_and_content: Peak locations in bed format. The peak file name contains how many reads were used for peak calling for that sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: androgen-sensitive human prostate adenocarcinoma cell line LNCaP

growth_protocol: LNCaP cells were cultured in RPMI 1640 (+) L-Glutamine medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin-streptomycin, and 1 mM sodium pyruvate. Cells were maintained in 5% CO2 at 37°C and cultured in 10 cm plates to a confluency of 70-80% before fixation.

extract_protocol:
Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Bioo ChIP libraries were prepared using the NEXTflex ChIP-Seq Kit (Bioo Scientific, now PerkinElmer) following the manufacturer’s protocol. "Diagenode" ChIP libraries were prepared using the Diagenode MicroPlex Library Preparation Kit v2 (Diagenode) following the manufacturer’s protocol. "KAPA" ChIP libraries were prepared using the KAPA HyperPrep Kit (Roche) following the manufacturer’s protocol. "NEB" ChIP-Seq libraries were prepared using the NEBNext® Ultra II™ DNA Library Prep Kit for Illumina® (New England BioLabs, Inc., Ipswich, MA) following the manufacturer’s protocol.

treatment_protocol: Not applicable

tag: cell line

tag: chip antibody

tag: input dna level

tag: library preparation protocol

value: Diagenode MicroPlex


title: KAPA, H3K4me3, Set1, 1ng

value: androgen-sensitive human prostate adenocarcinoma cell line LNCaP

value: Roche KAPA HyperPrep


title: Diagenode, H3K4me3, Set2, 1ng


title: Diagenode, H3K4me3, Set2, 250pg


title: Diagenode, H3K4me3, Set2, 10ng


title: Diagenode, Input, Set2


title: Diagenode, H3K4me3, Set2, 100pg


title: Diagenode, H3K4me3, Set1, 5ng


title: Diagenode, H3K4me3, Set1, 500pg


title: Diagenode, H3K4me3, Set1, 1ng


title: Diagenode, H3K4me3, Set1, 10ng


title: Diagenode, H3K4me3, Set1, 250pg


title: single cell RNAseq  in 14 to 14.5h Lola-I mutant ORC4 embryos using 10x Rep1

city: Kansas City

first: Julia

last: Zeitlinger

institute: Stowers Institute

library_source: transcriptomic single cell

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
Gene expression values were calculated following the cellranger pipeline from 10x genomics with a FlyBase release 6.21 GFF annotation file. Default parameters were used for the pipeline.
Assembly: dm6
Supplementary files format and content: h5 matrix

molecule: total RNA

organism: Drosophila melanogaster

source_name: Drosophila

extract_protocol:
The polyA selected mRNA from cells was extraced using in droplets using the 10x genomics instrument. 10x genomics manufacturer's insturtions were followed for mRNA extration and amplification
After RNA fragmentation and reverse transcription sequencing libraries were prepared following Illumina's instructions (see ChIP-seq)

treatment_protocol: Embryos were dechorionated in 5% bleach for ~2-3 min, washed with water. Embryos were then immediately processed for singlecell extraction. Single cell extraction was done by douncing the embryos in SFX medium+0.1% PF68. The cells werealso passed through a 22.5 gauge needle to maximize the single cell isolation efficiency. The debris were filterd by a 100micron filter followed by a 30micron filter. The cells were centrifuged and washed with SFX medium followed by wash in Schneider's medium. Mutant embryos were sorted for absense of GFP before isolation of the single cells.

tag: tissue

value: embryo

tag: developmental stage

tag: genotype

value: Lola-I mutant:ORC4


title: single cell RNAseq  in 14 to 14.5h Lola-I mutant ORC4 embryos using 10x Rep2


title: Diagenode, H3K27me3, Set2, 5ng


title: Diagenode, H3K27me3, Set2, 250pg


title: single cell RNAseq  in 14 to 14.5h wildtype OregonR embryos using 10x Rep1

molecule: polyA RNA


title: single cell RNAseq  in 14 to 14.5h wildtype OregonR embryos using 10x Rep2


title: Diagenode, H3K27me3, Set2, 10ng


title: Diagenode, H3K27me3, Set2, 500pg


title: Diagenode, H3K4me3, Set1, 100pg


title: mrna_wt_2to4h_3

library_source: transcriptomic

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
Gene expression values were calculated following the pseudoalignment strategy using the Kallisto aligner with a FlyBase release 6.21 GFF annotation file
Assembly: dm6
Supplementary files format and content: The calculated expression values are reported as tables.

source_name: polyA selected mRNAseq in 2 to 4h embryos Rep3

extract_protocol:
The total RNA from embryos was extraced using Maxwell simply RNA protocol according to the manufacturers protocol. mRNA-seq: polyA mRNA was purified from total RNA in two consecutive rounds of oligo(dT) selection. A
fter RNA fragmentation and reverse transcription sequencing libraries were prepared following Illumina's instructions (see ChIP-seq)

treatment_protocol: Embryos were dechorionated in 5% bleach for ~2-3 min, washed with water. Embryos were then imeidately processed for mRNA extraction.


title: Diagenode, H3K27me3, Set2, 1ng


title: mrna_wt_2to4h_1

source_name: polyA selected mRNAseq in 2 to 4h embryos Rep1


title: Diagenode, H3K27me3, Set2, 100pg


title: Diagenode, Input, Set3


title: mrna_ORC4_14to17h_4

source_name: polyA selected mRNAseq in Lola-I mutant ORC4 14 to 17h embryos Rep4


title: Diagenode, H3K4me3, Set2, 500pg


title: Diagenode, H3K27me3, Set1, 5ng


title: mrna_ORC4_14to17h_3

source_name: polyA selected mRNAseq in Lola-I mutant ORC4 14 to 17h embryos Rep3


title: mrna_ORC4_14to17h_2

source_name: polyA selected mRNAseq in Lola-I mutant ORC4 14 to 17h embryos Rep2


title: Diagenode, H3K27me3, Set1, 500pg


title: Diagenode, H3K27me3, Set1, 250pg


title: Diagenode, H3K27me3, Set1, 1ng


title: mrna_wt_2to4h_2

source_name: polyA selected mRNAseq in 2 to 4h embryos Rep2


title: mrna_wt_14to17h_2

source_name: polyA selected mRNAseq in wildtype OregonR 14 to 17h embryos Rep2


title: mrna_wt_14to17h_1

source_name: polyA selected mRNAseq in wildtype OregonR 14 to 17h embryos Rep1


title: Diagenode, CTCF, Set3

value: CTCF


title: Diagenode, H3K27me3, Set1, 100pg


title: Diagenode, H3K27me3, Set1, 10ng


title: Diagenode, CTCF, Set2


title: Diagenode, CTCF, Set1


title: Dme_emb_orc4_14-17h_WCE_1

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
For ChIP-seq samples, reads were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Genome-wide coverage counts were calculated, and saved in BigWig format
Assembly: dm6
Supplementary files format and content: BigWig files contain pileup counts for each base

source_name: WCE in 14-17hrs Lola-I mutant ORC4 embryos Rep1

extract_protocol:
ChIP-seq were performed as follows. ~100 mg embryos were used per ChIP, and 5 µg chromatin was used for tissue-specific ChIP-seq experiments. Fixed embryos were homogenized by douncing in an ice cold A1 buffer (15 mM HEPES (pH 7.5), 15 mM NaCl, 60 mM KCl, 4 mM MgCl, 0.5% Triton X-100, 0.5mM DTT, protease inhibitors) and A2 buffer (15 mM HEPES (pH 7.5), 140 mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 0.5% N-lauroylsarcosine, protease inhibitors) in a tissue grinder for 10-15 times in A1 and A2 buffer each. Then the sonication of the chromatin was performed with a Bioruptor Pico for four-five rounds of 30 s on and 30 s off cycles. The sonicated chromatin was cleared by centrifugation and the supernatant was used for ChIP. Chromatin was incubated with antibodies pre-bound to Dynal magnetic beads (IgA or IgG) overnight with end-to-end rotation at 4°C and washed with an ice cold RIPA buffer (50 mM HEPES (pH 7.5), 1mM EDTA, 0.7% sodium deoxycholate, 1% NP-40 (IGEPAL CA-630), 0.5M LiCl). Eluted, reverse cross-linked DNA was then purified using phenol-chloroform-isoamylalcohol phase separation and ethanol precipitation.
ChIP-seq libraries were prepared from 5-15 ng ChIP DNA or 100 ng input DNA according to the manufacturer’s instructions (NEBNext ChIP-Seq Library Prep kit).

treatment_protocol: Embryos were dechorionated in 5% bleach for ~2-3 min, washed with water, fixed for 15 min shaking on a vortexer, speed 7 with 1.8% formaldehyde in heptane, washed with PBT-glycine and PBT, and frozen in liquid nitrogen until used.

value: embryos

value: WCE


title: Dme_emb_orc4_14-17h_WCE_3

source_name: WCE in 14-17hrs Lola-I mutant ORC4 embryos Rep3


title: Bioo, TotalH3, Set2, 10ng

value: total H3

value: Bioo (now PerkinElmer) NEXTflex


title: Bioo, TotalH3, Set1, 10ng


title: Bioo, Input, Set3


title: Bioo, Input, Set2


title: Dme_emb_orc4_14-17h_Rpb3_1

source_name: Pol II ChIP in 14-17hrs Lola-I mutant ORC4 embryos Rep1

value: anti-RPB3 rabbit polyclonal, custom (GenScript)


title: Dme_emb_orc4_14-17h_Rpb3_2

source_name: Pol II ChIP in 14-17hrs Lola-I mutant ORC4 embryos Rep2


title: Dme_emb_orc4_14-17h_GAF_3

source_name: GAF ChIP in 14-17hrs Lola-I mutant ORC4 embryos Rep3

value: anti-GAF rabbit polyclonal, custom (GenScript)


title: Bioo, Input, Set1


title: Bioo, H3K4me3, Set2, 5ng


title: Bioo, H3K4me3, Set2, 500pg


title: Dme_emb_orc4_14-17h_GAF_1

source_name: GAF ChIP in 14-17hrs Lola-I mutant ORC4 embryos Rep1


title: Bioo, H3K4me3, Set2, 250pg


title: mrna_ORC4_14to17h_1

source_name: polyA selected mRNAseq in Lola-I mutant ORC4 14 to 17h embryos Rep1


title: Bioo, H3K4me3, Set2, 1ng

source_name: androgen-sensitive human prostate adenocarcinoma cell line LNCaP


title: Dme_emb_2-4h_WCE_1

source_name: WCE in 2-4hrs OregonR embryos Rep1


title: Dme_emb_orc4_14-17h_GAF_2

source_name: GAF ChIP in 14-17hrs Lola-I mutant ORC4 embryos Rep2


title: Dme_emb_2-4h_Rpb3_1

source_name: Pol II ChIP in 2-4hrs OregonR embryos Rep1


title: Dme_emb_orc4_14-17h_WCE_2

source_name: WCE in 14-17hrs Lola-I mutant ORC4 embryos Rep2


title: Dme_emb_2-4h_GAF_1

source_name: GAF ChIP in 2-4hrs OregonR embryos Rep1


title: Bioo, H3K4me3, Set2, 100pg


title: Dme_emb_14-17h_WCE_2

source_name: WCE in 14-17hrs OregonR embryos Rep2


title: Dme_emb_14-17h_WCE_3

source_name: WCE in 14-17hrs OregonR embryos Rep3


title: Bioo, H3K4me3, Set1, 5ng


title: Bioo, H3K4me3, Set2, 10ng


title: Dme_emb_orc4_14-17h_Rpb3_3

source_name: Pol II ChIP in 14-17hrs Lola-I mutant ORC4 embryos Rep3


title: Dme_emb_14-17h_WCE_1

source_name: WCE in 14-17hrs OregonR embryos Rep1


title: Bioo, H3K4me3, Set1, 500pg


title: Bioo, H3K4me3, Set1, 250pg


title: Dme_emb_14-17h_Rpb3_1

source_name: Pol II ChIP in 14-17hrs OregonR embryos Rep1


title: Dme_emb_14-17h_Rpb3_2

source_name: Pol II ChIP in 14-17hrs OregonR embryos Rep2


title: Bioo, H3K4me3, Set1, 10ng


title: Dme_emb_14-17h_Lola_I_2

source_name: Lola-I ChIP in 14-17hrs OregonR embryos Rep2

value: anti-Lola-I rabbit polyclonal, custom (GenScript)


title: Bioo, H3K4me3, Set1, 1ng


title: Bioo, H3K4me3, Set1, 100pg


title: Dme_emb_14-17h_Lola_I_1

source_name: Lola-I ChIP in 14-17hrs OregonR embryos Rep1


title: Dme_emb_14-17h_Rpb3_3

source_name: Pol II ChIP in 14-17hrs OregonR embryos Rep3


title: Bioo, H3K27me3, Set2, 5ng


title: Bioo, H3K27me3, Set2, 250pg


title: Bioo, H3K27me3, Set2, 500pg


title: Trachea_8807_INTACT_WCE_14-17h_2

source_name: WCE in 14-17hrs INTACT embryos in Trachea Rep2

extract_protocol:
Nuclei were isolated from INTACT embryos 14-17h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). The nuclei were further dissociated using syringe (22.5 gauge needle) 10 times. After washins with HBS buffer, nuclei were incubated with Dynabeads® M-280 Streptavidin beads( Invitrogen, # 11205D) for 30 minutes with end to end rotation at 4°C. A magnet was used to separate the bead bound nuclei, and the beads were washed thoroughly with HBS buffer. Purity of nuclei isolation was determined by staining nuclei with DAPI, and presence of free nuclei, unbound to beads, were used as indicators of contamination. Isolated nuclei were used for ChIP-seq. ChIP-seq was performed as follows. ~100 mg embryos were used per ChIP, and 5 µg chromatin was used for tissue-specific ChIP-seq experiments. Fixed embryos were homogenized by douncing in an ice cold A1 buffer (15 mM HEPES (pH 7.5), 15 mM NaCl, 60 mM KCl, 4 mM MgCl, 0.5% Triton X-100, 0.5mM DTT, protease inhibitors) and A2 buffer (15 mM HEPES (pH 7.5), 140 mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 0.5% N-lauroylsarcosine, protease inhibitors) in a tissue grinder for 10-15 times in A1 and A2 buffer each. Then the sonication of the chromatin was performed with a Bioruptor Pico for four-five rounds of 30 s on and 30 s off cycles. The sonicated chromatin was cleared by centrifugation and the supernatant was used for ChIP. Chromatin was incubated with antibodies pre-bound to Dynal magnetic beads (IgA or IgG) overnight with end-to-end rotation at 4°C and washed with an ice cold RIPA buffer (50 mM HEPES (pH 7.5), 1mM EDTA, 0.7% sodium deoxycholate, 1% NP-40 (IGEPAL CA-630), 0.5M LiCl). Eluted, reverse cross-linked DNA was then purified using phenol-chloroform-isoamylalcohol phase separation and ethanol precipitation.
ChIP-seq libraries were prepared from 5-15 ng ChIP DNA or 100 ng input DNA according to the manufacturer’s instructions (NEBNext ChIP-Seq Library Prep kit).

value: Trachea

value: wildtype


title: Trachea_8807_INTACT_WCE_14-17h_1

source_name: WCE in 14-17hrs INTACT embryos in Trachea Rep1


title: Bioo, H3K27me3, Set2, 10ng

source_name: androgen-sensitive human prostate adenocarcinoma cell line LNCaP


title: Dme_emb_14-17h_GAF_2

source_name: GAF ChIP in 14-17hrs OregonR embryos Rep2


title: Trachea_8807_INTACT_Rpb3_14-17h_2

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Trachea Rep2


title: Bioo, H3K27me3, Set2, 100pg


title: Bioo, H3K27me3, Set1, 5ng


title: Trachea_8807_INTACT_Rpb3_14-17h_1

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Trachea Rep1


title: Bioo, H3K27me3, Set1, 250pg


title: Neuron_elav_INTACT_WCE_14-17h_1

source_name: WCE in 14-17hrs INTACT embryos in Neuron Rep1

value: Neuron


title: Neuron_elav_INTACT_WCE_14-17h_2

source_name: WCE in 14-17hrs INTACT embryos in Neuron Rep2


title: Bioo, H3K27me3, Set1, 1ng


title: Neuron_elav_INTACT_Rpb3_14-17h_1

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Neuron Rep1


title: Neuron_elav_INTACT_Rpb3_14-17h_2

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Neuron Rep2


title: Muscle_mef2_INTACT_WCE_14-17h_2

source_name: WCE in 14-17hrs INTACT embryos in Muscle Rep2

value: Muscle


title: Bioo, H3K27me3, Set1, 100pg


title: Muscle_mef2_INTACT_WCE_14-17h_1

source_name: WCE in 14-17hrs INTACT embryos in Muscle Rep1


title: Muscle_mef2_INTACT_Rpb3_14-17h_2

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Muscle Rep2


title: Bioo, CTCF, Set2


title: Bioo, CTCF, Set1


title: Bioo, H3K27me3, Set2, 1ng


title: Muscle_mef2_INTACT_Rpb3_14-17h_1

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Muscle Rep1


title: Dme_emb_14-17h_GAF_1

source_name: GAF ChIP in 14-17hrs OregonR embryos Rep1


title: Gut_110394_INTACT_WCE_14-17h_2

source_name: WCE in 14-17hrs INTACT embryos in Gut Rep2

value: Gut


title: mrna_ORE50_ORC4_14to17h_3

source_name: polyA selected mRNAseq in Lola-I mutant transheterozygous ORE50/ORC4 14 to 17h embryos Rep3

value: Lola-I mutant:ORE50/ORC4


title: mrna_ORE50_ORC4_14to17h_2

source_name: polyA selected mRNAseq in Lola-I mutant transheterozygous ORE50/ORC4 14 to 17h embryos Rep2


title: Gut_110394_INTACT_Rpb3_14-17h_2

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Gut Rep2


title: A.borealis A6 control 3

city: Sopron

first: Boris

last: Indic

address: Bajcsy-Zsilinszky u. 4

department: Functional Genomics and Bioinformatics Group

country: Hungary

institute: Institute of Forest and Natural Resource Management, University of Sopron

data_processing:
100 ng RNA was enriched using RiboCop rRNA Depletion Kits (Lexogen, Austria).
The RNA was fragmented, end prepped and adapter-ligated.
The libraries were amplified according to the manufacturers instructions.
The quality of the libraries was checked on Agilent 4200 TapeSation System using D1000 Screen Tape (Agilent Technologies, Palo Alto, CA, USA), the quantity was measured on Qubit 3.0. Illumina sequencing was performed on the NovaSeq 6000 instrument (Illumina, San Diego, CA, USA) with 2 151 run configuration.
Raw RNA-Seq reads were aligned against the A. borealis (JGI: Armillaria borealis FPL87.14 v1.0) genome using STAR v2.7 .5a.
The level of expression was estimated using RSEM v1.3.9
Assembly: JGI: Armillaria borealis FPL87.14 v1.0

organism: Armillaria borealis

extract_protocol:
RNA was isolated from the frozen samples using the RNeasy Plant Midi Kit (Qiagen Inc.) according to the manufacturer’s protocol
The libraries for Illumina sequencing were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswitch, MA, USA)

tag: strain

value: high virulent

tag: treatment

value: control


title: Gut_110394_INTACT_WCE_14-17h_1

source_name: WCE in 14-17hrs INTACT embryos in Gut Rep1


title: Bioo, H3K27me3, Set1, 500pg

source_name: androgen-sensitive human prostate adenocarcinoma cell line LNCaP


title: mrna_ORE50_ORC4_14to17h_4

source_name: polyA selected mRNAseq in Lola-I mutant transheterozygous ORE50/ORC4 14 to 17h embryos Rep4

value: embryo


title: Gut_110394_INTACT_Rpb3_14-17h_1

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Gut Rep1


title: mrna_ORE50_ORC4_14to17h_1

source_name: polyA selected mRNAseq in Lola-I mutant transheterozygous ORE50/ORC4 14 to 17h embryos Rep1


title: Bioo, H3K27me3, Set1, 10ng

value: androgen-sensitive human prostate adenocarcinoma cell line LNCaP


title: mrna_wt_14to17h_6

source_name: polyA selected mRNAseq in wildtype OregonR 14 to 17h embryos Rep5


title: A.borealis A6 control 1


title: Bioo, CTCF, Set3

value: CTCF


title: A.borealis A6 control 2


title: Dme_MNase_2-4h_1

data_processing:
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
For MNAse samples, reads were aligned to the reference genome using bowtie v2, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Fragemnts of size 100-200bp are used to calculate the nucleosome occupupancy. Genome-wide coverage counts were calculated, and saved in BigWig format
Assembly: dm6
Supplementary files format and content: BigWig files contain pileup counts for each base

source_name: MNase in 2-4hrs OregonR embryos Rep1

extract_protocol:
Cell lysates were digested with micrococcal nuclease and mononucleosomal DNA was purified.
Sequencing libraries were prepared following Illumina's instructions:

value: embryos


title: A.borealis A6 fresh stems 3

value: fresh stems


title: Dme_MNase_orc4_14-17h_1

source_name: MNase in 14-17hrs Lola-I mutant ORC4 embryos Rep1

value: Lola-I mutant:ORC4


title: Glia_repo_INTACT_WCE_14-17h_1

source_name: WCE in 14-17hrs INTACT embryos in Glia Rep1

value: Glia

value: WCE


title: Dme_MNase_14-17h_2

source_name: MNase in 14-17hrs wildtype OregonR embryos Rep2


title: A.borealis A6 fresh stems 2


title: Glia_repo_INTACT_WCE_14-17h_2

source_name: WCE in 14-17hrs INTACT embryos in Glia Rep2


title: A.borealis A6 fresh stems 1


title: Dme_MNase_14-17h_1

source_name: MNase in 14-17hrs wildtype OregonR embryos Rep1


title: dme_emb_act_Lola_I_orc4_14-17h_WCE_1

source_name: WCE in 14-17hrs Lola-I rescue embryos Rep1

value: Lola-I rescue:ORC4


title: dme_emb_act_Lola_I_orc4_14-17h_WCE_2

source_name: WCE in 14-17hrs Lola-I rescue embryos Rep2


title: dme_emb_act_Lola_I_orc4_14-17h_Rpb3_2

source_name: Pol II ChIP in 14-17hrs Lola-I rescue embryos Rep2

value: anti-RPB3 rabbit polyclonal, custom (GenScript)


title: Glia_repo_INTACT_Rpb3_14-17h_1

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Glia Rep1

value: wildtype


title: A.borealis A4 control 3

value: low virulent


title: A.borealis A4 control 2


title: Epidermis_7021_INTACT_WCE_14-17h_2

source_name: WCE in 14-17hrs INTACT embryos in Epidermis Rep2

value: Epidermis


title: dme_emb_act_Lola_I_orc4_14-17h_Rpb3_1

source_name: Pol II ChIP in 14-17hrs Lola-I rescue embryos Rep1


title: Dme_emb_2-4h_WCE_3

source_name: WCE in 2-4hrs OregonR embryos Rep3


title: Dme_emb_2-4h_WCE_2

source_name: WCE in 2-4hrs OregonR embryos Rep2


title: mrna_wt_14to17h_5

source_name: polyA selected mRNAseq in wildtype OregonR 14 to 17h embryos Rep4


title: Dme_MNase_orc4_14-17h_2

source_name: MNase in 14-17hrs Lola-I mutant ORC4 embryos Rep2


title: Dme_emb_2-4h_Rpb3_2

source_name: Pol II ChIP in 2-4hrs OregonR embryos Rep2


title: Epidermis_7021_INTACT_WCE_14-17h_1

source_name: WCE in 14-17hrs INTACT embryos in Epidermis Rep1


title: Epidermis_7021_INTACT_Rpb3_14-17h_2

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Epidermis Rep2


title: A.borealis A4 control 1


title: A.borealis A4 fresh stems 3


title: Dme_emb_2-4h_GAF_3

source_name: GAF ChIP in 2-4hrs OregonR embryos Rep3

value: anti-GAF rabbit polyclonal, custom (GenScript)


title: Dme_emb_2-4h_GAF_2

source_name: GAF ChIP in 2-4hrs OregonR embryos Rep2


title: Epidermis_7021_INTACT_Rpb3_14-17h_1

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Epidermis Rep1


title: Glia_repo_INTACT_Rpb3_14-17h_2

source_name: Pol II ChIP in 14-17hrs INTACT embryos in Glia Rep2


title: A.borealis A4 fresh stems 2


title: Dme_emb_14-17h_GAF_3

source_name: GAF ChIP in 14-17hrs OregonR embryos Rep3


title: Trachea_8807_INTACT_Lola_I_14-17h_2

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Trachea Rep2

value: Trachea

value: anti-Lola-I rabbit polyclonal, custom (GenScript)


title: Trachea_8807_INTACT_Lola_I_14-17h_1

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Trachea Rep1


title: ATAC-seq in wildtype INTACT Neuron 14-17hrs embryo Rep1

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 50 bp each and aligned to the UCSC Drosophila melanogaster dm6 genome with Bowtie 2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
BigWig files contain per-base coverage of aligned read pairs of size 0-100bp.
Assembly: dm6
Supplementary files format and content: BigWig files contain counts of the aligned reads for each coordinate

source_name: Drosophila

growth_protocol: Drosophila melanogaster embryos INTACT lines were collected for 3 hours and aged for 14 hours on molasses agar plates at 25 degree celsius to get 14-17hr embryos(AED).

extract_protocol:
Nuclei were isolated from INTACT embryos 14-17h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). The nuclei were further dissociated using syringe (22.5 gauge needle) 10 times. After washins with HBS buffer, nuclei were incubated with Dynabeads® M-280 Streptavidin beads( Invitrogen, # 11205D) for 30 minutes with end to end rotation at 4°C. A magnet was used to separate the bead bound nuclei, and the beads were washed thoroughly with HBS buffer. Purity of nuclei isolation was determined by staining nuclei with DAPI, and presence of free nuclei, unbound to beads, were used as indicators of contamination. Isolated nuclei were treated with Tn5 transposase((Illumina, #FC-121-1030).
Nextera index kit (Illumina, #FC-121-1011) was used to create libraries.

treatment_protocol: Embryos were then dechorionated with 50% bleach solution for 2-3 minutes.

value: Neuron

tag: flyline


title: A.borealis A4 fresh stems 1


title: Neuron_elav_INTACT_Lola_I_14-17h_3

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Neuron Rep3


title: mrna_wt_14to17h_3

source_name: polyA selected mRNAseq in wildtype OregonR 14 to 17h embryos Rep3

value: embryo


title: Tdrd3_null2 [NextSeq]

city: Baltimore

first: Xingliang

last: Zhu

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging, National Institutes of Health

data_processing:
RNAseq raw data were removed adaptor by TrimGalore
Data quality was checked by FastQC
Trimmed data were mapped to mm10 using RSEM with the STAR alignments
The bedgraph files were produced by BEDTools.
Read counts were normalized and caluculated by RSEM
Assembly: mm10
Supplementary files format and content: each sample contains a bedgraph file.

organism: Mus musculus

source_name: Brain

growth_protocol: 10-12 week old mice

extract_protocol:
RNA was extracted by Trizol.
RNA libraries for RNA-seq were prepared using published protocols (Joo et al., Nature Communications, 2020).

value: Brain

tag: cell type

value: Whole brain


title: ATAC-seq in wildtype INTACT Muscle 14-17hrs embryo Rep2

value: Muscle


title: Dme_emb_2-4h_Rpb3_3

source_name: Pol II ChIP in 2-4hrs OregonR embryos Rep3

value: embryos


title: Neuron_elav_INTACT_Lola_I_14-17h_1

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Neuron Rep1


title: Neuron_elav_INTACT_Lola_I_14-17h_2

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Neuron Rep2


title: ATAC-seq in wildtype INTACT Muscle 14-17hrs embryo Rep1


title: Muscle_mef2_INTACT_Lola_I_14-17h_3

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Muscle Rep3


title: Muscle_mef2_INTACT_Lola_I_14-17h_2

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Muscle Rep2


title: Muscle_mef2_INTACT_Lola_I_14-17h_1

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Muscle Rep1


title: WT2 [NextSeq]

value: WT


title: Trachea_8807_orc4_INTACT_Rpb3_14-17h_1

source_name: Pol II ChIP in 14-17hrs INTACT ORC4 embryos in Trachea Rep1

value: Lola-I mutant:ORC4


title: Gut_110394_INTACT_Lola_I_14-17h_2

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Gut Rep2

value: Gut


title: Gut_110394_INTACT_Lola_I_14-17h_1

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Gut Rep1


title: Tdrd3_null2

data_processing:
PROseq raw data were removed adaptor by TrimGalore.
Data quality was checked by FastQC.
Trimmed data were mapped to mm10 by bowtie2.
Mapped data were sorted and indexed by samtools.
Bedgraph files were produced by BEDTools.
Counts were calculated by featureCounts in subread.
Assembly: mm10
Supplementary files format and content: each sample contains a bedgraph file.
Library strategy: PRO-seq

extract_protocol:
the brain tissues were prepared by permeabilization buffer and treated by 2 × nuclear run on buffer, then RNA was extracted by Triozol-LS. Biotin RNA was enriched by prewashed Dynabeads™ M-280 Streptavidin beads (Invitrogen, #11206D)
The extracted RNA was used to perform reverse transcription, PCR amplification aaccording previously published protocol (Mahat et al., Nature Protocols, 2016).


title: Tdrd3_null1


title: WT1 [NextSeq]


title: Epidermis_7021_INTACT_Lola_I_14-17h_3

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Epidermis Rep3


title: ATAC-seq in wildtype INTACT Epidermis 14-17hrs embryo Rep1


title: Epidermis_7021_INTACT_Lola_I_14-17h_2

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Epidermis Rep2


title: Epidermis_7021_INTACT_Lola_I_14-17h_1

source_name: Lola-I ChIP in 14-17hrs INTACT embryos in Epidermis Rep1


title: ATAC-seq in wildtype OregonR 14-17hrs embryo Rep2

growth_protocol: Drosophila melanogaster embryos OregonR were collected for 3 hours and aged for 14 hours on molasses agar plates at 25 degree celsius to get 14-17hr embryos(AED).

extract_protocol:
Nuclei were isolated from Oregon-R embryos 2-4h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). Isolated nuclei were treated with Tn5 transposase((Illumina, #FC-121-1030).
Nextera index kit (Illumina, #FC-121-1011) was used to create libraries.

treatment_protocol: Embryos were then dechorionated with 50% bleach solution for 2-3 minutes


title: ATAC-seq in wildtype INTACT Neuron 14-17hrs embryo Rep2


title: ATAC-seq in wildtype OregonR 14-17hrs embryo Rep1


title: WT2


title: ATAC-seq in Lola-I mutant transheterozygous ORE50/ORC4 14-17hrs embryo Rep2


title: Tdrd3_null1 [NextSeq]


title: ATAC-seq in Lola-I mutant transheterozygous ORE50/ORC4 14-17hrs embryo Rep1


title: PTID 19 oral mucosa

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in three steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2; SMARTer adapter sequence trimming with fastq-mcf (FastqMcf tool, v.1.0.0); 3) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Samples were selected for further analysis by using these criteria: percent alignment > 75% & MEDIAN_CV_COVERAGE<=0.8 & fastq total reads > 500,000
Assembly: GRCh38
Supplementary files format and content: RawCounts.csv  contains unnormalized gene counts in comma separated values format
Supplementary files format and content: TMM_normalized_log2_transformed_counts.csv contains TMM normalized, log2(counts+1) transformed counts fo protein coding genes with HGNC symbols in comma separated values format

source_name: mucosa

extract_protocol:
Full-length cDNA was prepared from 250-1000 sorted CD8+ MAIT cells using SMARTer Ultra Low Input RNA Kit for Sequencing - v4 according to manufacturer’s instructions (Clontech, Mountain View, CA).
Libraries were prepared from amplified cDNA using the NexteraXT kit according to manufacturer’s instructions (Illumina, San Diego, CA).

value: mucosa

value: CD8+ MAIT

tag: patient id

tag: pathology score


title: PTID 53 healthy human blood

source_name: blood

value: blood


title: PTID 53 healthy human oral mucosa


title: ATAC-seq in Lola-I rescue 14-17hrs embryo Rep1

source_name: Drosophila

value: Lola-I rescue


title: ATAC-seq in Lola-I rescue 14-17hrs embryo Rep2


title: ATAC-seq in wildtype INTACT Epidermis 14-17hrs embryo Rep2

value: Epidermis

value: wildtype


title: PTID 49 Human oral mucosa


title: ATAC-seq in Lola-I mutant ORC4 14-17hrs embryo Rep2


title: ATAC-seq in Lola-I mutant ORC4 17-20hrs embryo Rep1


title: PTID 49 Human blood


title: ATAC-seq in Lola-I mutant ORC4 14-17hrs embryo Rep1


title: PTID 48 Human oral mucosa


title: ATAC-seq in Lola-I mutant ORC4 Trachea 14-17hrs embryo Rep2

value: Trachea


title: ATAC-seq in Lola-I mutant ORC4 Trachea 14-17hrs embryo Rep1


title: PTID 48 Human blood


title: HL60, DNR, Input

city: Montpellier

first: Mathias

last: Boulanger

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

data_processing:
Basecalls performed with Real-Time Analysis software (Illumina)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using CASAVA 1.8.2
Analysis of the aligned reads, scaling and input subtraction were performed using the R package Pasha
peak-calling performed using IGB browser with the following parameters (value=32, Max Gap < 100 and Min Run > 100)
Assembly: hg19
Supplementary files format and content: Bigwig files were generated using R package Pasha and the WigToBigwig UCSC tool; Scores represent the normalized binding of SUMO2/3
Supplementary files format and content: SUMO2/3 peaks as BED files

source_name: acute myeloid leukemia

growth_protocol: HL-60 cells were cultured in RPMI (Eurobio) supplemented with 10% decomplemented (30 min at 56°C) fetal bovine serum (FBS) and penicillin and streptomycin at 37°C in the presence of 5% CO2. After thawing, cells were spitted at 0.3.106/mL every 2 to 3 days for no more than 10 passages.

extract_protocol:
Lysates from fixed HL-60 (18 milions cells) were clarified for nuclei, then chromatin was sonicated and SUMO2/3-DNA complexes were isolated with SUMO2/3 antibody (2µg per IP). Three biological replicates were performed and pooled for sequencing.
Libraries were prepared according to Illumina's instructions TruSeq®ChIP Sample Preparation (Illumina)

treatment_protocol: HL-60 cells were seeded at 300,000/mL the day before the treatment with drugs.  Cells were treated with H2O (mock), DNR (1µM) or AraC(2µM) for 2 hours at 37°C

value: DNR


title: PTID 19 Blood


title: ATAC-seq in Lola-I mutant ORC4 Gut 14-17hrs embryo Rep1


title: ATAC-seq in Lola-I mutant ORC4 Gut 14-17hrs embryo Rep2


title: PTID 42 Healthy human oral mucosa


title: HL60, AraC, Input

value: AraC


title: HL60, mock, Input

value: mock


title: ATAC-seq in wildtype INTACT Trachea 14-17hrs embryo Rep2


title: WT1

source_name: Brain

value: Brain


title: PTID 40 Human blood


title: ATAC-seq in wildtype INTACT Trachea 14-17hrs embryo Rep1


title: ATAC-seq in Lola-I mutant ORC4 17-20hrs embryo Rep2


title: ATAC-seq in wildtype INTACT Gut 14-17hrs embryo Rep3


title: HL60, DNR, SUMO2


title: ATAC-seq in wildtype INTACT Gut 14-17hrs embryo Rep2


title: HL60, AraC, SUMO2


title: PTID 35 Mucosa


title: PTID 40 Inflamed human oral mucosa


title: ATAC-seq in wildtype INTACT Gut 14-17hrs embryo Rep1


title: HL60, mock, SUMO2


title: PTID 35 Blood


title: mRNA_Control29

type: RNA

city: Amsterdam

first: Silvia

last: D'Ambrosi

address: De Boelelaan 1118

country: Netherlands

institute: Amsterdam UMC

description: RNA hybridization with Human Immunology V2 Panel

hyb_protocol: Two different nCounter panels for the analysis of platelet-derived RNA. The Human Immunology V2 Panel (NanoString Technologies) targets 594 genes involved in the immune response such as cytokines, enzymes, interferons, and their receptors. For each sample, 6 ng of total platelet RNA was hybridized with the biotinylated capture probe and the reporter probe attached to color-barcode tags for 18 hours at 65°C. The second panel was a custom-made panel targeting 78 circRNAs (78-circRNA Panel), 6 linear reference genes and 4 mRNAs. For this analysis, 8 ng of total platelet RNA from each sample was hybridized with the capture and reporter probes for 18 hours at 67°C.

scan_protocol: The automated nCounter® Prep Station was used to process the samples. The samples were purified and immobilized in a sample cartridge for data collection, where the target mRNA and circRNA in each hybridized sample were quantified, using the nCounter Digital Analyzer.

data_processing:
Pre-processing and normalization of the data were performed using R (version 4.0.3) and Rstudio as graphical interface (version 2022.02.2). The quality of the raw RCC proprietary format data was initially assessed by using the NanoStringQCPro (version 1.22.0) package. Standard control metrics embedded by NanoString, such as Imaging, Binding Density, Positive Control Linearity, and Limit of Detection, were used to search for any potential outlier samples.
Additionally, all samples were also subjected to supplementary exploratory examination, including Principal Component Analysis (PCA) and Inter Quartile Range (IQR) method for outlier detection. Samples higher than the upper bound (Q3 + 1.5 * IQR) or lower than the lower bound (Q1 - 1.5 * IQR) were excluded from subsequent analysis.
Prior to normalization, negative control probes embedded to each panel were used to filter out targets with poor expression and high background noise. Consequently, the background values were firstly calculated, by taking the mean of each sample’s Negative Controls increased by two times the standard deviation, and then removed from each sample. Any transcript that indicated a score of less or equal to 0 in more than 75% of the examined samples, was excluded from further examination. After this filtering steps, the data was again evaluated using a PCA plot. Two different packages were compared for the normalization of the data: DESeq2 (version 1.30.1) and edgeR (version 3.32.1). The normalization performance was assessed using the standard relative log expression (RLE) plot. DESeq2 was chosen as default to perform the normalization of the data. Differential expression (DE) analysis was performed to find significantly differentially (|FC|>0.5 and p-adj < 0.05) expressed genes between the cancer and control groups.

label: biotin

source_name: platelets

label_protocol: According to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA).

extract_protocol: Platelets isolation from the whole blood specimens was performed by separating platelet-rich plasma (PRP) and nucleated blood cells, by centrifugation at 120 g for 20 minutes, followed by PRP centrifugation at 360 g for 20 minutes at room temperature. Resulting platelets pellet was re-suspended in RNAlater. Total RNA isolation was carried out using the mirVana RNA isolation kit according to the manufacturer's instructions (Ambion, Thermo Scientific, cat. no. AM1560). Extracted RNA was eluded in 30 μl of mirVana buffer

tag: disease state

value: control

tag: Stage

value: platelets

value: whole blood

tag: fraction

value: mRNA


title: ATAC-seq in wildtype INTACT Trachea 14-17hrs embryo Rep3


title: PTID 34 Mucosa


title: PTID 27 oral mucosa


title: mRNA_Control28

value: nodules


title: HMF1

city: Cambridge

first: Robert

middle: D.

last: Kamm

state: MA

address: 77 Massachusetts Avenue Bldg NE47-321

department: Department of Mechanical Engineering

institute: Massachusetts Institute of Technology

data_processing:
For each library, quality-control was performed to assess coverage depth, enrichment for messenger RNA (exon/intron and exon/intergenic density ratios), fraction of rRNA reads and number of detected genes using bespoke scripts. Sequences were aligned against the human genome hg19 using bwa 1.0. Gene expression was estimated based on reads mapping near the 3' end of transcripts using ESAT 11, based on the Refseq annotation. Results were summarised as counts per million mapped reads (CPMs), merged across samples, log-transformed and subjected to hierarchical clustering and visualization.
Gene expression was estimated based on reads mapping near the 3' end of transcripts using ESAT 11, based on the Refseq annotation. Results were summarised as counts per million mapped reads (CPMs), merged across samples, log-transformed and subjected to hierarchical clustering and visualization.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with gene x sample count matrix

source_name: Human Normal Lung Fibroblasts

growth_protocol: Human umbilical vein ECs and Normal Human Lung FBs (Lonza) were passaged and cultured in EGM-2MV and FGM-2 media (Lonza), respectively. Cells were initially expanded and cryopreserved to establish a consistent stock for all experiments. For an individual experiment, cells were plated onto collagen coated flasks and grown to confluency before seeding into the fluidic devices. Except conditioned media experiments, EGM-2MV medium was used exclusively after seeding into fluidic devices.

extract_protocol:
To isolate cells for RNA-sequencing, the extracted tissue was dissociated with 2.5% trypsin (Gibco) for 1 hr in an incubator with occasional mixing. The trypsin was then diluted 1:50, and the cells were passed through a 35μm strainer in preparation for FACS sorting with a BD FACSAria II Cell Sorter to separate GFP ECs and non-fluorescent FBs. Sorted ECs and FBs were independently pelleted and re-suspended in 1 ml Trizol (Invitrogen) and the manufacturer’s instructions (Invitrogen) were followed for RNA isolation.
Three prime digital gene expression libraries (HT3DGE) were prepared as described in Struntz et al. Cell Chem Biol. 26(5):711 https://pubmed.ncbi.nlm.nih.gov/30880155/, with minor modifications (0.7x SPRI final clean).

treatment_protocol: Prior to seeding into the devices, ECs and FBs were re-suspended at 16 million and 8 million cells/ml, respectively, in EGM-2MV supplemented with 4 U/ml bovine thrombin (Sigma). Equal volumes of the two cell suspensions were combined and gently mixed, except for experiments that investigated the effects of paracrine signalling or cell density. For each device, 50 µL of the combined cell suspension was added to 50 µL of bovine fibrinogen (6 mg/ml in  -/-PBS; Sigma) to form a final encapsulation suspension of 4 million cells /ml ECs and 2 million cells /ml FBs in 3 mg/ml fibrinogen with 2 U/ml thrombin. The suspension was mixed slowly several times over ice to avoid premature polymerisation, and then pipetted into the vascularisation channel, i.e. half the volume through each of the two gel filling ports. The device was immediately placed in a humidified chamber and incubated at room temperature for 30 min during fibrin polymerisation. Finally, the medium channels were filled with warm EGM-2MV through the medium access ports. The devices were incubated at 37o C and 5% CO2 for the remainder of the culture and the growth medium in the medium channels was replaced every day.

tag: culture

value: FB monoculture

tag: time

value: Day 1


title: mRNA_Control27


title: GMF1


title: PTID 27 Blood

value: CD8+ MAIT


title: mRNA_Control30


title: mRNA_Control26


title: mRNA_Control24


title: mRNA_Control25


title: FMF1


title: mRNA_Control22


title: ECH10

source_name: Human Umbilical Vein Endothelial Cells

value: HUVEC-FB coculture

value: Day 10


title: HL-60_RNA_ML-792-DNR, rep3

data_processing:
Basecalls performed with Real-Time Analysis software (Illumina)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 2.1.1 based on Bowtie2 2.3.5.1
Duplicated were removed using Picard. The reproducibility of replicate was quantified using cufflinks 2.2.1
The read count on gene performed using HTseq-count tool 0.11.1 and the differential expression analysis was performed with DESeq2
Assembly: hg19
Supplementary files format and content: txt file contaning the raw and normalised count matrix
Supplementary files format and content: tab-sep table of the DeSeq2 analysis

growth_protocol: HL-60 were cultured in RPMI (Eurobio) supplemented with 10% decomplemented (30 min at 56°C) fetal bovine serum (FBS) and penicillin and streptomycin at 37°C in the presence of 5% CO2. After thawing, cells were spitted at 0.3.106/mL every 2 to 3 days for no more than 10 passages.

extract_protocol:
Total RNAs were purified using the GenElute Mammalian Total RNA kit (Sigma-Aldrich), treated with DNase I (4U, New England Biolabs) and RNasin (2.5U, Promega) and re purified. RNA quality was assessed using a BioAnalyzer Nano 6000 chip (Agilent).
Libraries were prepared using TruSeq®Stranded mRNA Sample Preparation kit (Illumina)

treatment_protocol: HL-60 cells were seeded at 300,000/mL the day before the treatment with drugs.  Cells were treated with DMSO, DNR (1µM), ML-792 (0,5µM) and the combination of ML-792 (0,5µM) and DNR (1µM) for 3 hours at 37°C

tag: cell line

value: ML-792- DNR


title: ECF10


title: HL-60_RNA_ML-792, rep3


title: mRNA_Control21


title: mRNA_Control18


title: mRNA_Control20


title: mRNA_Control19


title: HL-60_RNA_DNR, rep3


title: ECH4

value: Day 4


title: ECF4


title: mRNA_Control15


title: mRNA_Control17


title: mRNA_Control16


title: HL-60_RNA_DMSO, rep3

value: DMSO


title: mRNA_Control23


title: DMF14

value: Day 14


title: mRNA_Cancer30

value: lung cancer


title: HL-60_RNA_ML-792, rep2


title: HL-60_RNA_ML-792-DNR, rep2


title: DCH10


title: DMF7

value: Day 7


title: HL-60_RNA_DMSO, rep2


title: mRNA_Cancer27


title: mRNA_Cancer25


title: mRNA_Cancer28


title: mRNA_Cancer26


title: mRNA_Cancer23


title: mRNA_Cancer24


title: HL-60_RNA_ML-792-DNR, rep1


title: DMH1

value: HUVEC monoculture


title: DCF1


title: mRNA_Control13

value: control


title: mRNA_Control12

value: platelets


title: mRNA_Control11

value: whole blood


title: CMF14


title: HL-60_RNA_ML-792, rep1


title: DCF10


title: HL-60_RNA_DNR, rep2

value: DNR


title: mRNA_Cancer29

value: mRNA


title: mRNA_Cancer20


title: mRNA_Cancer21


title: HL-60_RNA_DMSO, rep1


title: CCF14


title: mRNA_Cancer19


title: mRNA_Cancer18


title: mRNA_Control14


title: CCH14


title: mRNA_Cancer17


title: HL-60_4C_ML-792-DNR, rep3

data_processing:
Library strategy: 4C
Basecalls performed with Real-Time Analysis software (Illumina)
The pipeline used for the 4C analysis is available on github (https://github.com/Mathias-Boulanger/pipe4C)
The pipeline steps are the following: Reads filtering (trim-capture), mapping to reference genome, assignment of reads to their restriction fragment and creation of normalized score per fragment. Only reads containing the amplification sequence (CGTGACGCACGGAAACGTC) were kept for further analysis. Then, sequences downstream of the restriction enzyme cutting site of each selected reads were mapped to GRCH37p13 human reference genome with Bowtie2 aligner. Restriction fragment map was extrapolated from the reference genome using the cutting sequence of restriction enzymes. The interaction peak calling has been performed with  peakC and the differential profiling analysis by DESeq2.
Assembly: hg19
Supplementary files format and content: Bigwig files containing the normalized frequencies of interaction with the restriction fragment containing the viewpoint.

extract_protocol:
Nuclei were purified from lysates of fixed HL-60 (7 milions cells). Chromatin was then digested with NlaIII enzyme and ligated. After DNA purification, the chimeric DNAs were digested with DpnII enzyme and re-ligated. DNA was purified to proceed the library preparation.
4C libraries were amplified using specific primers composed of P5/P7 Illumina sequence supplemented with indexes and sequences corresponding to the promoter of NFkB2 (viewpoint). The “Expend Long Template PCR System” kit (Roche) was used using 300 ng of the 4C library following the manufacturer's instruction. The following amplification parameters were used: denaturation for 2 min at 94°C followed by 30 cycles (94°C - 15 seconds, 58°C - 1 minute and 68°C – 3 minutes) and 7 min at 68°C. Libraries were purified and concentrated with ampureXP beads.

treatment_protocol: HL-60 cells were seeded at 300,000/mL the day before the treatment with drugs.  Cells were treated with DMSO, DNR (1µM), ML-792 (0,5µM) and the combination of ML-792 (0,5µM) and DNR (1µM) for 2 hours at 37°C

tag: viewpoint

value: NFkB2 promoter


title: BMF14

value: FB monoculture


title: HL-60_4C_ML-792, rep3


title: BCF14


title: HL-60_4C_DNR, rep3


title: BCH14


title: mRNA_Cancer22


title: HL-60_4C_DMSO, rep3


title: HL-60_RNA_DNR, rep1


title: ACF14


title: HL-60_4C_ML-792-DNR, rep2


title: mRNA_Cancer15


title: HL-60_4C_ML-792, rep2


title: mRNA_Control7


title: mRNA_Cancer8


title: mRNA_Cancer9


title: HL-60_4C_DNR, rep2


title: mRNA_Control9


title: CCF10


title: ACH14


title: mRNA_Cancer14


title: mRNA_Cancer7


title: CCH10


title: mRNA_Cancer12


title: mRNA_Cancer13


title: mRNA_Cancer11


title: HL-60_4C_DMSO, rep2


title: mRNA_Control5

description:
RNA hybridization with Human Immunology V2 Panel
This sample did not pass the quality control steps necessary to be included in further analysis.


title: mRNA_Control6


title: HL-60_4C_ML-792-DNR, rep1


title: mRNA_Control3

description: This sample did not pass the quality control steps necessary to be included in further analysis.


title: mRNA_Cancer10


title: mRNA_Control4


title: ACH10


title: mRNA_Control2


title: CMF7


title: HL-60_4C_DNR, rep1


title: mRNA_Control1


title: BMF7


title: rSBP15OE_rep2

city: Piracicaba

first: Diego

last: Brito

state: São Paulo

address: Av. Padua Dias, 11

department: ESALQ

country: Brazil

institute: University of São Paulo

data_processing:
Raw sequencing reads were cleaned by removing adaptor sequences and low-quality reads.
The resulting high-quality reads were mapped to the tomato reference genome (SL4.0, Tomato Genome Consortium, 2012) and transcripts were assembled, mapped and quantified using the Hisat2, StringTie and Ballgown packages with default parameters (Pertea et al. 2016).
Read count normalization and differential expression analysis were normalized by FPKM (Fragments per Kilobase Million; Mortazavi et al., 2008) and statistical comparative analysis between WT (MT) and 156-OE, and between WT (MT) and rSBP15 plants were performed with the packages Ballgown and Limman (http://www.bioconductor.org/). DEGs in 156-OE and rSBP15 ABs compared with WT (MT), with adjusted P ≤ 0.05 and ratio ≥ 1.5, were filtered for further analysis.
Assembly: SL4.0
Supplementary files format and content: .txt tab delimited file containing logFC and p-value for every gene, comparing overexpressing genotypes against the wild-type control (MT).
Supplementary files format and content: .xlsx file with logFC, FC, p-value and annotation of significant DEGs (p-value<0.05) between overexpressing genotypes against the wild-type control (MT).

organism: Solanum lycopersicum

source_name: Axillary buds

growth_protocol: Plants were grown in soil:vermiculite at a 1:1 ratio, in standard greenhouse conditions. Dormant axillary buds of WT (MT), 156-OE and rSBP15 plants were at 25-day post germination (dpg), and immediately frozen in liquid nitrogen. Each sample is composed from around 20 axillary buds from 4-5 plants.

extract_protocol:
Total RNA was extracted by TRIzol reagent. RNA integrity was cheked by gel electrophoresis and samples were treated by Dnase I. Two RNA samples of each genotyping were sent to Fasteris (Switzerland) for library construction and sequencing.
At Fasteris, RNA QC was checked and polyA purification was performed. Libraries were constructed using the TruSeq stranded mRNA kit from Illumina.

value: Axillary buds

tag: cultivar

value: MT


title: CCF7

value: HUVEC-FB coculture


title: rSBP15OE_rep1

tag: tissue


title: 156OE_rep1


title: mRNA_Cancer2


title: mRNA_Cancer4


title: mRNA_Cancer1


title: mRNA_Cancer3


title: mRNA_Cancer6


title: BCH7


title: MT_rep1

value: WT


title: MT_rep2


title: AMF7


title: S_EV3

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Oryctolagus cuniculus reference genome (OryCun2.0) using Bowtie2 (2.2.2)
Mapped reads were used for annotation against rabbit mature and precursor miRNAs listed in the mirBase database (release 22)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as TMM-adjusted Counts Per Million (CPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: OryCun2.0
Supplementary files format and content: xlsx file include CPM values for each sample

organism: Oryctolagus cuniculus

source_name: Seminal Plasma

extract_protocol:
EVs were isolated from SP groups (3 biological replicates/group; 2.5 mL SP/replicate) using Ultracentrifugation and PURE-EV® (HansaBioMed Life Sciences) size exclusion chromatography (SEC). Total RNA was isolated from EV samples using Trizol and miRNeasy Micro Kit.
Small-RNA libraries were prepared using QIAseq miRNA Library Kit

value: Seminal Plasma

value: Extracellular Vesicles

tag: group

value: Sub-fertile

tag: breed

value: California x New Zealand white rabbits


title: CCH7

value: Day 7


title: S_EV2


title: HL-60_4C_DMSO, rep1

value: DMSO


title: ACF7


title: S_EV1


title: mRNA_Cancer5

value: lung cancer


title: BCF7


title: 156OE_rep2

tag: genotype


title: HDAC1_set2_UD

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark St

institute: Northwestern University

data_processing:
STAR was used for ChIP-seq alignment and samtools was used for quality filtering. Peaks were called using MACS2.
Assembly: hg38
Supplementary files format and content: ChIP-seq peaks are presented in a table format with chromosome start and stop locations.

source_name: human keratinoctyes

growth_protocol: Prior to treatment, keratinocytes were cultured in keratinocyte SFM and Cascade Biologics Medium 154 supplemented with Human keratinocyte Growth supplement, antibiotic antibiotic-antimycotic, and antibiotic penicillin streptomycin. Cells were grown at 37 C, 5% CO2 and maintained under 60% confluency at all times.

extract_protocol:
genomic DNA was extracted by first doing nuclei extraction and lysis. DNA. Was then sheared to ~200 bp by sonication.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina was used to prepare ChIP-seq libraries.

treatment_protocol: For retroviral HA-RAE1 expression, keratinocytes were seeded to 20% confluency prior to spin infection.  the Retrovirus was diluted and added to keratinocytes along with 20 ug/mL of polybrene. Spin infection was performed at 32 C,  1250 rpm for 1 hour. The infected keratinocytes were then washed gently with PBS twice and keratinocyte media was added. One day post infection, cells were split to maintain confluency below 60%. For keratinocyte differentiation, cells were seeded at 100% confluency and 1.2 mM CaCl2 containing keratinocyte media was added for 4 days.

tag: treatment

value: primary human neonatal keratinocytes

value: Foreskin

tag: chip antibody


title: F_EV3

tag: cell type

value: Fertile


title: HDAC1_set1_UD


title: F_EV1


title: CMH4

value: HUVEC monoculture

value: Day 4


title: NUP98_ChIP-seq_keratinocytes_set2_UD

description: ChIP-seq

data_processing:
RNA-seq: RTA2 was used for base calling. Reads were aligned using STAR. Alignments were quality filtered using samtools. Counting mapped reads was done using Salmon count. DESeq2 was used to determine differential expression.
ChIP-seq: STAR was used for ChIP-seq alignment and samtools was used for quality filtering. Peaks were called using MACS2.
Assembly: hg38
Supplementary files format and content: ChIP-seq peaks are presented in a table format with chromosome start and stop locations.

treatment_protocol: For retroviral HA-RAE1 expression, keratinocytes were seeded to 20% confluency prior to spin infection. the Retrovirus was diluted and added to keratinocytes along with 20 ug/mL of polybrene. Spin infection was performed at 32 C, 1250 rpm for 1 hour. The infected keratinocytes were then washed gently with PBS twice and keratinocyte media was added. One day post infection, cells were split to maintain confluency below 60%. For keratinocyte differentiation, cells were seeded at 100% confluency and 1.2 mM CaCl2 containing keratinocyte media was added for 4 days.

value: SC-74553 (Santa Cruz Biotech)


title: HA-RAE1_Rep2

description: ChIP-seq

value: pLZRS-HA-RAE1 expression

value: 66006, proteintech


title: Ovary, tumor, rep 1

city: Berkeley

first: David

last: Bilder

state: CA

address: 535 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Replicate 1 for RNA collected from ovarian tumors

data_processing:
Sequencing reads were aligned to the Drosophila genome using Kallisto under default parameters for single-end reads.
Assembly: Drosophila melanogaster reference genome 6.26
Supplementary files format and content: Tab-delimited text files contain Flybase IDs, lengths, counts, and TPM for each replicate

source_name: Ovary

growth_protocol: Drosophila maintained at 29 degrees Celsius for twenty days. Drosophila flipped onto fresh food every other day.

extract_protocol:
RNA isolated using RNeasy mini kit (QIAGEN, 74104)
Libraries prepared for sequencing following standard Illumina protocols.

treatment_protocol: Control ovary tissue was dissected to isolate pre-vitellogenic follicles that were subsequently dissociated by incubating with Bacillus licheniformis protease in DPBS. Ovary tumors were dissected and then dissociated by incubating with Bacillus licheniformis protease in DPBS.

value: Ovary (tumor)

tag: developmental stage

value: Adult

tag: Sex

value: Female

value: tj-GAL4, tubulinGal80ts; UAS-aPKC{delta}N UAS-RasV12

value: 20 days at 29 degrees Celsius


title: Ovary, tumor, rep 2

description: Replicate 2 for RNA collected from ovarian tumors


title: CCF4

value: HUVEC-FB coculture


title: Ovary, control, rep 2

description: Replicate 2 for RNA collected from control ovaries

value: Ovary  (control)

value: tj-GAL4, tubulinGal80ts


title: Ovary, control, rep 1

description: Replicate 1 for RNA collected from control ovaries

value: Ovary (control)


title: CCH4


title: ACF10

value: Day 10


title: NUP98_ChIP-seq_keratinocytes_set2_DF

description: ChIP-seq

value: primary human neonatal keratinocytes

value: Foreskin


title: D3a8-MitoQ

city: Bar Harbor

first: Jennifer

last: Trowbridge

state: Maine

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: 10X Genomics

data_processing:
Illumina base call files for all libraries were demultiplexed and converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina).
A filtered digital gene expression matrix was generated for each single cell gene expression library against the 10X Genomics mm10 reference build (version 2020-A, GRCm38 assembly with GENCODE M23 annotations) using 10X Genomics CellRanger count version6.0.0for all samples.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode. For all samples, R2 contains a 91bp biological read.
The resultant counts matrices were input into PartekFlow (version 10.0.22.0428) for downstream analysis and visualization.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: column labels (cell barcodes) of gene expression counts matrix
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: row labels (genes) of gene expression counts matrix
Supplementary files format and content: matrix.mtx.gz
Supplementary files format and content: digital counts matrix for gene expression (matrix market format)

source_name: Bone Marrow

extract_protocol:
BM cells were isolated from Dnmt3aMut or MxCre control mice, ckit enriched put into culture for 16hrs with MitoQ or vehicle treatment. Cells were harvested and stained with cell surface markers for HSPC and cells were sorted for Live/Lin-/Sca1+/ckit+ into tubes and submitted for sequencing.
The cells were immediately processed as follows. Cells were counted on a LUNA FX7 automated cell counter (Logos Biosystems).  , and 16,000 cells were loaded into one lane of a 10X Chromium HT microfluidic chip. Single cell capture, barcoding and library preparation were performed using the 10X Genomics Chromium Next GEM Single Cell 3’ HT Kit v3.1, according to the manufacturer’s protocol (#CG000315). cDNA and libraries were checked for quality on Agilent 4200 Tapestation and quantified by KAPA qPCR before sequencing. each gene expression library was sequenced at 30.00% of an Illumina NovaSeq 6000 S4 flow cell lane, targeting on average ~9,000 barcoded cells with an average sequencing depth of 75,000 reads per cell.

value: Bone Marrow

value: hematopoietic cells

value: Dnmt3a Mutant


title: D3a8-vehicle

description: 10X Genomics


title: BMH4

value: HUVEC monoculture

value: Day 4


title: HDAC1_set1_DF

description: ChIP-seq


title: WT7-MitoQ

description: 10X Genomics

value: Mx-Cre


title: WT7-vehicle

description: 10X Genomics


title: HDAC1_set2_DF

description: ChIP-seq


title: F_EV2

value: Seminal Plasma

value: Extracellular Vesicles

value: Fertile

value: California x New Zealand white rabbits


title: ACH7

value: HUVEC-FB coculture

value: Day 7


title: HA-RAE1

description: ChIP-seq

value: pLZRS-HA-RAE1 expression

value: 66006, proteintech


title: BCH4


title: BCF4


title: D3a6-MitoQ

description: 10X Genomics


title: WT5-Vehicle

description: 10X Genomics


title: D3a6-Vehicle

description: 10X Genomics


title: ACF4


title: D4a-Vehicle

description: 10X Genomics


title: D4a-MitoQ

description: 10X Genomics


title: NUP98-ChIP_SAHA

data_processing:
RNA-seq: RTA2 was used for base calling. Reads were aligned using STAR. Alignments were quality filtered using samtools. Counting mapped reads was done using Salmon count. DESeq2 was used to determine differential expression.
ChIP-seq: STAR was used for ChIP-seq alignment and samtools was used for quality filtering. Peaks were called using MACS2.
Assembly: hg38
Supplementary files format and content: RNA-seq data analysis is presented in a table format with normalized counts data for each gene and DESeq2 output information. ChIP-seq peaks are presented in a table format with chromosome start and stop locations.

source_name: human keratinocytes

extract_protocol:
RNA was extracted and DNase treated using the Quick-RNA Miniprep Kit by Zymo Research. For ChIP-seq samples, cells were crosslinked with 1% formaldehyde for 10 minutes and then quenched with glycine. Nuclei were extracted in nuclei extraction buffer (10 mM HEPES pH7.4, 1.5 mM MgCl2, 10 mM KCl, and 0.2% NP-40) and lysed using a 27(1/2) gauge needle. DNA in nuclei lysate was fragmented to ~200 bp using sonication. Sonicated lysated was incubated with protein G beads conjugated with antibody. Beads were washed and DNA was eluted.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina was used to prepare RNA-seq libraries. NEBNext® Ultra™ II DNA Library Prep Kit for Illumina was used to prepare ChIP-seq libraries.

treatment_protocol: For shRNA-mediated knockdown, keratinocytes were seeded to 20% confluency prior to spin infection. shRNA lentivirus was diluted and added to keratinocytes along with 20 ug/mL of polybrene. Spin infection was performed at 32 C, 1250 rpm for 1 hour. The infected keratinocytes were then washed gently with PBS twice and keratinocyte media was added. One day post infection, cells were split to maintain confluency below 60%. Two days post infection, 2 ug/mL of puromycin was added to infected cells. Puromycin selection was done for 48 hours. Two days post puromycin selection, the cells were collected. For HDAC inhibitor drug treatment, 10 uM of SAHA or 100 nm of romidepsin was added to keratinocytes for 24 hrs.

value: SAHA

value: SC-74553 (Santa Cruz Biotech)


title: NUP98-ChIP_ROM

value: ROM

value: primary human neonatal keratinocytes

value: Foreskin


title: ACH4


title: WT3-MitoQ

description: 10X Genomics

value: Bone Marrow

value: hematopoietic cells


title: NUP98-ChIP_DMSO

value: DMSO


title: CMH1

value: HUVEC monoculture

value: Day 1


title: WT3-Vehicle

description: 10X Genomics

value: Mx-Cre


title: D3a-MitoQ

description: 10X Genomics

value: Dnmt3a Mutant


title: HDAC1-ChIP-seq_UDKC_rep2


title: WT1-Vehicle

description: 10X Genomics


title: WT5-MitoQ

description: 10X Genomics


title: HDAC1-ChIP-seq_UDKC


title: CCH1


title: WT1-MitoQ

description: 10X Genomics


title: SAHA-2


title: Stacc_TDP43_1C_rep3

city: Beijing

first: Fengling

last: Chen

state: Beijing

address: 30 Shuangqing Rd.

country: China

institute: Tsinghua University

data_processing:
Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 and then mapped to the mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat annotation from the UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data

source_name: Zygotes

growth_protocol: TDP-43 mice were maintained in a hybrid background of C57BL/6J and ICR under  guidelines of the Animal Care and Use Committee of the Institute of Zoology, Chinese Academy of Sciences.Oocytes and embryos were isolated in M2 medium, early embryos were culture in KOSM meduim.

extract_protocol:
The oocytes and embryos were collected as Smart-seq2 or Stacc-seq protocols in the paper, and the extraction was amplificated or used for the library directly as in the paper.
For RNA-seq, RNA libraries for RNA-seq were prepared using a kit of Vazyme (TD502) and performed as the protocol of manufacture. For stacc-seq, Stacc-seq libraries performed according to the previous report.1 μl fully dissolved 5% digitonin  was added to Buffer1 (10 mM Tris-HCl pH = 7.4, 150 mM NaCl, 0.5 mM spermidine, 1 × EDTA-free Roche complete protease inhibitor). 0.5 μl PA/G-Tn5  and 0.5 μg TDP-43 or Pol II antibody was added to prepared Buffer1 and incubated at 4℃ for 30 min. Meanwhile, oocytes and embryos were treated gently with Tyrode’s solution for removing the zona pellucida, then were put into 200ml low-binding tube contained 6ml prepared Buffer1 and incubate 4℃ for 10 min . Then 35 ml the prepared Buffer1, mixture of PA/G-Tn5, and the antibody and 12.5 ml TTBL were added for cleaving the chromatin around the binding sites and transposing with adaptors. Then the DNA were purified and PCR as the stacc-seq steps in previously reported

treatment_protocol: Oocytes or enbryos were  isolated from 7-8-week-old female mice after intraperitoneal injection PMSG  or HCG. For FGO, PMSG48h;For MII oocytes, HCG 13h;For embryos, 30h, 36h and 48h.The zona pellucida  of oocytes and embryos were  removed using Tyrode’s solution before they were collected.

value: Zygotes

tag: antibody

value: TDP-43(Proteintech 12892-1-AP)

value: WT


title: Stacc_TDP43_1C_rep2


title: BMH1


title: D3a-Vehicle

description: 10X Genomics


title: Stacc_PolII_FGO_TDP43KO_rep2

source_name: FGO oocytes

value: FGO oocytes

value: Pol II(Active Motif 102660)

value: TDP-43 oocyte knockout


title: SAHA-1

value: SAHA


title: BCF1

value: HUVEC-FB coculture


title: ROM-2

value: Rom

value: primary human neonatal keratinocytes


title: Stacc_PolII_FGO_Ctrl_rep2


title: BCH1


title: Stacc_PolII_FGO_Ctrl_rep1


title: Stacc_PolII_L2C_TDP43KO_rep2

source_name: late 2-cell mouse embryos

value: late 2-cell mouse embryos


title: ROM-1

value: Foreskin


title: Stacc_PolII_L2C_TDP43KO_rep1


title: ACF1


title: Stacc_PolII_L2C_Ctrl_rep2


title: CCF1


title: DMSO-2

value: DMSO


title: Stacc_PolII_L2C_Ctrl_rep1


title: DMSO-1


title: RAE1-shC

value: RAE1 shRNA


title: ACH1

value: Day 1


title: Stacc_TDP43_L2C_rep2

data_processing:
Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 and then mapped to the mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat annotation from the UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data
Library strategy: Stacc-Seq

value: TDP-43(Proteintech 12892-3-AP)


title: pif_end48 (biol rep 3)

city: Geneva

first: Urszula

last: Piskurewicz

address: 30, Quai Ernest-Ansermet

department: 30, Quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

data_processing:
Low-quality reads were filtered out by the fastqc program (RRID:SCR_005539) with the option –q 20 and –p 90.
The  reads were mapped to the Col-0 genome (TAIR10) with the TopHat program (RRID:SCR_013035)
Assembly: Transcript assembly and normalization was performed with the Cufflinks program (RRID:SCR_ 013307), and gene expression levels were calculated in FPKM (Fragments Per Kilobase of exon per Million mapped fragments) units.
Supplementary files format and content: Differential gene expression analysis was performed by Cuffdiff (RRID:SCR_001647), a part of the Cufflinks package
Supplementary files format and content: tab-delimited text files include average FPKM values

organism: Arabidopsis thaliana

source_name: endosperm

extract_protocol:
total RNA was isolated from 200 mature endosperms or embryos
cDNA libraries were prepared from 200 ng total RNA using a TruSeq mRNA Library Prep Kit (Illumina, Switzerland).

value: endosperm

value: pif3-1 mutant

value: 30C for 48 h


title: Stacc_TDP43_FGO_rep3

value: TDP-43(diagenode C15410266)

value: WT


title: Stacc_TDP43_L2C_rep1


title: Stacc_PolII_FGO_TDP43KO_rep1

value: FGO oocytes

value: Pol II(Active Motif 102660)


title: pif_end48 (biol rep 2)


title: RAE1-shB


title: Stacc_TDP43_FGO_rep1

value: TDP-43(Proteintech 12892-2-AP)


title: pif_end48 (biol rep 1)


title: RNA_TrimAway_2C_NC_rep2

value: TDP-43 zygotes knockdown


title: Stacc_TDP43_1C_rep1

value: Zygotes

value: TDP-43(Proteintech 12892-1-AP)


title: Col_end48 (biol rep 3)

value: WT (Col)


title: RAE1-shA

value: primary human neonatal keratinocytes

value: Foreskin


title: RNA_TrimAway_2C_NC_rep1

value: late 2-cell mouse embryos


title: RNA_TrimAway_2C_KD_rep2


title: RNA_TrimAway_2C_KD_rep1


title: CTRL-shA

value: Ctrl shRNA for RAE1 KD (GFP)


title: RNA_MII_KO_rep1

source_name: MII oocytes

value: MII oocytes

value: TDP-43 oocyte knockout


title: Col_end48 (biol rep 1)

value: endosperm


title: RNA_MII_KO_rep2


title: RNA_MII_Ctrl_rep2


title: NUP98_ChIP-seq_keratinocytes_set1_DF

value: SC-74553 (Santa Cruz Biotech)


title: RNA_MII_Ctrl_rep1


title: pif_emb48 (biol rep 3)

source_name: embryo

value: embryo

value: pif3-1 mutant

value: 30C for 48 h


title: Stacc_TDP43_FGO_rep2

value: FGO oocytes

value: TDP-43(Proteintech 12892-3-AP)

value: WT


title: RNA_L2C_KO_rep2


title: pif_emb48 (biol rep 2)


title: NUP98-ChIP-seq_UDKC_rep3


title: RNA_L2C_KO_rep1


title: mRNA_Control10

tag: disease state

value: control

tag: Stage

value: platelets

value: whole blood

value: mRNA


title: RNA_L2C_Ctrl_rep1


title: RNA_L2C_Ctrl_rep2


title: pif_emb48 (biol rep 1)


title: RNA_FGO_KO_rep2


title: CTRL-shB

value: Ctrl shRNA for RAE1 KD (non-targeting)

value: primary human neonatal keratinocytes

value: Foreskin


title: NUP98-shC

data_processing:
RNA-seq: RTA2 was used for base calling. Reads were aligned using STAR. Alignments were quality filtered using samtools. Counting mapped reads was done using Salmon count. DESeq2 was used to determine differential expression.
ChIP-seq: STAR was used for ChIP-seq alignment and samtools was used for quality filtering. Peaks were called using MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq data analysis is presented in a table format with normalized counts data for each gene and DESeq2 output information. ChIP-seq peaks are presented in a table format with chromosome start and stop locations.

treatment_protocol: For shRNA-mediated knockdown, keratinocytes were seeded to 20% confluency prior to spin infection. shRNA lentivirus was diluted and added to keratinocytes along with 20 ug/mL of polybrene. Spin infection was performed at 32 C,  1250 rpm for 1 hour. The infected keratinocytes were then washed gently with PBS twice and keratinocyte media was added. One day post infection, cells were split to maintain confluency below 60%. Two days post infection, 2 ug/mL of puromycin was added to infected cells. Puromycin selection was done for 48 hours. Two days post puromycin selection, the cells were collected. For HDAC inhibitor drug treatment, 10 uM of SAHA or 100 nm of romidepsin was added to keratinocytes for 24 hrs.

value: NUP98 shRNA


title: NUP98_ChIP-seq_keratinocytes_set1_UD


title: NUP98-shB


title: RNA_FGO_KO_rep1

value: TDP-43 oocyte knockout


title: Col_end48 (biol rep 2)

value: endosperm

value: WT (Col)


title: MonoMAC B cell line_20

city: Bethesda

first: Weixin

last: Wang

state: MD

address: 9000 Rockville Pike

department: DLM/CC

institute: NIH

hyb_protocol: Hybridization was done at 56ºC and 20 rpm for 20 h.

scan_protocol: Array images were scanned on Agilent’s G2505C scanner using settings for high-density miRNA arrays.

data_processing:
The scanned images were processed with Agilent’s Feature Extraction software (v.10.7.3.1).
Signal intensity values normalized by all control probes (including spike-ins) on the array.

source_name: MonoMAC B cell line_20

label_protocol: Total RNA (100 ng) was reverse transcribed and Cyanine3-pCp labeled using the Agilent microRNA labeling kit according to the manufacturer’s protocol.  Labeled cRNA was purified with Micro Bio-Spin 6 columns.

extract_protocol: Total RNA was isolated from the human B cell lines using miRNeasy Mini Kit (Qiagen, Germantown, MD). RNA concentration and quality was determined using an Agilent Bioanalyzer 2100 (Agilent, Wilmington, DE) and NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE).

value: lymphocytes

tag: phenotype

value: monoMAC


title: MonoMAC B cell line_21

source_name: MonoMAC B cell line_21


title: mRNA_Cancer16

source_name: platelets

value: lung cancer

tag: fraction


title: NUP98-shA


title: Col_emb48 (biol rep 2)

value: embryo

value: 30C for 48 h


title: HL-60_4C_ML-792, rep1

source_name: acute myeloid leukemia

tag: cell line

value: NFkB2 promoter


title: MonoMAC B cell line_16

source_name: MonoMAC B cell line_16


title: Col_emb48 (biol rep 1)


title: CTRL-sh2

value: Ctrl shRNA for NUP98 KD (non-targeting)


title: RNA_FGO_Ctrl_rep1

value: FGO oocytes

value: WT


title: RNA_E2C_KO_rep2

source_name: early 2-cell mouse embryos

value: early 2-cell mouse embryos


title: pif_end24 (biol rep 3)

value: pif3-1 mutant

value: 30C for 24 h


title: pif_end24 (biol rep 2)


title: CTRL-sh1

value: Ctrl shRNA for NUP98 KD (GFP)

value: primary human neonatal keratinocytes

value: Foreskin


title: MonoMAC B cell line_11

source_name: MonoMAC B cell line_11


title: pif_end24 (biol rep 1)

value: endosperm


title: Col_emb48 (biol rep 3)

value: WT (Col)


title: RNA_E2C_Ctrl_rep2


title: RNA_E2C_KO_rep1

value: TDP-43 oocyte knockout


title: MonoMAC B cell line_10

source_name: MonoMAC B cell line_10

value: lymphocytes

value: monoMAC


title: NFAT5-KO-UMR106+NaCl 2

city: Zurich

first: Ganesh

last: Pathare

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zurich

description:
KO2+NaCl
KO-NaCl+NaCl.xlsx

data_processing:
In brief, amplified cDNA samples were subjected to different quality control standards. RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®.
Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, the insert size of the library was validated on an Agilent 2100 and quantified using quantitative qPCR.
. Libraries were then sequenced on Illumina NovaSeq 6000 S4 flow cell with PE150 according to results from library quality control and expected data volume.
Assembly: mm10
Supplementary files format and content: .xls files included raw counts for each sample

organism: Rattus norvegicus

source_name: bone

growth_protocol: Cell were grown in DMEM supplemented with 10% FBS

extract_protocol:
RNA was isolated using a Nucleospin kit
RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®.

treatment_protocol: cell were treated with low (-20 mM) or high (+20 mM) NaCl

value: bone

value: osteoblast

value: High NaCl for 24h


title: Col_end24 (biol rep 3)


title: NFAT5-KO-UMR106+NaCl 3

description:
KO3+NaCl
KO-NaCl+NaCl.xlsx


title: RNA_E2C_Ctrl_rep1


title: RNA_FGO_Ctrl_rep2


title: MonoMAC B cell line_4

source_name: MonoMAC B cell line_4


title: MonoMAC B cell line_19

source_name: MonoMAC B cell line_19


title: RNA_1C_KO_rep2

source_name: Zygotes

value: Zygotes


title: Col_end24 (biol rep 2)


title: Col_end24 (biol rep 1)


title: NFAT5-KO-UMR106-NaCl 3

description:
KO3-NaCl
KO-NaCl+NaCl.xlsx

value: Low NaCl for 24h


title: MonoMAC B cell line_3

source_name: MonoMAC B cell line_3


title: MonoMAC B cell line_12

source_name: MonoMAC B cell line_12


title: RNA_1C_KO_rep1


title: pif_emb24 (biol rep 3)

value: embryo


title: NFAT5-KO-UMR106-NaCl 2

description:
KO2-NaCl
KO-NaCl+NaCl.xlsx


title: MonoMAC B cell line_1

source_name: MonoMAC B cell line_1


title: control B cell line_30

source_name: control B cell line_30

value: control


title: NFAT5-KO-UMR106-NaCl 1

description:
KO1-NaCl
KO-NaCl+NaCl.xlsx


title: pif_emb24 (biol rep 2)

source_name: embryo

value: pif3-1 mutant


title: MonoMAC B cell line_5

source_name: MonoMAC B cell line_5


title: Control-UMR106+NaCl 3

description:
Ctrl3+NaCl
Control-NaCl+NaCl.xlsx

value: WT


title: pif_emb24 (biol rep 1)

value: 30C for 24 h


title: RNA_1C_Ctrl_rep2


title: NFAT5-KO-UMR106+NaCl 1

description:
KO1+NaCl
KO-NaCl+NaCl.xlsx


title: Control-UMR106+NaCl 2

description:
Ctrl2+NaCl
Control-NaCl+NaCl.xlsx


title: Col_emb24 (biol rep 3)


title: Control-UMR106+NaCl 1

description:
Ctrl1+NaCl
Control-NaCl+NaCl.xlsx


title: Col_emb24 (biol rep 2)


title: Control-UMR106-NaCl 3

description:
Ctrl3-NaCl
Control-NaCl+NaCl.xlsx


title: Control-UMR106-NaCl 2

description:
Ctrl2-NaCl
Control-NaCl+NaCl.xlsx


title: Col_emb24 (biol rep 1)


title: control B cell line_27

source_name: control B cell line_27


title: control B cell line_26

source_name: control B cell line_26


title: control B cell line_29

source_name: control B cell line_29


title: control B cell line_25

source_name: control B cell line_25


title: control B cell line_28

source_name: control B cell line_28


title: control B cell line_24

source_name: control B cell line_24


title: Tet2_wildtype_RNAseq_rep3

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

description: RNA-seq

data_processing:
For RNA-seq RNA was extracted using Omega E.Z.N.A. Total RNA kit I (R6834). Library preparation and mRNA sequencing were performed at Novogene using their Illumina Novoseq 6000 platform. Adaptors were trimmed using trim galore (v0.6.5) and clean reads were mapped to the mouse genome (mm10) using STAR (v2.7.3a) with default parameters. Gene counts were extracted from mapped reads using featureCounts with --largestOverlap parameter. Raw counts were used to identify differentially expressed genes with DESeq2 (FDR <0.05 and fold-change >1.5), following the standard package documentation.
For CUT&Tag cleaned reads were mapped to the mouse genome (mm10) using Bowtie2 (Version 2.2.3) (Langmead and Salzberg, 2012) with options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700. Peak calling was performed using MACS2 (Version 2.1.0) (Zhang et al., 2008) with options -f BAMPE --keep-dup all.
For WGBS, DNA was extracted by Quick-DNA miniprep kit (Zymo, D3024) following the manufacturer’s instructions. Bisulfite conversion and sequencing were performed at BGI Genomics (https://en.genomics.cn/). Lamda DNA spike-in confirmed a >99.4% bisulfite conversion efficiency. The libraries were subjected to 100 bp pair-end sequencing on a HiSeq 4000 Illumina platform. The raw reads were filtered by SOAPnuke (v1.5.5) (https://github.com/BGI-flexlab/SOAPnuke) with the parameters -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2 -G to remove adaptors and filter out low-quality reads. Clean reads were mapped to mouse genome mm10 using Bismark (v0.22.3) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine extracted with bismark_methylation_extractor
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files were generated using bamCoverage from deepTools, and bigwig files were analyzed using plotProfile and plotHeatmap.Peaks annotation were implemented by R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Mouse ESCs

growth_protocol: ESCs were cultured on gelatin in serum/LIF and then harvested for subsequent high-throughput sequencing.

extract_protocol:
For RNA-seq, RNA extraction was performed using Omega E.Z.N.A Total RNA kit. For WGBS, DNA extraction was performed using Zymo Quick-DNA Miniprep Kit.
RNA-seq libraries were prepared by Novogene (https://en.novogene.com/). WGBS libraries were prepared by BGI company (https://en.genomics.cn/). CUT&Tag libraries were prepared by NEBNext HiFi 2x PCR Master mix.
RNA-seq, CUT&Tag, WGBS

treatment_protocol: For CUT&Tag, ESCs were crosslinked, bound to Con-A beads, incubated with primary antibody and treated with pre-loaded pA-Tn5 adapter complex.

value: Embryonic stem cells

tag: strain

value: V6.5 Male mixed 129/C57BL/6

value: Tet2 wildtype


title: Tet2_wildtype_RNAseq_rep2

description: RNA-seq


title: Tet2_mutant_RNAseq_rep1

description: RNA-seq

value: Tet2 mutant


title: Tet2_knockout_RNAseq_rep1

description: RNA-seq

value: Tet2 knockout


title: Control-UMR106-NaCl 1

description:
Ctrl1-NaCl
Control-NaCl+NaCl.xlsx

source_name: bone


title: Tet2_knockout_RNAseq_rep2

description: RNA-seq


title: RNA_1C_Ctrl_rep1


title: Tet2_knockout_WGBS

description: WGBS


title: control B cell line_9

source_name: control B cell line_9

value: lymphocytes


title: E. coli C3000 + M13 phage – nontargeting - rep 2

city: Skolkovo

first: Matvei

last: Kolesnik

address: 3 Nobel str

department: Life Sciences

country: Russia

institute: Skoltech

data_processing:
Raw RNA sequencing reads were filtered by quality with the simultaneous adapters removal using trimmomatic v. 0.36. The exact parameters of trimmomatic run could be found in raw_data_processing.sh file.
Processed reads were mapped onto reference sequences (RefSeq: NC_000913.3 supplemented with pC002 and pC008 plasmids in case of nontargeting samples and NC_000913.3 supplemented with pC003_RFP_spacer and pC008 plasmids in case of targeting samples) using bowtie2 v. 2.3.4.3 producing corresponding SAM files. In case of the analysis of data obtained from in vitro experiments on isolated E. coli total RNAб reads were mapped only onto the NC_000913.3 sequence. The exact parameters of bowtie2 run could be found in read_mapping.sh file.
For each nucleotide position of each strand of reference sequences the number of 5’ ends of aligned fragments were counted producing corresponding tables (see return_fragment_coords_table.py file for details).
The obtained tables were joined using merge_ends_count_tables.py script. The differences between the numbers of mapped 5’ ends in targeting and nontargeting samples were analyzed using edgeR package v.  3.26.3. The features (here, strand specific nucleotide positions) with low counts were excluded from the analysis. The TMM normalization method implemented in edgeR was applied. Next, the edgeR likelihood ratio test was performed. The obtained p-values were corrected using Benjamini-Hochberg method, and the result tables containing analyzed features with assigned log2FC and adjusted p-values were written to separate files (see TCS_calling.R file for details). The obtained trascript cleavage sites were overlapped with annotated genomic features using GenomicRanges package.
Assembly: NC_000913.3

organism: Escherichia coli

growth_protocol: E. coli cells were grown overnight in LB supplemented with 25 µg/ml chloramphenicol and 100 µg/ml ampicillin. Cell cultures were diluted 1:100 in fresh LB with double selection and grown for 1 hour at 37 °C with continuous shaking. After 1 hour, target expression was induced with 500 ng/ml anhydrotetracyline.

extract_protocol:
Total RNA was isolated from cells pelleted at 5 minutes (E. coli C3000 5 min samples) or 30 minutes (E. coli C3000 + M13 phage samples) post RFP induction. Cell lysis was done using Max Bacterial Enhancement Reagent (Invitrogen) for 4 min and then with TRIzol reagent (Invitrogen) for 5 min. RNA was extracted by chloroform and precipitated with isopropanol. RNA pellets were washed with 70% ethanol and then dissolved in nuclease free water and then treated with Turbo DNA-free kit (Invitrogen).
Total RNA samples were treated with MICROBExpress Bacterial mRNA Enrichment Kit (Invitrogen) for rRNA depletion prior to library preparation. To obtain both primary (5’ PPP) and processed (5’ P/5’ OH) transcripts, RNA samples were treated with RNA 5' Pyrophosphohydrolase (RppH) (NEB) for 30 min at 37C which removes pyrophosphate from 5’ end from triphosphorylated RNA to leave a 5’ monophoshphate RNA. Fragmentation was carried out by sonication using the Covaris protocol to obtain fragments of 200 nt size. T4 PNK (NEB) treatment was done to obtain 5’P ends for adapter ligation during library preparation. Samples were purified using the Zymo Research Oligo Clean and Concentrator kit. Library preparation for RNA sequencing was done using the NEBNext Multiplex Small RNA Library Prep Set for Illumina according to manufacturer’s protocol. BluePippin size selection was done using 2% agarose gel cassette (Sage Science) to select for 100 - 600 bp products. QC at each step was carried out by both Qubit and fragment analyzer.

treatment_protocol: Expression of target transcript was induced with 500 ng/ml anhydrotetracyline


title: E. coli C3000 + M13 phage – nontargeting - rep 3


title: Tet2_mutant_WGBS

description: WGBS


title: E. coli C3000 + M13 phage – nontargeting - rep 1


title: E. coli C3000 + M13 phage - targeting - rep 3


title: control B cell line_8

source_name: control B cell line_8


title: Tet2_wildtype_RNAseq_rep1

description: RNA-seq


title: Tet2_wildtype_WGBS

description: WGBS


title: Tet2_mutant_RNAseq_rep2

description: RNA-seq


title: E. coli C3000 + M13 phage - targeting - rep 2


title: SAG, replicate 1, scRNAseq

city: College Station

first: Fei

last: Liu

address: 206 Olsen Blvd

institute: Texas A&M University Health Science Center

description: 10x Genomics

data_processing:
The Cell Ranger Suite version 2.0.2 software was used to perform sample barcode processing and single-cell gene UMI (unique molecular index) counting Alignment, filtering, barcode counting and unique molecular identifier counting were performed using Cell Ranger 3.1.0 with default parameters. Reads were aligned to mouse reference mm10.
Assembly: mm10
Supplementary files format and content: Hierarchical Data Format. Matrix containing features, cell-barcodes and read.

source_name: SMG

extract_protocol:
Freshly collected SMGs at day 4 after SAG treatment were minced and digested for 1 h with RPMI 1640 medium containing 1 mg/ml mg/mL collagenase IV, 5mM CaCl2, 50 mg DNase I, and 8% fetal bovine serum with continuous shaking at room temperature.
scRNA-seq libraries were generated using the 10x Chromium platform and the version 3 Chromium Single Cell 3` reagent kit following the manufacturers instructions (10x Genomics).

treatment_protocol: SAG Millipore 566660, 25 μg/gland once

value: Various

value: SMG

tag: age

value: 6-8 weeks old


title: control B cell line_7

source_name: control B cell line_7


title: NT, replicate 1, scRNAseq

description: 10x Genomics

extract_protocol:
Freshly collected SMGs were minced and digested for 1 h with RPMI 1640 medium containing 1 mg/ml mg/mL collagenase IV, 5mM CaCl2, 50 mg DNase I, and 8% fetal bovine serum with continuous shaking at room temperature.
scRNA-seq libraries were generated using the 10x Chromium platform and the version 3 Chromium Single Cell 3` reagent kit following the manufacturers instructions (10x Genomics).

treatment_protocol: No treatment

tag: tissue


title: Bone Marrow Derived Macrophage -Cigarette Smoke exposure 3

city: Santa Cruz

first: Susan

last: Carpenter

address: Red Hill Rd, Biomedical Sciences

department: MCD

institute: UC Santa Cruz

description:
macviv_cig_ctl_er056
DESeq2_results.txt
juncBASE_Output.txt
rMATS_RI_JCEC.txt

data_processing:
All samples were sequenced together on an Illumina HiSeq system (paired-end 150bp), and sequencing reads were mapped to mm10 using STAR. For analysis of differential genes, STAR outputs were processed using DESeq2.
Prior to alternative splicing steps (rMATS, juncBASE ), non-canonical chromosome reads were removed with Samtools v1.9 as samtools view -b -@ 8 <in.bam> chr{1..19} chrX chrY > chr_$<in.bam>
rMATS v4.1.1 was run as: rmats_turbo_v4_1_1/rmats.py --b1 <samples1.txt> --b2 <samples2.txt> --nthread 4 -t paired --readLength 100 --gtf merged.gtf --od <out> --libType fr-unstranded --allow-clipping
juncBASE was run using Docker container "mgmarin/juncbase:0.9" with the "--by_chr" option used wherever allowed. The full list of commands is available here: https://github.com/ericmalekos/alt_splicing_scripts/blob/main/tool_usage.txt
juncBASE counts were used as input to DRIMSeq v1.2. DRIMSeq was run as described in the manual with default settings except the filter step which was run as dmFilter(d, min_samps_gene_expr = 6, min_samps_feature_expr = 3, min_gene_expr = 10, min_feature_expr = 0)
Events from both rMATS and DRIMSeq statistical analysis were kept if they met the following criteria: FDR < 0.1, |PSI| > 0.1, number of reads supporting event > 10
Common retained intron events were identified with Bedtools v2.27.1 bedtools intersect -wa -u -f -r 0.85 -a <rmatsIR.bed> -b <drimIR.bed>
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2, juncBASE, rMATS files are TSV format containing the direct output of above commands
Supplementary_files_format_and_content: merged_annotations.gtf is GTF format
Supplementary_files_format_and_content: DESeq2 normalized gene counts and statistics
Supplementary_files_format_and_content: juncBASE event counts
Supplementary_files_format_and_content: rMATS retained intron counts and statistics

source_name: Bone Marrow Derived Macrophage

growth_protocol: Mouse bone marrow-derived macrophages (BMDMs) were generated by culturing erythrocyte-depleted bone-marrow cells in DMEM medium supplemented with 10% FCS, 5 mL pen/strep (100X), 500μl ciprofloxacin (10mg/ml) and 10% L929 supernatant for 7-12 days, with the replacement of culture medium every 2-3 days.

extract_protocol:
Total RNA was purified from bone marrow cells or BMDMs using Direct-zol RNA MiniPrep Kit (Zymo Research) and TRIzol reagent (Ambion) according to the manufacturer’s instructions.
Total RNA was used to generate libraries using a NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific, $5138-07) according to the manufacturer’s instructions. Samples were quality assessed using TapeStation (Agilent, Santa Clara, CA) and read on a High-Seq System (Illumina, San Diego, CA.

treatment_protocol: Bone marrow erythrocyte-depleted cells from each mouse were split into two fractions, 1) to be immediately harvested in Trizol for RNA isolation (Day 0), and 2) to be differentiated into BMDMs upon addition of 10% L929 in culture media until harvest (Day 11).

value: Bone Marrow Derived Macrophage

value: Cigarette Smoke Exposure

value: Wild-type (WT)


title: Top3b_null3 [HiSeq]

city: Baltimore

first: Xingliang

last: Zhu

address: 251 Bayview Blvd

institute: National Institute on Aging, National Institutes of Health

data_processing:
RNAseq raw data were removed adaptor by TrimGalore
Data quality was checked by FastQC
Trimmed data were mapped to mm10 using RSEM with the STAR alignments
The bedgraph files were produced by BEDTools.
Read counts were normalized and caluculated by RSEM
Assembly: mm10
Supplementary files format and content: each sample contains a bedgraph file.

source_name: Brain

extract_protocol:
RNA was extracted by Trizol.
RNA libraries for RNA-seq were prepared using published protocols (Joo et al., Nature Communications, 2020).

value: Brain

value: Whole brain


title: Bone Marrow Derived Macrophage -Cigarette Smoke exposure 2

description:
macviv_cig_ctl_er055
DESeq2_results.txt
juncBASE_Output.txt
rMATS_RI_JCEC.txt


title: E. coli C3000 5 min - nontargeting - rep 3


title: 28LL-treatment3

city: London

first: Efthymia

last: Papaevangelou

address: Guy's Hospital

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: King's College London

description: subcutaneous tumor model

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mis-match was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome GRCm38 using the STAR aligner v.2.5.2b. The STAR aligner uses a splice aligner that detects intron/exon junctions and helps align the entire read sequences.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
The gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include hit counts for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with TPM values for every gene and every sample

source_name: TRAMP-C2 tumor

growth_protocol: Male C57BL/6J mice, 6–8 weeks old, were injected with 5 x 10^6 TRAMP-C2 cells in 0.1 mL PBS subcutaneously into the right flank.

extract_protocol:
At day 6, tumors were removed, flash frozen on dry ice, and RNA was harvested using an RNeasy Mini Kit (Qiagen). NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice with tumors of an approximate 200mm^3 volume were randomly divided into four treatment cohorts and treated intratumorally with 3 doses (every other day) of 50 µl HBSS (Hank’s balanced salt solution, vehicle control) or 2 doses of 10µg cyto-IL-15 or with 3 doses of 50µg (in 50µl) of ADU-S100 or combination of ADU-S100 (3 doses) and cyto-IL-15 (2 doses). Treatments were given as three doses injected at days 0, 2 and 4 for ADU-S100 and at days 0 and 4 for cyto-IL-15.

value: tumor

tag: tumor type

value: prostate

value: Combination (cyto-IL-15 plus ADU-S100)


title: E. coli C3000 5 min - nontargeting - rep 2


title: Bone Marrow Derived Macrophage -Cigarette Smoke exposure 1

description:
macviv_cig_ctl_er054
DESeq2_results.txt
juncBASE_Output.txt
rMATS_RI_JCEC.txt


title: 22-treatment3

description: subcutaneous tumor model


title: Top3b_null1 [HiSeq]


title: Top3b_null2 [HiSeq]


title: E. coli C3000 5 min - nontargeting - rep 1


title: Bone Marrow Derived Macrophage - Room Air exposure 3

description:
macviv_air_ctl_er053
DESeq2_results.txt
juncBASE_Output.txt
rMATS_RI_JCEC.txt

value: Room Air Exposure


title: E. coli C3000 5 min - targeting - rep 3


title: 20L-treatment3

description: subcutaneous tumor model


title: WT2 [HiSeq]

value: WT


title: 22LR-treatment2

description: subcutaneous tumor model


title: WT1 [HiSeq]


title: 18R-treatment2

description: subcutaneous tumor model


title: 17LL-treatment2

description: subcutaneous tumor model