title: PU.1_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_PU1_Veh6h_rep2_YA_l20201107_GGCTAC
PU.1_WT_Veh_KLA_merged_allRawTags.txt

value: Bone marrow-derived macrophages


title: PGC1b_WT_Veh rep1

status: Public on Dec 21 2023

type: SRA

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr.

department: CMM

country: USA

institute: University of California, San Diego

description:
mouse_C57Bl6_Veh_BMDM_ChIP_PGC1b_rep1_YA_l20210517_GGTAGC
PGC1b_WT_Veh_KLA_merged_allRawTags.txt

library_source: genomic

data_processing:
FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2.  Peaks were called with HOMER (findPeaks) using parameters “-style factor -minDist 200 -size 200”.  After merging these peaks, correlations among replicates from the same cell subset/treatment were evaluated by correlation using tag counts.  The two most highly correlated samples were used for identifying the most robust peaks using the irreproducible discovery rate (IDR) method.  For this step, peaks were called with HOMER’s findPeaks, using parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”.  IDR peaks from different conditions involved in a comparison merged with HOMER’s mergePeaks and annotated with HOMER’s annotatePeaks.pl.  The raw tags of all samples which had reasonable correlation were quantified with HOMER (annotatePeaks.pl) using parameter “-noadj”.  Peaks which contained at least 4 tags in at least 1 sample were used to identify differentially bounded peaks (DBP) by DESeq2.  Peaks were categorized as distal peaks which are 2 kb away from known TSS and promotor peaks which are located within 2 kb region of known TSS sites.
ChIP peak single was normalized to the sequence depth.
Assembly: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow-derived macrophages

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed in biological replicates as previously described (Heinz et al., 2018: Sakai et al., 2019) with modifications as follows.  For H3K27ac ChIP assays, cells were cross-linked with 1% (vol/vol) formaldehyde (Thermo Fisher Scientific) in PBS for 10 min at room temperature.  For NCoR, HDAC3, PU.1, p65, Fosl2, PGC1b, ERK1 and p300 ChIP assays, cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min.  The crosslinking reaction was quenched by 0.125 M glycine (Thermo Fisher Scientific).  Cells were washed once with cold PBS and pelleted at 1,000 g for 5 min at 4°C.  Crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1 mM PMSF (Sigma), 0.5 mM sodium butyrate (Sigma), 1X protease inhibitor cocktail (Sigma)), and centrifuged at 1,000 g for 5 min at 4°C to obtain a nuclear fraction.  Nuclear pellets were resuspended in 100 ml of either LB3 buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurosylsarcosine, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail for H3K27ac ChIP) or PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail, for NCoR, HDAC3, PU.1, p65, Fosl2, PGC1b, ERK1 and p300 ChIP).  Chromatin DNA was sonicated in a 96 Place microTUBE Rack (Covaris) using a Covaris E220 for 12-18 cycles with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were centrifuged at 15,000 rpm for 10 min at 4°C, and the supernatant was used for immunoprecipitation.  LB3 lysate was diluted 1.1-fold with 10% Triton X-100.  1% of the lysate was kept as ChIP input.  The lysates were rotated with each antibody pre-bound to 20 ml of beads (10 ml of Dynabeads protein A (Invitrogen) + 10 ml of Dynabeads protein G (Invitrogen)) overnight at 4°C.  After the immunoprecipitation, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), wash buffer III (10 mM Tris-HCl (pH 7.5), 250 mM LiCl, 1% Triton X-100, 0.7% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail) and twice with TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2% Tween-20, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), and then resuspended in 25 ml of TT (10mM Tris-HCl (pH 7.5), 0.05% Tween-20).
The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions.  DNA in 46.5 ml of NEB reactions was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K (NEB) and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  DNA was purified with 2 ml of SpeedBeads (GE Healthcare) in 20% PEG 8000/1.5 M NaCl (Final 12% PEG 8000), and eluted with 25 ml of TT.  The eluted DNA was amplified for 14 cycles in 50 ml of PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix and 0.5 mM each of primers Solexa 1GA and Solexa 1GB.  The amplified libraries were purified with 2 ml of SpeedBeads in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 20 ml of TT, size selected using PAGE/TBE gel (Invitrogen) for 225-325 bp fragments by gel extraction, and single-end sequenced on HiSeq 4000.  ChIP input material (1% of sheared DNA) in 46.5 ml of TE was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  The input DNA was purified with SpeedBeads as described above, and eluted with 25 ml of TT.  The eluted input DNA was prepared for libraries and amplified as described for ChIP samples.

tag: genotype

value: Wild type

tag: treatment

value: Veh

tag: cell type

tag: chip antibody


title: Control 2

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

country: Germany

institute: Freiburg Medical Center

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Drosophila_melanogaster.BDGP6.32
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: not specified

extract_protocol:
Nuclei were extracted and sorted from Hml-dsRed.nuc flies as described previously in Hersperger et al., 2023 (PMID: 37639115)
Library was performed according to the manufacter’s instructions (single cell 3’ Regent kits v3.1 protocol, 10x Genomics)
snRNA-seq

treatment_protocol: Flies were maintained at 29°C for six days prior to treatment. On day six they were starved for 6 hours. A filter paper soaked in 5% sucrose solution with or without 15mM Paraquat (PQ, Methyl viologen hydrate, Acros Organics) was added after starvation. Flies were fed for 18 hours on the PQ containing food in groups of ten. The PQ treatment was performed at 29°C in the dark.

tag: tissue

value: not specified

value: 5% sucrose solution


title: AB5260

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: MARSseq

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q_annotated.txt

molecule: total RNA

source_name: GL261 tumor

growth_protocol: GL261 cells were grown in full DMEM medium.

extract_protocol:
Isolation of tumor cells and tumor-infiltrating immune cells was performed from tumor-bearing brain hemispheres. Briefly mice were perfused with PBS and the tumor-bearing brain hemisphere was collected in Roswell Park Memorial Institute (RPMI) medium containing 0.4 mg/ml Collagenase IV and 0.1 mg/ml DNase I (both Sigma-Aldrich). The tissue was then incubated for 40 min at 37°C and further homogenize using a 18G needle. Myelin was removed using a 30% Percoll centrifugation step (Sigma-Aldrich).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single-cell RNA-sequencing for gene expression quantitation

treatment_protocol:
Groups of mice were treated with anti-TREM2 antibodies or isotype control (anti-hILT1) at days 2 and 7 post tumor implantation. See Molgora et al 2020, Cell.
All mice were implanted with 2x10^4 GL261 cells intracerebrally. 11-12 days later mice received i.v. fluorescent CD45 antibody time stamps. On day 13 mice were sacrificed and tumors were extracted for single cell processing.

value: GL261 tumor

tag: strain

tag: age

value: 10-12 weeks

value: no treatment

tag: day of_tumor_harvest

tag: biological replicate

value: Mouse 7


title: AB5263

description: MARSseq

value: Mouse 8


title: H3K27ac_Pgc1b_flox_Cre_KLA rep2

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_H3K27ac_PGC1bfloxLysMCre_rep2_YA_l20210619_CTATAC
H3K27ac_Pgc1b_flox_Cre_Veh_KLA_merged_allRawTags.txt

value: PGC1b flox/flox, LysMCre

value: KLA


title: HCC_rep2

type: RNA

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

country: Japan

institute: Chuo University

description: Gene expression in liver of HCC patient

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Hmn GE 8x60K Microarray (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially to detrend Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: HCC,liver,replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.075 ug RNA using the Low Input Quick Amp Labeling Kit, One-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was prepared using the mirVana miRNA isolation kit (Ambion) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Twenty-four samples were surgically resected from hepatocallular carcinoma and twenty-four samples of chronic hepatitis type C were obtained by fine needle biopsy

value: hepatocallular carcinoma

value: liver

tag: gender

value: male

tag: age(yrs)


title: PU.1_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_PU1_KLA6h_rep2_YA_l20201107_GTCCGC
PU.1_WT_Veh_KLA_merged_allRawTags.txt


title: PU.1_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_PU1_KLA6h_rep1_YA_l20201107_AGTTCC
PU.1_WT_Veh_KLA_merged_allRawTags.txt


title: HCC_rep1

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 1


title: Control 1


title: AB5261

description: MARSseq


title: Paraquat 1

value: 15mM paraquat in 5% sucrose solution


title: CTCFd_RNA-seq

city: Shanghai

first: Mo

last: Zhang

address: 800 Dongchuan Road

country: China

institute: Shanghai Jiaotong University

library_source: transcriptomic

data_processing:
RNA-seq raw FASTQ files were aligned to GRCh37/hg19 using STAR (v2.7.3a) with the default parameters.
The bam files were feed to Cufflinks (v2.2.1) to generate expression levels of transcripts in FPKM (fragments per kilobase of exon per million fragments mapped).
Deeptools was used to convert the bam file to bedGraph file for visualizing in UCSC genome browser.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: Human HEC-1-B cells and derived cell lines were cultured in MEM, 200mM L-Glutamine, Earle’s Balanced Salts (Hyclone) supplemented with 1mM sodium pyruvate (Sigma), 1% penicillin-streptomycin (Gibco) and 10% fetal bovine serum (Gibco). Human HCT-116 RAD21-AID-mClover cells (Natsume et al., 2016) were cultured in RPMI Medium 1640 L-Glutamine (Gibco), 1% penicillin-streptomycin (Gibco 15140122) and 10% fetal bovine serum (Gibco). The cells were cultured at 37°C in the incubator supplied with 5% (v/v) of CO2.

extract_protocol:
About 1 million cells were used for each RNA-seq experiment. Cells were washed twice using PBS and lysed by 1 mL Trizol (Invitrogen 15596026) for 15 min at room temperature. 0.2 mL chloroform was added and incubated for 2-3 minutes at room temperature. The upper phase was transferred into a new tube after centrifuged at 12,000rpm for 15 min at 4°C, and mixed with 0.5 mL isopropanol. After incubation at room temperature for 10 minutes, the total RNA was precipitated by centrifuging at 12,000 rpm for 10 minutes at 4°C. The precipitated DNA was washed by 75% ethanol to remove salt. Air-dried RNA was dissolved by 100 nuclease-free H2O.
The RNA was purified using the RNeasy kit (QIAGEN 75142) to remove residual DNA. 1ug RNA was used for extract mRNA by NEBNext poly(A) mRNA Magnetic Isolation Module (NEB E7490S), and RNA-seq library was constructed using NEBNext®Ultra™II RNA Library Prep Kit. The library was sequenced on the Illumina HiSeq platform.

tag: cell line

value: Human Uterine Adenocarcinoma Cells

value: CTCF-AID

value: IAA, 24h


title: CTCF-AID_RNA-seq

value: IAA, 0h


title: PU.1_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_PU1_Veh6h_rep1_YA_l20201107_TAGCTT
PU.1_WT_Veh_KLA_merged_allRawTags.txt

value: Wild type

value: Veh

value: Bone marrow-derived macrophages


title: HCC_rep4

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 4


title: WT [2]

city: Nagoya

first: Hossam

middle: Hassan

last: Shawki

state: Aichi

address: Mizuho Ward, Ōtachō, 3-chōme−1

department: Comparative and Experimental medicine

institute: Nagoya City University

data_processing:
Illumina Basespace Onsite software
FASTQ files were imported to CLC Genomics Workbench (Version 7.5.1), mapped to mm10 mouse genome and quantified for annotated genes in ENSEMBLE database to obtain RPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file format include RPKM values for each Sample

source_name: Sertoli cells

extract_protocol:
Total RNA was extracted by Nucleospin RNA XS kit (TaKaRa; 740902) according to the manufacturer's instructions. Concentration and purity of RNA were determined by automated optical density evaluation (OD 260/OD 280 ≥ 1.8 and OD 260/OD 230 ≥ 1.8) using Nanodrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six weeks old mice carrying loxP-flanked Mafb allele with Cre-ERT2 as well as control wild type mice were received 75 mg tamoxifen/kg body weight intraperitoneally once daily for 5 consecutive days. Eight weeks old mice were injected busulfan 20mg/kg. Five weeks later, Sertoli cells were sorted by FACs and the purity of the isolated cells was confirmed by immunocytochemical staining. Total RNA were then extracted and stored immediately in -80 C.

value: Wild Type (Control)

value: 13 weeks

value: Sertoli cells


title: p65_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_p65_KLA6h_rep1_YA_l20201107_ACTTGA
p65_WT_Veh_KLA_merged_allRawTags.txt


title: WT_H3K27me3,ChIP

data_processing:
Reads of ChIP-seq were mapped to human genome GRCh37/hg19 with bowtie2.
The peaks were called by MACS2 with default parameters.
All of the mapped Sam files were sorted and indexed by Samtools (v1.12) and normalized to RPKM by Deeptools BamCoverage function.
The BedGraph file generated from Deeptools was uploaded into USCS browser for visualizing.
Assembly: hg19
Supplementary files format and content: bigWig, broadPeak

growth_protocol: Human HEC-1-B cells and derived cell lines were cultured in MEM, 200mM L-Glutamine, Earle’s Balanced Salts (Hyclone) supplemented with 1mM sodium pyruvate (Sigma), 1% penicillin-streptomycin (Gibco) and 10% fetal bovine serum (Gibco). The cells were cultured at 37°C in the incubator supplied with 5% (v/v) of CO2.

extract_protocol:
After washed twice by PBS, ~10-20 million cells digested by trypsin and resuspended by 10mL medium. Formaldehyde (Thermo 28908) was added to a final concentration of 1% to cross-link protein and DNA. After incubation at room temperature for 10 minutes, the glycine solution reached a final concentration of 125mM and incubated at room temperature for 5 minutes to quench the cross-linking reaction. Cells were centrifuged at 2,500g for 10 minutes at 4°C to precipitate cells. The cell pellet was washed by ice-cold PBS and quickly frozen by liquid nitrogen. The cell pellet was stored at -80°C until the next step. Cell pellet was resuspended by 1mL ice-cold ChIP buffer 1 (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150 mM NaCl, 1x protease inhibitors), and lysed twice by ChIP buffer 1 at 4°C for 10 minutes with slow rotation. After centrifuged at 2,500g for 5 minutes at 4°C, the pellet was resuspended by 0.7mL ChIP buffer 1 and incubated at ice for 10 minutes. The cell suspension was sonicated to fragment DNA using Bioruptor Plus Sonicator by high intensity (30 seconds on, 30 seconds rest, 30 cycles), and the DNA size should be 100-10000 bp. After spinning at 14,000g for 10 minutes at 4°C, the supernatant was transferred to a new tube with 50 μL agarose protein A beads (16-157 Millipore) were added. After incubation at 4°C with slow rotation for 1 hour, the supernatant was transferred into a new tube and the primary antibody was added to incubate it at 4°C with slow rotation overnight. 50 μL agarose protein A beads were added and incubated at 4°C with slow rotation for 3 hours. The protein-DNA complexes were sequenced and washed by ChIP buffer 1, ChIP buffer 2 (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 400 mM NaCl), ChIP buffer 3 (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) and ChIP buffer 4 (50 mM HEPES pH 7.5, 1 mM EDTA, 1% NP-40, 0.7% sodium deoxycholate, 500 mM LiCl). DNA-protein complexes were eluted using 100 μL elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) by incubation at 65°C for 30 minutes. The above step was repeated again and a total of 200 μL solution of DNA-protein complexes was collected. The DNA-protein complexes solution was mixed with 200 μL TE buffer, and incubated at 65°C overnight to be reversely cross-linked. The DNA-protein complexes were digested by 2 μL RNase A at 37°C for 2 hours and 8 μL proteinase K at 55°C for 2 hours. The DNA was purified using 400μl of phenol-chloroform. The DNA was precipitated by adding 40 μL 3M NaAc pH 5.2, 1.5 μL glycogen (Thermo R0561), and 1mL absolute ethanol, and frozen at -80°C for 30 minutes. After centrifuged at 17,000g for 30 minutes at 4°C, the DNA pellet was washed by 75% ethanol, air-dried, and then solved by 20 μL nuclease-free water.
DNA concentration was measured by PicoGreen reagents. 10 ng DNA was used for the library constructed with NEBNext®Ultra™ II DNA Library Prep Kit for Illumina. Library was sequenced on the Illumina HiSeq platform.

value: H3K4me3 (cell signaling #9733)

value: wild type


title: late stationary NaCl 5

city: Madison

first: Daniel

last: Pensinger

state: WI

address: 1550 Linden Dr., MSB Rm3435

department: Department of Gastroenterology and Department of Medical Microbiology and Immunology

institute: UW-Madison

description:
Late Stationary All Quantified Genes.tsv
1157 Differentially Expressed Genes In L.But vs L.Na.tsv
L_Na5

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v3.9.3).
Assembly: GCF_000009205.2
Supplementary files format and content: Differentially Expressed Genes, Quantified Genes

organism: Clostridioides difficile

extract_protocol:
At the appropriate time points, 5mL aliquots of the cultures were diluted 1:1 in chilled 1:1 Ethanol:Acetone to preserve RNA [45]. These samples were then centrifuged for 5 minutes at 3000 x g at room temperature and cell pellets were frozen at -80˚C. Immediately prior to RNA extraction, cell pellets were centrifuged at 4˚C at 3000 x g for 1minute. Residual supernatant was removed from the cell pellets, which were subsequently washed with 5mL nuclease free PBS. Washed pellets were centrifuged at 4˚C at 3000 x g for 1minute, the supernatant was removed, and the resulting pellet was resuspended in 1mL TRIzol and processed using a TRIzol Plus RNA Purification Kit (Thermo) with on-column DNase treatment according to the manufacturer’s instructions. Purified RNA was frozen at -80C and RNA integrity was confirmed via BioAnalyzer (Agilent) prior to proceeding.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

value: WT

value: 50mM NaCl


title: AB5257

description: MARSseq

value: GL261 tumor

value: 10-12 weeks

value: no treatment

value: Mouse 7


title: late stationary NaCl 2

description:
Late Stationary All Quantified Genes.tsv
1157 Differentially Expressed Genes In L.But vs L.Na.tsv
L_Na2


title: late stationary NaCl

description:
Late Stationary All Quantified Genes.tsv
1157 Differentially Expressed Genes In L.But vs L.Na.tsv
L_Na


title: AB5259

description: MARSseq


title: Paraquat 2

value: not specified

value: 15mM paraquat in 5% sucrose solution


title: MafB-cKO [2]

value: MafB knockout


title: p65_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_p65_Veh6h_rep2_YA_l20201107_CTTGTA
p65_WT_Veh_KLA_merged_allRawTags.txt

value: Wild type


title: AB5258

description: MARSseq


title: late stationary butyrate 5

description:
Late Stationary All Quantified Genes.tsv
1157 Differentially Expressed Genes In L.But vs L.Na.tsv
L_But5

value: 50 mM butyrate


title: AB5256

description: MARSseq


title: p65_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_p65_Veh6h_rep1_YA_l20201107_CAGATC
p65_WT_Veh_KLA_merged_allRawTags.txt

value: Veh

value: Bone marrow-derived macrophages


title: late stationary NaCl 1

description:
Late Stationary All Quantified Genes.tsv
1157 Differentially Expressed Genes In L.But vs L.Na.tsv
L_Na1


title: AB5255

description: MARSseq


title: Input_Fosl2_p65_PU.1_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_input_KLA6h_rep2_YA_l20201107_CAACTA
Fosl2_WT_Veh_KLA_merged_allRawTags.txt

value: KLA


title: AB5254

description: MARSseq


title: late stationary butyrate 4

description:
Late Stationary All Quantified Genes.tsv
1157 Differentially Expressed Genes In L.But vs L.Na.tsv
L_But4


title: p65_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_p65_KLA6h_rep2_YA_l20201107_GATCAG
p65_WT_Veh_KLA_merged_allRawTags.txt


title: late stationary butyrate 3

description:
Late Stationary All Quantified Genes.tsv
1157 Differentially Expressed Genes In L.But vs L.Na.tsv
L_But3


title: AB5252

description: MARSseq


title: Input_Fosl2_p65_PU.1_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_input_Veh6h_rep1_YA_l20201107_ACTGAT
Fosl2_WT_Veh_KLA_merged_allRawTags.txt


title: Input_Fosl2_p65_PU.1_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_input_KLA6h_rep1_YA_l20201107_ATTCCT
Fosl2_WT_Veh_KLA_merged_allRawTags.txt


title: AB5253

description: MARSseq


title: AB5251

description: MARSseq


title: Input_Fosl2_p65_PU.1_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_input_Veh6h_rep2_YA_l20201107_ATGAGC
Fosl2_WT_Veh_KLA_merged_allRawTags.txt


title: AB5250

description: MARSseq


title: AB5249

description: MARSseq


title: Adult_2

city: SHANG HAI

first: XUETING

last: WANG

state: Not US or Canada

address: 100 Hai Ke ROAD, shanghai, china

institute: IRCBC

data_processing:
All sequencing reads were processed with Trim Galore (v0.6.6) with the parameters “--nextseq 30 --paired” to remove the adapter sequences (AGATCGGAAGAGC) from NovaSeq-platforms, and reads longer than 20 bp were kept. Reads that passed the quality control procedure were kept and mapped to Drosophila melanogaster genome r6.36 and Mus musculus genome GRCm39 using STAR (2.7.6a) with default parameters, respectively. Uniquely mapped read pairs were counted against annotations from Mus musculus (Ensembl: GRCm39) and Drosophila melanogaster (Flybase: dmel-all-r6.36) using featureCounts (v2.0.1) with parameters “-p -B -C” and summarized as gene-level counts, respectively.
Assembly: GRCm39 and dmel-all-chromosome-r6.36
Supplementary files format and content: Counts from featurecounts output were merged into csv table with each gene in rows and each sample in columns.

source_name: Fly

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108)
RNA libraries were prepared according to instructions of Fast RNA-seq Lib Prep Kit V2 (Abclonal, catalog: RK20306)

value: Whole fly

tag: condition

value: Adult (3d)

tag: assay

value: RNAseq


title: Fosl2_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_Fosl2_KLA6h_rep1_YA_l20201107_GAGTGG
Fosl2_WT_Veh_KLA_merged_allRawTags.txt


title: Fosl2_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_Fosl2_Veh6h_rep2_YA_l20201107_CGTACG
Fosl2_WT_Veh_KLA_merged_allRawTags.txt


title: AB5248

description: MARSseq


title: Adult_1


title: AB5247

description: MARSseq

value: Mouse 3


title: Pupa_2

value: Pupa (7d AEL)


title: AB5246

description: MARSseq

value: GL261 tumor


title: Fosl2_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_Fosl2_Veh6h_rep1_YA_l20201107_GTGGCC
Fosl2_WT_Veh_KLA_merged_allRawTags.txt


title: Fosl2_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_Fosl2_KLA6h_rep2_YA_l20201107_GGTAGC
Fosl2_WT_Veh_KLA_merged_allRawTags.txt


title: AB5245

description: MARSseq

value: 10-12 weeks


title: Pupa_3


title: Pupa_1


title: Adult_3


title: AB5244

description: MARSseq

value: no treatment


title: Larva_3

value: Larva (4d AEL)


title: AB5243

description: MARSseq


title: AB5242

description: MARSseq


title: Larva_1


title: AB5239

description: MARSseq


title: Embryo_2

value: Embryo (14h-16h AEL)


title: Input_NCoR_HDAC3_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_input_Day4_rep2_YA_l20201221_CTATAC
NCoR_WT_Veh_KLA_merged_allRawTags.txt


title: HDAC3_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_HDAC3_Veh6h_rep1_YA_l20201221_GATCAG
HDAC3_WT_Veh_KLA_merged_allRawTags.txt


title: HDAC3_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_HDAC3_KLA6h_rep1_YA_l20201221_GGCTAC
HDAC3_WT_Veh_KLA_merged_allRawTags.txt


title: Input_NCoR_HDAC3_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_input_Day4_rep1_YA_l20201221_CATGGC
NCoR_WT_Veh_KLA_merged_allRawTags.txt


title: HDAC3_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_HDAC3_Veh6h_rep2_YA_l20201221_TAGCTT
HDAC3_WT_Veh_KLA_merged_allRawTags.txt


title: HDAC3_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_HDAC3_KLA6h_rep2_YA_l20201221_GTCCGC
HDAC3_WT_Veh_KLA_merged_allRawTags.txt


title: Larva_2


title: Embryo_1


title: AB5240

description: MARSseq


title: Embryo_3


title: midlog NaCl 1

description:
Midlog All Quantified Genes.tsv
1199 Differentially Expressed Genes In M.But vs M.Na.tsv
M_Na1

value: WT

value: 50mM NaCl


title: early stationary NaCl 5

description:
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_Na5


title: Adult_enrich_2

value: Enrich


title: early stationary NaCl 2

description:
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_Na2


title: early stationary butyrate 1

description:
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_But1

value: 50 mM butyrate


title: midlog NaCl 2

description:
Midlog All Quantified Genes.tsv
1199 Differentially Expressed Genes In M.But vs M.Na.tsv
M_Na2


title: midlog butyrate 5

description:
Midlog All Quantified Genes.tsv
1199 Differentially Expressed Genes In M.But vs M.Na.tsv
M_But5


title: early stationary NaCl 1

description:
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_Na1


title: midlog NaCl

description:
Midlog All Quantified Genes.tsv
1199 Differentially Expressed Genes In M.But vs M.Na.tsv
M_Na


title: early stationary butyrate 3

description:
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_But3


title: early stationary butyrate 4

description:
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_But4


title: early stationary butyrate 5

description:
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_But5


title: late stationary butyrate 1

description:
Late Stationary All Quantified Genes.tsv
1157 Differentially Expressed Genes In L.But vs L.Na.tsv
L_But1


title: early stationary NaCl

description:
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_Na


title: midlog NaCl 5

description:
Midlog All Quantified Genes.tsv
1199 Differentially Expressed Genes In M.But vs M.Na.tsv
M_Na5


title: AB5236

description: MARSseq


title: Input_NCoR_HDAC3_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_input_Day0_rep1_YA_l20201221_CACCGG
NCoR_WT_Veh_KLA_merged_allRawTags.txt

value: Wild type

value: Veh


title: NCoR_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_NCoR1_KLA6h_rep2_YA_l20201221_ACTTGA
NCoR_WT_Veh_KLA_merged_allRawTags.txt

value: KLA

value: Bone marrow-derived macrophages

value: NCoR


title: Input_NCoR_HDAC3_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_input_Day0_rep2_YA_l20201221_CACTCA
NCoR_WT_Veh_KLA_merged_allRawTags.txt


title: AB5235

description: MARSseq


title: AB5238

description: MARSseq


title: midlog butyrate 3

description:
Midlog All Quantified Genes.tsv
1199 Differentially Expressed Genes In M.But vs M.Na.tsv
M_But3


title: midlog butyrate 4

description:
Midlog All Quantified Genes.tsv
1199 Differentially Expressed Genes In M.But vs M.Na.tsv
M_But4


title: Pupa_enrich_2

value: Whole fly


title: Adult_enrich_1

value: Adult (3d)


title: midlog butyrate 1

description:
Midlog All Quantified Genes.tsv
1199 Differentially Expressed Genes In M.But vs M.Na.tsv
M_But1


title: AB5237

description: MARSseq

value: Mouse 3


title: NCoR_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_NCoR1_KLA6h_rep1_YA_l20201221_CGTACG
NCoR_WT_Veh_KLA_merged_allRawTags.txt


title: Pupa_enrich_1

value: Pupa (7d AEL)


title: Larva_enrich_2


title: AB5234

description: MARSseq

value: GL261 tumor

value: 10-12 weeks


title: MB21 cells, control, 1 day, rep3

city: Boston

first: Rosalind

middle: A

last: Segal

state: MA

address: 360 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
Sequences from each replicate were then aligned to mouse (GRCm39) or human (GRCh38.p13) reference genomes using STAR (version 2.7.9a, default alignment settings) and mapping quality was assessed using Qualimap (version 2.2.1)27.
Raw genewise counts were obtained for each replicate using featureCounts (Subreads package, version 2.0.3)28. Counts matrices were then imported into R (version 4.1.0) and analyzed using the edgeR sequencing analysis package (version 3.14)28.
Briefly, lowly expressed genes were filtered out prior to analysis (filterByExpr, default arguments), then filtered counts were converted to counts per million (cpm, default arguments).
The mean relative expression value for each gene was then calculated using the formula “Relative Expression of Gene X = (Mean count value of X for all samples in group)/(Mean(Sum(Count values for all genes for all samples in group)))”
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Non-adherent cells were cultured in DMEM/F12 media, 2% B27, 1% Pen/Strep.

extract_protocol:
RNA was harvested using a Qiagen RNeasy Mini Kit (#74004) according to the manufacturer’s protocol
Library preparation was performed using the Roche Kapa mRNA Hyper Prep kit (#KK8580, automated using Biomek i7 platform)

treatment_protocol: 1 day treatment of 10 uM of DS-1-38 or vehicle

value: medulloblastoma

value: ptch mutant

value: DMSO control 1 day


title: Embryo_enrich_2

value: Embryo (14h-16h AEL)


title: MB21 cells, DS38, 1 day, rep3

value: DS38 treated 1 day


title: MB21 cells, DS38, 1 day, rep2


title: MB21 cells, DS38, 1 day, rep1


title: Larva_enrich_1

value: Larva (4d AEL)

value: Enrich


title: Adult_input_2

value: Input


title: MB21 cells, control, 1 day, rep1


title: Adult_input_1


title: Embryo_enrich_1


title: MB21 cells, control, 1 day, rep2


title: H3K27ac_WT_KLA rep1

description:
mouse_C57Bl6_NWT_BMDM_ChIP_H3K27ac_KLA6h_rep1_YA_l20210121_GGCTAC
H3K27ac_WT_NKO_Veh_KLA_merged_allRawTags.txt

value: NCoR flox/flox

value: KLA


title: NCoR_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_NCoR1_Veh6h_rep1_YA_l20201221_GTCCGC
NCoR_WT_Veh_KLA_merged_allRawTags.txt

value: Wild type

value: Veh

value: Bone marrow-derived macrophages

value: NCoR


title: H3K27ac_WT_KLA rep2

description:
mouse_C57Bl6_NWT_BMDM_ChIP_H3K27ac_KLA6h_rep2_YA_l20210121_GTCCGC
H3K27ac_WT_NKO_Veh_KLA_merged_allRawTags.txt


title: H3K27ac_NKO_KLA rep1

description:
mouse_C57Bl6_NKO_BMDM_ChIP_H3K27ac_KLA6h_rep1_YA_l20210121_ACTGAT
H3K27ac_WT_NKO_Veh_KLA_merged_allRawTags.txt

value: NCoR flox/flox, LysMCre


title: H3K27ac_NKO_KLA rep2

description:
mouse_C57Bl6_NKO_BMDM_ChIP_H3K27ac_KLA6h_rep2_YA_l20210121_ATGAGC
H3K27ac_WT_NKO_Veh_KLA_merged_allRawTags.txt


title: NCoR_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_NCoR1_Veh6h_rep2_YA_l20201221_GTGGCC
NCoR_WT_Veh_KLA_merged_allRawTags.txt


title: MB21 cells, DS38, 5 days, rep4

treatment_protocol: 5 day treatment of 10 uM of DS-1-38 or vehicle

value: DS38 treated 5 days


title: Pupa_input_2

value: Whole fly

value: Pupa (7d AEL)


title: MB21 cells, DS38, 5 days, rep3

value: medulloblastoma

value: ptch mutant


title: Pupa_input_1


title: ATAC_WT_KLA_RGFP966 rep2

description:
mouse_C57Bl6_RGFP966_BMDM_ATAC_KLA6h_rep2_YA_l20201023_AGTCGATT
ATAC_WT_KLA_Veh_merged_allRawTags.txt

data_processing:
FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2.  Peaks were called with HOMER (findPeaks) using parameters “-style factor -minDist 200 -size 200”.  After merging these peaks, correlations among replicates from the same cell subset/treatment were evaluated by correlation using tag counts.  The two most highly correlated samples were used for identifying the most robust peaks using the irreproducible discovery rate (IDR) method.  For this step, peaks were called with HOMER’s findPeaks, using parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”.  IDR peaks from different conditions involved in a comparison merged with HOMER’s mergePeaks and annotated with HOMER’s annotatePeaks.pl.  The raw tags of all samples which had reasonable correlation were quantified with HOMER (annotatePeaks.pl) using parameter “-noadj”.  Peaks which contained at least 4 tags in at least 1 sample were used to identify differentially bounded peaks (DBP) by DESeq2.  Peaks were categorized as distal peaks which are 2 kb away from known TSS and promotor peaks which are located within 2 kb region of known TSS sites.
ATAC peak quantification was normalized to the total tags in peaks.
Assembly: mm10
Supplementary files format and content: allRawTags

extract_protocol:
70000 cultured cells were washed once with PBS and once with cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40).  The cells were suspended in 50 µl of 1X Reaction Buffer (25 ul of Tagment DNA Buffer, 2.5 ul of Tagment DNA enzyme I, and 22.5 ul of water) (Nextera DNA Library Preparation Kit, Illumina).  Transposase reactions were carried out at 37°C for 30 min, and then DNA was purified using ChIP DNA Clean & Concentrator Kit (Zymo Research).
DNA was amplified using the Nextera primer Ad1 and a unique Ad2.n barcoding primer using NEBNext High-Fidelity 2X PCR Master Mix (NEB) for 7 cycles.  The amplified libraries were purified with 2 ul of SpeedBeads (GE Healthcare) in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 15 ul of EB (Zymo Research), size selected using PAGE/TBE gel (Invitrogen) for 175-225 bp fragments by gel extraction, and single-end sequenced on HiSeq 4000 (Illumina).

tag: time


title: ATAC_WT_KLA_RGFP966 rep1

description:
mouse_C57Bl6_RGFP966_BMDM_ATAC_KLA6h_rep1_YA_l20201023_ATCTGTCG
ATAC_WT_KLA_Veh_merged_allRawTags.txt


title: MB21 cells, DS38, 5 days, rep1


title: MB21 cells, DS38, 5 days, rep2


title: ATAC_WT_KLA rep2

description:
mouse_C57Bl6_Veh_BMDM_ATAC_KLA6h_rep2_YA_l20201023_CCAACTCG
ATAC_WT_KLA_Veh_merged_allRawTags.txt


title: MB21 cells, control, 5 days, rep3

value: DMSO control 5 days


title: ATAC_WT_KLA rep1

description:
mouse_C57Bl6_Veh_BMDM_ATAC_KLA6h_rep1_YA_l20201023_ACCAGGCG
ATAC_WT_KLA_Veh_merged_allRawTags.txt


title: MB21 cells, control, 5 days, rep2


title: scRNAseq_human_small_intestine_Sample2.1

city: San Francisco

first: Rachel

middle: Klapper

last: Zwick

address: 513 Parnassus Ave.

institute: University of California, San Francisco

description: 10x Chromium single cell data

data_processing:
Kallisto-bustools v.0.46.2 was used to produce the raw gene count matrix files from the "GEX" fastq files
Kallisto-bustools v.0.46.2 with the kite script was used to produce the raw MULTIseq barcode count matrix files from the "ADT" fastq files
DropletUtils v1.12.3 was used to filter gene count matrixess
DropletUtils v1.12.3 was used to demultiplex datasets
Assembly: Human GRCh38.95
Supplementary files format and content: Matrix, barcodes, and features tables with raw gene counts for every gene and every sample

source_name: small intestine

extract_protocol:
The intestine was washed, cut into 30 pieces of equal length, and incubated with media supplemented with 5mM EDTA and 10mM DTT at 37°C with 5% CO2. Cells were triturated, strained, washed, and labelled with barcodes unique to each segment using the MULTIseq method. The target population was FACS sorted.
10x libraries were prepared for sequencing using standard 10x genomics protocols adapted for MULTIseq as described in McGinnis et al. Nat Methods 2019.
Chromium Single Cell 3'

value: Epithelial zonation along the mammalian small intestine defines five discrete metabolic domains

value: FACS sorted intestinal epitheilal cells (CD45-, EpCAM+)

value: small intestine

tag: developmental stage

value: female adult, homeostasis


title: ATAC_WT_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_ATAC_Veh6h_rep1_YA_l20201023_AAGGAACG
ATAC_WT_KLA_Veh_merged_allRawTags.txt


title: MB21 cells, control, 5 days, rep4


title: H3K27ac_WT_Veh rep2

description:
mouse_C57Bl6_NWT_BMDM_ChIP_H3K27ac_Veh_rep2_YA_l20210121_TAGCTT
H3K27ac_WT_NKO_Veh_KLA_merged_allRawTags.txt

value: NCoR flox/flox


title: H3K27ac_NKO_Veh rep2

description:
mouse_C57Bl6_NKO_BMDM_ChIP_H3K27ac_Veh_rep2_YA_l20210121_GGTAGC
H3K27ac_WT_NKO_Veh_KLA_merged_allRawTags.txt


title: H3K27ac_NKO_Veh rep1

description:
mouse_C57Bl6_NKO_BMDM_ChIP_H3K27ac_Veh_rep1_YA_l20210121_GAGTGG
H3K27ac_WT_NKO_Veh_KLA_merged_allRawTags.txt


title: H3K27ac_WT_Veh rep1

description:
mouse_C57Bl6_NWT_BMDM_ChIP_H3K27ac_Veh_rep1_YA_l20210121_GATCAG
H3K27ac_WT_NKO_Veh_KLA_merged_allRawTags.txt


title: MB21 cells, control, 5 days, rep1


title: ATAC_WT_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_ATAC_Veh6h_rep2_YA_l20201023_GCTAAACG
ATAC_WT_KLA_Veh_merged_allRawTags.txt


title: Larva_input_1

value: Larva (4d AEL)

value: Input


title: Embryo_input_1

value: Embryo (14h-16h AEL)


title: Embryo_input_2


title: GSC-20, M2 Macrophage CM, Day 28, core fraction_rep2

city: Berkeley

first: Sanjay

last: Kumar

address: Stanley Hall, University Dr

department: Bioengineering

institute: University of California, Berkeley

description: CM_Core_biol rep2

data_processing:
Data filtering was performed to remove low-quality reads or reads with adapters
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. Mapped regions were classified as exons, introns, or intergenic regions.
Gene expression quantification was performed using featureCounts v1.5.0-p3, which was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: genome_gene.fa.gz
Supplementary files format and content: gene_fpkm.xls; Includes FPKM values for each sample; excel format
Supplementary files format and content: gene_count.xls; Includes gene counts for each sample; excel format

extract_protocol:
All samples were treated with 10k U/ml Hyaluronidase from bovine testes, Type IV-S (Sigma-Aldrich, H3884) for 15 min with agitation until the hydrogel was fully degraded. Afterwards, RNA was extracted using TRIzol Reagent (Invitrogen, 15596018) according to manufacturer’s recommendations. In brief, 1M cells were mixed with 100 µl TRIzol Reagent and the solution was vortexed for 30 seconds. 20 µL chloroform (Sigma, c2432) was added to the mixture and the solution was placed on ice for 15 minutes. Sample were centrifuged at 14000 rpm for 10 minutes and the clear RNA layer was carefully transferred to a new Eppendorf tube. Each RNA sample was mixed with a 1:1 volume of 2-Propanol (Sigma-Aldrich, 190764-4L) and 0.5 µL Glycogen, RNA grade (Thermo Scientific, R0551). After an overnight incubation at -20˚C, samples were centrifuged at 14000 rpm for 10 minutes at 4˚C and the RNA pellet was rinsed twice by aspirating the supernatant, adding 400 µL 75% Ethanol and centrifuging at 14000 rpm for 1 minute. Following the second rinse, the supernatant was carefully and completely removed, and RNA pellets were incubated at room temperature until visibly dry. RNA was dissolved in 30 µL RNase-free DNase-free distilled H2O and RNA concentration and purity was measured with Nanodrop.
Isolated RNA was sent to Novogene Corporation Inc. (Sacramento, CA) for library construction, quality control and sequencing. In brief, 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. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: glioblastoma stem cells


title: GSC-20, Control Media, Day 28, full channel_rep2

description: gsc20_Ctrl_biol rep2


title: GSC-20, M2 Macrophage CM, Day 28, core fraction_rep1

description: CM_Core_biol rep1


title: GSC-20, M2 Macrophage CM, Day 28, invasive fraction_rep3

description: CM_Inv_biol rep3


title: GSC-20, M2 Macrophage CM, Day 28, invasive fraction_rep1

description: CM_Inv_biol rep1


title: GSC-20, M2 Macrophage CM, Day 28, invasive fraction_rep2

description: CM_Inv_biol rep2


title: GSC-20, M2 Macrophage CM, Day 28, core fraction_rep3

description: CM_Core_biol rep3


title: GSC-20, Control Media, Day 28, full channel_rep1

description: gsc20_Ctrl_biol rep1


title: Larva_input_2


title: GSC-20, Control Media, Day 28, full channel_rep3

description: gsc20_Ctrl_biol rep3


title: scRNAseq_human_small_intestine_Sample2.2

description: 10x Chromium single cell data

value: FACS sorted intestinal epithelial progenitor cells (CD45-, EpCAM+, CD44+)


title: scRNAseq_human_small_intestine_Sample2.5

description: 10x Chromium single cell data


title: scRNAseq_human_small_intestine_Sample2.3

description: 10x Chromium single cell data


title: scRNAseq_human_small_intestine_Sample2.4

description: 10x Chromium single cell data


title: Without_yDcpS_enrich_4

source_name: Liver tissue

value: Liver

value: yDcpS-

value: Enrich


title: ATAC_NWT_Veh rep2

description:
mouse_C57Bl6_NCoRWT_BMDM_ATAC_Veh6h_rep2_YA_l20201015_TTGACCCT
ATAC_NWT_merged_allRawTags.txt

value: Bone marrow-derived macrophages

value: NCoR1 flox/flox

value: Veh


title: ATAC_NWT_Veh rep1

description:
mouse_C57Bl6_NCoRWT_BMDM_ATAC_Veh6h_rep1_YA_l20201015_TGGTCACA
ATAC_NWT_merged_allRawTags.txt


title: Mutant 3

city: Los Angeles

first: Fei

last: Pei

address: 2250 Alcazar St

institute: USC

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed and aligned using TopHat (Version 2.0.8) with the mm10 genome
RPKM was used to normalize the data and differential expression was calculated by selecting transcripts that changed with p < 0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: molar

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol: cDNA library preparation and sequencing were performed at the Technology Center for Genomics & Bioinformatics at the University of California, Los Angeles (UCLA).

treatment_protocol: molar samples from Fgfr2fl/fl (control) and Gli1-CreER;Fgfr2fl/fl (mutant) mice were collected at PN7.5 after TMX for RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol

value: molar

value: TMX induction


title: Without_yDcpS_enrich_3


title: anther, Mv 17-09 control rep3

city: Martonvásár

first: Attila

last: Fábián

address: Brunszvik 2

country: Hungary

institute: Centre for Agricultural Research

data_processing:
Sequencing results were analyzed by FASTQC v0.11.8 (Babraham Bioinformatics, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to assess the read quality.
Trimming and adapter removal were performed using CLC Genomics Workbench v23.3 (Qiagen).
The trimmed short reads were mapped to the IWGSC RefSeq v2.1 reference genome assembly (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies) by CLC Genomics Workbench v23.3.
Expression values were normalized by the TMM method using CLC Genomics Workbench v23.3.
Assembly: IWGSC RefSeq v2.1
Supplementary files format and content: tab-delimited text file includes  RPKM values for each sample

organism: Triticum aestivum

source_name: anther

extract_protocol:
Anther tissue was ground using a mortar and pestle in liquid nitrogen. Total RNA was extracted using Direct-zol™ RNA MiniPrep Kit, following the manufacturer’s protocol (Zymo Research, Irvine, CA, USA).
The libraries for RNA-seq were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswitch, MA, USA). Briefly, ribosomal RNA was depleted from 400 ng of total RNA using the QIAseq FastSelect rRNA Plant Kit (Qiagen, Hilden, Germany). The depleted RNA was fragmented, end-prepped, adapter ligated, and the libraries were amplified according to the manufacturer’s instructions.

value: anther

tag: cultivar

tag: stress

value: control


title: anther, Mv 17-09 treated rep1

value: treated


title: anther, Mv 17-09 treated rep2


title: anther, Mv 17-09 treated rep3


title: Without_yDcpS_enrich_2


title: anther, Mv 17-09 control rep2


title: Without_yDcpS_enrich_1


title: Mutant 2

tag: genotype

tag: treatment


title: With_yDcpS_enrich_3

value: yDcpS+


title: PBMC, HBV-ACLF1, Jiang, CD4+BTLA+

city: Quanzhou

first: Xueping

last: Yu

state: Fujian

address: No. 250 East Street

department: Infection Disease

institute: Fujian Medical University Affiliated First Quanzhou hospital

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GRCh38(hg38) using TopHat（version:2.0.9）
The number of Fragments of each gene after TopHat comparison was counted by HTSeq, and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCh38(hg38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: PBMC

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Cat# 217004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
According to the instructions of the experiment, the purified Total RNA was remove rRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: PBMC

tag: cell type

value: HBV-ACLF

value: Jiang, male

value: No


title: PBMC, HBV-ACLF2, Chen, CD4+BTLA+

tag: tissue

value: Chen, male


title: PBMC, HBV-ACLF2, Chen, CD4+BTLA-


title: Lymphocytes, cartridge_12, abseq library

city: Newcastle upon Tyne

first: Kenneth

middle: Frank

last: Baker

address: Framlington Place

department: Translational and Clinical Research Institute

country: United Kingdom

institute: Newcastle University

description: Rhapsody

data_processing:
Raw FASTQ sequencing files were uploaded to the SevenBridges Genomics platform and processed using the standard BD Rhapsody deconvolution, alignment and V(D)J sequencing pipelines. In addition to the standard pipelines, cells with both TCR and BCR paired reads (i.e. T/B cell doublets) were excluded.
Assembly: BD Rhapsody Immune Response Panel
Supplementary files format and content: Matrix of marker counts, where rows are markers and columns are cells. Suffix ".pAbO" in marker name denotes surface protein (i.e. Abseq antibody).

source_name: Circulating lymphocytes

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from fresh whole blood by density centrifugation, and stored in foetal calf serum with 10% DMSO at -150°C. PBMC samples were subsequently thawed and stained with fluorescent antibodies for fluorescence-activated cell sorting (FACS). After removal of debris, doublets and dead cells, three subsets were isolated from each sample: CD3+CD4+CD45RO+PD1hi T cells, CD3+CD8+CD45RO+PD1hi T cells, and CD19+ B cells. Isolated cells were immediately processed according to the BD Rhapsody protocol, including staining with oligo-tagged Abseq surface antibodies, loading onto a Rhapsody cartridge (ratio 2:2:1 CD4+:CD8+:B cells), and cell lysis. Sample tags were used to combine 6 individual cell isolates from a single patient on each cartridge (two visit time points, three isolates per time point), with a unique index tag for each cartridge. Beads were then processed according to the standard BD Rhapsody protocol with additional V(D)J steps.
Beads were stored at 4°C for <4 months prior to library preparation, which was performed simultaneously across all samples using the BD Immune Response Panel with additional custom primers. Five libraries (antibody, mRNA, TCR, BCR, SMK sample tag) were prepared and sequenced in two runs: NovaSeq 6000 S2 300 cycle (75 x 225bp) + 10% PhiX (mRNA, TCR, BCR, SMK sample tag libraries), and NovaSeq 6000 S2 100 cycle (2 x 50bp) + 20% PhiX (antibody library).

value: Circulating lymphocytes

value: CD3+CD4+CD45RO+PD1hi T cells, CD3+CD8+CD45RO+PD1hi T cells, CD3-CD19+ B cells


title: Mutant 1


title: PBMC, HBV-ACLF1, Jiang, CD4+BTLA-


title: anther, Ellvis treated rep3

value: Ellvis


title: anther, Ellvis treated rep2


title: anther, Mv 17-09 control rep1


title: anther, Ellvis treated rep1


title: With_yDcpS_enrich_4

tag: strain

value: Liver

value: Enrich


title: Control 2

value: wild type


title: Lymphocytes, cartridge_12, rna_vdj_smk library

description: Rhapsody


title: Lymphocytes, cartridge_11, abseq library

description: Rhapsody


title: With_yDcpS_enrich_2


title: With_yDcpS_enrich_1


title: Lymphocytes, cartridge_10, abseq library

description: Rhapsody


title: anther, Ellvis control rep3


title: anther, Ellvis control rep2


title: Distal jejunum Aster-B/C global KO fed diet with ezetimibe rep3

city: Dallas

first: Lara

last: Bideyan

state: TX

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

data_processing:
For RNA-Seq, data quality analysis was performed via FastQC
The reads were aligned to the mm10 genome using STAR (version 2.6.0c).
Differential expression analysis was performed with DESeq2 and genes were classified as significantly regulated if adjusted P value < 0.05.
Genes were annotated using biomaRt package in R (https://www.R-project.org/).
Assembly: mm10
Supplementary files format and content: csv file showing the normalized counts from RNA-Seq for each gene for each sample obtained from DESeq2
Supplementary files format and content: csv file showing the RNA-Seq results from DESeq2

source_name: distal jejunum

extract_protocol:
Total RNA from frozen tissue was extracted through TRIzol (Invitrogen).
Total RNA libraries were made with NEBNext Ultra II RNA Library Prep Kit for Illumina (New Ingland Biolabs, Ipswich, MA, USA)

treatment_protocol: Mice were fed special diets (control diet: 0.08% cholesterol; ezetimibe diet: 0.08% cholesterol + 0.01% ezetimibe)

value: distal jejunum

tag: age

value: 13-15 weeks old

tag: Sex

value: male

value: Aster-B/C global KO

value: low cholesterol diet + 0.01% ezetimibe


title: Control 3

value: molar

value: TMX induction


title: Distal jejunum Aster-B/C global KO fed diet with ezetimibe rep4


title: Lymphocytes, cartridge_10, rna_vdj_smk library

description: Rhapsody


title: Without_yDcpS_input_3

value: yDcpS-

value: Input


title: anther, Ellvis control rep1

value: anther

value: control


title: Without_yDcpS_input_1


title: Lymphocytes, cartridge_09, rna_vdj_smk library

description: Rhapsody

value: Circulating lymphocytes


title: Lymphocytes, cartridge_09, abseq library

description: Rhapsody

value: CD3+CD4+CD45RO+PD1hi T cells, CD3+CD8+CD45RO+PD1hi T cells, CD3-CD19+ B cells


title: Distal jejunum Aster-B/C global KO fed diet with ezetimibe rep2


title: Distal jejunum Aster-B/C global KO fed diet with ezetimibe rep1


title: Distal jejunum Aster-B/C global KO fed control diet rep3

value: low cholesterol diet


title: Lymphocytes, cartridge_11, rna_vdj_smk library

description: Rhapsody


title: Without_yDcpS_input_2

value: Liver


title: Distal jejunum Aster-B/C global KO fed control diet rep2


title: With_yDcpS_input_3

value: yDcpS+


title: Lymphocytes, cartridge_08, rna_vdj_smk library

description: Rhapsody


title: Control 1

value: wild type


title: With_yDcpS_input_4


title: Lymphocytes, cartridge_08, abseq library

description: Rhapsody


title: Without_yDcpS_input_4


title: Lymphocytes, cartridge_07, abseq library

description: Rhapsody


title: Distal jejunum Aster-B/C global KO fed control diet rep1

value: distal jejunum


title: With_yDcpS_input_2


title: Lymphocytes, cartridge_07, rna_vdj_smk library

description: Rhapsody


title: Distal jejunum wildtype fed diet with ezetimibe rep4

value: 13-15 weeks old

value: WT


title: With_yDcpS_input_1


title: T47D_Starved_Estrogen_rep1

city: Charlottesville

first: Thomas

middle: G

last: Scott

state: VA

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://guertinlab.github.io/TRPS1_ER/Vignette.html
Assembly: hg38
Supplementary files format and content: bigWig counts files
Supplementary files format and content: Peak counts file

growth_protocol: T47D cells from ATCC were were grown in Roswell Park Memorial Institute (RPMI) 1640 medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate

extract_protocol:
At the time of harvest, cells were moved to ice and scraped in 1mL ice cold PBS, and 100μL (∼5 x 10^4 cells) were transferred to 1.5 mL tubes. Cells were centrifuged at 500 x g for 5 minutes at 4°C, and the pellets were resuspended in 50 μL cold lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, adjusted to pH 7.4) and incubated on ice for 3 minutes. Samples were washed with 1 mL cold wash buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20). Cells were centrifuged at 500 x g for 10 minutes at 4°C, and pellets were resuspended in the transposition reaction mix (25 μL 2X TD buffer (Illumina), 2.5 μL TDE1 Tn5 transposase (Illumina), 16.5 μL PBS, 0.5 μL 1% Digitonin, 0.5 μL 10% Tween-20, 5 μL nuclease-free water) and incubated in a thermomixer at 37°C and 100rpm for 30 minutes.
DNA was extracted with the DNA Clean and Concentrator-5 Kit (Zymo Research). Sequencing adapters were attached to the transposed DNA fragments using NEBNext Ultra II Q5 PCR mix (New England Biolabs), and libraries were amplified with 8 cycles of PCR. PEG-mediated size fractionation (Lis 1980) was performed on the libraries by mixing SPRIs-elect beads (Beckman) with each sample at a 0.5:1 ratio, then placing the reaction vessels on a magnetic stand. The right side selected sample was transferred to a new reaction vessel, and more beads were added for a final ratio of 1.8:1. The final size-selected sample was eluted into nuclease-free water. This size selection protocol was repeated to further remove large fragments.

treatment_protocol: For each Complete sample, 5x10^5 cells were grown for 1 day in complete medium. After 1 day, a final concentration of 100nM fulvestrant, raloxifene, or tamoxifen or 0.1% volume/volume DMSO was added, and the cells were incubated for 1 hour. For each Starved sample, 3.3x10^5 cells were grown for 3 days in phenol red free RPMI 1640 medium containing 10% charcoal stripped FBS, 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate. After 3 days, a final concentration of 1nM beta estradiol or 0.1% volume/volume DMSO was added, and the cells were incubated for 1 hour.

value: 1nM beta estradiol for 1 hour


title: T47D_Starved_DMSO_rep4

value: 0.1% v/v DMSO for 1 hour


title: T47D_Starved_Estrogen_rep3


title: T47D_Starved_Estrogen_rep4


title: T47D_Starved_Estrogen_rep2


title: Lymphocytes, cartridge_06, abseq library

description: Rhapsody


title: Distal jejunum wildtype fed diet with ezetimibe rep3

value: male

value: low cholesterol diet + 0.01% ezetimibe


title: NAD5_enrich_4

value: 5% NAD-RNA spike-in

value: Enrich


title: Distal jejunum wildtype fed diet with ezetimibe rep2


title: NAD5_enrich_3


title: Lymphocytes, cartridge_06, rna_vdj_smk library

description: Rhapsody


title: Lymphocytes, cartridge_05, rna_vdj_smk library

description: Rhapsody


title: Lymphocytes, cartridge_05, abseq library

description: Rhapsody


title: NAD5_enrich_2


title: NAD5_enrich_1


title: Distal jejunum wildtype fed control diet rep4


title: Distal jejunum wildtype fed diet with ezetimibe rep1


title: Lymphocytes, cartridge_04, abseq library

description: Rhapsody


title: NAD1_enrich_4

value: 1% NAD-RNA spike-in


title: Distal jejunum wildtype fed control diet rep3


title: Lymphocytes, cartridge_04, rna_vdj_smk library

description: Rhapsody


title: Distal jejunum wildtype fed control diet rep2


title: NAD1_enrich_3


title: NAD1_enrich_2


title: T47D_Starved_DMSO_rep2


title: Distal jejunum wildtype fed control diet rep1


title: T47D_Starved_DMSO_rep1


title: T47D_Complete_Tamoxifen_rep3

value: 100nM Tamoxifen for 1 hour


title: Exd2+/+ rep 2 [RNA-seq]

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

data_processing:
Reads were sorted into individual libraries based on the barcodes. For small-RNAseq reads the 3′ adapter sequences were clipped from the reads using cutadapt (DOI:http://dx.doi.org/10.14806/ej.17.1.200) and only sequences of at least 15 nucleotides were left for further analysis (cutadapt parameters: -a AGATCGGAAGAGCACACGTCT -m 15 -e 0.2 -O 4 -q 10 --match-read-wildcards). The reads were mapped to the mouse genome (GRCm38: Ensembl release 95) using STAR (parameters: --runThreadN 10 -outFilterType BySJout --limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000). For small RNA-seq samples only the reads of 25nt-32nt were considered to represent piRNAs and selected for further analysis.
To compare the piRNA production from individual pachytene piRNA clusters, the piRNA counts for each cluster were compared between Exd2∆ and Exd2+/+ using edgeR. In case of overlapping clusters, only the longest ones were retained.
Genome_build: GRCm38
Supplementary_files_format_and_content: The excel file contains differential expression analysis from pachytene piRNA clusters obtained by edgeR.

source_name: Testes

growth_protocol: Exd2∆ mice were generated at the mouse transgenic facility of the EMBL Monterotondo, Rome, Italy. Genome of single mouse embryos of the C57BL6 background were edited using guide RNA/Cas9 endonuclease complex to remove the 3' end of exon 2 of the mouse Exd2 gene locus and part of the downstream intron.

extract_protocol:
RNA was extracted from testes with TRIzol™ Reagent (Invitrogen). RNA pellets were resuspended in 100 µl RNase free water. RNA concentration was quantified with NanoDrop (Thermo Fisher Scientific). For isolation of small RNAs, 10 µg of total RNA was run into a 15% denaturating Urea-PAGE gel, the region of gel containing small RNAs was cut out, and small RNAs were extracted rom the Urea PAGE gel slices with 400µl of NaCl 0.4M. After incubation, the solution was filtered by spinning full speed for 2 min, and RNA was precipitated by adding 40 µl of 7.5 M ammonium acetate, pH 5.5, 1 µl of Glycogen RNA grade (20 ng/ml) and 1 ml of 100% EtOH, incubating 5 h at -20°C. After centrifugation, RNA pellets were washed with 80% EtOH and suspended in RNase free H2O for Illumina library preparation.
Small RNA-seq libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina®, and the quality of the libraries were validated in 2% agarose gel. For size selection, libraries were run into a 3.6% Agarose (MetaPhorTM) gel, region of desired size was cut out and DNA was extracted from gel slices with QIAGEN MinElute Gel extraction Kit. For the preparation of RNA-seq libraries, ribosomal RNA was depleted from 1 µg of total RNA using NEBNext® rRNA Depletion Kit v2 and libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. Both small RNA-seq and RNA-seq libraries were sequenced at the GENOMICS Platform of the University of Geneva using Illumina HiSeq 4000 platform with single-end run with a read length of 50 nt.

value: adult

tag: experiment

value: long RNA-seq


title: T47D_Starved_DMSO_rep3


title: T47D_Complete_Tamoxifen_rep2


title: T47D_Complete_Tamoxifen_rep4


title: Lymphocytes, cartridge_03, abseq library

description: Rhapsody

value: Circulating lymphocytes

value: CD3+CD4+CD45RO+PD1hi T cells, CD3+CD8+CD45RO+PD1hi T cells, CD3-CD19+ B cells


title: T47D_Complete_Raloxifene_rep4

value: 100nM Raloxifene for 1 hour


title: Lymphocytes, cartridge_03, rna_vdj_smk library

description: Rhapsody


title: T47D_Complete_Tamoxifen_rep1


title: NAD1_enrich_1

value: Liver


title: Exd2+/+ rep 1 [RNA-seq]


title: T47D_Complete_Raloxifene_rep3


title: NAD0_enrich_4

value: 0% NAD-RNA spike-in


title: Lymphocytes, cartridge_02, abseq library

description: Rhapsody


title: T47D_Complete_Raloxifene_rep2


title: T47D_Complete_Raloxifene_rep1


title: Exd2∆ rep 1 [RNA-seq]


title: Lymphocytes, cartridge_02, rna_vdj_smk library

description: Rhapsody


title: Exd2∆ rep 2 [RNA-seq]


title: NAD0_enrich_2


title: NAD0_enrich_3


title: Lymphocytes, cartridge_01, abseq library

description: Rhapsody


title: T47D_Complete_Fulvestrant_rep4

value: 100nM Fulvestrant for 1 hour


title: Lymphocytes, cartridge_01, rna_vdj_smk library

description: Rhapsody


title: NAD0_enrich_1


title: MesHMLE, QKI kd, rep3

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description:
genewise-count.csv
genewise-info.csv
genewise-tail-count.csv
genewise-tail.csv

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four un-templated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 2000 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Comma-separated files: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains counts of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis with the statistics package "Fitnoise". gene.csv lists the genomic locations of the genes that were used. Locations are 1-based.
Assembly: human genome, build hg38
Supplementary files format and content: Comma-separated files: genewise-count.csv, genewise-info.csv, genewise-tail-count.csv, genewise-tail.csv

source_name: mesHMLE

growth_protocol: The immortalized human mammary epithelial cell line (HMLE) was cultured in HuMEC Ready Media (ThermoFisher) with HuMEC Supplement Kit (ThermoFisher) and passaged at a 1:5 ratio every 72 hours. The TGF-β-treated mammary epithelial cell line (mesHMLE) was derived by culturing immortalized human mammary epithelial cells (HMLE) in mesHMLE culturing media (DMEM/F12- Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 supplemented with 5% Foetal Bovine Serum, 20 ng/ml EGF, 10 μg/ml insulin and 0.5 μg/ml hydrocortisone) with 2.5 ng/μL TGF-β1 for at least 14 days. Once established, mesHMLE cells were cultured in mesHMLE culturing media and passaged at a 1:10 ratio every 72 hours.

extract_protocol:
RNA was extracted using Trizol (ThermoFisher) following the standard manufacturer’s protocol.
Library construction was by the PAT-seq approach. Breifly this involves a modified the ePAT approach to tagging adenylated RNA to generate libraries suitable for deep sequencing. Briefly, adenylated RNA is sequence specifically extended by dNTPs using Klenow polymerase and an annealed DNA anchor oligonucleotide. This takes advantage of the native function of DNA polymerase to extend an RNA primer from a DNA template in second strand synthesis. Importantly, any unwanted priming to internal poly(A)-tracts in RNA is avoided by a requirement for 3’ extension in subsequent fragment selection and reverse transcription. No ribosome depletion is necessary. Here, the anchor sequence was compatible with the Illumina index primers and included a 5’ biotin moiety to facilitate handling. In a second step, the 3’ tagged RNA was subject to limited fragmentation by RNase T1. This cleaves RNA after G-residues and ensures that cleavage is only possible within the body of the RNA, not the poly(A)-tract or the DNA sequence of the extended tag. The fragmented RNA was 5’ phosphorylated to allow RNA Ligase 2 mediated ligation of an Illumina compatible splinted-linker to the RNA fragments. Reverse transcription was primed from the anchor sequence. Note: All manipulations after limited fragmentation were performed in association with streptavidin magnetic beads. The cDNA PAT-seq libraries was eluted from beads, size-selected by Urea PAGE and amplified with primers that introduce the features for directional Illumina sequencing and indexing. In samples analysed here, the window of selection was between 120-300 bases. This size range was selected to allow for ≥ 25 bases of 3’UTR sequence to map reads to the genome, the an average yeast poly(A)-tail of ~25 bases (maximum ~90 bases), the majority of reads would contain heterogeneous 5’ sequence of sufficient length to map uniquely to the yeast genome. Note: all reads run in 5’ to 3’ direction from unique sequence into a variable length of poly(A) homopolymers. This means that color balance is preserved and that any low fidelity within the homopolymers is limited to the end of the read.
Illumina directional RNA-seq

treatment_protocol: mesHMLE cells were treated with control or QKI-5 targeting siRNAs for 72hr prior to RNA extraction. QKI-5 siRNA #1 sequence was 5'-CUGGUAAUCGCCUUUGCUU UU-3'. QKI-5 siRNA #2 sequence was 5'-CUAUUAACCCACAGCAUUA UU-3'.

value: mesHMLE

value: breast

value: QKI-5 siRNA #1

value: QKI knockdown

tag: replicate

tag: index 1 (i7)

value: TCGACGTC

tag: index 2 (i5)

value: ATAGAGAG


title: NAD5_input_4

tag: condition

value: 5% NAD-RNA spike-in

value: Input


title: NAD5_input_2

tag: assay


title: T47D_Complete_Fulvestrant_rep2

tag: cell line


title: Exd2∆ rep 1 [small RNA-seq]

value: small RNA-seq


title: MesHMLE, QKI kd, rep1

value: CGATCAGT


title: MesHMLE, QKI kd, rep2

value: TGCAGCTA


title: Exd2∆ rep 2 [small RNA-seq]

value: adult


title: Exd2+/+ rep 1 [small RNA-seq]


title: T47D_Complete_DMSO_rep4


title: NAD5_input_3


title: T47D_Complete_Fulvestrant_rep3


title: NAD5_input_1


title: T47D_Complete_Fulvestrant_rep1


title: T47D_Complete_DMSO_rep3


title: MesHMLE, rep3

value: Control siRNA

value: WT

value: CCTAAGAC


title: MesHMLE, rep2

value: ACTGAGCG


title: NAD1_input_4

value: Liver

value: 1% NAD-RNA spike-in


title: T47D_Complete_DMSO_rep2

value: 0.1% v/v DMSO for 1 hour


title: NAD1_input_3


title: T47D_Complete_DMSO_rep1


title: Exd2+/+ rep 2 [small RNA-seq]


title: NAD1_input_2


title: MesHMLE, rep1

value: mesHMLE

value: breast

value: TAGCGCTC


title: T47D_Complete_Tamoxifen, rep2

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://github.com/guertinlab/Nascent_RNA_Methods
Assembly: hg38
Supplementary files format and content: Stranded bigWig counts files
Supplementary files format and content: Gene counts files
Library strategy: PRO-seq

treatment_protocol: For each sample, 2x10^6 cells were grown for 3 days in complete medium. After 3 days, a final concentration of 100nM fulvestrant, raloxifene, or tamoxifen or 0.1% volume/volume DMSO was added, and the cells were incubated for 1 hour.

value: 100nM Tamoxifen for 1 hour

tag: molecule subtype

value: nascent RNA


title: HMLE, rep3

source_name: HMLE

value: HMLE

value: ATGCGCAG

value: ATAGAGAG


title: NAD1_input_1

value: Input


title: HMLE, rep2

value: TACGCTGC


title: HMLE, rep1

value: CGGAGCCT


title: NAD0_input_4

value: 0% NAD-RNA spike-in


title: NAD0_input_3


title: T47D_Complete_Tamoxifen, rep1


title: T47D_Complete_Raloxifene, rep2

value: 100nM Raloxifene for 1 hour


title: T47D_Complete_Raloxifene, rep1


title: T47D_Complete_Fulvestrant, rep2

value: 100nM Fulvestrant for 1 hour


title: NAD0_input_2

value: Liver


title: HCT116, size-matched input

city: Shenzhen

first: Wei

last: Chen

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

department: School of Life Sciences

institute: Southern University of Science and Technology

data_processing:
First, adapters were removed by cutadapt v 1.18 with parameters -m 20 -q 20,20.
Then, the clean reads were aligned against human interspersed repeats and low complexity DNA sequences (downloaded from http://www.repeatmasker.org/) by bowtie2 with default parameters.
Reads that unmapped to the repeats were aligned by STAR v 2.7.8a against human hg38 genome using GENCODE v37 annotations with parameters --outFilterScoreMin 10 --alignEndsType Local --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0
After removing PCR duplicates using barcode_collapse_pe.py (https://github.com/YeoLab/gscripts/blob/master/gscripts/clipseq/barcode_collapse_pe.py), peaks were called using the second read in the pair by CLIPper v 2.0.0 and normalized to size-matched input (SMInput) control.
Assembly: hg38
Supplementary files format and content: bigWig, Peaks bed (except for Input sample).

growth_protocol: HCT116 cells were cultured in recommended media with 10% FBS (Gibco, #10270106) and 1% P/S (Gibco, #15070063) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Cells were lysed, Turbo DNase/RNase I treated, sonicated, and then subjected to immunoprecipitation with two different anti-DDX6 antibody  precoupled with protein G/A beads. After stringent washes, the RNA/protein complex was dephosphorylated with T4 polynucleotide kinase and FastAP alkaline phosphatase, and then ligated to an RNA adaptor at the 3ʹ end. Next, the resulting sample was eluted through LDS sample buffer. 10% of the eluted sample was used for western gel and the remaining 90% for CLIP gel. The region of the CLIP gel above the 54 kDa protein was isolated followed by proteinase K digestion to release RNA.
The purified RNA was reverse transcribed with AffinityScript enzyme and AR17 primer. Then, a DNA adaptor was ligated to the purified cDNA 3ʹ ends. After cleanup, the library was amplified using Q5 DNA polymerase and F-D501 and R-D701 primers, and purified through a 2% low melting temp agarose gel, recycling the library from 175-400bp gels. The final library was used for paired-end Illumina sequencing.

treatment_protocol: Cells are cross-linked with 254nm UV light at 400 mJ/cm2 in ice-cold PBS.

value: human colon cancer cell line

tag: chip _antibody


title: NAD0_input_1


title: T47D_Complete_Fulvestrant, rep1


title: HCT116, DDX6 eCLIP, rep2

value: Anti-DDX6 antibody


title: HCT116, DDX6 eCLIP, rep1


title: hHGFtg-hMETtg-Ctnnb1-PBCre

city: Duarte

first: Zijie

last: Sun

address: 1500 E. Duarte Rd.

institute: City of Hope

data_processing:
The library purity and size was validated by capillary electrophoresis using 2,100 Bioanalyzer (Agilent Technologies)
The library quantity was measured fluorometrically using Qubit dsDNA HS Assay Kit from Invitrogen
The libraries were sequenced with a NovaSeq 6000 instrument (Illumina) to a depth of ~100k reads per cell. Raw sequencing data were processed using the 10x Genomics’ Cell Ranger pipeline (version 6.0.2) to generate FASTQ files and were aligned to the mm10 genome with added hHGFtg and hMETtg sequences to generate gene expression counts
Assembly: mm10 reference genome with added hHGFtg and hMETtg sequence
Supplementary files format and content: Txt file with counts for each cell corresponding to each gene

source_name: Prostatic carcinoma

extract_protocol:
Prostatic adenocarcinoma and carcinoma were trimmed and dissociated to single cells using collagenase and TrypLE (Gibco)
The library was prepared using 10x Genomics Chromium Single Cell 3' Solution with v3 chemistry following manufacturer protocols (10x Genomics)

value: Prostate

tag: normal/modified

value: Prostatic carcinoma


title: HCT116, batch3, DDX6KO_shHMGA2, rep2

data_processing:
First, adapters were removed by cutadapt v 1.18 with parameters -m 20 -q 20,20.
Then, the clean reads were aligned by STAR v 2.7.8a against the human hg38 genome using GENCODE v37 annotations with parameters --outFilterMultimapNmax 1.
Unique mapped read counts for individual genes were calculated by featureCounts v 2.0.1 with parameter -p -g gene_name -s 2.
Differential expression analysis was performed using DESeq2 package with default processes. Differentially expressed genes were genes with |fold change| > 2 and false discovery rate (FDR) < 0.05.
The bigwig files were generated from BAM files by home-made script and visualized by Integrative Genomics Viewer (IGV, https://software.broadinstitute.org/software/igv/).
Assembly: hg38
Supplementary files format and content: bigWig, Tab-delimited text files include TPM values for each sample.

extract_protocol:
Total RNA was extracted by TRIzol® Reagent (Ambion).
mRNA sequencing libraries were prepared according to the standard protocol provided by Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (YEASEN, #12309ES96) with starting material of 1ug total RNA.

treatment_protocol: The Cas9-expressing cell clone was established by using LentiCas9-Blast virus  (Addgene) and single cell sorting. To generate KO cell clones, Cas9-expressing cells were transiently transfected with plasmid (pCRISPRia-v2-RFP derived from pCRISPRia-v2) expressing gRNAs. Gene knockdown mediated by shRNA was performed using pLKO.1-Blast plasmid, which was modified from pLKO.1-TRC.

tag: genotype

value: DDX6 KO, shHMGA2


title: T47D_Complete_DMSO, rep2

tag: treatment

value: 0.1% v/v DMSO for 1 hour


title: hHGFtg-hMETtg-PBCre

source_name: Prostatic adenocarcinoma

value: Prostatic adenocarcinoma


title: HCT116, batch3, DDX6KO_shHMGA2, rep1

tag: cell type


title: Healthy controls 05

city: Guangzhou

first: Yingqin

last: Li

address: Room 927, Building 2, No. 651 Road Dong Feng East

institute: Sun Yat-sen University Cancer Center

description: circRNA expression data from nasopharyngeal mucositis

hyb_protocol: 1.65 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number 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 with using R software. Differentially expressed circRNAs with statistical significance between groups were identified through P-value/FDR filtering.
Quantile normalization and subsequent data processing were performed with using R software.

source_name: nasopharyngeal mucositis

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: Nasopharyngeal carcinoma biopsy samples obtained through nasopharyngoscope before treatment.

extract_protocol: Total RNA was extracted from frozen fresh tissues using the AllPrep DNA/RNA Mini Kit (QIAGEN GmbH, Hilden, Germany)

tag: tissue

value: nasopharyngeal mucositis


title: T47D_Complete_DMSO, rep1

value: nascent RNA


title: HCT116, batch3, DDX6KO_shNC, rep2

value: DDX6 KO, shNC


title: HCT116, batch3, DDX6KO_shNC, rep1


title: Healthy controls 04


title: T47D_Clone39_dTAG13_rep4

description:
T47D_Clone39_dTAG13_rep4_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig

data_processing:
Adapter trimming: cutadapt v1.8.1
UMI trimming and reverse complementing: seqtk v1.3
FASTQ deduplication: https://github.com/guertinlab/fqdedup v1.0.0
FASTQ pairing: fastq_pair v1.0
Alignment: bowtie2 v2.4.4
File manipulation: samtools v1.9
File manipulation: https://github.com/guertinlab/seqOutBias v1.3.1
All details and code: https://guertinlab.github.io/TRPS1_ER/Vignette.html
Assembly: hg38
Supplementary files format and content: Stranded bigWig counts files
Supplementary files format and content: Gene counts file
Library strategy: PRO-seq

growth_protocol: T47D cells (RRID:CVCL_0553) (ATCC) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gemini) and 10ug/ml insulin from bovine pancreas (Sigma, made as a 1000x solution in 1% aqueous glacial acetic acid).

extract_protocol:
Cell permeabilization was performed as previously described (Mahat et al. 2016), with modifications. At the time of harvest, cells were scraped in 10mL ice cold PBS and washed in 5mL buffer W (10mM Tris-HCl pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, 0.5mM DTT, 0.004U/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)). Cells were permeabilized by incubating with buffer P (10 mM Tris-HCl pH 7.5, KCl 10 mM, 250 mM sucrose , 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40, 0.5 mM DTT, 0.004 units/mL SUPERaseIN RNase inhibitor (Invitrogen), Complete protease inhibitors (Roche)) for 3 minutes on ice. Cells were washed with 10 mL buffer W before being transferred into 1.5mL tubes using wide bore pipette tips. Finally, cells were resuspended in 50μL buffer F (50mM Tris-HCl pH 8, 5mM MgCl2, 0.1mM EDTA, 50% Glycerol, 0.5 mM DTT). Cells were snap frozen in liquid nitrogen and stored at -80°C.
PRO-seq libraries were prepared as previously described (Judd et al. 2020), with modifications. RNA extraction after the run-on reaction was performed with 500μL Trizol LS (Thermo Fisher) followed by 130μL chloroform (Sigma). The equivalent of 1μL of 50μM for each adapter was used. A random eight base unique molecular identifier (UMI) was included at the 5′ end of the adapter ligated to the 3′ end of the nascent RNA. 37°C incubations were performed with rotation with 1.5mL tubes placed in 50mL conical tubes in a hybridization oven. For the reverse transcription reac- tion, RP1 was used at 100μM and dNTP mix was used at 10mM each. Libraries were amplified by PCR for a total of 8 cycles in 100μL reactions with Phusion polymerase (New England Biolabs). No PAGE purification was performed to ensure that our libraries were not biased against short nascent RNA insertions.

treatment_protocol: 4 replicates were performed from cells treated and collected at different times in the same day. 4*10^6 cells per sample were plated in 10cm dishes 1 day before harvest. Cells were treated with DMSO or 100nM dTAG-13 in DMSO for 90 minutes and collected simultaneously.

value: 100nM dTAG-13 for 90 minutes


title: BM neutrophils, KO, Rep2

city: Beijing

first: Yang

last: Liu

address: Dongdan Santiao 5

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

data_processing:
The adapters and low quality bases were removed.
The Fastq files were aligned to the reference genome (mm10) using Hisat2 (v2.2.1).
Reads mapped to tRNA and rRNA are removed for the following analysis.
Stringtie (v2.1.4) was used to calculate the TPM of each gene to represent their mRNA expression level.
The differential genes were identified by a negative binomial model using the DEseq2 package.
Assembly: mm10
Supplementary files format and content: txt

source_name: Mouse bone marrow neutrophils

extract_protocol:
Total RNA was isolated from bone marrow neutrophils with TRIzol reagent (Invitrogen) and subjected to Poly(A)+ mRNA purification via Dynabeads mRNA Purification Kit ( Invitrogen) following the manufacturer’s instructions
RNA libraries were prepared for RNA-seq using standard Illumina protocols

value: Mouse bone marrow neutrophils

value: 12h after CLP-induced sepsis


title: Healthy controls 01


title: nasopharyngeal carcinoma patients without posttreatment metastasis 25

description: circRNA expression data from nasopharyngeal carcinoma

source_name: primary nasopharyngeal carcinoma without posttreatment relapse

value: Nasopharyngeal carcinoma


title: BM neutrophils, KO, Rep1


title: nasopharyngeal carcinoma patients without posttreatment metastasis 24


title: Healthy controls 02


title: Healthy controls 03


title: T47D_Clone39_dTAG13_rep3

description:
T47D_Clone39_dTAG13_rep3_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: HCT116, batch2, EDC4 KO, rep2

value: EDC4 KO


title: nasopharyngeal carcinoma patients without posttreatment metastasis 22


title: nasopharyngeal carcinoma patients without posttreatment metastasis 23


title: BM neutrophils, WT, Rep2

value: Wild-type


title: nasopharyngeal carcinoma patients without posttreatment metastasis 21


title: HCT116, batch2, EDC4 KO, rep1


title: T47D_Clone39_dTAG13_rep2

description:
T47D_Clone39_dTAG13_rep2_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: BM neutrophils, WT, Rep1


title: nasopharyngeal carcinoma patients without posttreatment metastasis 19


title: nasopharyngeal carcinoma patients without posttreatment metastasis 20


title: T47D_Clone39_dTAG13_rep1

description:
T47D_Clone39_dTAG13_rep1_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: T47D_Clone39_DMSO_rep4

description:
T47D_Clone39_DMSO_rep4_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig

value: 0.1% v/v DMSO for 90 minutes


title: HCT116, batch2, negative control, rep1

value: human colon cancer cell line

value: WT


title: HCT116, batch2, negative control, rep2


title: HCT116, batch1, DDX6 KO, rep1

value: DDX6 KO


title: HCT116, batch1, DDX6 KO, rep2


title: HCT116, batch1, negative control, rep4


title: nasopharyngeal carcinoma patients 18


title: HCT116, batch1, negative control, rep3


title: T47D_Clone39_DMSO_rep2

description:
T47D_Clone39_DMSO_rep2_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: T47D_Clone39_DMSO_rep3

description:
T47D_Clone39_DMSO_rep3_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: T47D_Clone39_DMSO_rep1

description:
T47D_Clone39_DMSO_rep1_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: HCT116, batch1, negative control, rep2


title: HCT116, batch1, negative control, rep1


title: dHL-60 cells, KO, Rep1

data_processing:
The adapters and low quality bases were removed.
The Fastq files were aligned to the reference genome (hg38) using Hisat2 (v2.2.1).
Reads mapped to tRNA and rRNA are removed for the following analysis.
Stringtie (v2.1.4) was used to calculate the TPM of each gene to represent their mRNA expression level.
The differential genes were identified by a negative binomial model using the DEseq2 package.
Assembly: hg38
Supplementary files format and content: txt

source_name: HL-60 neutrophil-like cells

extract_protocol:
Total RNA was isolated from dHL-60 neutrophils with TRIzol reagent (Invitrogen) and subjected to Poly(A)+ mRNA purification via Dynabeads mRNA Purification Kit ( Invitrogen) following the manufacturer’s instructions
RNA libraries were prepared for RNA-seq using standard Illumina protocols

value: HL-60 neutrophil-like cells

value: Infection with Escherichia coli


title: dHL-60 cells, KO, Rep2


title: dHL-60 cells, WT, Rep2


title: dHL-60 cells, WT, Rep1


title: NCI-H1299, IP_IgG

first: Donglai

last: Wang

address: #5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
The raw reads were aligned to the human reference genome hg38 using BWA (Burrows Wheeler Aligner, v0.7.12).
After mapping reads to the reference genome, the model-based analysis of ChIP-seq (MACS, v1.4.2) was used for peak calling that identified regions of ZBTB11 enrichment over the normal IgG background.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak (except for Input sample)

growth_protocol: NCI-H1299 cells were cultured in DMEM supplemented with 10% (vol/vol) FBS.

extract_protocol:
Cells were fixed with 1% formaldehyde, followed by lysis with ChIP lysis buffer. After sonication and further processing, DNA was extracted using a PCR purification Kit (Qiagen, 28106).
The library was prepared by using the NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) according to the manufacturer’s protocol.

treatment_protocol: None treatment

value: Human lung adenocarcinoma

tag: chip antibody

value: IgG (CST, 2729S)


title: T47D_Clone35_DMSO_rep4

description:
T47D_Clone35_DMSO_rep4_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: T47D_Clone35_dTAG13_rep4

description:
T47D_Clone35_dTAG13_rep4_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: T47D_Clone28_dTAG13_rep4

description:
T47D_Clone28_dTAG13_rep4_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: T47D_Clone35_DMSO_rep1

description:
T47D_Clone35_DMSO_rep1_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: T47D_Clone35_DMSO_rep3

description:
T47D_Clone35_DMSO_rep3_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: T47D_Clone35_dTAG13_rep1

description:
T47D_Clone35_dTAG13_rep1_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: T47D_Clone35_DMSO_rep2

description:
T47D_Clone35_DMSO_rep2_combined
TRPS1_PRO_gene_counts.txt
T47D_DMSO_plus_PE1_combined_normalized.bigWig
T47D_DMSO_minus_PE1_combined_normalized.bigWig


title: T47D_Clone35_dTAG13_rep3

description:
T47D_Clone35_dTAG13_rep3_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: T47D_Clone35_dTAG13_rep2

description:
T47D_Clone35_dTAG13_rep2_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: NCI-H1299, IP_ZBTB11

value: ZBTB11 (Bethyl, A303-240A)


title: ckb1 ckb2 cka1, basal, rep3

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

data_processing:
The adapter sequences were trimmed from the sequencing reads by using Cutadpat v3.4 with Python 3.7.4. The reference genome sequence of Cryptococcus neoformans H99 and annotation data were downloaded from the NCBI ftp server
The reads were aligned to the Cryptococcus neoformans H99 genome sequence using Hisat2 v2.2.1 with the Hisat and Bowtie2 algorithm and processed as previously reported. Hisat2 was performed with “-p 30”and “– dta -1”option and other parameters set as default. Aligned reads were converted and then sorted by Samtools v1.9 with “-Sb -@ 8”option for converting, and “-@ 20 –m 2000000000” option for sorting and the other parameters set as default
Transcript assembly and abundance estimation were performed using Stringtie v2.1.1 by using “-p 12” option, and also “-B” option to run the Ballgown analysis.
Assembled transcripts were merged to single GTF ﬁle, and the relative transcript abundances were calculated via Fragments Per Kilobase ofexon per Million fragments mapped (FPKM). The FPKM and readcount matrix was generated by R package “isoformswitchanalyzerR” and analyzed by DESeq2.
Differentially expressed genes (DEG) analysis was performed using DESeq2 v1.24.0 with default sets with the Ballgown. Volcano plot was illustrated by using R v4.1.0, with the cutoff (more than two-fold changes with p< 0.05).
Assembly: Cryptococcus neoformans var. grubii H99 GCA_000149245.3 CNA3
Supplementary files format and content: tab-delimited excel files include gene counts for each Sample
Supplementary files format and content: tab-delimited excel files include DEG analysis value for each Sample

organism: Cryptococcus neoformans

growth_protocol: C. neoformans strains grown overnight in YPD medium weretransferred to 50 mL of fresh YPD medium and incubated at 30°C until the OD600 reached 0.8.

extract_protocol:
The cells were then harvested by centrifugation and lyophilized. Total RNAs were isolated by Easy-BLUE (iNtRON), treated with DNase I (Qiagen), and puriﬁed with RNeasy MiniElute clean up kit (Qiagen) following the manufacturer’s instruction
Cultured samples were prepared independently three times for each strain, the cDNA library was constructed with the 1 µg of total RNAs for each sample by Illumina TruSeq mRNA library kit (Illumina) and sequenced by Illumina platform.

value: Fungi

value: ckb1 ckb2 cka1 knockout

value: basal


title: ckb1 ckb2 cka1, basal, rep2


title: ckb1 ckb2 cka1, basal, rep1


title: T47D_Clone28_dTAG13_rep3

description:
T47D_Clone28_dTAG13_rep3_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig

value: 100nM dTAG-13 for 90 minutes


title: NCI-H1299, Input


title: cka1, basal, rep3

value: cka1 knockout


title: cka1, basal, rep2


title: T47D_Clone28_dTAG13_rep2

description:
T47D_Clone28_dTAG13_rep2_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig


title: TFP 72 hr, biological rep2

city: Taipei

first: MingYing

last: Lan

address: No.201, Sec. 2, Shipai Rd., Beitou District

department: Department of Otolaryngology-Head and Neck Surgery

country: Taiwan

institute: Taipei Veterans General Hospital, Taipei, Taiwan

description: gene expression after 72 hours TFP treatment in NPC cell line

data_processing:
The original data obtained by high-throughput sequencing (NovaSeq 6000; Illumina) were converted into raw se-quenced reads by CASAVA base calling and stored in FASTQ format.
Read pairs from each sample were aligned to the reference genome (H. sapiens) using the HISAT2 software (v2.1.0)
FeatureCounts v2.0.0 was performed to calculate the read numbers mapped to individual genes
For gene expression, the relative log expression (RLE) normalization was performed us-ing DESeq2 (v1.26.0) with a biological duplicate.
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were conducted using clusterProfiler (v3.14.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: Map_stat.txt
Supplementary_files_format_and_content: Original_read_count.txt
Supplementary_files_format_and_content: Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway files

source_name: Nasopharyngeal carcinoma cells

growth_protocol: The NPC cell line was maintained in DMEM with 10% FBS at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NPC cells treated with or without TFP for 72 hours at 37°C

value: Nasopharyngeal carcinoma cells

tag: passage

value: passage at p3-p10

value: TFP


title: TFP 72 hr, biological rep1


title: cka1, basal, rep1


title: T47D_Clone28_dTAG13_rep1

description:
T47D_Clone28_dTAG13_rep1_combined
TRPS1_PRO_gene_counts.txt
T47D_dTAG13_plus_PE1_combined_normalized.bigWig
T47D_dTAG13_minus_PE1_combined_normalized.bigWig