title: eCLIP-Seq, HCT116, MYC, IP, rep2

city: Pittsburgh

first: Da

last: Yang

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

data_processing:
Briefly, we followed CLIP Tool Kit (CTK) pipeline for most of the data processing steps and used MACS2 to do peak calling.
For each cell line, eCLIP-Seq data were first demultiplexed using fastx_barcode_splitter.pl from fastx-toolkit, with default parameters, yielding two IP replicates and one input sample. The adapters were trimmed using Cutadapt with “--match-read-wildcards --times 1 --quality-cutoff 5 -O 1 -m 15 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGGCTA -a ATTGCTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a ACAAGCCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a AACTTGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG -a AGGACCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG ” parameters and the low-quality reads were dropped.
Then, the analysis was mainly based on CTK pipeline. Briefly, the exact PCR duplicates were collapsed using fastq2collapse.pl with default parameters. The 10-nt random-mers were removed from read 2 and stored in the read ID for further analysis, using stripBarcode.pl with default parameters. The processed read 2 sequences were mapped to the hg38 genome using bwa (Li and Durbin, 2009), with parameters “-t 4 -n 0.06 -q 20”. Only uniquely mapped reads were kept for further analysis. Tags from rRNA and repetitive RNA were removed using tagoverlap.pl with recommended parameters. Then, based on the random-mers, the PCR duplicates were collapsed using tag2collpase.pl with recommended parameters. For each replicate, we separated the reads into plus and minus strand.
Next, we used MACS2 to do peak calling by the following steps. (1) For each replicate, we first call peaks in IP to identify the potential RNA binding sites with “--keep-dup all --nomodel -s $tagsize --extsize 100 --max-gap 50 -q 1e-2” parameters. Since the length eCLIP-Seq reads various a lot after adapter trimming, the average “tagsize” was calculated by an ad hoc script. These peaks are considered as “IP-only” peaks. (2) To identify MYC-specific binding peaks, we called peak by comparing IP versus input with the same parameters. These peaks are considered as “enriched” peaks. (3) “IP-only” peaks that are overlapped with the “enriched” peaks are considered as MYC-specific binding sites (enriched in IP). (4) Then the overlapped MYC-specific binding sites from the two replicates were considered as the reproducible MYC-specific binding sites. (5) To make downstream analysis simple and get a uniform peak list for each cell line, replicates of IP were merged and then used to call peaks by comparing the merged IP with input using the same parameters. The peaks that overlap with the reproducible MYC-specific binding sites will be considered as the final peak list and used for following analysis. Finally, for each sample, peaks from plus and minus strands were merged as the MYC eCLIP-Seq peaks for each sample.
For visualization in the UCSC genome browser, based on the bed files of aligned and processed reads, bedgraph files were first generated using CTK “tag2profile.pl” with “-ss -exact --normalize multiply==$factor -of bedgraph” in which factor indicates the counts per million (CPM) normalization factor. Then the bedgraph files were converted into bigwig files using “bedGraphToBigWig” tool.
Assembly: hg38
Supplementary files format and content: The bw files contain the read distribution across the genome.
Supplementary files format and content: The narrowPeak files contain the peak details.
Library strategy: eCLIP-Seq

growth_protocol: MCF-7, U2OS, K562, HepG2, HCT116, and MCF10A cell lines were obtained from the American Type Culture Collection (ATCC) and maintained as suggested by ATCC’s guidelines.

extract_protocol:
Protein-associated RNAs by eCLIP and input RNAs were extracted using acid phenol:chloroform:isoamyl alcohol (25:24:1, pH 6.6) (Invitrogen) and RNA cleanup was performed with RNA Clean & Concentrator-5 columns (Zymo). After reverse transcription, qPCR was performed to the Ct value of the cDNA with Power SYBR Green Master Mix (Applied Biosystems).
eCLIP-seq libraries were prepared with primers containing Illumina adapter sequences using Q5 High-Fidelity 2× Master Mix (NEB) for 9 to 18 cycles and PCR products were purified with Agencourt AMPureXP beads (Beckman Coulter). After separating on a 3% Nusieve GTG agarose gel (Lonza), DNA ranging from 175 - 300 bp gel fragments was excised and extracted using the MinElute Gel Extraction Kit (Qiagen) and libraries were validated using the 1× High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: Cells at the exponential phase were washed twice with ice-cold PBS, UV-crosslinked on ice with 254 nm at 400 mJ/cm2 with a UV crosslinker (XL-1000, Spectrolinker). For each reaction, 20 million cells were lysed in eCLIP lysis buffer for 15 min on ice and incubated at 37°C for 5 min with RNase I (Ambion) and Turbo DNase (Ambion) on a ThermoMixer C (Eppendorf).

tag: eclip antibody


title: Wiild type, HSCs mouse 3 [WC-3_S47]

status: Public on May 08 2025

type: SRA

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Sequencing quality was checked using FASTQC/MultiQC v0.11.5
Sequencing adptors were trimmed and low-quality reads were removed using Trimmomatic v0.40
Sequencing reads were mapped against reference genome mm10 using STAR v2.5
Differentially expressed genes were identified using edgeR v3.28.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and logRPKM for each sample

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
total RNA was isolated using Clontech SMART-Seq v4 Ultra Low Input RNA Kit
sequencing library was constructed using Nextera XT DNA Lib Kit for Illumina

tag: tissue

value: Bone marrow

tag: cell line

value: primary mouse cells

tag: cell type

value: hematopoietic stem and progenitor cells

tag: genotype

value: Wildtype


title: PLX8394 Day 14 rep3

city: La Jolla

first: Jingting

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC (v0.11.8) and mapped to the hg19 human genome using the STAR aligner (v2.5.3a) with default parameters.
Raw or TPM (Transcripts Per Kilobase Million) gene expression was quantified across all the exons of RefSeq genes with analyzeRepeats.pl in HOMER (v4.11.1), which used the top-expressed isoform as proxy for gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Homo sapiens

source_name: SK-MEL-2 human melanoma cells

growth_protocol: SKMEL-2 cells were grown in EMEM (HyClone) supplemented with 10% fetal bovine serum (Atlanta Biologicals) and Penicillin-Streptomycin (Gibco).

extract_protocol:
The total RNA was extracted from SKMEL-2 human melanoma cells using E.Z.N.A. Total RNA Kit I (Omega Bio-Tek).
Libraries were sequenced on the HiSeq 2500 following standard protocols.

treatment_protocol: Cells were treated with the vehicle (DMSO), PLX8394 (10μM), or Vemurafenib (10 μM) for 0, 3, 7, 14, or 21 days.

tag: time point

value: Day 14

tag: treatment


title: eCLIP-Seq, HCT116, MYC, IP, rep1

state: PA


title: Male 3 Early Polysome RNA (F7-9)

city: College Station

first: Darrell

last: Pilling

state: Texas

address: 301 Old Main Drive

department: Biology

institute: Texas A&M University

description:
Library name: Male 3 early polysome
120619M-F7-9_S26

data_processing:
RNA sequencing data were analyzed using the QuantSeq Data Analysis Pipeline on the BlueBee Genomic Platform. The quality of sequences was evaluated using FastQC software (version 0.11.5) after adapter trimming with BBDUK software (version 35.92).
Assembly: hg38
Supplementary files format and content: CSV files for total and fractionated datasets

source_name: blood

extract_protocol:
Human neutrophils were isolated from blood using  Polymorphprep
Neutrophils were lysed with polysome buffer. One fraction was retained as total lysate (total cell RNA), the rest was fractionated on sucrose gradients to collect free RNA, monosome RNA, and early and late polysome RNA.
RNAseq libraries were created using a QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), with 2 µg of RNA used as the starting material.
RNAseq libraries were created using a QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), with 2 µg of RNA used as the starting material. Libraries were sequenced using an Illumina NextSeq 500 platform

value: blood

value: neutrophil


title: Wiild type, HSCs mouse 1 [WC-1_S45]


title: eCLIP-Seq, HCT116, input


title: PLX8394 Day 14 rep1


title: Mel18 knock out, mouse 6 [Mel18_KO_44_S37]

data_processing:
Sequencing quality was checked using FASTQC/MultiQC v0.11.5
Sequencing adptors were trimmed and low-quality reads were removed using Trimmomatic v0.40
Sequencing reads were mapped against reference genome mm10 using STAR v2.5
Differentially expressed genes were identified using edgeR v3.28.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and log2FPKM for each sample

value: Mel18 knock out


title: eCLIP-Seq, MCF10A, MYC, IP, rep2


title: Mel18 knock out, mouse 4 [Mel18_KO_4_S7]


title: Mel18 knock out, mouse 5 [Mel18_KO_6_S9]


title: Male 3 Free RNA (F1-3)

description:
Library name: Male 3 free
120619M-F1-3_S11


title: DMSO Day 14 rep3

value: vehicle (DMSO)


title: DMSO Day 14 rep2


title: Wiild type, mouse 3 [WT_7_S10]


title: Female 3 Late Polysome RNA (F10-12)

description:
Library name: Female 3 late polysome
120619F1-F10-12_S34


title: eCLIP-Seq, MCF10A, input


title: eCLIP-Seq, HepG2, MYC, IP, rep2


title: vemurafenib Day 14 rep1

value: vemurafenib


title: DMSO Day 14 rep1


title: Wiild type, mouse 2 [WT_5_S8]


title: Female 3 Early Polysome RNA (F7-9)

description:
Library name: Female 3 early polysome
120619F1-F7-9_S27


title: vemurafenib Day 7 rep3

value: Day 7


title: eCLIP-Seq, HepG2, MYC, IP, rep1


title: Female 3 Monosome RNA (F4-6)

description:
Library name: Female 3 monosome
120619F1-F4-6_S19


title: PLX8394 Day 14 rep2


title: Female 3 Free RNA (F1-3)

description:
Library name: Female 3 free
120619F1-F1-3_S12


title: vemurafenib Day 7 rep2


title: eCLIP-Seq, HepG2, input


title: Male 3 Monosome RNA (F4-6)

description:
Library name: Male 3 monosome
120619M-F4-6_S18


title: Male 2 Total cell RNA (Total)

description:
Library name: Male 2  Total
120419M-Total_S2


title: SREBP1_ko_uterus_LPS_biol_replicate_2

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

description: 7 days after injection

data_processing:
Reads were aligned to the mm10 mouse genome using STAR.
Aligned read files were analyzed using HOMER.  Differentially expressed genes were analyzed using svaseq and DESeq2.
bedGraph files were generated using HOMER.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: endometrial tissue

extract_protocol:
Total RNA was extracted using Rneasy column (Qiagen) according to the manufacturer's protocol.
Poly-A mRNA was extracted from total RNA by using an NEBNext Poly(A) mRNA magnetic Isolation module (NEB), after which RNA-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.

value: endometrial tissue

value: LPS injection


title: SREBP1_ko_uterus_LPS_biol_replicate_3

description: 7 days after injection


title: PLX8394 Day 7 rep3


title: vemurafenib Day 7 rep1


title: Female 3 Total cell RNA (Total)

description:
Library name: Female 3 Total
120619F1-Total_S5


title: eCLIP-Seq, MCF10A, MYC, IP, rep1


title: eCLIP-Seq, K562, MYC, IP, rep2


title: Male 2 Late Polysome RNA (F10-12)

description:
Library name: Male 2 late polysome
120419M-F10-12_S31


title: eCLIP-Seq, K562, MYC, IP, rep1


title: SREBP1_ko_uterus_LPS_biol_replicate_1

description: 7 days after injection


title: PLX8394 Day 7 rep2


title: Male 2 Early Polysome RNA (F7-9)

description:
Library name: Male 2 early polysome
120419M-F7-9_S24


title: eCLIP-Seq, K562, input


title: eCLIP-Seq, U2OS, MYC, IP, rep2


title: Male 2 Monosome RNA (F4-6)

description:
Library name: Male 2 monosome
120419M-F4-6_S16


title: SREBP1_ko_uterus_biol_replicate_3

description: 7 days after injection

value: PBS injection


title: PLX8394 Day 7 rep1


title: SREBP1_ko_uterus_biol_replicate_2

description: 7 days after injection


title: Wiild type, mouse 1 [WT_3_S6]


title: DMSO Day 7 rep3


title: SREBP1_ko_uterus_biol_replicate_1

description: 7 days after injection


title: eCLIP-Seq, U2OS, MYC, IP, rep1


title: DMSO Day 7 rep2


title: Male 2 Free RNA (F1-3)

description:
Library name: Male 2 free
120419M-F1-3_S9


title: Female 2 Total cell RNA (Total)

description:
Library name: Female 2 Total
120419F-Total_S3


title: ChIP-Rx, Dox, MYC-7A, IP, rep2

library_source: genomic

data_processing:
The adapters were trimmed using Cutadapt with “--match-read-wildcards --trim-n -O 1 -m 25” parameters. Since the library contains reads from both human and mouse samples, we first generated a “genome” concatenated by human (hg19) and mouse (mm10) genome. To distinguish the chromosome names, we added a suffix “__mm10” to all mouse chromosome names. A custom Bowtie2 library was built based on this combined genome sequence using “bowtie2-build” command. Reads were first mapped using bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 800”.
Reads with MAPQ >= 30 were kept (uniquely mapped reads) using samtools. Duplicates were removed using Picard MarkDuplicates. Then the reads were split to two files such that hg38 reads were stored in one file and mm10 reads were stored in the other one. All suffix “__mm10” were removed for the mm10 SAM file. Alignment files were then parsed and converted in a bed format using MACS2 “filterdup” command with “--keep-dup -f BAMPE” parameters.
Next, the peaks were called by MACS2 with “--keep-dup all -f BEDPE” parameters using the similar steps with eCLIP-Seq. Specifically, the two IP samples without Dox induction are considered as “input” samples. Final peaks overlapped with “blacklist” regions were removed.
For visualization in the UCSC genome browser, based on the bed files of aligned and processed reads, bedgraph files were first generated using MACS2 “pileup” command with “-f BEDPE” parameters. Then the counts in the bedgraph were RRPM (reference-adjusted reads per million) normalized using MACS2 “bdgopt” command. Next, the bedgraph files were converted into bigwig files using “bedGraphToBigWig” tool.
Assembly: hg38
Supplementary files format and content: The bw files contain the read distribution across the genome.
Supplementary files format and content: The narrowPeak files contain the peak details.

molecule: genomic DNA

growth_protocol: U2OS cells were maintained in McCoy's 5A medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37°C. Mouse embryonic fibroblast cell line NIH/3T3 was maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS, 1% MEM non-essential amino acids (Gibco), 10 mM HEPES (Gibco), and 1% penicillin/streptomycin.

extract_protocol:
After reverse cross-linking, RNase A, and proteinase K treatment on MYC-DNA adducts enriched with anti-FLAG antibodies, DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1, pH 8.0).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). 5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 9 cycles on the thermocycler. Post-amplification libraries were size selected at 200 - 500 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the 1× dsDNA High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: Both NIH3T3 cells at exponential growth phase and U2OS cells induced for 24 h with 1 µg/mL of doxycycline (Dox) or without Dox treatment were fixed with 1% formaldehyde for 10 min. After quenching by glycine, 10% of NIH3T3 cells were  mixed with U2OS cells, mixed chromatin were sheared to a size of 200 - 500 bp using a Bioruptor Pico (Diagenode) and incubated for overnight with an anti-FLAG (Sigma, F3165) antibody at 4°C.

tag: chip antibody

value: FLAG (Sigma, #F3165)

value: Doxycycline (Dox)


title: eCLIP-Seq, U2OS, input


title: ChIP-Rx, Dox, MYC-7A, IP, rep1


title: Female 2 Late Polysome RNA (F10-12)

description:
Library name: Female 2 late polysome
120419F-F10-12_S32


title: vemurafenib Day 3 rep3

value: Day 3


title: Female 2 Early Polysome RNA (F7-9)

description:
Library name: Female 2 early polysome
120419F-F7-9_S25


title: vemurafenib Day 3 rep2


title: WT_uterus_LPS_biol_replicate_1

description: 7 days after injection

value: Wild-type


title: ChIP-Rx, Dox, MYC-3A, IP, rep2


title: Female 2 Monosome RNA (F4-6)

description:
Library name: Female 2 monosome
120419F-F4-6_S17


title: WT_uterus_biol_replicate_3

description: 7 days after injection


title: ChIP-Rx, Dox, MYC-3A, IP, rep1


title: vemurafenib Day 3 rep1


title: Female 2 Free RNA (F1-3)

description:
Library name: Female 2 free
120419F-F1-3_S10


title: WT_uterus_biol_replicate_2

description: 7 days after injection


title: Male 1 Late Polysome RNA (F10-12)

description:
Library name: Male 1 late polysome
112519M-F10-12_S29


title: ChIP-Rx, Dox, MYC-WT, IP, rep2


title: PLX8394 Day 3 rep3


title: WT_uterus_biol_replicate_1

description: 7 days after injection


title: ChIP-Rx, Dox, MYC-WT, IP, rep1


title: DMSO Day 7 rep1


title: PLX8394 Day 3 rep2


title: ChIP-Rx, no Dox, MYC-WT, IP, rep2


title: Male 1 Monosome RNA (F4-6)

description:
Library name: Male 1 monosome
112519M-F4-6_S14


title: ChIP-Rx, no Dox, MYC-WT, IP, rep1


title: KO_PM_1

city: Xiamen

first: Binbin

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

country: China

institute: Xiamen University

data_processing:
The sequencing reads were mapped to the reference mouse genome GRCm39 by HISAT 2.2.1
Read counts per gene locus were obtained with featureCounts
Assembly: mm10
Supplementary files format and content: table-delimitted txt files containing raw counts for each smaplws

molecule: polyA RNA

source_name: Peritoneal macrophages

growth_protocol: Cd163-/- mice on a C57BL/6 genetic background were generated as our previous report. Cd163-/- male mice and their littermate WT male mice were housed in specific pathogen free facilities on a 12 h light/dark cycle at 22–23C in Xiamen University. All experiments were conducted in accordance with the National Institutes of Health guidelines for the Care and Use Laboratory Animal, and the protocol were approved by Animal Care and Protection Committee of Xiamen University (Protocol No. XMULAC20200150). Peritoneal macrophages were harvested from the peritoneal cavity three days after stimulation with thioglycolate-containing medium. Following centrifugation, the macrophages were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 5% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S) at 37 °C in a 5% CO₂ environment. The cells were allowed to adhere for 2–3 hours, and non-adhere  nt cells were removed

extract_protocol:
RNAs were purified from the livers  by Trizol Reagent
A cDNA library was prepared by using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: Cd163-/- mice received subcutaneous injections of mouse recombinant IL-10 (50 μg/kg/day) on days 0, 1, 3, 5, 7, 10, 13, 16, 19, 22, 25, and 27 following TAC surgery. The  cells were treated with 100 nM dexamethasone for 48 hours.

value: Peritoneal macrophages

value: macrophages

value: 100 nM dexamethasone


title: PLX8394 Day 3 rep1


title: WT_uterus_LPS_biol_replicate_3

description: 7 days after injection


title: DMSO Day 3 rep3


title: WT_uterus_LPS_biol_replicate_2

description: 7 days after injection


title: DMSO Day 3 rep2


title: Male 1 Free RNA (F1-3)

description:
Library name: Male 1 free
112519M-F1-3_S7


title: WT_PM_2

value: Wild type


title: ChIP-Rx, Dox, MYC-WT, input


title: Female 1 Total cell RNA (Total)

description:
Library name: Female 1 Total
112519F-Total_S1

value: blood


title: DMSO Day 3 rep1


title: WT_PM_1


title: ChIP-Rx, No Dox, MYC-WT, input


title: Day 0 rep3

value: Day 0

value: Nothing added


title: Female 1 Late Polysome RNA (F10-12)

description:
Library name: Female 1 late polysome
112519F-F10-12_S30

value: neutrophil


title: CUT&RUN, RNase, TBP, IP, rep2

data_processing:
The adapters were trimmed using Cutadapt with “--match-read-wildcards --trim-n -O 1” parameters. Similar to rChIP-Seq, reads were first mapped to the human genome (hg38) using bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 800”.
Reads with MAPQ >= 30 were kept (uniquely mapped reads) using samtools. Alignment files were then parsed and converted in a bed format using MACS2 “filterdup” command with “--keep-dup -f BAMPE” parameters.
Since there are no input samples in CUT&RUN, the peaks were called in a simpler way as follows. (1) For each replicate, we first call peaks in IP to identify the potential RNA binding sites with “--keep-dup all -f BEDPE -q 1e-2” parameters. These peaks are considered as MYC-specific binding sites. (2) Then the overlapped MYC-specific binding sites from the two replicates were considered as the reproducible MYC-specific binding sites. (3) To make downstream analysis simple and get a uniform peak list for each sample, replicates of IP were merged and then used to re-do the peak calling. The peaks that overlap with the reproducible MYC-specific binding sites will be considered as the final peak list and used for following analysis. Final peaks overlapped with “blacklist” regions were removed.
For visualization in the UCSC genome browser, based on the bed files of aligned and processed reads, bedgraph files were first generated using MACS2 “pileup” command with “-f BEDPE” parameters. Then the counts in the bedgraph were CPM normalized using MACS2 “bdgopt” command. Next, the bedgraph files were converted into bigwig files using “bedGraphToBigWig” tool.
Assembly: hg38
Supplementary files format and content: The bw files contain the read distribution across the genome.
Supplementary files format and content: The narrowPeak files contain the peak details.
Library strategy: CUT&RUN

growth_protocol: MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
After DNA digestion and release, DNA purification was conducted with a DNA Clean & Concentrator-5 Kit.
DNA library was constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) according to the manufacturer's protocols.

treatment_protocol: Cells at the exponential phase were directly harvested and fixed with Concanavalin A conjugated magnetic beads (Bans Laboratories). After treatment for 90 min with 5 U of RNase A per one million cells at room temperature, cells were incubated overnight with 2.5 µg of anti-MYC antibody, or anti-TBP antibody, or control rabbit IgG at 4°C.

value: RNase A


title: Heart_IL10_3

source_name: heart

value: heart


title: Day 0 rep2


title: Heart_IL10_2


title: Female 1 Early Polysome RNA (F7-9)

description:
Library name: Female 1 early polysome
112519F-F7-9_S23


title: CUT&RUN, RNase, TBP, IP, rep1


title: Heart_IL10_1


title: Day 0 rep1


title: Male 1 Early Polysome RNA (F7-9)

description:
Library name: Male 1 early polysome
112519M-F7-9_S22


title: KO_PM_2


title: CUT&RUN, RNase, MYC, IP, rep2


title: Female 1 Free RNA (F1-3)

description:
Library name: Female 1 free
112519F-F1-3_S8


title: CUT&RUN, RNase, MYC, IP, rep1


title: eCLIP-Seq, MCF-7, MYC, IP, rep2


title: Heart_NS2

value: saline


title: Heart_NS1


title: eCLIP-Seq, MCF-7, MYC, IP, rep1


title: CUT&RUN, RNase, IgG, IP, rep2


title: Heart_NS3


title: 4T1 cells, 11A_rep3 (RNAseq)

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality checks were performed using FastQC (v0.11.8), summarised with MultiQC (v1.9). Reads were then subsampled. Alignment to the mouse reference genome (build GRCm38.100) was performed using STAR (v2.7.0a) with default parameters. The counts of the aligned reads corresponding to exons were obtained using featureCounts program against the exon annotations obtained from the ensembl database (annotation file Mus_musculus.GRCm38.100.gtf). Density plots, boxplots, MA plots, and PCA were performed as further quality checks.
Noise filtering was performed using noisyR [Moutsopoulos et al, 2021; https://academic.oup.com/nar/article/49/14/e83/6291165] on the raw count matrix. The data was normalised using quantile normalisation [Bolstad2003].
Differential expression analysis was performed using DESeq2 1.26.0 [Love2014] and edgeR [Robinson2010].
Enrichment analysis on the set of differentially expressed genes against a background of all genes expressed in the dataset using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.1.9) [Raudvere2009].
Genome_build: mm10 (GRCm38.100)
Supplementary_files_format_and_content: two count matrices containing raw and normalized, respectively, gene expression

source_name: 4T1 cells, 11A

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen). Cell cultures in T25 flasks were first washed with cold PBS, and 350 µl of RLT was added. Cells were scraped, passed through a 20G syringe five times and resuspended in RLT, and RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacturer instructions.
RNA was submitted for library preparation by the Wellcome-MRC Cambridge Stem Cell Institute. Initial QC was performed using Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and TapeStation Analysis software (Agilent Technologies). 1000 ng RNA was used for library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB), ERCC spike-ins, and the QIAseq FastSelect RNA Removal Kit (Qiagen). Libraries were subsequently measured using the Qubit system and visualized on a TapeStation D5000. Sequencing was performed as one lane of PE150 using the HiSeq 4000 at the CRUK-CI Genomics Core.
RNA-seq, PE150

tag: shRNA sequence


title: 4T1 cells, control_rep3 (RNAseq)

department: Wellcome-MRC Cambridge Stem Cell Institute

source_name: 4T1 cells, control

value: control


title: CUT&RUN, RNase, IgG, IP, rep1


title: eCLIP-Seq, MCF-7, input


title: SC52_2_OE_AAI

city: Stony Brook

first: Sandeep

last: Mallipattu

state: NY

address: 101 Nicolls Road

institute: Stony Brook University

data_processing:
Illumina software used for basecalling
CellRanger used for raw processing
Seurat R-package
Signac R-package
Archr R-package
Assembly: mm10
Supplementary files format and content: CellRanger barcoded and aligned output files fragments.tsv.gz

source_name: Kidney cortex

extract_protocol:
A 2 mm3 section of tissue collected from perfused cortex stored at -80C was rinsed briefly with PBS and minced before adding 1 mL of lysis buffer containing 20 mM Tris-HCl (pH 8), 320 mM sucrose, 5 mM CaCl2, 3 mM MgAc2, 0.1 mM EDTA, 0.1% TritonX-100, 0.1% RNAse Inhibitor and 0.1% DAPI. The tissue was initially dissociated by pipetting up and down 10X with a p-1000 tip and then being passed through a 25G syringe 10X. The tissue was incubated on ice for 10 minutes and then passed through a 30 µm CellTrics filter. Nuclei were pelleted by centrifugation (5 min, 500g, 4°C) and washed with PBS after removal of supernatant. Nuclei were pelleted again and resuspended in 1 mL of PBS containing 0.04% BSA and RNAse inhibitor (0.2u/µL) and then passed through a 40 µm FlowMI filter before generating counts with hemocytometer. Nuclei were then diluted and prepared for snATA-seq with the 10X Chromium System according to the manufacturer’s instructions (10X Genomics)
ATAC libraries were prepared for sequencing using standard 10X Genomics and Illumina protocols

value: Kidney cortex

tag: strain

value: mixed

tag: Sex

value: male

value: AAI


title: ChIP-Seq, MCF-7, TBP, RNase, IP, rep2

data_processing:
Reads were first mapped to the human genome (hg38) using bowtie2 with parameters “--local --very-sensitive-local --no-unal”.
Reads with MAPQ >= 30 were kept (uniquely mapped reads) using samtools. Duplicates were removed using Picard MarkDuplicates. Alignment files were then parsed and converted in a bed format using MACS2 “filterdup” command with “--keep-dup -f BAM” parameters.
Then the peaks were called by MACS2 “callpeak” command with “--keep-dup all -f BED-q 1e-5” parameters using similar steps with eCLIP-Seq. Final peaks overlapped with “blacklist” regions were removed.
For visualization in the UCSC genome browser, based on the bed files of aligned and processed reads, bedgraph files were first generated using MACS2 “pileup” command with “--extsize 100 -f BED” parameters. Then the counts in the bedgraph were CPM normalized using MACS2 “bdgopt” command. Next, to smooth the read distribution in the bedgraph files, bedtools “makewindows” were used to separate the hg38 genome to a list of 100-bp windows in a bed file format. “bigwigAverageOverBed” was used to average the signals in bedgraph files along the 100-bp windows. Finally, the bedgraph files were converted into bigwig files using “bedGraphToBigWig” tool.
Assembly: hg38
Supplementary files format and content: The bw files contain the read distribution across the genome.
Supplementary files format and content: The narrowPeak files contain the peak details.

extract_protocol:
After reverse cross-linking, RNase A, and proteinase K treatment on MYC-DNA adducts enriched with anti-MYC or anti-TBP antibodies, DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1, pH 8.0).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). 5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 9 cycles on the thermocycler. Post-amplification libraries were size selected at 200 - 500 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the 1× dsDNA High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: Cells at the exponential phase were fixed with 1% formaldehyde for 10 min. After quenching by glycine and cell lysis, chromatins were sheared to a size of 200 - 500 bp using a Bioruptor Pico (Diagenode), followed by the treatment with RNase A or without RNase A, then incubated overnight with an anti-MYC (CST) antibody or anti-TBP (CST) antibody at 4°C.


title: Female 1 Monosome RNA (F4-6)

description:
Library name: Female 1 monosome
112519F-F4-6_S15


title: 4T1 cells, CHD8_rep3 (RNAseq)

source_name: 4T1 cells, CHD8


title: 4T1 cells, 11A_rep2 (RNAseq)


title: SC52_3_OE


title: CUT&RUN, no RNase, TBP, IP, rep1


title: CUT&RUN, no RNase, MYC, IP, rep2


title: 4T1 cells, control_rep2 (RNAseq)


title: ChIP-Seq, MCF-7, TBP, RNase, IP, rep1


title: 4T1 cells, CHD8_rep2 (RNAseq)


title: CUT&RUN, no RNase, TBP, IP, rep2


title: ChIP-Seq, MCF-7, TBP, no RNase, IP, rep2


title: SC52_1_Control_AAI


title: CUT&RUN, no RNase, MYC, IP, rep1


title: 4T1 cells, CHD8_rep1 (RNAseq)


title: SC52_4_Control


title: Cas9-sgMef2d-2

first: Bowen

last: Dong

state: Pennsylvania

address: 4200 Fifth Ave, Pittsburgh, PA 15260

data_processing:
Fastq files generated with CASAVA
Sequenced reads were mapped to GRCm38 reference GENCODE annotation M22 using STAR aligner
Read counts are obtained using Subread
Assembly: GRCm38
Supplementary files format and content: Raw counts csv file format

growth_protocol: DMEM medium with10% FBS supply with 100 units/ml penicillin, 100 µg/ml streptomy-cin. Cells were cultured in a humidified atmosphere of 95% air and 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Life Technologies) according to the manufacturer’s protocol.
RNA library were processed for next generation sequencing at Roswell genomic core facility.Briefly, the sequencing libraries were prepared with the mRNA HyperPrep kit (Roche) from 500 ng total RNA. Following the manufacturer’s instructions, the first step selected for PolyA RNA using the mRNA Capture Beads (KAPA BIOSYSTEMS).
Fragmented RNA was then reverse transcribed into first strand cDNA using random pri-mers. The next step removed the RNA template and synthesized a replacement strand, in-corporating dUTP in place of dTTP to generate double strand cDNA (ds-cDNA). Pure Beads (Roche) were used to separate the ds-cDNA from the second strand reaction mix resulting in blunt-ended cDNA. A single “A” nucleotide was then added to the 3′ ends of the blunt fragments. Multiple indexing adapters, containing a single “T” nucleotide on the 3′ end of the adapter, were ligated to the ends of the ds-cDNA, thereby preparing these samples for hybridization onto a flow cell. Adapter ligated libraries were amplified by PCR, purified using Pure Beads, and validated for an appropriate size on a 4200 TapeSta-tion D1000 Screentape (Agilent Technologies, Inc.).

treatment_protocol: sgCon versus sgMEF2D

value: mouse mammary epithelial cells


title: 4T1 cells, 11A_rep1 (RNAseq)


title: ChIP-Seq, MCF-7, MYC, RNase, IP, rep2


title: ChIP-Seq, MCF-7, TBP, no RNase, IP, rep1


title: CUT&RUN, no RNase, IgG, IP, rep2


title: 4T1 cells, control_rep1 (RNAseq)


title: CUT&RUN, no RNase, IgG, IP, rep1


title: Cas9-sgCon-3

value: sgControl


title: ChIP-Seq, MCF-7, MYC, RNase, IP, rep1


title: Cas9-sgMef2d-1


title: 4T1 cells, input:7c (ChIPseq)

data_processing:
Quality checks were performed using FastQC (v0.11.8), summarised with MultiQC (v1.9). Reads trimming was performed using cutadapt (v2.10) then subsampled. Alignment to the mouse reference genome (build GRCm38.100) was performed using STAR (v2.7.0a) with default parameters. Peaks were called using macs2 2.2.7.1 using default parameters. Density plots, boxplots, MA plots, and PCA were performed as further quality checks.
Peaks were matched between samples if the midpoint of a peak in each sample was within the peak in the other sample. Bigwig files were produced for each sample using bamCompare 3.4.1 and amplitudes for peaks in each sample were calculated using pyBigWig 0.3.17. The resulting amplitudes were normalised using quantile normalisation and noise was removed using a fixed threshold of 20 (only peaks entirely under the threshold were discarded and 20 was added to other abundances [Mohorianu2017]).
Differential expression analysis was performed using edgeR (v3.28.1) [Robinson2010] and DESeq2 [Love2014].
Genome_build: mm10 (GRCm38.100)
Supplementary_files_format_and_content: peak bed files

source_name: 4T1 cells, input:7c

extract_protocol:
ChIP-Seq experiments were performed as described (Schmidt et al Methods 2009). Antibodies used were BCL11A (Bethyl, A300-382A and Abcam ab191401) and CHD8 (Novus NB100-60417 and Bethyl A301-225A-M). Briefly 2 × 15 cm plates per cell line were formaldehyde crosslinked, nuclear fraction was isolated and chromatin sonicated using Bioruptor Pico (Diagenode). IP was performed using 100 μl of Dynabeads Protein G (Thermo Fisher Scientific) and 10 μg of antibody. The samples were then reverse crosslinked and DNA was eluted using Qiagen MinElute column. Samples were then processed for library prep and sequencing.
ChIP-Seq libraries were prepared using the ThruPLEX DNA-seq Kit. The pool was run as a PE150 run type on one lane of a HiSeq 4000.
ChIPseq, PE150

value: input control


title: Cas9-sgCon-2


title: HCC-PDX tumor, CD133 positive, H3K4me3

city: Hangzhou

first: Jiaqi

last: Wang

state: Zhejiang

address: Yuhangtang No.866

institute: Zhejiang University

data_processing:
We use FastQC performs basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were preprocessed through Trimmomatic software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 (Burrows Wheeler Aligner) and clean reads were aligned to the reference genome using BWA mem v0.7.12.
All peak calling was performed with MACS2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

source_name: HCC-PDX tumor

growth_protocol: HuH-7 cell were cultured in DMEM medium supplemented with 10% fetal bovine serumand 1% penicillin/streptomycin.Cells were kept in a humidified atmosphere (5% CO2) at 37°C.

extract_protocol:
The cells are bound to Concanavalin A-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposase precisely binds the DNA sequence near the  target protein under the antibody guidance and results in factor-targeted tagmentation.
DNA sequence is tagmented, with adapters added at the same time at both ends, which can be enriched by PCR to form the sequencing-ready libraries. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: HCC-PDX tumor

value: Human hepatocellular carcinoma

value: WT

tag: cell subtype

value: CD133-negative subpopulation obtained by MACS


title: ChIP-Seq, MCF-7, MYC, no RNase, IP, rep2


title: 4T1 cells, CHD8_KD_CHD8_IP (ChIPseq)

source_name: 4T1 cells, CHD8_KD_CHD8_IP

value: CHD8 KD


title: Cas9-sgCon-1


title: ChIP-Seq, MCF-7, MYC, no RNase, IP, rep1


title: HCC-PDX tumor, CD133 negative, H3K4me3

value: CD133-positive subpopulation obtained by MACS


title: ChIP-Seq, MCF-7, no RNase, input, rep2


title: HuH7 cells, CD133 positive, H3K4me3

value: CD133-negative subpopulation obtained by FACS


title: 4T1 cells, 11A_KD_CHD8_IP (ChIPseq)

source_name: 4T1 cells, 11A_KD_CHD8_IP

value: 11A KD


title: 4T1 cells, CHD8_KD_11A_IP (ChIPseq)

source_name: 4T1 cells, CHD8_KD_11A_IP


title: ChIP-Seq, MCF-7, no RNase, input, rep1


title: HuH7 cells, CD133 negative, H3K4me3

value: CD133-positive subpopulation obtained by FACS


title: Balb/c mice,Lung tissue,IAV-infection,day10,biol rep 6

city: chengdu

first: HUAN

last: LEI

state: Sichuan

address: No.1166 Liutai Avenue, Wenjiang District, Chengdu

institute: Chengdu university of traditional Chinese medicine

description:
Library name: M1006
model

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: lung tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction of sequencing libraries
RNA lilbraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: lung tissue

value: Alveolar Type I Cells


title: Balb/c mice,Lung tissue,IAV-infection,day10,biol rep 4

description:
Library name: M1004
model


title: 4T1 cells, 11A_KD_11A_IP (ChIPseq)

source_name: 4T1 cells, 11A_KD_11A_IP


title: 786-O HA-HLF input Rep2

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

description: Library name: 786-O_HA_HLF_input_Rep2

data_processing:
The data was analyzed as described previously (https://doi.org/10.1016/j.molcel.2020.01.009). GSEA analysis and GO analysis were performed by using the WebGestalt (WEB-based Gene SeT AnaLysis Toolkit).
Peaks were called using MACS2, under default settings and using the -f BAM flag. MACS2 was run twice, once for were each replicate of HA-HLF. However, each HA-HLF MACS2 calls used both input samples as the control in the -c flag.
Assembly: hg19
Supplementary files format and content: BigWig files show the genome-wide, read-depth normalized signal from each replicate across all ChIP-seq samples
Supplementary files format and content: narrowPeak files contain the MACS2 callpeak output from each HA-HLF replicate using both input replicates as control.

growth_protocol: The cell lines used in this study were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM,Gibco) high glucose medium supplemented with 10% fetal bovine serum (FBS) and 1%penicillin/streptomycin unless specifically indicated. The normal kidney cell line HK-2 was grownin keratinocyte serum-free medium (K-SFM, Gibco). The PDX cell lines, acquired from Dr. James Brugarolas’s lab at UT Southwestern, were grown in DMEM high glucose supplemented with 10% FBS, 1% Pen/Strep, 1X MEM Non-essential amino acids (Gibco, 11140050), 0.01µg/ml EGF (Bio-Techne, 236-EG), and 0.4µg/ml Hydrocortisone (STEMCELL, 07925). All cells werecultured in a humidified incubator at 37°C with 5% CO2. All cells were tested negative for mycoplasma by using the mycoplasma detection kit (Lonza, LT07–218) or mycoplasmaelimination reagent-plasmocin (Invivogen, ant-mpt).

extract_protocol:
Samples were then lysed in lysis buffer (10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton x-100) and sonicated by using the BioRuptor. Dynabeads were incubated with FLAG or HA antibody at 4°C overnight with rotation, followed by incubation with sonicated samples overnight. Then the samples were washed and collected by applying a magnetic stand, eluted and reverse crosslinked. RNase A (sigma, 70856-3) was used for RNA degradation, and Proteinase K (sigma, 3115828001) was used for protein degradation. DNA was purified by using Qiagen PCR purification kit (Qiagen, 28106).
DNA libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), followed by followed by sequencing at the CRI’s Sequencing Facility at UT Southwestern.

tag: hlf status


title: Balb/c mice,Lung tissue,IAV-infection,day10,biol rep 5

description:
Library name: M1005
model


title: Xenograft harvested from mice treated with PT2399 at ZT12 3

city: SAN DIEGO

first: Rebecca

last: Mello

address: 11093 CLAIREMONT MESA BLVD

institute: The Scripps Research Institute

description:
Library name: ZT12_PT2399_3
sample17_combined

data_processing:
STAR alignment with SeqMan NGen 17
Counts table with ArrayStar 17
DESeq2 using GenePattern online tool
Assembly: hg38
Supplementary files format and content: normalized counts output by DESeq2 where drug treatment defined the grounps and time of drug treatment was the confounding variable

source_name: cell line derived xenograft tumor

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium + 10% fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin (Gibco), and maintained in an atmosphere containing 5% CO2 at 37°C.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN #74104) and QIAshredder (QIAGEN #79654)
DNBSEQ stranded mRNA library by BGI

value: cell line derived xenograft tumor

value: Adenocarcinoma; Renal Cell


title: 4T1 cells, control_CHD8_IP (ChIPseq)

source_name: 4T1 cells, control_CHD8_IP

value: control


title: 786-O HA-HLF input Rep1

description: Library name: 786-O_HA_HLF_input_Rep1


title: 4T1 cells, control_11A_IP (ChIPseq)

source_name: 4T1 cells, control_11A_IP


title: Balb/c mice,Lung tissue,IAV-infection,day10,biol rep 3

description:
Library name: M1003
model


title: Xenograft harvested from mice treated with PT2399 at ZT12 1

description:
Library name: ZT12_PT2399_1
sample15_combined


title: Balb/c mice,Lung tissue,IAV-infection,day10,biol rep 2

description:
Library name: M1002
model


title: Xenograft harvested from mice treated with vehicle control at ZT12 4

description:
Library name: ZT12_VC_4
sample14_combined

value: vehicle control


title: 786-O HA-HLF ChIP Rep2

description: Library name: 786-O_HA_HLF_ChIP_Rep2


title: 4T1 cells, CHD8_rep2 (ATACseq)

data_processing:
Quality checks were performed using FastQC (v0.11.8), summarized with MultiQC (v1.9). Reads trimming was performed using cutadapt (v2.10) then subsampled. Alignment to the mouse reference genome (build GRCm38.100) was performed using STAR (v2.7.0a) with default parameters. Peaks were called using macs2 (v2.2.7.1) using default parameters. Density plots, boxplots, MA plots, and PCA were performed as further quality checks.
Peaks were matched between samples if the midpoint of a peak in each sample was within the peak in the other sample. Bigwig files were produced for each sample using bamCompare 3.4.1 and amplitudes for peaks in each sample were calculated using pyBigWig (v0.3.17). The resulting amplitudes were normalised using quantile normalisation and noise was removed using noisyR [Moutsopoulos2021].
Differential expression analysis was performed using edgeR (v3.28.1) [Robinson2010].
Genome_build: mm10 (GRCm38.100)
Supplementary_files_format_and_content: peak bed files

extract_protocol:
ATACseq assay were performed using Illumina kits. Briefly, a homogenous cell pellet was lysed and resuspended in a transposition mix. The samples were then incubated at 37deg for 30mins and then purified using the Qiagen MinElute PCR Purification Kit. Eluted sample were then processed for library prep and sequencing.
Libraries were prepared using the PCR steps (12 cycles) in the Illumina Nextera DNA library preparation kit. The pool was run as a PE150 run type on one lane of a HiSeq 4000.
ATACseq, PE150


title: Balb/c mice,Lung tissue,IAV-infection,day10,biol rep 1

description:
Library name: M1001
model


title: 786-O HA-HLF ChIP Rep1

description: Library name: 786-O_HA_HLF_ChIP_Rep1


title: 4T1 cells, CHD8_rep1 (ATACseq)


title: Xenograft harvested from mice treated with vehicle control at ZT12 3

description:
Library name: ZT12_VC_3
sample13_combined


title: Stem cell-derived alpha cells treated with tunicamycin, biological replicate 6

city: Rochester

first: Quinn

last: Peterson

state: MN

address: 150 3rd St SW

institute: Mayo Clinic

description:
Library name: ER-stress 6
Column name in All_Samples_Raw_Countmatrix.csv: ER-stress 6

data_processing:
Adapter content was trimmed using cutadapt (v4.4).
Trimmed sequencing reads were mapped to the GRCh38 human reference genome with HISAT2 (v2.1.0).
Aligned sequencing reads were counted using featureCounts (v2.0.6).
Assembly: GRCh38
Supplementary files format and content: .csv file with raw counts for each sample

growth_protocol: Human pluripotent stem cells were differentiated into stem cell-derived pancreatic alpha cells following the protocol from Peterson, et. al., Nature Communications, 2020.

extract_protocol:
The Qiagen RNeasy Mini Kit was used to isolate total RNA from the stem cell-derived alpha cells.
The NEBNext Ultra II RNA Library Prep for Illumina was used to prepare RNA sequencing libraries.

treatment_protocol: Vehicle samples were treated with DMSO vehicle and ER-stress samples were treated with 5 uM tunicamycin.

value: Tunicamycin (5 uM)

tag: batch


title: Balb/c mice,Lung tissue,Vehicle,day10,biol rep 6

description:
Library name: K1006
vehicle


title: Xenograft harvested from mice treated with vehicle control at ZT12 2

description:
Library name: ZT12_VC_2
sample12_combined


title: 4T1 cells, 11A_rep2 (ATACseq)


title: Stem cell-derived alpha cells treated with DMSO vehicle, biological replicate 6

description:
Library name: Vehicle 6
Column name in All_Samples_Raw_Countmatrix.csv: Vehicle 6

value: stem cell-derived pancreatic alpha cells

value: DMSO


title: Balb/c mice,Lung tissue,Vehicle,day10,biol rep 4

description:
Library name: K1004
vehicle


title: Balb/c mice,Lung tissue,Vehicle,day10,biol rep 5

description:
Library name: K1005
vehicle


title: Stem cell-derived alpha cells treated with tunicamycin, biological replicate 5

description:
Library name: ER-stress 5
Column name in All_Samples_Raw_Countmatrix.csv: ER-stress 5


title: Xenograft harvested from mice treated with vehicle control at ZT12 1

description:
Library name: ZT12_VC_1
sample11_combined


title: 4T1 cells, 11A_rep1 (ATACseq)


title: 4T1 cells, control_rep2 (ATACseq)

source_name: control


title: Xenograft harvested from mice treated with PT2399 at ZT0 5

description:
Library name: ZT0_PT2399_5
sample10_combined


title: Xenograft harvested from mice treated with PT2399 at ZT12 2

description:
Library name: ZT12_PT2399_2
sample16_combined


title: Balb/c mice,Lung tissue,Vehicle,day10,biol rep 3

description:
Library name: K1003
vehicle


title: 4T1 cells, control_rep1 (ATACseq)


title: Xenograft harvested from mice treated with PT2399 at ZT0 4

description:
Library name: ZT0_PT2399_4
sample9_combined


title: Stem cell-derived alpha cells treated with tunicamycin, biological replicate 4

description:
Library name: ER-stress 4
Column name in All_Samples_Raw_Countmatrix.csv: ER-stress 4


title: Balb/c mice,Lung tissue,Vehicle,day10,biol rep 2

description:
Library name: K1002
vehicle


title: Stem cell-derived alpha cells treated with DMSO vehicle, biological replicate 5

description:
Library name: Vehicle 5
Column name in All_Samples_Raw_Countmatrix.csv: Vehicle 5


title: SC-A Replicate 3

description: Library name: 061020_A

library_source: transcriptomic single cell

data_processing:
Data demultiplexing, barcode processing, and gene counting was performed using CellRanger version 4.0.0.
Assembly: GRCh38
Supplementary files format and content: Tab separated values (.tsv) files and matrix (.mtx) files

source_name: Cell Culture

growth_protocol: Human pluripotent stem cells were differentiated into SC-α cells following the protocol from Peterson, et. al., 2020

extract_protocol:
Differentiated SC-α clusters were washed twice with ice cold PBS and then dispersed using TrypLE (10 minutes at 37 °C). TrypLE reaction was quenched with 2% BSA containing media and cells were centrifuged (200 xg, 5 min, 4 °C). Cells were washed with ice cold PBS, re-centrifuged, and resuspended in fresh ice cold PBS. Cells were counted and diluted to a concentration of 0.5 million cells/mL in ice cold PBS.
The 10x Genomics Single Cell 3' v3 library was constructed for according to manufacturer guidelines.

value: SC-A


title: Xenograft harvested from mice treated with PT2399 at ZT0 3

description:
Library name: ZT0_PT2399_3
sample8_combined


title: Balb/c mice,Lung tissue,Vehicle,day10,biol rep 1

description:
Library name: K1001
vehicle


title: Stem cell-derived alpha cells treated with DMSO vehicle, biological replicate 4

description:
Library name: Vehicle 4
Column name in All_Samples_Raw_Countmatrix.csv: Vehicle 4


title: Xenograft harvested from mice treated with PT2399 at ZT0 2

description:
Library name: ZT0_PT2399_2
sample7_combined


title: Stem cell-derived alpha cells treated with tunicamycin, biological replicate 3

description:
Library name: ER-stress 3
Column name in All_Samples_Raw_Countmatrix.csv: ER-stress 3


title: SC-A Replicate 1

description: Library name: 021020_A


title: Balb/c mice,Lung tissue,IAV-infection,day8,biol rep 6

description:
Library name: M806
model


title: Xenograft harvested from mice treated with PT2399 at ZT0 1

description:
Library name: ZT0_PT2399_1
sample6_combined


title: Stem cell-derived alpha cells treated with DMSO vehicle, biological replicate 3

description:
Library name: Vehicle 3
Column name in All_Samples_Raw_Countmatrix.csv: Vehicle 3


title: Stem cell-derived alpha cells treated with tunicamycin, biological replicate 2

description:
Library name: ER-stress 2
Column name in All_Samples_Raw_Countmatrix.csv: ER-stress 2


title: Xenograft harvested from mice treated with vehicle control at ZT0 5

description:
Library name: ZT0_VC_5
sample5_combined


title: 143B cells, sgaELMSAN1 -2

city: Boston

first: Ting

last: Zhao

state: MA

address: 185 Cambridge st, Simches Building, CPZN4400

institute: MGH

description:
TZ8
RNA-seq raw count_ELMSAN1-OE and KD.csv

data_processing:
RNA-seq reads were mapped to the hg19 reference genome using STAR v. 2.7.3a. Read counts for individual genes were produced using count feature in HTSeq v. 0.6.0
Assembly: hg19
Supplementary files format and content: genes based raw counts of sequencing reads  were prepeared using htseq

source_name: 143B cells

extract_protocol:
Total RNA was isolated using Direct-zol RNA MiniPrep Kit. mRNA was purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module.
Libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: 143B cells

value: ELMSAN1 overexpression


title: Balb/c mice,Lung tissue,IAV-infection,day8,biol rep 4

description:
Library name: M804
model


title: Xenograft harvested from mice treated with vehicle control at ZT0 4

description:
Library name: ZT0_VC_4
sample4_combined


title: Stem cell-derived alpha cells treated with DMSO vehicle, biological replicate 2

description:
Library name: Vehicle 2
Column name in All_Samples_Raw_Countmatrix.csv: Vehicle 2


title: 143B cells, sgGal4 -2

description:
TZ6
RNA-seq raw count_ELMSAN1-OE and KD.csv

value: control (overexpression)


title: Xenograft harvested from mice treated with vehicle control at ZT0 3

description:
Library name: ZT0_VC_3
sample3_combined


title: 143B cells, sgaELMSAN1 -1

description:
TZ7
RNA-seq raw count_ELMSAN1-OE and KD.csv


title: Stem cell-derived alpha cells treated with tunicamycin, biological replicate 1

description:
Library name: ER-stress 1
Column name in All_Samples_Raw_Countmatrix.csv: ER-stress 1


title: Balb/c mice,Lung tissue,IAV-infection,day8,biol rep 2

description:
Library name: M802
model


title: 143B cells, sgGal4 -1

description:
TZ5
RNA-seq raw count_ELMSAN1-OE and KD.csv


title: Balb/c mice,Lung tissue,IAV-infection,day8,biol rep 1

description:
Library name: M801
model


title: Stem cell-derived alpha cells treated with DMSO vehicle, biological replicate 1

description:
Library name: Vehicle 1
Column name in All_Samples_Raw_Countmatrix.csv: Vehicle 1


title: 143B cells, shRenilla -2

description:
TZ2
RNA-seq raw count_ELMSAN1-OE and KD.csv

value: control (knockdown)


title: Xenograft harvested from mice treated with vehicle control at ZT0 1

description:
Library name: ZT0_VC_1
sample1_combined


title: ESCC, T4-4

city: Hong Kong

first: Xin

middle: Yuan

last: Guan

state: -- Country other than USA or Canada --

address: Room L10-56, 10/F, Laboratory Block, 21 Sassoon Road, Hong Kong

department: Department of Clinical Oncology

institute: The University of Hong Kong

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

data_processing:
Beginning with raw base call (BCL) files generated by Illumina HiSeq X Ten system, CellRanger-4.0.0 package with “cellranger mkfastq” commend was used to demultiplex the BCLs files to generate raw FASTQs. By using “cellranger count” commend, raw FASTQs files was aligned to the human reference genome (build GRCh38), filtered, barcode counted and UMI counted to generate single cell gene expression profile. To remove the bias, the “cellranger aggr” commend was used to aggregate the gene expression count of all samples from “cellranger count” to normalize those counts to the same sequencing depth and then to recompute the feature-barcode single cell gene expression matrices.
The output from “cellranger aggr” was converted to a Seurat object using the R Seurat package (version 4.0.1) for downstream analysis.
We applied Single-Cell Remover of Doubelts (Scrublet) with default parameters to infer and remove cell doublets in each sample individually.
To remove low quality cells, we have visualized the various metrics distribution of our data and applied the following thresholds: nUMI >= 300, nGene >= 200, log10GenesPerUMI > 0.8 and mitoRatio < 0.2.
To avoid the reduction of average expression for a cell caused by genes with zero count or only expressed in a handful of cells, we keep only genes which are expressed in 10 or more cells. The remaining expression matrix was normalized to account for differences in sequencing depth per cell for each sample with “NormalizeData” function in Seurat package. By regressing out cell-cycle phage (S, G2/M) scores, mitochondrial expression with CellCycleScoring and SCTransform function in Seurat package, the normalized matrix was further scaled to eliminate cell-cycle and mitochondrial effects and to generate a final single cell gene expression matrix with high quality.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: The primary tumor site of esophageal carcinoma

extract_protocol:
The fresh tissue samples endoscopic biopsied from ESCC patients were rinsed with PBS on ice.
The Gel Bead & Multiplex Kit and Chip Kit (10× Genomics, Pleasanton, CA, USA) was used to construct a chromium single-cell 3′-library according to the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq X Ten system, and mapped to the human reference genome (build GRCh38) using CellRanger-4.0.0 (10× Genomics)

tag: patient id

tag: disease state

value: ESCC

value: Esophageal Carcinoma

value: No


title: Xenograft harvested from mice treated with vehicle control at ZT0 2

description:
Library name: ZT0_VC_2
sample2_combined


title: 143B cells, shRenilla -1

description:
TZ1
RNA-seq raw count_ELMSAN1-OE and KD.csv


title: ESCC, T4-3

value: The primary tumor site of esophageal carcinoma


title: SC-A Replicate 2

description: Library name: 042721_A


title: ESCC, T4-2


title: Balb/c mice,Lung tissue,IAV-infection,day8,biol rep 5

description:
Library name: M805
model

value: lung tissue

value: Alveolar Type I Cells


title: Balb/c mice,Lung tissue,Vehicle,day8,biol rep 4

description:
Library name: K804
vehicle


title: HW4, hindlimb, interdigital webbing between digit IV and digit V

city: Shenyang

first: Bai

last: Shibin

address: 120 Dongling Road

institute: Shenyang Agriculture University

description:
Library name: Sample8
wild type

data_processing:
Reads were mapped to the Ensemble Chines soft-shell turtle genome assembly (PelSin_1.0) using HISAT2 version 2.2.1.
Transcript assembly by StringTie v2.1.7
Use prepDE.py3 script of StringTie to get raw counts and TPM counts
Assembly: Pelodiscus_sinensis.PelSin_1.0.113.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM counts for each Sample

organism: Pelodiscus sinensis

source_name: hindlimb interdigital webbing

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen, Hilden, Germany), with on-column DNase to remove contaminating genomic DNA. RNA concentration and purity were measured using NanoDrop 2000. (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: hindlimb interdigital webbing

value: anti-ICD


title: HW3, hindlimb, interdigital webbing between digit III and digit IV

description:
Library name: Sample7
wild type


title: ESCC, T4-1


title: Balb/c mice,Lung tissue,IAV-infection,day8,biol rep 3

description:
Library name: M803
model


title: Balb/c mice,Lung tissue,Vehicle,day8,biol rep 3

description:
Library name: K803
vehicle


title: ESCC, T3


title: HW1, hindlimb, interdigital webbing between digit I and digit II

description:
Library name: Sample5
wild type


title: Brain_AD_4_rep1

type: RNA

first: Ami

last: Kobayashi

address: 60 Fenwood Rd

department: Neurology

institute: Brigham & Women's Hospital

hyb_protocol: The labeled RNA was hybridized onto Arraystar Human small RNA Microarray (8x15K, Arraystar) .

scan_protocol: The array was scanned by an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: brain, frozen tissue

label_protocol: 100 ng total RNA was firstly dephosphorylated to form the 3-OH end. The 3-OH ended RNA was then denatured by DMSO and enzymatically labeled with Cy3.

extract_protocol: Total RNA was extracted from tissues using Trizol (Invitrogen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Temporal cortex

tag: gender

value: Female


title: ESCC, T2


title: Balb/c mice,Lung tissue,Vehicle,day8,biol rep 1

description:
Library name: K801
vehicle


title: Balb/c mice,Lung tissue,Vehicle,day8,biol rep 6

description:
Library name: K806
vehicle


title: Brain_AD_3_rep1

value: Male


title: ESCC, T1


title: FW3, forelimb, interdigital webbing between digit III and digit IV

description:
Library name: Sample3
wild type

source_name: forelimb interdigital webbing

value: forelimb interdigital webbing

value: ICD


title: Balb/c mice,Lung tissue,Vehicle,day8,biol rep 5

description:
Library name: K805
vehicle


title: ESCC, N4-4

source_name: Normal tissue adjacent to the primary tumor of esophageal carcinoma


title: FW2, forelimb, interdigital webbing between digit II and digit III

description:
Library name: Sample2
wild type


title: Brain_AD_5_rep1


title: Brain_AD_1_rep1


title: Balb/c mice,Lung tissue,IAV-infection,day6,biol rep 5

description:
Library name: M605
model


title: Balb/c mice,Lung tissue,IAV-infection,day6,biol rep 4

description:
Library name: M604
model


title: ESCC, N4-3

value: Normal tissue adjacent to the primary tumor of esophageal carcinoma


title: Brain_Control_5_rep1


title: ESCC, N4-2


title: HW2, hindlimb, interdigital webbing between digit II and digit III

description:
Library name: Sample6
wild type


title: Balb/c mice,Lung tissue,Vehicle,day8,biol rep 2

description:
Library name: K802
vehicle


title: Balb/c mice,Lung tissue,IAV-infection,day6,biol rep 3

description:
Library name: M603
model


title: SCOP3

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

data_processing:
The completed libraries were qualified with Agilent 2100 Bioanalyzer and sequenced on DNBSEQ platform. Quality control (QC) is then performed on the raw reads with SOAPnuke.
The clean reads were aligned to the reference gene sequence (GRCm38.p6) by Bowtie2. Then, RSEM was used to calculate the gene expression level of each sample. Differentially expressed genes were calculated with R package DESeq2.
Assembly: Genome_build: GRCm38.p6
Supplementary files format and content: Excel include FPKM and count values for each gene and each sample

source_name: Lacrimal gland

extract_protocol: 1~2 μg total RNA was used to prepare the sequencing library. mRNA was enriched by oligo(dT) magnetic beads. RNA-seq library preparation using Hieff NGS C102P1 Ultima Dual-mode mRNA Kit (YEASEN).

treatment_protocol: Control: mice received no treatment  SCOP: The female C57/BL6J mice were injected with scopolamine hydrobromide three times a day and placed in an air-drying device for 7 consecutive days.  OHDA: Scopolamine injection is considered day 0, 6-OHDA injections were performed daily for 4 days firstly (from -6 to -3 day), then every three day (from -3 to 7 day) during the treatment.

value: Lacrimal gland

tag: age

value: 10 to 12 weeks old

value: injected with SCOP


title: ESCC, N4-1

value: ESCC

tag: tissue


title: Brain_Control_4_rep1


title: Brain_Control_3_rep1


title: Brain_AD_2_rep1


title: Brain_Control_2_rep1


title: Brain_Control_1_rep1


title: OHDA2

value: injected with SCOP and 6-OHDA


title: Balb/c mice,Lung tissue,Vehicle,day6,biol rep 5

description:
Library name: K605
vehicle


title: FW4, forelimb, interdigital webbing between digit IV and digit V

description:
Library name: Sample4
wild type


title: ESCC, N3

value: Esophageal Carcinoma

value: No


title: ESCC, N1


title: Balb/c mice,Lung tissue,IAV-infection,day6,biol rep 6

description:
Library name: M606
model

value: lung tissue


title: ESCC, N2


title: Balb/c mice,Lung tissue,IAV-infection,day6,biol rep 1

description:
Library name: M601
model

value: Alveolar Type I Cells


title: SynNotch (+)GFP 4

city: Nashville

first: Jonathan

last: Brunger

state: Tennessee

address: 2400 Highland Ave

institute: Vanderbilt University

description: Library name: 11476-CH-0016

data_processing:
Novaseq X series PE150 sequencing; raw sequencing reads were demultiplexed and converted to FASTQ format
Assembly: Reads were aligned to the human reference genome (Feb. 2022 GRCh38.p14) using HISAT2 (v2.2.1) with default parameters. Gene expression levels were quantified using featureCounts (v2.0.1) within the Subread package. Differential expression analysis was performed using EdgeR (v3.34.0) and limma (v3.46.0) R packages.
Supplementary files format and content: Normalization of gene expression data was performed using the trimmed mean of M-values method implemented in EdgeR, followed by log-transformation for downstream analysis. Genes with a count per million >4 in at least one sample were retained for analysis, and differential expression was identified using a false discovery rate threshold of <0.05. Functional enrichment analysis was conducted using the WEB-based Gene Set Analysis Toolkit (WebGestalt).

extract_protocol:
mRNA was prepared using the PureLink™ RNA Mini Kit (ThermoFisher Scientific 12183018A)
Stranded mRNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit according to the manufacturer's protocol. Libraries were then QC-checked and submitted for sequencing

tag: cell line

value: hESC


title: Balb/c mice,Lung tissue,Vehicle,day6,biol rep 6

description:
Library name: K606
vehicle

tag: cell type


title: SCOP2


title: SCOP1


title: SynNotch (+)GFP 3

description: Library name: 11476-CH-0015


title: ESCC, L4-4

source_name: Normal lymph node site of esophageal carcinoma


title: ESCC, L4-3

value: Normal lymph node site of esophageal carcinoma


title: OHDA1


title: SynNotch (-)GFP 4

description: Library name: 11476-CH-0012


title: FW1, forelimb, interdigital webbing between digit I and digit II

description:
Library name: Sample1
wild type

tag: genotype


title: Control3

value: no treatment


title: SynNotch (+)GFP 1

description: Library name: 11476-CH-0013


title: OHDA3


title: SynNotch (-)GFP 3

description: Library name: 11476-CH-0011


title: Balb/c mice,Lung tissue,Vehicle,day6,biol rep 2

description:
Library name: K602
vehicle


title: Balb/c mice,Lung tissue,IAV-infection,day6,biol rep 2

description:
Library name: M602
model


title: SynNotch (+)GFP 2

description: Library name: 11476-CH-0014


title: SynNotch (-)GFP 2

description: Library name: 11476-CH-0010


title: Control2


title: Balb/c mice,Lung tissue,Vehicle,day6,biol rep 4

description:
Library name: K604
vehicle


title: ESCC, L4-1


title: Balb/c mice,Lung tissue,IAV-infection,day4,biol rep 6

description:
Library name: M406
model


title: SynNotch (-)GFP 1

description: Library name: 11476-CH-0009


title: ESCC, L2

source_name: Metastatic lymph node site of esophageal carcinoma


title: Balb/c mice,Lung tissue,Vehicle,day6,biol rep 3

description:
Library name: K603
vehicle


title: ESCC, L3

value: Metastatic lymph node site of esophageal carcinoma


title: WT (+)SHH 2

description: Library name: 11476-CH-0006


title: Control1


title: Balb/c mice,Lung tissue,IAV-infection,day4,biol rep 4

description:
Library name: M404
model


title: KT3

last: Liu

description: CD163-/-TAC heart

data_processing:
The data generated from BGI platform were used for bioinformatics analysis. All of the  analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology.  The major software and parameters are as follows
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis  step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a  string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N  (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain  clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2  software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.

source_name: heart

growth_protocol: Cd163−/− mice on a C57BL/6J genetic background were generated as our previous report 19. WT and Cd163−/− male mice were housed in specific pathogen free facilities on a 12 h light/dark cycle at 22–23°C in Xiamen University. All experiments were conducted in accordance with the National Institutes of Health guidelines for the Care and Use Laboratory Animal, and the protocol were approved by Animal Care and Protection Committee of Xiamen University (Protocol No. XMULAC20200150).

extract_protocol:
Total RNA was extracted from the heart tissue using TRIzol® Reagent according the  manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280  absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA  was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only  qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China)  following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo  (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated  temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs  were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA  fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I,  RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapterligated  for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR  amplification. PCR products were purified (AMPure XP system) and library quality was assessed on  an Agilent Bioanalyzer 4150 system. Finally, the library preparations were sequenced on an  MGISEQ-T7  and 150 bp paired-end reads were generated.

treatment_protocol: 8-week-old male mice were anesthetized with 2% isoflurane and incubated with 0.5–1 L/min oxygen mixed with 1.5–2% isoflurane during surgery. The transverse aorta was exposed and tied with a 27-gauge blunt needle by 6-0 silk string. The needle was removed later. The chest and skin were closed, and mice were allowed to recover from anesthesia. Sham surgery was carried out as above without aortic ligation

value: heart

value: TAC


title: RNA-seq of mus musculus: mouse brain cortex, CKO1-8

city: Beijing

first: Xing-jun

last: Chen

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

institute: Chinese Institute for Brain Research, Beijing(CIBR)

description: Library name: XG8_CKO

data_processing:
RNA-seq
RNA-seq raw data were initially filtered with “FastQC” to obtain clean data after quality control. Clean data were aligned to the reference genome (Version: GRCm38) downloaded from Gencode by HISAT. Raw counts for each gene were calculated by FeatureCounts.
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
The heat map was generated by heatmap with the z-score of each gene. Gene Set Enrichment Analysis (GSEA) was performed using the ClusterProfiler package in R, with an adjusted p-value less than 0.05
Assembly: Hisat2 GRCm38
Supplementary files format and content: Deseq2 normalized count, XG_Tak1_cKO_raw_counts_diff_combined-RNA-seq.xlsx

source_name: Brain, P90

extract_protocol:
Total RNA was extracted fromcerebral cortex using RNeasy Micro Kit (Qiagen, 74104) following the manufacturer's protocol
DNA library for sequencing was prepared following the protocol of DNA SMART ChIP Seq Kit (TAKARA #101617)

value: Brain, P90

value: Tamoxifen


title: WT (+)SHH 3

description: Library name: 11476-CH-0007


title: Balb/c mice,Lung tissue,Vehicle,day6,biol rep 1

description:
Library name: K601
vehicle

source_name: lung tissue


title: KT5

description: CD163-/-TAC heart


title: WT (+)SHH 4

description: Library name: 11476-CH-0008


title: WT (+)SHH 1

description: Library name: 11476-CH-0005


title: ESCC, L4-2


title: KS3

description: CD163-/- sham heart

value: sham


title: RNA-seq of mus musculus: mouse brain cortex, CKO1-7

description: Library name: XG7_CKO


title: KT1

description: CD163-/-TAC heart


title: Balb/c mice,Lung tissue,IAV-infection,day4,biol rep 5

description:
Library name: M405
model


title: Balb/c mice,Lung tissue,IAV-infection,day4,biol rep 2

description:
Library name: M402
model


title: KS2

description: CD163-/- sham heart


title: Balb/c mice,Lung tissue,IAV-infection,day4,biol rep 3

description:
Library name: M403
model


title: WT (-)SHH 4

description: Library name: 11476-CH-0004


title: KS1

description: CD163-/- sham heart


title: RNA-seq of mus musculus: mouse brain cortex, CKO1-6

description: Library name: XG6_CKO


title: WT (-)SHH 3

description: Library name: 11476-CH-0003


title: ESCC, L1


title: Balb/c mice,Lung tissue,Vehicle,day4,biol rep 6

description:
Library name: K406
vehicle


title: WT5

description: c57bl6j TAC heart

value: WT


title: WT (-)SHH 2

description: Library name: 11476-CH-0002


title: RNA-seq of mus musculus: mouse brain cortex, Ctrl1-4

description: Library name: XG4_Ctrl


title: Balb/c mice,Lung tissue,Vehicle,day4,biol rep 4

description:
Library name: K404
vehicle


title: RNA-seq of mus musculus: mouse brain cortex, Ctrl1-3

description: Library name: XG3_Ctrl


title: WT (-)SHH 1

description: Library name: 11476-CH-0001


title: Balb/c mice,Lung tissue,Vehicle,day4,biol rep 5

description:
Library name: K405
vehicle


title: WT3

description: c57bl6j TAC heart


title: RNA-seq of mus musculus: mouse brain cortex, Ctrl1-2

description: Library name: XG2_Ctrl


title: WS3

description: c57bl6j sham heart


title: siB AAI_rep3

description:
Library name: A12
A12

data_processing:
fastq files were aligned and transcript counts performed using https://maayanlab.cloud/biojupies/
Assembly: hg38
Supplementary files format and content: A txt file containing log CPM values

extract_protocol:
Trizol
Messenger RNA 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, size selection, amplification, and purification.

treatment_protocol: 25uM AAI dissolved in DMSO or equivalent volume of DMSO for 24 hours, with simultaneous transfection of SCR or siB Trilencer-27 siRNA duplex.

value: kidney

value: DMSO


title: WT1

description: c57bl6j TAC heart


title: RNA-seq of mus musculus: mouse brain cortex, Ctrl1-1

description: Library name: XG1_Ctrl


title: siB AAI_rep2

description:
Library name: A11
A11


title: Balb/c mice,Lung tissue,Vehicle,day4,biol rep 3

description:
Library name: K403
vehicle


title: siB AAI_rep1

description:
Library name: A10
A10


title: SCR AAI_rep3

description:
Library name: A9
A9


title: Balb/c mice,Lung tissue,IAV-infection,day4,biol rep 1

description:
Library name: M401
model


title: Balb/c mice,Lung tissue,Vehicle,day4,biol rep 1

description:
Library name: K401
vehicle


title: WS2

description: c57bl6j sham heart


title: WS1

description: c57bl6j sham heart


title: CckGFP small intestine and nodose neurons

city: DURHAM

first: Diego

middle: V.

last: Bohórquez

state: North Carolina

address: 203 RESEARCH DR, Room 221

department: Medicine

institute: Duke University

description:
Library name: CckGFP
SCRB-Seq

data_processing:
Pairwise comparisons between genes from the PyyGFP+ and PyyGFP- groups were made using DESeq2.
Assembly: STAR was used with the mm10 mouse reference genome to align reads, and counts tables were generated using featureCounts.
Supplementary files format and content: csv files include counts for each dataset (Cck or Pyy)

source_name: proximal 1/3 small intestine, vagal nodose neurons

extract_protocol:
RNA was extracted from single cell suspensions using Single Cell RNA Purification Kit (Norgen).
All samples were assessed with a Bioanalyzer (Agilent), and only samples with RIN scores > 8.0 were used for downstream analysis. Given the rarity of the cells, SCRB-seq was used to generate libraries. Libraries were sequenced on an Illumina NextSeq 500.

value: small intestinal epithelial, neuron

value: CckGFP


title: Pero-Media-M2

first: Jeffrey

last: Bourgeois

address: 136 Harrison Ave

institute: Tufts University

description: Library name: Pero-Media-M2

data_processing:
All analyses were performed separately for P. leucopus and M. musculus. Published P. leucopus (GCF_004664715.2) and Mus musculus M. musculus (GRCm39) genomes were used for read mapping using STAR version 2.6.1. Gene expression was summarized using RSEM version 1.3.1. Annotations were based on the NCBI annotated genes. All differential gene expression analyses were performed with R (version 4.3.1) using DESeq2 version 1.40.2 using standard parameters. Only genes with ≥10 reads across all conditions (summed) were included in the analysis. Differential gene expression, modeling gene ~ condition, was determined using DESeq2—where the condition term differentiated macrophages based on mock treatment, treatment with LPS, or B. burgdorferi infection. Corrected p-values were generated using a Wald test and a Nejamini-Hochberg calculated false discovery rate.
Assembly: P. leucopus GCF_004664715.2; M. musculus GRCm39
Supplementary files format and content: Each individual sample's processed file includes a data table containing the gene_id, transcript id(s), transcript length, effective length, expected_count (aka raw count), TPM (transcripts per million), and FPKM (fragments per kilobase of transcript per million mapped reads)
Supplementary files format and content: B6_TPM.csv and Pero_TPM.csv contain the transcripts per million for each sample within each species

organism: Peromyscus leucopus

source_name: Bone marrow derived macrophages

growth_protocol: These bones were individually placed in needle-perforated PCR tubes within 1.7 mL Eppendorf tubes with ~900 mL of DMEM and pulse spun at a maximum force of 350xg to remove the marrow from the bones. These pellets of bone marrow were resuspended and combined before differentiation in media specific to each rodent species.  To generate M. musculus differentiation medium, L-929 cells were cultured for two passages. During the third passage the L-929 culture was allowed to reach >80% confluency, and two days after achieving 80% density the cell culture supernatant was collected and frozen at -20°C for later use as conditioned media for murine BMDM differentiation. Bone marrow from C57BL/6J M. musculus was differentiated in DMEM supplemented with 30% L-929 cell supernatant and 20% heat inactivated FBS in 100 x 15 mm2 sterile dishes or in 6-well plates. Alternative differentiation was carried out with 20 ng/mL recombinant murine MCSF in DMEM + 20% FBS.  To generate P. leucopus M-CSF, transduced HEK293T cells were passaged to approximately 50% confluence in the presence of 1ug/mL puromycin and allowed to reach 80% confluency. The culture was continued for two additional days and supernatant was collected, filtered through a 0.22 um PES syringe filter, and stored at -20C for use in BMDM differentiation. Bone marrow from P. leucopus was differentiated in DMEM supplemented with 30% HEK293TM-CSF cell supernatant and 20% heat inactivated FBS in 100 x 15 mm2 sterile dishes or in 6-well plates.  For both species, 1 x 106 cells were plated in 100 x 15 mm dishes with 10 mL of differentiation media, and 1 x 106 cells in 12 mL differentiation media in 6-well plates with 2 mL per well. Cells were supplemented with an additional 0.5 volumes of their original plating at days two days and four of differentiation. On day six of differentiation, cells were lifted via cell-scraper, counted with Countess III (ThermoFisher), and resuspended at the desired density for subsequent experiments in DMEM + 10% FBS. During differentiation, phase contrast microscopy images were captured on days zero, three, and six of differentiation in order to track cell morphology changes.

extract_protocol:
Samples were thawed, pelleted at 500xg, and lysed in 700µL QIAzol. RNA was extracted using the miRNAeasy isolation kit (Qiagen). DNA was depleted using TURBO DNase (Invitrogen AM2238). DNase was removed and samples were concentrated using the Monarch® Spin RNA Cleanup Kit (New England Biolabs T2050S).
Samples were submitted to Azenta Life Sciences/Genewiz for RNA quality assessment, library preparation, and sequencing (Illumina NovaSeqX+ 2x150bp). Ribosomal RNA were depleted by polyA enrichment.

treatment_protocol: Differentiated, lifted macrophages were plated into 6-well plates at 1.0 x 106 cells per well (5.0 x 105 cells/mL) and allowed to adhere overnight at 37°C, 5% CO2. The following day the cells were stimulated with B. burgdorferi B31, MOI 100 or 100 ng/mL S. enterica serovar Minnesota LPS (Invivogen tlrl-smlps) for 10 hours at 37°C, 5% CO2. Cells were scraped, washed, and preserved in RNAlater (ThermoFisher AM7020). Samples were incubated in RNAlater overnight at 4ºC before storage at -80°C.

value: Bone marrow derived macrophages

value: Male

value: Mock (media)


title: RNA-seq of mus musculus: mouse brain cortex, CKO1-5

description: Library name: XG5_CKO


title: SCR AAI_rep2

last: Mallipattu

description:
Library name: A8
A8


title: KO podo3

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

data_processing:
The gene counts were normalized by rlog transformation and analyzed by the DeSeq2 pipeline.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

source_name: kidney

extract_protocol:
FACS sorted mouse kidney cells
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

value: podocyte

value: EMCN-/-


title: Pero-Media-F2

description: Library name: Pero-Media-F2

value: Female


title: B6-Media-F2

description: Library name: B6-Media-F2


title: SCR AAI_rep1

first: Sandeep

address: 101 Nicolls Road

description:
Library name: A7
A7


title: KO podo2


title: PyyGFP colon and dorsal root neurons

description:
Library name: PyyGFP
SCRB-Seq

source_name: colon, dorsal root neurons

value: colon, dorsal root neurons

value: colonic epithelial, neuron

value: PyyGFP


title: Pero-Media-F1

description: Library name: Pero-Media-F1


title: siB DMSO_rep3

description:
Library name: A6
A6


title: Wt podo2

value: EMCN+/+


title: Pero-LPS-F2

description: Library name: Pero-LPS-F2

value: 100ng/mL LPS


title: Pero-LPS-M2

description: Library name: Pero-LPS-M2


title: Wt podo3


title: B6-LPS-F2

description: Library name: B6-LPS-F2


title: siB DMSO_rep1

description:
Library name: A4
A4


title: B6-Media-F1

description: Library name: B6-Media-F1


title: SCR DMSO_rep3

description:
Library name: A3
A3


title: Pero-LPS-F1

description: Library name: Pero-LPS-F1


title: siB DMSO_rep2

description:
Library name: A5
A5


title: B6-LPS-F1

description: Library name: B6-LPS-F1


title: Pero-Bb-M2

description: Library name: Pero-Bb-M2

value: B. burgdorferi B31


title: KO Endo3

value: endothelium


title: SCR DMSO_rep2

description:
Library name: A2
A2

value: kidney


title: Wt Endo3


title: Balb/c mice,Lung tissue,Vehicle,day4,biol rep 2

description:
Library name: K402
vehicle

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction of sequencing libraries
RNA lilbraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: lung tissue

value: Alveolar Type I Cells


title: B6-LPS-M2

description: Library name: B6-LPS-M2


title: B6-Bb-M2

description: Library name: B6-Bb-M2


title: B6-Media-M2

description: Library name: B6-Media-M2


title: B6-Bb-F2

description: Library name: B6-Bb-F2


title: Pero-Bb-F2

description: Library name: Pero-Bb-F2


title: SCR DMSO_rep1

description:
Library name: A1
A1

value: DMSO


title: Wt Endo2


title: BMDM, hom, Sal_03

status: Public on May 07 2025

city: Philadelphia

first: Ken

last: Cadwell

address: 421 Curie Blvd

institute: Perelman School of Medicine University of Pennsylvania

data_processing:
Reads that passed FASTQC were aligned to the most recent UCSC mouse genome assembly using STAR. Raw transcript counts were extracted by FeatureCount, DEseq2 was used to generate normalized count table and  analyze differential gene expression.
Assembly: UCSC mouse genome
Supplementary files format and content: count table in excel file

source_name: Bone Marrow Derived Macrophages

extract_protocol:
Cells were collected and resuspended in 700uL of RLT buffer (Mini RNeasy Kit) and homogenized using TissueRuptor (Qiagen). RNA was then isolated using the RNeasy Mini Kit (Qiagen) as per manufacturer’s instructions, DNase treatment was performed using RNeasy DNase kit (Qiagen) and protocol
cDNA libraries were prepared with the Ovation Ultralow RNA-seq System V2 (NuGEN)

value: Bone Marrow Derived Macrophages

value: Atg16L1 A/A

value: Salmonella


title: B6-Bb-F1

description: Library name: B6-Bb-F1

value: Bone marrow derived macrophages


title: BMDM, hom, Sal_02


title: Pero-Bb-F1

description: Library name: Pero-Bb-F1


title: BMDM, hom, mock_03

value: Mock


title: BMDM, hom, Sal_01


title: KO Endo2

value: EMCN-/-


title: BMDM, hom, mock_01


title: BMDM, het, Sal_01

value: Atg16L1 T/A


title: BMDM, wt, Sal_03

value: Atg16L1 T/T


title: BMDM, wt, Sal_02


title: BMDM, het, mock_02


title: BMDM, het, mock_03


title: BMDM, wt, Sal_01


title: BMDM, wt, mock_03


title: BMDM, wt, mock_01


title: BMDM, wt, mock_02


title: BMDM, het, mock_01


title: mKate::PRG-1 (adult) - IP, replicate 2

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

description: Library name: Sample 23

library_source: other

data_processing:
Small RNA libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Sequences were parsed from adapters using FASTQ/A Clipper (options: -Q33 -l 17 -c -n -a TGGAATTCTCGGGTGCCAAGG) and quality filtered using the FASTQ Quality Filter (options: -Q33 -q 27 -p 65) from the FASTX-Toolkit
Contamination from reads mapping to 18-mer and 28-mer size standards were filtered out using Cutadapt (version 3.4)
Filtered reads were mapped to the C. elegans genome WS258 using Bowtie2 v. 2.5.0 (default parameters)
Reads were assigned to genomic features using featureCounts (options: -t exon -g gene_id -O --fraction –largestOverlap) which is part of the Subread v. 2.0.1 package.
Assembly: WS258
Supplementary files format and content: Processed data files are tab-delimited text files including total reads mapping to each gene generated by FeatureCounts.

molecule: other

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Sychronized animals were grown on enriched peptone plates seeded with OP50 E. coli at 20°C or 25°C for 68 hours post-hatching (for 1-day-old adults ).

extract_protocol:
For immunoprecipitation, ~100,000 synchronized 1-day-old adult animals were collected in IP Buffer (50 mM Tris-Cl pH 7.4, 100 mM KCl, 2.5 mM MgCl2, 0.1% Igapal CA-630, 0.5 mM PMSF, cOmplete Protease Inhibitor Cocktail, and RNaseOUT Ribonuclease Inhibitor), frozen in liquid nitrogen, and homogenized using a mortar and pestle. After further dilution into IP buffer (1:10 packed worms:buffer), insoluble particulate was removed by centrifugation and a sample was taken as “input.”  The remaining lysate was used for the immunoprecipitation. Immunoprecipitation was performed at 4°C for 1 hour, then washed at least 3 times in immunoprecipitation buffer. Trizol reagent was added to the remainder of each sample, followed by chloroform extraction, and isopropanol precipitation.
Small RNAs (18 to 30-nt) were size selected on denaturing 15% polyacrylamide gels from total RNA samples. Small RNAs were treated with 5’ RNA polyphosphatase and ligated to 3’ pre-adenylated adapter with Truncated T4 RNA ligase. Small RNAs were then hybridized to the TruSeq reverse transcription primer, ligated to the 5’ adapter with T4 RNA ligase), and reverse transcribed with Superscript III. Small RNA libraries were amplified using Q5 High-Fidelity DNA polymerase and size selected on a 10% polyacrylamide gel. Library concentration was determined using the Qubit 1X dsDNA HS Assay kit and quality was assessed using the Agilent BioAnalyzer.

value: Whole worm

tag: developmental stage

value: 1-day-old adult

value: prg-1(cmp220[(mKate2 + loxP + 3xMyc)::prg-1])

tag: antibody

value: anti-c-Myc (clone 9E10) (ThermoFisher 20168)


title: mKate::PRG-1 (adult) - IP, replicate 3

description: Library name: Sample 24

tag: treatment


title: mKate::PRG-1(3xAG) (adult) - IP, replicate 2

description: Library name: Sample 29

value: prg-1(cmp220[mKate2 + loxP + 3xMyc::prg-1] & cmp270[3x RG to AG]) I


title: mKate::PRG-1(3xAG) (adult) - input, replicate 2

description: Library name: Sample 26


title: mKate::PRG-1(3xAG) (adult) - IP, replicate 1

description: Library name: Sample 28


title: mKate::PRG-1(3xAG) (adult) - IP, replicate 3

description: Library name: Sample 30


title: mKate::PRG-1(3xAG) (adult) - input, replicate 1

description: Library name: Sample 25


title: mKate::PRG-1(3xAG) (adult) - input, replicate 3

description: Library name: Sample 27


title: BMDM, hom, mock_02


title: BMDM, het, Sal_03


title: mKate::PRG-1 (adult) - IP, replicate 1

description: Library name: Sample 22


title: mKate::PRG-1 (adult) - input, replicate 3

description: Library name: Sample 21


title: BMDM, het, Sal_02


title: mKate::PRG-1 (adult) - input, replicate 1

description: Library name: Sample 19


title: prg-1(3xAG) (adult) - 25°C, replicate 2

description: Library name: Sample 17


title: mKate::PRG-1 (adult) - input, replicate 2

description: Library name: Sample 20


title: prg-1(3xAG) (adult) - 20°C, replicate 3

description: Library name: Sample 15


title: prg-1(3xAG) (adult) - 20°C, replicate 2

description: Library name: Sample 14


title: prg-1(3xAG) (adult) - 20°C, replicate 1

description: Library name: Sample 13


title: prg-1 (adult) - 25°C, replicate 3

description: Library name: Sample 12


title: wild-type (adult) - 25°C, replicate 1

description: Library name: Sample 4

value: wild-type


title: prg-1 (adult) - 20°C, replicate 1

description: Library name: Sample 7


title: wild-type (adult) - 25°C, replicate 2

description: Library name: Sample 5


title: wild-type (adult) - 25°C, replicate 3

description: Library name: Sample 6


title: prg-1 (adult) - 25°C, replicate 2

description: Library name: Sample 11


title: prg-1 (adult) - 25°C, replicate 1

description: Library name: Sample 10


title: prg-1 (adult) - 20°C, replicate 2

description: Library name: Sample 8


title: prg-1 (adult) - 20°C, replicate 3

description: Library name: Sample 9


title: wild-type (adult) - 20°C, replicate 2

description: Library name: Sample 2


title: wild-type (adult) - 20°C, replicate 3

description: Library name: Sample 3


title: wild-type (adult) - 20°C, replicate 1

description: Library name: Sample 1


title: GFP::DMD-3, L4 males (strain DF301), Replicate 2, (Input)

city: New York

first: Porfirio

last: Fernandez

address: 29 Washington Place

institute: New York University

description:
Library name: Input, Rep2
Input, Rep2

data_processing:
Adapter sequences from raw reads were trimmed and filtered using the Bbduk shell script from BBmap Version 38.42
single-end reads were aligned to the C. elegans genome version WBcel235/ce11 using bowtie2 version 2.3.2 under the default parameters.Duplicate reads were removed using MAC2 version 2.1.1 and BAM files were sorted and indexed using Samtools version 1.6.
DeepTools version 3.3.1 was employed for coverage generations and normalization by subtracting by input via bamCompare settings: CPM, bin-size of 10 bp, ignore duplicates, extend reads to 391-400 bp, exclude chrM, minMappingQuality 20 and to remove blacklisted regions
Using MACS2, we predicted the estimated fragment size and called peak enrichment regions. Peaks were called on each individual replicate sample along with a merged BAM file using a threshold false discovery rate (FDR) of 0.05
Bedtools Intersect, we identified overlapping enrichment peak regions between replicates and the merged BAM; only peaks present in at least two of the three replicates were chosen as the final peaks to be reported
Assembly: WBcel235/ce11
Supplementary files format and content: bigWig,  narrowPeak (except for input samples)

source_name: whole-worm

extract_protocol:
Samples were cross-linked by adding formaldehyde (2%) and incubating on a rocker at room temperature for 30 minutes. Glycine was added to a final concentration of 125mM and incubated at room temperature for 5 minutes.samples were dounce homogenized in FA-buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl). Sarkosyl (0.1% sodium lauroyl sarcosinate) was added to samples before sonication. Samples were sonicated to enrich chromatin fragments between 200 and 800 bp in length
ChIP-DNA samples were ligated to barcode adaptors from the NEXTflex ChIPseq Barcodes kit (Bioo Scientific) using the NEXTflex ChIP-seq kit (Bioo Scientific) following the manufacturer’s protocol with the following alterations: the initial size selection step (step B1) was skipped, the number of PCR cycles in the amplification step was 15. After amplification, 200-600 bp fragments were size-selected using SPRIselect beads (Beckman Coulter).

value: whole-worm

value: Male

value: dpy-28(y1 ts,mat) III;dmd-3(ny21[GFP::3xFLAG::dmd-3]) him-5(e1490) V

value: L4 stage

tag: chip antibody


title: GFP::DMD-3, L4 males (strain DF301), Replicate 3, (ChIP)

description:
Library name: GFP::DMD3, ChIP, Rep3
GFP::DMD3, ChIP, Rep3

tag: strain

value: anti-GFP (ab290)


title: GFP::DMD-3, L4 males (strain DF301), Replicate 3, (Input)

description:
Library name: Input, Rep3
Input, Rep3

tag: Sex


title: GFP::DMD-3, L4 males (strain DF301), Replicate 2, (ChIP)

description:
Library name: GFP::DMD3, ChIP, Rep2
GFP::DMD3, ChIP, Rep2


title: prg-1(3xAG) (adult) - 25°C, replicate 3

description: Library name: Sample 18


title: prg-1(3xAG) (adult) - 25°C, replicate 1

description: Library name: Sample 16


title: GFP::DMD-3, L4 males (strain DF301), Replicate 1, (ChIP)

description:
Library name: GFP::DMD3, ChIP, Rep1
GFP::DMD3, ChIP, Rep1


title: GFP::DMD-3, L4 males (strain DF301), Replicate 1, (Input)

description:
Library name: Input, Rep1
Input, Rep1


title: Patient-10

city: Chandigarh

first: Priyanka

last: Srivastava

state: Chandigarh

address: PGIMER, Sector-12

department: Pediatrics

country: India

institute: PGIMER

description: Library name: RS-10

data_processing:
The adapter sequences, low-quality bases, and reads shorter than 17 bp were removed using Trim-galore v0.6.6 and fastp program. The QC passed reads were mapped onto indexed human reference genome (GRCh38.p13) using mapper.pl script of miRDeep2 v2.0.1.2. Reads mapped to the reference genome were used to identify miRNAs with miRDeep2 using known and novel miRNA identification parameters. Human mature miRNAs from miRbase v22.1 were used for miRNA prediction. miRNAs with miRDeep score< 1 were excluded from the analysis resulting in total 1,569 novel and 679 known miRNAs. Expression levels of miRNAs were estimated using miRDeep2 quatifiler.pl script. Differential expression analysis was carried out using DESeq2 package after normalizing the data using relative log expression normalization method. miRNAs with absolute log2 fold change ≥ 1 and p-value ≤0.05 were considered significant.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: blood

extract_protocol:
The total RNA was extracted from the EVs using Total Exosome RNA and Protein Isolation Kit (Cat. 4478545,Invitrogen, CA, USA) using the manufacturer’s protocol. The RNA was quantified using Tape Station System (Agilent Technologies, Santa Clara, USA).
These samples were then processed for sequencing. The miRNA sequencing library was constructed using the QIAseq miRNA Library Kit (Qiagen, Germany). Briefly, to prepare the miRNA library, total RNA of each sample was used. 3′-and 5′-adaptor ligations were followed by cDNA synthesis, PCR amplification, and gel purification. Quantification was done with Qubit (Thermo Fisher, USA), and quality assessment was done using Agilent D1000 ScreenTape System in a 4150 TapeStation System. The libraries were then sequenced using Illumina NovaSeq 6000 platform (Illumina, USA).

value: blood