title: ATAC_12h_Bioreplicate 1 (reanalyzed)

description:
Re-analysis of Sample GSM4988037 to new Sp 5.0 version of the genome. It Should be included as SubSeries in  SubSeries GSE234139
ATAC_12h6_ATAC12h7_RPM.bw
12h_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed


title: DEN1013A_Day0_Shot1_run2_PBMC

status: Public on Jul 27 2023

type: SRA

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

library_source: transcriptomic

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed reads were aligned to the GRCh38 reference genome (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a
RseQC was used to assess strand specificity for all transcripts
HTSeq was used to estimate transcript abundance from unique mapped reads
Raw reads were normalized using DESeq2 v1.26.0
Assembly: GRCh38
Supplementary files format and content: counts

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
RNEasy micro-kit (QIAGEN)
TruSeq Stranded Total RNA Library Prep kit after rRNA and globin mRNA removal using the Globin-Zero Gold rRNA removal kit.

tag: batch

tag: timepoint

tag: immunization

tag: participant

tag: breadth

value: high

tag: serostatus before immunization

value: Seronegative


title: DRG, spinal nerve ligation (SNL), Day14, rep3

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

data_processing:
The reads were aligned to the Rattus norvegicus USCS rn5 reference genome with RefSeq gene annotation and were constructed into transcripts using RNA-Seq Alignment v1.0
FPKM values were calculated by Cufflinks Assembly & DE v2.0.
Assembly: rn5
Supplementary files format and content: FPKM values

organism: Rattus norvegicus

source_name: DRG

extract_protocol:
Total RNA was extracted using RNAiso plus (Takara Bio, Shiga, Japan).
A polyadenylated RNA library was prepared using a TruSeq stranded mRNA LT sample Prep Kit (Illumina, San Diego, CA).

tag: tissue

value: DRG

tag: strain

value: Sprague Dawley

tag: Sex

value: male

tag: treatment

value: SNL

tag: time

value: Day 14 after SNL


title: DRG, control AAV vector + SNL, Day14, rep1

value: control AAV vector + SNL


title: DEN1011A_Day0_Shot1_run2_PBMC


title: xenograft-6R

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

description:
RAB27A KD Biological replicate 4
human-VJ-3468-6R_S10.featurecounts.txt
mouse-VJ-3468-6R_S10.featurecounts.txt

data_processing:
Trimming with fastp
Alignment with hista2
deconvolution of mouse and human reads in xenograft sequence data with XenofilteR
Assembly: Homo_sapiens.GRCh38 & Mus_musculus.GRCm39
Supplementary files format and content: tab-delimited text files include quantified reads from FeatureCounts

organism:
Homo sapiens
Mus musculus

source_name: xenograft formed by subcutaneously injected human cSCC cells (UT-SCC-7) and infiltrating mouse stroma cells

growth_protocol: UT-SCC-7 cells were cultured in DMEM with 10% FBS, 1% HEPES, 1% NEA and 1% P+S in vitro, and subcutaneously injected into NOD SCID gamma (NSG) mice for xenograft experiments. Cell suspension in 100 µl of ice-cold medium was mixed at 1:1 volume ratio with Matrigel right before the injection.

extract_protocol:
RNA was extracted using miRNeasy Mini Kit  (QIAGEN).
Library preparation was constructed using the TruSeq stranded mRNA library preparation kit with polyA selection (Illumina Inc.) according to the manufacturer’s instructions

treatment_protocol: Stable RAB27A knockdown and control UT-SCC-7 cell lines were established by lentiviral transduction with TurboRFP as a selection marker (GeneCopoeia). The transduced cells were selected based on the expression of RFP within the cells using fluorescent-activated cell sorter (FACS).

tag: cell type

tag: genotype

value: RAB27A knockdown

value: shRAB27A lentiviral transduction


title: xenograft-6L_2

description:
WT Technical replicate 4
human-VJ-3468-6L_S9.featurecounts.txt
mouse-VJ-3468-6L_S9.featurecounts.txt

value: xenograft formed by subcutaneously injected human cSCC cells (UT-SCC-7) and infiltrating mouse stroma cells

value: WT

value: scramble lentiviral transduction


title: DRG, spinal nerve ligation (SNL), Day14, rep1


title: DEN1010A_Day0_Shot1_run2_PBMC

value: low


title: FC2

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

country: USA

institute: University of Arizona

data_processing:
data quality was validated for RNAseq analysis using FastQC Version 0.11.9.
aligned with the sequencing data using Salmon
Integrated differential expression and pathway analysis were conducted with iDep.96 web-based applications
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: txt file format - contains TPM

organism: Ovis aries

source_name: Perirenal Adipose Tissue

extract_protocol:
adipose tissue was thawed in Trizol and homogenized using 3 pulses, 4-6 seconds each. Then, 0.2 mL of chloroform was added per 1 mL of Trizol (0.1 mL per sample). Samples were centrifuged for 15 minutes at 14,000 x g (4 ˚C) and the mixture separated into a lower red phenol-chloroform, interphase, and a colorless upper aqueous solution. The aqueous phase containing RNA was transferred to a new tube very carefully to ensure proteins and other cell components did not contaminate the RNA. Then, 250 µl of isopropanol was added to the aqueous phase (0.5 ml/ ml of Trizol) and incubated for 10 minutes. The sample was centrifuged for 10 minutes at 14,000 x g (4˚C) and the RNA precipitate formed a white gel-like pellet at the bottom of the tube. The supernatant was discarded and the sample was vortexed briefly before centrifugation for 5 minutes at 8000 x g (4˚C). The supernatant was discarded and the RNA pellet was air-dried for 10 minutes. Pellets were resuspended in 50 µl of RNase-free water. The RNA was further purified by Zymo Purelink RNA columns.
library was constructed from samples using a Swift RNA Library Kit – (Catalog # R1024) and Swift Dual Combinatorial Indexing Kit – (Catalog # X8096)

value: Perirenal Adipose Tissue

value: Female

value: Control


title: DRG, spinal nerve ligation (SNL), Day14, rep2


title: xenograft-6L

description:
WT Biological replicate 4
human-VJ-3468-6L_S9.featurecounts.txt
mouse-VJ-3468-6L_S9.featurecounts.txt

value: human cSCC cells (UT-SCC-7) and infiltrating mouse stroma cells


title: FC3


title: DEN1009A_Day0_Shot1_run2_PBMC

value: Seronegative


title: DEN1008A_Day0_Shot1_run2_PBMC

value: high


title: FC1


title: DRG, Control, Day14, rep3

value: DRG

value: Sprague Dawley

value: Contralateral


title: DRG, control AAV vector + SNL, Day14, rep3

value: male

value: Day 14 after SNL


title: DRG, Control, Day14, rep2


title: MFGR4

value: Male

value: Hyperthermia


title: DEN1007A_Day0_Shot1_run2_PBMC


title: MFGR3


title: DRG, Control, Day14, rep1


title: xenograft-3R

description:
RAB27A KD Biological replicate 3
human-VJ-3468-3R_S6.featurecounts.txt
mouse-VJ-3468-3R_S6.featurecounts.txt

value: xenograft formed by subcutaneously injected human cSCC cells (UT-SCC-7) and infiltrating mouse stroma cells

value: RAB27A knockdown

value: shRAB27A lentiviral transduction


title: xenograft-3R_2

description:
RAB27A KD Technical replicate 3
human-VJ-3468-3R_S6.featurecounts.txt
mouse-VJ-3468-3R_S6.featurecounts.txt


title: tet-MTR4-Dox-2

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Reads were trimmed using Trim Galore
Reads were mapped on the S. cerevisiae reference genome (R64-2-1, including the 2-micron plasmid) and ERCC spike-in RNA sequences, using HISAT2 V2.2.0, with default parameters and maximum intron size of 5000.
Gene count was obtained with featureCounts v2.0.0.
Gene count was normalized using estimatesizefactorsformatrix() function from DESeq2 package (R software), using ERCC counts.
Normalized densities were computed for each sample as: normalized gene count / gene length
Assembly: R64-2-1
Supplementary files format and content: tab delimited file, containing normalized tag/nt for each sample

organism: Saccharomyces cerevisiae

source_name: MATa ade2-1 his3-11,15 leu2-3,112 trp12 ura3-1 can1-100 kanMX6- tetOFF::MTR4

growth_protocol: Yeast cells were grown to mid-log phase (OD600 0.5) at 30°C in YPD medium.

extract_protocol:
Total RNA was extracted from cells grown to mid-log phase (OD600 0.5) using standard hot phenol procedure. Extracted RNA was ethanol-precipitated, resuspended in nuclease-free H2O (Ambion) and quantified using a NanoDrop 2000c spectrophotometer and/or a Qubit fluorometer with the Qubit RNA HS Assay kit (Life Technologies)
RNA-seq libraries were prepared from 125 ng of rRNA-depleted RNAs using the TruSeq Stranded Total RNA kit (Illumina)

treatment_protocol: At mid-logphase, addition of doxycycline at 10 μg/mL (final concentration) for 6 hours. During this treatment, cells were maintained to mid-log phase (OD600 0.5) by dilution into preheated YPD medium with 10 μg/mL doxycyline

value: MATa ade2-1 his3-11,15 leu2-3,112 trp1{delta}2 ura3-1 can1-100 kanMX6- tetOFF::MTR4

value: Doxycyclin


title: MFGR2

value: Perirenal Adipose Tissue


title: MFGR1


title: xenograft-3L_2

description:
WT Technical replicate 3
human-VJ-3468-3L_S5.featurecounts.txt
mouse-VJ-3468-3L_S5.featurecounts.txt

value: WT

value: scramble lentiviral transduction


title: tet-MTR4-Dox-1


title: YBX1K2A-2

city: Leipzig

first: Berend

last: Isermann

address: Paul List Str. 13/15

department: Medical Faculty

country: Germany

institute: University of Leipzig

data_processing:
RNA libraries were sequenced on the Illumina HiSeq2500 using TruSeq SBS Kit v3- HS (50 cycles, single ended run) with an average of 3 x107 reads per RNA sample.
The general workflow comprised the following steps: quality control; trimming of barcodes; mapping of reads; counting and differential expression analysis
Specifically, the reads were quality controlled with fastqc (v0.11.9) and MultiQC (v1.10.1) as raw reads and after each processing stage. Adapter remains where trimmed with trimgalore (v0.6.3),followed by mapping of reads against the Mus musculus genome (mm10) using STAR (v2.7.3a). Unique mapping reads were extracted and counted using featureCounts (v2.0.1) followed by analysis of differentially expressed genes with DESeq2 (v1.30.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text file inculdes raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: secretion-deficient Ybx1-mutant specifically in podocytes

growth_protocol: Wild-type mice (C57BL/6N) were obtained from Janvier Lab (S.A.S., St. Berthevin Cedex, France).

extract_protocol:
RNA was extracted from renal tissue using RNeasy Mini Kit (QIAGEN, Germany).RNA integrity and quality were checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 500ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification. The ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) was used to prepare the RNA sequencing library according to the manufacturer's protocols.

treatment_protocol: Mice were sacrificed at the end of study period and kidney samples were isolated and RNAseq was performed.

value: renal tissue

value: Ybx1 mutant lacking the two lysine residues required for Ybx1 acetylation-dependent secretion  (K299A and K302A in exon 7)

tag: strain background


title: YBX1K2A-3


title: xenograft-2R_2

description:
RAB27A KD Technical replicate 2
human-VJ-3468-2R_S4.featurecounts.txt
mouse-VJ-3468-2R_S4.featurecounts.txt

value: human cSCC cells (UT-SCC-7) and infiltrating mouse stroma cells


title: MC3

value: Control


title: xenograft-2R

description:
RAB27A KD Biological replicate 2
human-VJ-3468-2R_S4.featurecounts.txt
mouse-VJ-3468-2R_S4.featurecounts.txt


title: YBX1ΔPod-3

source_name: YBX1 deletion from podocytes


title: WT-Dox-1


title: YBX1ΔPod-2


title: WT-Dox-2


title: DEN1003A_Day0_Shot1_run2_PBMC

value: high

value: Seronegative


title: MC2


title: xenograft-2L_2

description:
WT Technical replicate 2
human-VJ-3468-2L_S3.featurecounts.txt
mouse-VJ-3468-2L_S3.featurecounts.txt


title: xenograft-2L

description:
WT Biological replicate 2
human-VJ-3468-2L_S3.featurecounts.txt
mouse-VJ-3468-2L_S3.featurecounts.txt


title: MC1


title: xenograft-3L

description:
WT Biological replicate 3
human-VJ-3468-3L_S5.featurecounts.txt
mouse-VJ-3468-3L_S5.featurecounts.txt


title: YBX1ΔPod-1


title: xenograft-1R_2

description:
RAB27A KD Technical replicate 1
human-VJ-3468-1R_S2.featurecounts.txt
mouse-VJ-3468-1R_S2.featurecounts.txt


title: xrn1-2

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 xrn1::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 xrn1{delta}::kanMX4


title: dbp2-1

source_name: MATa his30 leu20 met- lys? ura30 dbp2::KanMX6

value: MATa his3{delta}0 leu2{delta}0 met- lys? ura3{delta}0 dbp2{delta}::KanMX6


title: YBX1WT-3

source_name: Control


title: eBW4, scRNAseq

city: Princeton

first: Bruce

last: Wang

state: NJ

address: Lewis Thomas Lab

institute: Prinnceton University

library_source: transcriptomic single cell

data_processing:
The demultiplexing, alignment, and data processing were performed from the raw basecalls using custom scripts here: https://github.com/brwaang55/m3seq_scripts . Raw basecall files were converted into a single ended bam file as loaded here.
Assembly: B. subtilis 168 (assembly ASM904v1, assembly accession GCF_000009045.1); E. coli MG1655 (assembly ASM584v2, assembly accession GCF_000005845.2); E. coli Nissle (assembly ASM71459v1, assembly accession GCF_000714595.1).
Supplementary files format and content: *.csv: Comma-separated gene name files, cell annotation files, and matrix files.
Supplementary files format and content: bw_scifi*.samples.csv include demultiplexing information (barcodes, etc.).

organism:
Pseudomonas aeruginosa
Escherichia coli
Bacillus subtilis

source_name: bacterial cells

growth_protocol: Cells were grown in LB media for 90 minutes, then treated with antibiotics or phage.

extract_protocol:
Cells were fixed in formaldehyde overnight, washed 2x, permeabilized using lysozyme, then washed 2x more. Cells then underwent an in-situ RT for r1 indices, after which the cells were pooled. Cells were then loaded onto the 10X scATAC platform. Following droplet generation, emulsions were broken, cells were lysed, and processed according to the M3-Seq protocol.
Briefly, RNA was stripped from DNA using RNase H, followed by second strand synthesis using random primers. Following second strand synthesis, DNA library was tagmented, amplified, and then in vitro transcribed. The library was rRNA-depleted, and then reverse transcribed using a P5-specific primer. The final library was amplified and indexed using indexing primers.

treatment_protocol: Cells were treated for each experiment as described in M3-Seq.

value: bacterial cells


title: xenograft-1R

description:
RAB27A KD Biological replicate 1
human-VJ-3468-1R_S2.featurecounts.txt
mouse-VJ-3468-1R_S2.featurecounts.txt

value: xenograft formed by subcutaneously injected human cSCC cells (UT-SCC-7) and infiltrating mouse stroma cells


title: eBW3, scRNAseq

organism:
Escherichia coli
Bacillus subtilis


title: YBX1WT-2


title: xrn1-1


title: YBX1K2A-1


title: MC4

value: Male


title: YBX1WT-1


title: WT-2

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: dbp2-2


title: xenograft-1L

description:
WT Biological replicate 1
human-VJ-3468-1L_S1.featurecounts.txt
mouse-VJ-3468-1L_S1.featurecounts.txt


title: eBW2, scRNAseq


title: WT-1


title: Parental ES anti-CRM1 (Bethyl), ChIP

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

library_source: genomic

data_processing:
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore.
Sequence reads were aligned to the reference mouse genome (mm10) and human genome (GRCh38) using Bowtie2.
bigWig files for each samples were generated using deepTools with following options "--binSize 100 --normalizeUsing CPM".
Assembly: GRCh38(human), mm10(mouse)
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: mouse embryonic stem cells (mESCs)

extract_protocol:
Cross-linked chromatin was sheared by sonication, and MNase treatment.
The ChIP library was prepared using ThruPLEX DNA-seq kit (Takara Bio), according to the manufacturer’s instructions.

value: mouse embryonic stem cells (mESCs)

tag: genotype/variation

value: Parental

tag: chip antibody

value: anti-CRM1 (CST, A300-469A)


title: SI_IEL_TRM_HC_R3

city: La Jolla

first: Miguel

last: Reina-Campos

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Aligned with STAR 2.5.4a to mouse genome
Gene-level quantification calculated by featureCounts
Assembly: mm10
Supplementary files format and content: Gene counts by sample as an .xlsx file

source_name: Small Intestine CD8 T cells

extract_protocol:
Ultra-low-input RNA Seq was performed on sort purified cells, polyadenylated mRNA was converted to cDNA. Illumina adapters were added and product was PCR amplified for sequencing
Immgen ULI-RNAseq

value: Small Intestine CD8 T cells

value: P14 CD8 T cells

value: High cholesterol-containing diet for 7 days


title: dbp2-aa-R-2

source_name: MATalpha ade 2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 GAL psi+ tor1-1 fpr1::NAT RPL13A-2×FKBP12::TRP1 DBP2-FRB-GFP-KanMX6

treatment_protocol: At mid-logphase, addition of rapamycin at 1 µg/mL (final concentration) for 1 hour.

value: MATalpha ade 2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 GAL psi+ tor1-1 fpr1::NAT RPL13A-2xFKBP12::TRP1

value: rapamycin


title: MEFs, Rapalink1-3

city: Chicago

first: Sejeong

last: Shin

state: IL

address: 909 S Wolcott Ave.

institute: University of Illinois at Chicago

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited table formatted, Unique hit counts per each sample

source_name: Embryonic fibroblasts

growth_protocol: Cells were maintained in DMEM containing 10% FBS at 37°C with 5% CO2

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen)
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions

treatment_protocol: Cells were treated with rapamycin (20 ng/ml), Torin1 (250 nM), and RapaLink-1 (10 nM) for 24 hours

value: Embryonic fibroblasts


title: SI_IEL_TRM_HC_R2


title: PS-R-2

source_name: MATalpha ade 2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 GAL psi+ tor1-1 fpr1::NAT RPL13A-2×FKBP12::TRP1


title: eBW1, scRNAseq


title: dbp2-aa-R-1


title: NUP98HOXA9 (WT), anti-FLAG_ChIP

value: NUP98HOXA9 (WT)

value: FLAG (SIGMA, F1804)


title: MEFs, Torin1-3


title: MEFs, Rapalink1-1


title: SI_IEL_TRM_HC_R1


title: SI_IEL_TRM_LC_R3

value: Low cholesterol-containing diet for 7 days


title: MEFs, Torin1-2


title: Parental ES anti-CRM1 (Bethyl), INPUT

value: INPUT


title: NUP98HOXA9 (N51S mutant), anti-FLAG_ChIP

value: NUP98HOXA9 (N51S mutant)


title: PS-R-1


title: NUP98HOXA9 (WT), INPUT


title: xenograft-1L_2

description:
WT Technical replicate 1
human-VJ-3468-1L_S1.featurecounts.txt
mouse-VJ-3468-1L_S1.featurecounts.txt

value: xenograft formed by subcutaneously injected human cSCC cells (UT-SCC-7) and infiltrating mouse stroma cells

value: WT

value: scramble lentiviral transduction


title: SI_IEL_TRM_LC_R2


title: MEFs, Torin1-1


title: oocyte from antral follicle stage 1, gilt 803, rep2

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Raw sequencing reads were trimmed to remove low-quality reads and adaptors by TrimGalore (v0.4.3)
Hisat2 (v2.1.0) was used to align reads to the reference genome
A count matrix was generated using featureCounts with the Ensembl gene annotation (v93)
A TPM matrix was generated using STRINGTIE(v1.2.2) with the Ensembl gene annotation (v94)
Assembly: Sscrofa 11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM for each Sample

molecule: cytoplasmic RNA

organism: Sus scrofa

source_name: ovary

growth_protocol: 208-210-day-old pubertal Landrace  Yorkshire pigs that were grown up in natural envrionment

extract_protocol:
Firstly, single oocyte in cell lysis buffer was vortexed for 2 min then centrifugated at 1200 g for 10 min at 4 ℃, resulting in the physical separation of mRNA and genomic DNA. The supernatant containing cytoplasm transcriptome was subjected to Smart-seq2 protocol for single-cell full-length cDNA library construction
Briefly, the full-length cDNA synthesis was performed by addition of template switch oligo and SuperScript II reverse transcriptase (Invitrogen) to the 4 μL of supernatant and incubated at 42 ℃ for 90 min following by 10 cycles of 50 ℃ 2 min and 42℃ for 2 min. The reverse transcriptase was inactivated at 70 ℃ for 15 min. The single stranded cDNA was subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at 1 x concentration for 16 cycles. The amplified cDNA was purified using AMpure XP beads (Beckman) and then used for library construction using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). Smart-seq2

treatment_protocol: pigs were intraperitoneally injected with 5 IU of pregnant mare serum gonadotropin (PMSG) (Sigma Corporation, Guangdong, China) to stimulate antral follicular development. After 48 h, ovaries were dissected from gilts at a local slaughterhouse and transported to the laboratory within 2 hours in iced 0.1% DEPC PBS

value: ovary

value: oocyte


title: SI_IEL_TRM_LC_R1


title: dbp2-aa-2


title: NUP98HOXA9 (N51S mutant), INPUT

value: mouse embryonic stem cells (mESCs)


title: MEFs, Rapalink1-2


title: MEFs, Rapamycin3

value: Rapamycin


title: NUP98HOXA9 (AG mutant), anti-FLAG_ChIP

value: NUP98HOXA9 (AG mutant)


title: MEFs, Rapamycin2


title: PS-2


title: MH-S cells, infection ATAC-seq rep2 [CP2]

city: chengdu

first: yang

last: yang

address: No.17, Section 3, South Renmin Road

institute: Sichuan University

data_processing:
RNA-seq:
Before applying any data filtering criteria, RNA-Seq reads were adapter trimmed using Trim Galore (v0.6.7) for removing low-quality data, and FastQC (v0.11.9) software was used to assess data quality.
Reads were mapped to the mouse reference genome (mm10) using HISAT2 software (v2.2.1).
The mapped reads were assembled into transcripts or genes by featureCounts (v2.0.2) software and genome annotation (mm10.gtf).
ATAC-seq:
The unmapped reads were first processed with trim_galore (v0.6.7) with the parameters "-q 30 --phred33 --stringency 3 --length 35".
Sequencing reads are mapped to the mouse genome (mm10) by bowtie (v1.3.1) with the parameter "-m1 --best --strata -X 2000".
The bam files were then merged and processed using sambamba (v0.8.1) markdup function to remove duplicate reads and then filter out reads that mapped to the mitochondrial genome and to select unique, non-chrM reads from the bam files using samtools (v1.9).
To normalize and visualize the data, the BAM files were converted to bigWig format using RPKM's "bamCoverage".
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mapped reads for each Sample
Supplementary files format and content: bigWig

source_name: Lung

growth_protocol: RNA-seq: Wild-type Pseudomonas aeruginosa PAO1 was routinely cultured in LB (Luria-Bertani) broth with shaking (220 r.p.m.) at 37°C.  Mouse alveolar macrophages MH-S cell line (ATCC CRL-2019) maintained in RPMI-1640 and DMEM (Gibco) supplemented with 10% FBS (Gibco).

extract_protocol:
For RNA extraction, a 1% agarose gel was used to detect RNA degradation and contamination.
RNA-seq: Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, E7530L) and index codes were added to the attribute sequences of each sample and sequenced using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, PE-401-3001) on the cBot Cluster Generation System to cluster the index-coded samples.
ATAC-seq: Resuspended the cell pellets with 50 μL of lysis buffer and the nuclei were pelletized by centrifugation at 500 × g for 10 min at 4°C.   The supernatant was discarded and the nuclei were resuspended with a reaction buffer containing Tn5 transposase 2.5 μL and TD (Nextera Illumina) 22.5 μL.   Incubate at 37°C for 30 minutes.   Labeled DNA was isolated using the MinElute PCR Purification Kit (Qiagen).
ATAC-seq: 10 cycles of libraries amplification and 2 × SPRI Cleanup (Agencourt) were used to purify. Using the LabChip GXII Touch HT (PerkinElmer), library sizes were calculated. NextSeq500 (Illumina) was then used to do 2 × 75 paired-end sequencings, which produced an average of 50 M reads/sample.

treatment_protocol:
RNA-seq: In the mouse model, overnight-cultured P. aeruginosa was collected and diluted in sterile saline. C57BL/6 female mice were anesthetized by isoflurane. A total of 1.0 × 10^7 CFU planktonic bacterial cells were washed three times, suspended in 50 µl of sterile saline, and then injected into the trachea of each mouse.
RNA-seq: MH-S cells were infected with P. aeruginosa (MOI of 50) for 2h.

value: Lung

tag: cell line

value: MH-S cells

value: Murine alveolar macrophages

value: infection


title: NUP98HOXA9 (AG mutant), INPUT


title: MEFs, Rapamycin1

value: Embryonic fibroblasts


title: MH-S cells, infection ATAC-seq rep1 [CP1]


title: PS-1

value: MATalpha ade 2-1 trp1-1 can1-100 leu2-3,112 his3-11,15 ura3 GAL psi+ tor1-1 fpr1::NAT RPL13A-2xFKBP12::TRP1


title: MEFs, Control3

value: DMSO


title: MH-S cells, control ATAC-seq rep1 [CC1]

value: control


title: MEFs, Control2


title: Lung tissues, infection ATAC-seq rep2 [TP2]

value: Lung tissues


title: Lung tissues, infection ATAC-seq rep1 [TP1]


title: dbp2-aa-1


title: CFT073, rep 1

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

description: High Output 75bp

data_processing:
We performed pan-genome analysis of 34 E. coli strains gene annotation by Roary with default parameter setting.
Kallisto was used to estimate the read counts on transcripts for each library by using all transcripts from 34 E. coli strains.
We quantified gene expression at group level by using gene groups defined from Roary and summing estimated read counts from all transcripts clustered into this group.
Assembly: All transcripts from 34 E. coli strains grouped by Roary.
Supplementary files format and content: A matrix of estimated read counts per group per sample.
Supplementary files format and content: A matrix of estimated TPM (transcript per million transcripts) per group per sample.

organism: Escherichia coli

extract_protocol:
Once grown, cells were collected by centrifugation at maximum speed for 10 minutes at 4 degrees Celsius. Media was decanted and pellets frozen overnight a -80 degrees Celsius. The next day, pellets were thawed on ice and 700 microliters of buffer RLT added. Buffered cells are mechanically lysed using a bead beater set the highest setting for 45 five seconds a cycle for three cycles with a 5 minute rest between cycles. During the rest, the cells are stored on ice. Once lysed, a Qiagen RNeasy mini kit was used to collect RNA. Contaminating DNA was removed though RNase-free DNase digestion of at least 10 micrograms of RNA determined by nanodrop. To remove the DNase and concentrate the RNA, a GeneJet RNA isolation and concentration kit was used.
Lexogen RiboCop rRNA depletion kit for Bacteria followed by Illumina Truseq Stranded mRNA library prep kit.

value: UPEC

value: Group B2


title: UTI89, rep 2

description: High Output 75bp


title: MEFs, Control1


title: Lung tissues, control ATAC-seq rep2 [TC2]

value: WT


title: macrophage cells-M3

city: beijing

first: wenjuan

last: xu

address: Beijing University of Chinese Medicine, No.11 North 3rd Ring East Road, Chao-Yang District, Beijing

institute: Beijing University of Chinese Medicine

description: macrophage cells-M3

data_processing:
Illumina Hiseq 4000 platform used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: macrophage cells

extract_protocol:
RNA of ox-LDL induced macrophage cells was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: macrophage


title: CFT073, rep 3

description: High Output 75bp


title: Lung tissues, control ATAC-seq rep1 [TC1]


title: LNCaP-DHT-24hr-R2

type: RNA

city: Boston

first: Shaoyong

last: Chen

state: Massachusetts

address: 3 Blackfan Circle, CLS-432

department: Hem/Onc

institute: Boston BIB

description: LNCaP cells in androgen depleted-medium, treated with DHT (1nM of Dihydrotestosterone) for 24hrs, repeat 2

hyb_protocol: Hybridized to Affymetrix U133A oligonucleotide microarrays as described (PMID: 10521349).

data_processing: The expression files were normalized across the arrays, and genes expressed below 10 were filtered out.

label: Biotin-labeled cRNA

source_name: LNCaP cell tissue culture

label_protocol: Biotin-labeled cRNA was generated.  hybridized to Affymetrix U133A oligonucleotide microarrays as described

growth_protocol: LNCaP cells were cultured in androgen-depleted medium (RPMI1640 + 5% of Charcoal/Dextran treated Fetal Bovine Serum) for 2 days.

extract_protocol: Total RNA was isolated with TriZOL reagent.

treatment_protocol: Cells were either untreated or treated for 2 hours, 4 hours, 8 hours, or 24 hours with Vehicle (Ethanol), CPA (10µM of cyproterone acetate), or DHT (1nM of Dihydrotestosterone). Two repeats for each setting.

value: Prostate cancer LNCaP cell line


title: UTI89, rep 1

description: High Output 75bp


title: LNCaP-Veh-24hr-R1

description: LNCaP cells in androgen depleted-medium, treated with Vehicle (Ethanol) for 24hrs, repeat 1


title: MH-S cells, control ATAC-seq rep2 [CC2]


title: CFT073, rep 2

description: High Output 75bp


title: macrophage cells-M1

description: macrophage cells-M1


title: control macrophage cells-C3

description: macrophage cells-C3


title: LNCaP-DHT-24hr-R1

description: LNCaP cells in androgen depleted-medium, treated with DHT (1nM of Dihydrotestosterone) for 24hrs, repeat 1


title: LNCaP-Veh-24hr-R2

description: LNCaP cells in androgen depleted-medium, treated with Vehicle (Ethanol) for 24hrs, repeat 2


title: LNCaP-CPA-24hr-R2

description: LNCaP cells in androgen depleted-medium, treated with CPA (10µM of cyproterone acetate) for 24hrs, repeat 2


title: control macrophage cells-C2

description: macrophage cells-C2


title: PTBP1 in vivo iCLIP, HeLa, rep5

city: Mainz

first: Stefanie

last: Ebersberger

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with non-default parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcodes.fasta (using sample barcodes: FUBP1 in vivo iCLIP, HeLa, rep1: NNNNNACATCGNNNN; FUBP1 in vivo iCLIP, HeLa, rep2: NNNNNTGGTCANNNN; FUBP1 in vivo iCLIP, HeLa, rep3: NNNNNGATCTGNNNN; FUBP1 in vivo iCLIP, HeLa, rep4: NNNNNATTGGCNNNN; FUBP1 in vivo iCLIP, HeLa, rep5: NNNNNTCAAGTNNNN; SF1 in vivo iCLIP, HeLa, rep1: NNNNNACATCGNNNN; SF1 in vivo iCLIP, HeLa, rep2: NNNNNGCCTAANNNN; SF1 in vivo iCLIP, HeLa, rep3: NNNNNTGGTCANNNN; SF3B1 in vivo iCLIP, HeLa, rep1: NNNNNCGTGATNNNN; SF3B1 in vivo iCLIP, HeLa, rep2: NNNNNACATCGNNNN; SF3B1 in vivo iCLIP, HeLa, rep3: NNNNNGCCTAANNNN; SF3B1 in vivo iCLIP, HeLa, rep4: NNNNNTGGTCANNNN; U2AF2 in vivo iCLIP in FUBP1 KD, HeLa, 2017, rep1: NNNTATTNN; U2AF2 in vivo iCLIP in FUBP1 KD, HeLa, 2017, rep2: NNNTACGNN; U2AF2 in vivo iCLIP in FUBP1 KD, HeLa, 2017, rep3: NNNGCGTNN; U2AF2 in vivo iCLIP in FUBP1 KD, HeLa, 2017, rep4: NNNCACANN; U2AF2 in vivo iCLIP, HeLa, 2017, rep1: NNNATCGNN; U2AF2 in vivo iCLIP, HeLa, 2017, rep2: NNNCGAGNN; U2AF2 in vivo iCLIP, HeLa, 2017, rep3: NNNAGAANN; U2AF2 in vivo iCLIP, HeLa, 2017, rep4: NNNGAAANN; U2AF2 in vivo iCLIP, HeLa, 2019, rep1: NNNNNTCAAGTNNNN; U2AF2 in vivo iCLIP, HeLa, 2019, rep2: NNNNNCTGATCNNNN; PTBP1 in vivo iCLIP, HeLa, rep1: NNNGGTTNN; PTBP1 in vivo iCLIP, HeLa, rep2: NNNTGGCNN; PTBP1 in vivo iCLIP, HeLa, rep3: NNNCGGANN; PTBP1 in vivo iCLIP, HeLa, rep4: NNNTTAANN; PTBP1 in vivo iCLIP, HeLa, rep5: NNNGGCANN)
Mapping: STAR (v2.6.1b) with non-default parameters: --genomeDir Gencode_release31_GRCh38.p12 --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang MAX_READLENGTH_AFTER_TRIMMING-1 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
Duplicate removal: UMI-tools (v1.0.0) with non-default parameter: umi_tools dedup --method unique
BAM to BED shifting one base upstream: bedtools (v2.27.1): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.27.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
Assembly: GRCh38.p12 (Gencode release 31)
Supplementary files format and content: bigWig (crosslink events per nucleotide)

source_name: HeLa

extract_protocol:
In vivo iCLIP is used to study protein-RNA interactions on individual nucleotide resolution by means of UV crosslinking and immunoprecipitation (PMID: 20601959). For the U2AF2 in vivo iCLIP, data from two iCLIP experiments were combined. The first U2AF2 iCLIP  and PTBP1 iCLIP were performed as previously described in (PMID: 24184352 ). The second U2AF2 iCLIP as well as in vivo iCLIPs for FUBP1, SF1, and SF3B1, were performed using the iCLIP2 protocol as described in (PMID: 31610236). Briefly, HeLa cells were irradiated with 150  mJ/cm2 in a UV-C crosslinker to covalently bind the RNA-binding proteins to the bound nucleic acids. For FUBP1 in vivo iCLIP, cross-linking was achieved by 4sU-mediated cross-linking. HeLa cells were 4sU-labelled by adding a 0.1 M 4-Thiouridine (4sU, Sigma) in DMSO to a final concentration of 100 μM/10 cm cell culture dish. Cells were incubated for 16 h at 37 °C, 5% CO2, under exclusion of light. After incubation, the cells were moved onto ice, shielded from light and irradiated at 365 nm, 800 mJ. During subsequent cell lysis, RNA was partially digested to create 50-200 nt long fragments. Immunoprecipitation of the investigated proteins was performed with antibodies listed in Table S9. The anti-PTBP1 Antibody was a kind gift of Chris Smith (PMID: 17679092). Radioactive labelling at the 3’ end of the precipitated RNA enables visualisation of the RNP-complex by SDS-PAGE and transfer to a nitrocellulose membrane. After recovery of protein-RNA complexes from the membrane, a proteinase K digestion results in protein-free RNA.
cDNA was synthesised by reverse transcription which stops at the cross-linked site, leading to truncation reads in the sequencing. The cDNA is cleaned twice with MyONE beads. PCR amplification and ProNex size selection are performed to amplify and purify the library, respectively. In vivo iCLIP libraries (except PTBP1 iCLIP libraries) were sequenced on an Illumina NextSeq 500 sequencing machine as 92 nt single-end reads including a 6 nt (or 4 nt in case of the first U2AF2 iCLIP) sample barcode as well as 5+4 nt (or 3+2 nt) UMIs. PTBP1 iCLIP libraries were sequenced on an Illumina GA-II machine (https://doi.org/10.15252/embj.201489852) and then resequenced on an Illumina HiSeq 2000 machine as 50 nt single-end reads including a 4 nt sample barcode as well as 3+2 nt UMIs.

value: HeLa


title: UTI89, rep 3

description: High Output 75bp


title: PTBP1 in vivo iCLIP, HeLa, rep3


title: ECOR62

description: High Output 75bp


title: PTBP1 in vivo iCLIP, HeLa, rep4


title: ECOR60

description: High Output 75bp


title: LNCaP-CPA-24hr-R1

description: LNCaP cells in androgen depleted-medium, treated with CPA (10µM of cyproterone acetate) for 24hrs, repeat 1


title: macrophage cells-M2

description: macrophage cells-M2


title: LNCaP-DHT-8hr-R2

description: LNCaP cells in androgen depleted-medium, treated with DHT (1nM of Dihydrotestosterone) for 8hrs, repeat 2


title: control macrophage cells-C1

description: macrophage cells-C1


title: ECOR56

description: High Output 75bp


title: PTBP1 in vivo iCLIP, HeLa, rep2


title: ECOR55

description: High Output 75bp


title: ECOR64

description: High Output 75bp


title: PTBP1 in vivo iCLIP, HeLa, rep1


title: ECOR66

description: High Output 75bp

value: NPEC


title: U2AF2 in vivo iCLIP, HeLa, 2019, rep2


title: control of lung cancer 3

city: Nanjing

first: Shuwen

last: Cheng

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

data_processing:
raw data were trimmed by fastp
clean data were aligned to genome by STAR
bam files were quantified by stringtie
Assembly: hg38
Supplementary files format and content: count.csv,the count value of all samples

source_name: lung

extract_protocol: Trizol with standard protocol

value: lung

tag: patient number

tag: disease state

value: paratumor non-cancerous tissue

tag: patient diagnosis

value: NSCLC


title: lung cancer 3

value: lung cancer


title: control of lung cancer 2


title: U2AF2 in vivo iCLIP, HeLa, 2019, rep1


title: ECOR61

description: High Output 75bp


title: LNCaP-Veh-8hr-R1

description: LNCaP cells in androgen depleted-medium, treated with Vehicle (Ethanol) for 8hrs, repeat 1


title: ECOR54

description: High Output 75bp


title: control of lung cancer 1


title: U2AF2 in vivo iCLIP, HeLa, 2017, rep4


title: LNCaP-Veh-8hr-R2

description: LNCaP cells in androgen depleted-medium, treated with Vehicle (Ethanol) for 8hrs, repeat 2


title: U2AF2 in vivo iCLIP, HeLa, 2017, rep3


title: LNCaP-DHT-4hr-R2

description: LNCaP cells in androgen depleted-medium, treated with DHT (1nM of Dihydrotestosterone) for 4hrs, repeat 2


title: LNCaP-CPA-8hr-R1

description: LNCaP cells in androgen depleted-medium, treated with CPA (10µM of cyproterone acetate) for 8hrs, repeat 1


title: ECOR53

description: High Output 75bp


title: LNCaP-DHT-8hr-R1

description: LNCaP cells in androgen depleted-medium, treated with DHT (1nM of Dihydrotestosterone) for 8hrs, repeat 1


title: lung cancer 1


title: LNCaP-DHT-4hr-R1

description: LNCaP cells in androgen depleted-medium, treated with DHT (1nM of Dihydrotestosterone) for 4hrs, repeat 1


title: U2OS, input

city: London

first: Sara

last: Rohban

state: London

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: input

data_processing:
Adapters were trimmed from the 3’ ends of the reads using Trimmomatic v0.36.
Obtained sequences were mapped to the human hg38 reference genome with Bowtie2.
PCR duplicates were removed with Picard MarkDuplicates tools.
bigwig files were generated for each bam file with bamCoverage tool (deepTools).
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: DMEM supplemented with 10% FBS at 37C in 5% CO2 incubator.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor Pico (Diagenode) to obtain DNA fragment size distribution of 150-300 bp.
Library preparation was performed using NEBNext Ultra II DNA Library Prep kit for Illumina.

value: human osteosarcoma


title: U2AF2 in vivo iCLIP, HeLa, 2017, rep2


title: ECOR52

description: High Output 75bp


title: U2OS, siINTS11, RNAPII-ChIP, rep2

value: RNAPII (Bethyl Laboratories # A304-405A)


title: U2AF2 in vivo iCLIP, HeLa, 2017, rep1


title: lung cancer 2


title: PNK004, rep 3

description: High Output 75bp

value: Group D


title: ECOR51

description: High Output 75bp


title: LNCaP-CPA-8hr-R2

description: LNCaP cells in androgen depleted-medium, treated with CPA (10µM of cyproterone acetate) for 8hrs, repeat 2


title: U2AF2 in vivo iCLIP in FUBP1 KD, HeLa, 2017, rep4


title: LNCaP-CPA-4hr-R1

description: LNCaP cells in androgen depleted-medium, treated with CPA (10µM of cyproterone acetate) for 4hrs, repeat 1


title: U2OS, siINTS11, RNAPII-ChIP, rep1


title: LNCaP-CPA-4hr-R2

description: LNCaP cells in androgen depleted-medium, treated with CPA (10µM of cyproterone acetate) for 4hrs, repeat 2


title: U2AF2 in vivo iCLIP in FUBP1 KD, HeLa, 2017, rep3


title: LNCaP-DHT-2hr-R2

description: LNCaP cells in androgen depleted-medium, treated with DHT (1nM of Dihydrotestosterone) for 2hrs, repeat 2


title: PNK004, rep 1

description: High Output 75bp


title: LNCaP-DHT-2hr-R1

description: LNCaP cells in androgen depleted-medium, treated with DHT (1nM of Dihydrotestosterone) for 2hrs, repeat 1


title: U2AF2 in vivo iCLIP in FUBP1 KD, HeLa, 2017, rep2


title: LNCaP-CPA-2hr-R2

description: LNCaP cells in androgen depleted-medium, treated with CPA (10µM of cyproterone acetate) for 2hrs, repeat 2


title: U2OS, siCtrl, RNAPII-ChIP, rep1

value: siCtrl-transfected


title: ECOR50

description: High Output 75bp


title: U2AF2 in vivo iCLIP in FUBP1 KD, HeLa, 2017, rep1


title: ECOR48

description: High Output 75bp


title: U2OS, siINTS11, DRB_30min, rep2

description:
siINTS11_DRB_30min_rep2
nascent RNA
Directional RNA-seq

data_processing:
Adapters were trimmed from the 3’ ends of the reads using Trimmomatic v0.36.
Reads mapping to rRNA genes were removed using BBDuk in the BBTools package v36.20.
The rRNA cleaned reads were then mapped to the human reference genome (hg38) with STAR aligner v2.7.
Putative PCR duplicates were marked and removed using MarkDuplicates.
bigWig files (in forward and reverse direction) were generated using bamCoverage (deepTools), normalized with library size.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Total RNA was extracted with TRIzol, digested with DNaseI and purified. Around 100 ug purified RNA was fragmented to approximately 100-300 nucleotide fragments by sodium hydroxide treatment. 4sU-RNA was then biotinylated using 0.1 mg/ml MTSEA biotin-XX linker. Biotinylated RNA was purified and captured by streptavidin MicroBeads. After elution from beads, RNA was purified using RNeasy MinElute Cleanup kit.
40 ng RNA was used for library preparation using NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: Forty-eight hours after siRNA transfection, DRB was added to the medium of the cells. After 3 hours, cells were washed three times with PBS equilibrated at 37C, and pre-warmed fresh medium was then added to the cells. 4sU (1 mM final concentration) was added to the medium during the last 10 min before cell harvesting. 10-, 20- and 30-min post DRB release, cells were harvested directly on the plate with TRIzol reagent.


title: SF3B1 in vivo iCLIP, HeLa, rep4


title: U2OS, siINTS11, DRB_30min, rep1

description:
siINTS11_DRB_30min_rep1
nascent RNA
Directional RNA-seq


title: SF3B1 in vivo iCLIP, HeLa, rep3


title: LNCaP-CPA-2hr-R1

description: LNCaP cells in androgen depleted-medium, treated with CPA (10µM of cyproterone acetate) for 2hrs, repeat 1


title: ECOR49

description: High Output 75bp


title: PNK004, rep 2

description: High Output 75bp


title: LNCaP-Control-R2

description: LNCaP cells in androgen-depleted medium, no treatment, repeat 2

value: Control


title: U2OS, siCtrl, RNAPII-ChIP, rep2


title: U2OS, siINTS11, DRB_20min, rep2

description:
siINTS11_DRB_20min_rep2
nascent RNA
Directional RNA-seq


title: SF3B1 in vivo iCLIP, HeLa, rep2


title: Hypothalamic neurons, male, 3

city: Los Angeles

first: John

middle: Edward

last: van Veen

state: CA

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

data_processing:
Assembly to mouse transcriptome with Kallisto version 0.46.2
merge kallisto output with tximport Version 1.10.0
DEseq2 Galaxy Version 2.11.40.6+galaxy1
Assembly: mm10
Supplementary files format and content: TPM values in tsv file

source_name: hypothalamus

extract_protocol:
Qiagen RNA micro
SMARTer® Stranded Total RNA-Seq Kit v2 followed by Illumina V2

value: hypothalamus

tag: agent

value: AAV2-flex-tdTomato (addgene#28306)

value: Neurons

value: Ssttm2.1(cre)Zjh/J / +

value: male


title: ECOR47

description: High Output 75bp


title: ECOR44

description: High Output 75bp


title: SF3B1 in vivo iCLIP, HeLa, rep1


title: U2OS, siINTS11, DRB_20min, rep1

description:
siINTS11_DRB_20min_rep1
nascent RNA
Directional RNA-seq


title: U2OS, siINTS11, DRB_10min, rep2

description:
siINTS11_DRB_10min_rep2
nascent RNA
Directional RNA-seq


title: LNCaP-Control-R1

description: LNCaP cells in androgen-depleted medium, no treatment, repeat 1

value: Prostate cancer LNCaP cell line


title: Hypothalamic neurons, male, 4


title: U2OS, siINTS11, DRB_10min, rep1

description:
siINTS11_DRB_10min_rep1
nascent RNA
Directional RNA-seq


title: PNK006, rep 3

description: High Output 75bp

value: UPEC

value: Group A


title: SF1 in vivo iCLIP, HeLa, rep3

value: HeLa


title: Hypothalamic neurons, male, 1


title: PNK006, rep 2

description: High Output 75bp


title: Hypothalamic neurons, female, 4

value: female


title: PNK006, rep 1

description: High Output 75bp


title: Hypothalamic neurons, female, 3


title: U2OS, siCtrl, DRB_30min, rep1

description:
siCtrl_DRB_30min_rep1
nascent RNA
Directional RNA-seq


title: Hypothalamic neurons, male, 2


title: ECOR14

description: High Output 75bp


title: FUBP1 in vivo iCLIP, HeLa, rep5


title: SF1 in vivo iCLIP, HeLa, rep1


title: FUBP1 in vivo iCLIP, HeLa, rep4


title: U2OS, siCtrl, DRB_20min, rep1

description:
siCtrl_DRB_20min_rep1
nascent RNA
Directional RNA-seq


title: Hypothalamic neurons, female, 2


title: ECOR11

description: High Output 75bp


title: SF1 in vivo iCLIP, HeLa, rep2


title: FUBP1 in vivo iCLIP, HeLa, rep3


title: U2OS, siCtrl, DRB_30min, rep2

description:
siCtrl_DRB_30min_rep2
nascent RNA
Directional RNA-seq


title: Hypothalamic neurons, female, 1


title: ECOR23

description: High Output 75bp

value: NPEC


title: U2OS, siCtrl, DRB_10min, rep1

description:
siCtrl_DRB_10min_rep1
nascent RNA
Directional RNA-seq


title: FUBP1 in vivo iCLIP, HeLa, rep2


title: FUBP1 in vivo iCLIP, HeLa, rep1


title: control Cut n Run rep 2

city: Munich

first: Nikolas

last: Eggers

address: Grosshaderner Strasse 9

department: Molecular Biology

institute: LMU Munich

data_processing:
RTA software von Illumina, version ist 1.18.66.3
sequenced reads were demultiplexed and trimmed using JE Demultiplexer
Demultiplexed reads were aligned to the dm6 genome using bowtie 2 version 2.2.9. with settings: -p 24 --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant  -X 400
filtering and sorting was done using samtools 1.9 with -q 10.
genomic tracks were made by Homer 4.9 and normalized to the negative control or the input.
replicates were summarized by subsampling them to the same read counts and summarizing them
peaks were called using findPeaks form Homer 4.9  with settings: -style factor -size 150 -F 10 -L 4
Assembly: dm6
Supplementary files format and content: .bw files

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were cultured in Schneiders Drosophila Medium until 90% confluent

extract_protocol:
The cells were then permeabilized in Antibody buffer containing 0.05% digitoninand 2 mM EDTA and incubated with rabbit α-MSL2 serum or pre-immune serum
libraries were prepared using NEBNext Ultra II DNA Library
These libraries are Cut and Run libraries

treatment_protocol: 106 S2 cells were harvested, washed and bound to pre-activated Concanavalin A-coated magnetic beads, in wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine and 1X cOmplete EDTA-free PIC)

tag: ip target

value: PPI


title: U2OS-AsiSI, siINTS11, rep3

description:
AsiSI_siINTS11_rep3_TTseq
nascent RNA
Directional RNA-seq

data_processing:
Adapters were trimmed from the 3’ ends of the reads using Trimmomatic v0.36.
Reads mapping to rRNA genes were removed using BBDuk in the BBTools package v36.20.
The rRNA cleaned reads were then mapped to the human reference genome (hg38) with STAR aligner v2.7.
Putative PCR duplicates were marked and removed using MarkDuplicates.
bigWig files (in forward and reverse direction) were generated using bamCoverage (deepTools), normalized with yeast spike-in scale factor.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: Tab-delimited text files include gene counts (calculated by featureCounts) for each sample compared to its control.

extract_protocol:
Total RNA was extracted with TRIzol, digested with DNaseI and purified. Around 100 ug purified RNA was spiked with 1 ug 4-thiouracil (4TU) labelled yeast RNA. The RNA mixture was fragmented to approximately 100-300 nucleotide fragments by sodium hydroxide treatment. 4sU-RNA was then biotinylated using 0.1 mg/ml MTSEA biotin-XX linker. Biotinylated RNA was purified and captured by streptavidin MicroBeads. After elution from beads, RNA was purified using RNeasy MinElute Cleanup kit.
500 ng RNA was used for library preparation using NEBNext Ultra II Directional RNA Library Prep kit.

value: human osteosarcoma


title: ECOR16

description: High Output 75bp


title: control Cut n Run rep 1


title: ECOR6

description: High Output 75bp


title: U2OS, siCtrl, DRB_10min, rep2

description:
siCtrl_DRB_10min_rep2
nascent RNA
Directional RNA-seq


title: ECOR8

description: High Output 75bp


title: MSL2 Cut n Run rep 3


title: U2OS, siCtrl, DRB_20min, rep2

description:
siCtrl_DRB_20min_rep2
nascent RNA
Directional RNA-seq


title: U2OS-AsiSI, siINTS11, rep2

description:
AsiSI_siINTS11_rep2_TTseq
nascent RNA
Directional RNA-seq


title: ECOR4

description: High Output 75bp


title: MSL2 Cut n Run rep 1


title: MSL2 Cut n Run rep 2


title: U2OS-AsiSI, siINTS11, rep1

description:
AsiSI_siINTS11_rep1_TTseq
nascent RNA
Directional RNA-seq


title: W3110, rep 3

description: High Output 75bp


title: U2OS-AsiSI, siCtrl, rep3

description:
AsiSI_siCtrl_rep3_TTseq
nascent RNA
Directional RNA-seq


title: chip msl2 negative control rep3

data_processing:
RTA software von Illumina, version ist 1.18.66.3
sequenced reads were demultiplexed and trimmed using JE Demultiplexer
Demultiplexed reads were aligned to the dm6 genome using bowtie 2 version 2.2.9. with settings: -p 24 --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant  -X 400
filtering and sorting was done using samtools 1.9 with -q 10.
genomic tracks were made by Homer 4.9 and normalized to the negative control or the input.
replicates were summarized by subsampling them to the same read counts and summarizing them
peaks were called using findPeaks form Homer 4.9  with settings: -style factor -size 150 -F 8 -L 2
Assembly: dm6
Supplementary files format and content: .bw files

source_name: BG-3 cells

growth_protocol: purified genomic DNA from bg-3 cells was assembled to chromatin for 5h.

extract_protocol:
DNA was purified using Phenol-Chloroform Extraction.
libraries were made using the NEB library Kit for Illumina

treatment_protocol: Respective Proteins were added to the chromatin and bound for 30 min. samples were crosslinked and partially digested by Mnase.

value: BG-3 cells


title: W3110, rep 2

description: High Output 75bp


title: HS6

city: Philadelphia

first: Camila

last: Farias Amorim

state: United States

address: 380 S University Ave

department: Pathobiology

institute: University of Pennsylvania

data_processing:
Samples were sequenced  five times on an Illumina NextSeq 500 to produce 75–base pair single-end reads. The raw reads were mapped to the human reference transcriptome (Ensembl; Mus musculus version 100) using Kallisto version 0.46.0.
All subsequent analyses were carried out using the statistical computing environment, R version 4.1.0 in RStudio version 1.4.1717 and Bioconductor, version 3.13
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package
Normalized data was variance stabilized using the VOOM function in limma
raw data file: Tab-delimited text raw data includes raw gene counts summarized by tximport package
normalized data file: Tab-delimited text filtered (for genes detected at <1 CPM in at least 6 samples), normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method)
study design file: Tab-delimited text file with study design

source_name: intact skin biopsy

growth_protocol: CL lesion biopsies and intact HS were thawed from RNAlater and homogenized with a tissue homogenizer

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions.
Complementary DNA (cDNA) sequence-ready libraries were carried out with the Illumina TruSeq Total Transcriptome kit with Ribo-Zero Gold for eukaryotic cytoplasmic and mitochondrial rRNA depletion (Illumina).
Quality assessment and quantification of RNA preparations and libraries were carried out using an Agilent 4200 TapeStation and Qubit 3, respectively.

tag: diagnosis

value: healthy

value: intact skin biopsy

tag: age

tag: lesion size mm2

tag: lymphadenophathy

tag: dth mm2

tag: treatment outcome

tag: healing time days

tag: microbiome cluster 16s-seq


title: U2OS-AsiSI, siCtrl, rep1

description:
AsiSI_siCtrl_rep1_TTseq
nascent RNA
Directional RNA-seq

tag: cell type

tag: genotype

tag: treatment


title: W3110, rep 1

description: High Output 75bp

tag: cell line


title: HS5

tag: tissue

tag: Sex


title: chip msl2 negative control rep2


title: chip msl2 negative control rep1


title: HS3


title: chip msl2 rep 2

tag: factors added


title: PU.1 ChIP L1

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
Fastq read files were trimmed using Cutadapt
The trimmed reads were mapped to mm10 mouse genome using HISAT2
Peak calling was conducted by HOMER program run in factor mode (false discovery rate < 0.001). The intergenic peaks nearest a TSS were annotated as the corresponding gene, and peaks within a gene were further categorized into exonic, intronic, 3′ or 5′ untranslated regions using HOMER mm10 annotation.
Assembly: mm10
Supplementary files format and content: BigWig format

source_name: BM hematopoietic cells

extract_protocol:
Cells were cross-linked in 0.75% formaldehyde, pelleted, and frozen until the ChIP procedure. Pellets were thawed on ice, resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCL [pH 8.1] plus protease inhibitor) for 10 min. Volume was brought up to 1 ml with ChIP dilution buffer (16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl, 0.01% SDS, 1.1% Triton X-100, and 1.2 mM EDTA plus protease inhibitor) and samples were sonicated with a Branson sonicator to shear chromatin. Chromatin was subsequently incubated with 1 µg PU.1 antibody (sc-390405; Santa Cruz Biotechnology) and rotated overnight at 4°C. Next, ChIPs were added to a 50:50 mix of prewashed Protein A/G Dynabeads (50 µl; 10001D/10009D; Thermo Fisher Scientific) and rotated overnight at 4°C. The next day, 175 µl RIPA/140 mM NaCl buffer (0.1% sodium deoxycholate, 0.1% SDS, 1% Triton X-100,140 mM NaCl, 1 mM EDTA, 20 mM Tris-HCl [pH 8.1]) was added to each tube and beads were transferred to a 96-well plate on a magnet, washed twice with cold RIPA/500 ml NaCl buffer (0.1% sodium deoxycholate, 0.1% SDS, 1% Triton X-100, 140 mM NaCl, 1 mM EDTA, and 20 mM Tris-HCl [pH 8.1]), twice with cold LiCl buffer (0.25 M LiCl, 1% NP-40, 1% Na deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl [pH 8.1]), and twice with RT TE buffer (10 mM Tris-HCl [pH 8.0] and 1 mM EDTA [pH 8.0]). Chromatin was eluted by adding 50 µl of elution buffer (10 mM Tris-Cl [pH 8.0], 5 mM EDTA, 300 mM NaCl, 0.1% SDS, and 5 mM dithiothreitol) and 8 µl of reverse cross-linking buffer (250 mM Tris-HCl [pH 6.5], 1.25 M NaCl, 62.5 mM EDTA, 5 mg/ml Proteinase K, and 62.5 μg/ml RNase A) and incubated at 65°C overnight. ChIP material was quantified on a Qubit spectrometer (Invitrogen) according to manufacturer’s instructions.
Library construction was performed first using an End-it DNA End-Repair Kit (ER0720; Epicenter) according to manufacturer’s instructions, followed by DNA ligase-based adapter ligation (M2200S; New England Biolabs) and enrichment of adapter-modified DNA fragments by PCR. PCR fragments were gel purified using a Qiagen Gel Purification Kit (Qiagen) a
PCR fragments were gel purified using a Qiagen Gel Purification Kit (Qiagen) and sequenced on an Illumina single-end flow cell. Sequencing of libraries was performed on Illumina HiSeq 2500v4 high-throughput sequencer.

value: BM hematopoietic cells

value: primary cells

value: LSK Flk2- CD150+

value: WT


title: WCE ChIP L2

description: WCE.bw


title: U2OS, siINTS11, rep2

description:
siINTS11_rep2_TTseq
nascent RNA
Directional RNA-seq


title: U2OS-AsiSI, siCtrl, rep2

description:
AsiSI_siCtrl_rep2_TTseq
nascent RNA
Directional RNA-seq


title: WCE ChIP L1

description: WCE.bw


title: U2OS, siINTS11, rep1

description:
siINTS11_rep1_TTseq
nascent RNA
Directional RNA-seq


title: HS4


title: Heat Shock+5phlAA B

first: Asif

last: Ali

state: Illinois

address: 929 E 57th St

department: Molecular Genetics and Cell Biology

institute: University of Chicago

data_processing:
Fastq files were generated by Illumina HiSeq 4000
Reads were mapped using an index for S.cerevisiae from Ensembl, which  kallisto recommends. https://github.com/pachterlab/kallisto-transcriptome-indices/releases
Assembly: The reads mapping were counted using the pseudosequencing software called Kallisto. kallisto quant --index=cenpk_kalindex --output-dir=quant90_orfcoding --single -s 20 -l 200 *.fastq.gz
Supplementary files format and content: tab-separated value format; includes raw counts and TPM

growth_protocol: Cells were grown at optimum growth temperature 30°C until OD600 was between 0.2-0.4 in YPD with 2% dextrose.

extract_protocol:
The extraction of total RNA was carried out by employing the Direct-zol RNA Miniprep kit (Zymo, catalog number R2052) in conjunction with Ambion TRI-reagent (Fisher, catalog number AM9738) and Zirconia/Silica 0.5 mm homogenization beads (Biospec, catalog number 11079105Z). To remove any contaminating DNA, the samples were treated with Dnase I (NEB, catalog number M0303S).
TruSeq RNA Library Prep Kit v2 (Illumina RS-122-2001), Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: easts were treated at 30°C/39°C for 5 min.  Acute and non-leaky depletion of Ifh1 is achieved by co-treatment with β-estradiol (1μM, Sigma #E8875) and 5ph-IAA (5μM, MedChemExpress #HY-134653) for 30 min.

tag: strain

tag: temperature

tag: biorep


title: Control+5phlAA B


title: chip msl2 rep 3

tag: ip target


title: chip msl2 rep 1


title: Heat Shock+5phlAA A


title: chip msl2 +clamp rep3

value: MSL2 + CLAMP


title: Control+5phlAA A


title: HS2

tag: diagnosis

tag: age

tag: lesion size mm2


title: U2OS, siCtrl, rep3

description:
siCtrl_rep3_TTseq
nascent RNA
Directional RNA-seq

value: siCtrl-transfected


title: Control B


title: U2OS, siCtrl, rep2

description:
siCtrl_rep2_TTseq
nascent RNA
Directional RNA-seq


title: chip msl2 +clamp rep2


title: Patient51

source_name: CL lesion skin biopsy

value: cutaneous leishmaniasis

value: CL lesion skin biopsy

value: male

tag: lymphadenophathy

value: yes

tag: dth mm2

tag: treatment outcome

value: Cure


title: U2OS, siINTS11, rep3

description:
siINTS11_rep3_TTseq
nascent RNA
Directional RNA-seq

tag: cell type


title: Control A


title: U2OS, siCtrl, rep1

description:
siCtrl_rep1_TTseq
nascent RNA
Directional RNA-seq

tag: genotype


title: PU.1 ChIP L2

tag: treatment

value: 1 µg PU.1 antibody (sc-390405; Santa Cruz Biotechnology)


title: Patient50

tag: healing time days

tag: microbiome cluster 16s-seq


title: Patient48

tag: tissue

tag: Sex

value: female

value: no

value: Failure


title: Heat Shock A

tag: strain


title: chip msl2 + clamp mutant rep2

tag: cell line

value: BG-3 cells

tag: factors added

value: MSL2 + CLAMP mutant


title: chip msl2 + clamp mutant rep3

tag: ip target


title: 14-442.Tumour

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
For in situ Hi-C library, the paired end reads were was mapped to the reference genome (hg38) using BWA-mem (‘–M’ option).
In-house script was used to remove low quality reads (MAPQ < 10), the reads that span ligation sites, chimeric reads, and self-interacting reads where two fragments are located within 15kb.
The read-pairs were merged together as paired-end aligned BAM files
PCR duplicates were removed with Picard.
Final usable cis-chromosomal (>15kb) paired reads were obtained.
To remove multiple sources of intrinsic biases of raw Hi-C data, we applied negative binomial model-based implicit normalization approaches, as previously described in [PMID: 29106613], and created 40kb resolution normalized interaction matrix.
We performed quantile-normalization across the samples to allow a robust comparative analysis in each chromosome.
Genome_build: hg38
Supplementary_files_format_and_content: 40kb resolution Hi-C contact matrix. 1st row/column indicates coordinate of the bins and matrix values are normalized interaction frequencies.

extract_protocol:
Patient tissue sample was pulverized by repeated hammering while frozen in liquid nitrogen to produce tissue powder. For in-situ Hi-C, tissue was crosslinked, lysed and disgested with MboI. The fragments were the labelled with biotin, proximally ligated, sonicated, and purified with AMPure XP beads. Ligated DNA was pulled down with streptavidin T1 beads, followed by manual library preparation.
In situ Hi-C library was sequenced with Illumina Hiseq4000 and Novaseq S4 platforms.

tag: experiment

value: in situ Hi-C

tag: disease

value: colorectal cancer


title: HS1

tag: diagnosis

value: healthy

value: intact skin biopsy

tag: age

tag: lesion size mm2


title: chip msl2 + clamp mutant rep1


title: 14-810.Tumour


title: chip flag clamp rep 2

value: FLAG-tag

value: CLAMP


title: chip flag clamp rep 1


title: Patient46

value: cutaneous leishmaniasis

tag: lymphadenophathy

tag: dth mm2

tag: treatment outcome


title: Patient45

value: CL lesion skin biopsy


title: 14-91.Tumour


title: Patient47


title: ECKO-CCL4-2

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng 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 GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), 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: GRCm38.p4 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (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 separated into mRNA, 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.

treatment_protocol: Tgfbr2f/f mice and Tgfbr2ECKO mice were intraperitoneally injected with CCl4  twice a week for 6 weeks.

value: liver

tag: cell type

value: LSECs

tag: genotype

value: Tgfbr2 ECKO

tag: treatment


title: ECKO-CCL4-3

tag: tissue


title: 14-114.Tumour


title: WT-CCL4-3


title: chip flag clamp mutant rep2

value: CLAMP mutant


title: ECKO-CCL4-1


title: Heat Shock B

tag: temperature

tag: biorep


title: Patient44

tag: Sex

value: male

value: yes

tag: healing time days

tag: microbiome cluster 16s-seq


title: WT-CCL4-2


title: chip msl2 +clamp rep1

tag: cell line

tag: ip target

tag: factors added

value: MSL2 + CLAMP


title: 14-132.Tumour

tag: experiment

tag: disease


title: WT-CCL4-1


title: chip flag clamp mutant rep1

value: BG-3 cells


title: chip flag negative control rep2


title: 13-257.Tumour


title: Patient43

tag: diagnosis

tag: age

value: female

tag: lesion size mm2

tag: lymphadenophathy

value: DOT


title: Patient42

tag: dth mm2

tag: treatment outcome

value: Cure


title: chip flag negative control rep1


title: MH-S cells, infection RNA-seq rep3 [CP3]

data_processing:
RNA-seq:
Before applying any data filtering criteria, RNA-Seq reads were adapter trimmed using Trim Galore (v0.6.7) for removing low-quality data, and FastQC (v0.11.9) software was used to assess data quality.
Reads were mapped to the mouse reference genome (mm10) using HISAT2 software (v2.2.1).
The mapped reads were assembled into transcripts or genes by featureCounts (v2.0.2) software and genome annotation (mm10.gtf).
ATAC-seq:
The unmapped reads were first processed with trim_galore (v0.6.7) with the parameters "-q 30 --phred33 --stringency 3 --length 35".
Sequencing reads are mapped to the mouse genome (mm10) by bowtie (v1.3.1) with the parameter "-m1 --best --strata -X 2000".
The bam files were then merged and processed using sambamba (v0.8.1) markdup function to remove duplicate reads and then filter out reads that mapped to the mitochondrial genome and to select unique, non-chrM reads from the bam files using samtools (v1.9).
To normalize and visualize the data, the BAM files were converted to bigWig format using RPKM's "bamCoverage".
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mapped reads for each Sample
Supplementary files format and content: bigWig

extract_protocol:
For RNA extraction, a 1% agarose gel was used to detect RNA degradation and contamination.
RNA-seq: Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, E7530L) and index codes were added to the attribute sequences of each sample and sequenced using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, PE-401-3001) on the cBot Cluster Generation System to cluster the index-coded samples.
ATAC-seq: Resuspended the cell pellets with 50 μL of lysis buffer and the nuclei were pelletized by centrifugation at 500 × g for 10 min at 4°C.   The supernatant was discarded and the nuclei were resuspended with a reaction buffer containing Tn5 transposase 2.5 μL and TD (Nextera Illumina) 22.5 μL.   Incubate at 37°C for 30 minutes.   Labeled DNA was isolated using the MinElute PCR Purification Kit (Qiagen).
ATAC-seq: 10 cycles of libraries amplification and 2 × SPRI Cleanup (Agencourt) were used to purify. Using the LabChip GXII Touch HT (PerkinElmer), library sizes were calculated. NextSeq500 (Illumina) was then used to do 2 × 75 paired-end sequencings, which produced an average of 50 M reads/sample.

tag: tissue

value: Lung

value: MH-S cells

tag: cell type

value: Murine alveolar macrophages

tag: genotype

value: WT

tag: treatment

value: infection

tag: strain


title: 13-1413.Tumour

value: in situ Hi-C

value: colorectal cancer


title: Patient41

value: cutaneous leishmaniasis

value: CL lesion skin biopsy

tag: Sex

value: no

value: Failure

tag: healing time days

tag: microbiome cluster 16s-seq


title: 14-426.Tumour


title: 14-494.Tumour


title: chip clamp rep2

tag: cell line

tag: ip target

value: CLAMP

tag: factors added


title: MH-S cells, infection RNA-seq rep1 [CP1]


title: 13-1410.Tumour

tag: experiment

tag: disease


title: Patient40

tag: diagnosis

tag: age

value: male

tag: lesion size mm2


title: Patient39

tag: lymphadenophathy

value: yes

tag: dth mm2

tag: treatment outcome


title: 13-1334.Tumour


title: chip clamp mutant rep2

value: BG-3 cells

value: CLAMP mutant


title: 13-1321.Tumour


title: MH-S cells, control RNA-seq rep3 [CC3]

tag: tissue

tag: cell type

tag: genotype

value: control


title: MH-S cells, infection RNA-seq rep2 [CP2]

value: Lung

tag: treatment

tag: strain


title: Patient38

tag: Sex

value: Cure

tag: healing time days

tag: microbiome cluster 16s-seq


title: chip clamp mutant rep1

tag: cell line

tag: ip target

tag: factors added


title: 11-1026.Tumour

tag: experiment

tag: disease


title: chip clamp rep1


title: MH-S cells, control RNA-seq rep1 [CC1]

value: MH-S cells

value: Murine alveolar macrophages


title: Patient37

tag: diagnosis

tag: age

tag: lesion size mm2

value: DOT


title: MH-S cells, control RNA-seq rep2 [CC2]

value: WT


title: Patient36

value: female

tag: lymphadenophathy

tag: dth mm2

tag: treatment outcome


title: 11-983.Tumour

value: in situ Hi-C

value: colorectal cancer


title: chip clamp mutant + msl2 rep2

value: MSL2 + CLAMP mutant


title: chip clamp mutant + msl2 rep1


title: 11-927.Tumour


title: Lung tissues, infection RNA-seq rep3 [TP3]

tag: tissue

tag: cell type

value: Lung tissues

tag: genotype

value: infection


title: Patient35

value: cutaneous leishmaniasis

value: CL lesion skin biopsy

tag: Sex

value: male

value: Failure


title: chip clamp + msl2 rep2

value: BG-3 cells

value: CLAMP

value: MSL2 + CLAMP


title: Lung tissues, infection RNA-seq rep2 [TP2]

value: Lung

tag: treatment

tag: strain


title: 14-1083.Tumour


title: chip clamp negative control rep2

tag: cell line


title: 14-431.Tumour


title: Patient34

value: no

value: Cure

tag: healing time days

tag: microbiome cluster 16s-seq


title: Patient32

value: yes


title: Lung tissues, infection RNA-seq rep1 [TP1]

value: WT


title: 13-545.Tumour

tag: experiment

value: in situ Hi-C


title: Lung tissues, control RNA-seq rep3 [TC3]

value: control


title: chip clamp negative control rep1

tag: ip target


title: Patient31

tag: diagnosis


title: Patient33

tag: age


title: chip clamp + msl2 rep1

tag: factors added


title: Lung tissues, control RNA-seq rep2 [TC2]


title: 09-376.Tumour

tag: disease

value: colorectal cancer


title: Patient30

value: female

tag: lesion size mm2

tag: lymphadenophathy

tag: dth mm2


title: 13-731.Tumour


title: Neutrophil, Hmgb1ΔMye-LPS, rep3

first: Natalia

last: Nieto

address: 909 South Wolcott Avenue

data_processing:
Data were aligned using RNA-Seq Alignment v.2.0.2 in basespce
Differential analysis was performed using RNA-Seq Differential Expression v: 1.1.0 in basespace
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Blood

extract_protocol:
miRNeasy micro kit (Qiagen, Germantown, MD)
The total RNAs were converted into individually barcoded polyadenylated mRNAseq libraries with the Universal Plus Total RNA with mouse probes library construction kit (Tecan, CA).

treatment_protocol: Mice were treated with saline or 0.5 mg/kg LPS for 16 hours, and neutrophils were isolated for RNAseq

tag: tissue

value: Blood

tag: cell type

value: Neutrophil

tag: gender

value: Female

value: LPS

tag: group


title: Reh-6MPR, His+6-MP

city: Jinan

last: Dong

state: Shandong Province

address: No. 107 Wenhua West Road

department: Department of Pediatrics

institute: Qilu Hospital of Shandong University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38(Ensembl GRCh38.104)
Supplementary files format and content: FPKM(.xls)

source_name: cell line

growth_protocol: Reh-6MPR cells were  cultured in 1640 RPMI medium containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S), at 37℃ in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted from the cell pellets using Trizol reagent.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Reh-6MPR cells were seeded in 6-cm dishes and treated with  PBS, histidine (4mM), 6-MP (1.0μg/mL), or a combination of histidine and 6-MP for 48h.

value: cell line

value: Reh

value: 6-MP resistant

tag: genotype

tag: treatment


title: Patient29

value: cutaneous leishmaniasis

value: CL lesion skin biopsy

tag: Sex

tag: treatment outcome

tag: healing time days


title: Reh-6MPR, 6-MP

tag: cell line


title: 13-731.Normal

tag: experiment

value: Normal


title: Reh-6MPR, His

value: His


title: Patient28

tag: diagnosis

tag: age

value: male

value: yes

value: Failure

tag: microbiome cluster 16s-seq


title: Neutrophil, Hmgb1ΔMye-Saline, rep3

institute: University of Illinois at Chicago

value: Saline


title: 12-251.Normal

value: in situ Hi-C

tag: disease


title: Patient26

tag: lesion size mm2

tag: lymphadenophathy

value: no


title: Neutrophil, Hmgb1ΔMye-Saline, rep2

tag: tissue

value: Blood


title: 12-251.Tumour

value: colorectal cancer


title: 11-1074.Tumour


title: LOUCY KPT-330, anti-MLL1C_ChIP

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

data_processing:
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore.
Sequence reads were aligned to the reference mouse genome (mm10) and human genome (GRCh38) using Bowtie2.
bigWig files for each samples were generated using deepTools with following options "--binSize 100 --normalizeUsing CPM".
Assembly: GRCh38(human), mm10(mouse)
Supplementary files format and content: bigWig

source_name: LOUCY

extract_protocol:
Cross-linked chromatin was sheared by sonication, and MNase treatment.
The ChIP library was prepared using ThruPLEX DNA-seq kit (Takara Bio), according to the manufacturer’s instructions.

value: LOUCY

tag: cell type

value: leukemia

tag: chip antibody

value: anti-MLL1C (CST, 14197)


title: LOUCY KPT-330, INPUT

value: INPUT


title: Patient25

tag: dth mm2

value: Cure


title: Neutrophil, Hmgb1ΔMye-Saline, rep1

city: Chicago

value: Neutrophil

tag: genotype

tag: gender

value: Female

tag: group


title: LOUCY DMSO, anti-MLL1C_ChIP

tag: treatment

value: DMSO


title: 11-52.Tumour


title: Patient27

value: cutaneous leishmaniasis

value: CL lesion skin biopsy

tag: Sex

value: female

tag: treatment outcome

tag: healing time days


title: LOUCY DMSO, INPUT

tag: cell line


title: Neutrophil, Hmgb1ΔMye-LPS, rep2

value: LPS


title: Patient24

tag: diagnosis

tag: age

value: male

value: yes

value: Failure


title: Patient23

tag: microbiome cluster 16s-seq


title: 11-52.Normal

tag: experiment

value: in situ Hi-C

tag: disease

value: Normal


title: Patient22

tag: tissue

tag: lesion size mm2

tag: lymphadenophathy


title: Neutrophil, WT-LPS, rep3

value: Blood

tag: cell type

value: WT

value: WT-LPS


title: Neutrophil, Hmgb1ΔMye-LPS, rep1

tag: genotype


title: Patient49

value: no

tag: dth mm2


title: 11-1074.Normal


title: Lung tissues, control RNA-seq rep1 [TC1]

last: yang

institute: Sichuan University

value: Lung

value: Lung tissues

value: control

tag: strain


title: Reh-6MPR, Blank

value: cell line

value: Reh

value: 6-MP resistant

tag: treatment

value: Blank


title: Patient20

value: cutaneous leishmaniasis

value: CL lesion skin biopsy

tag: Sex


title: 11-63.Normal


title: Patient19

value: male

value: yes

tag: treatment outcome

value: Cure


title: 13-542.Tumour

value: in situ Hi-C

value: colorectal cancer


title: Patient21

tag: healing time days


title: Neutrophil, WT-Saline, rep3

value: Blood

value: Neutrophil

value: WT

tag: gender

value: Female

value: Saline

tag: group

value: WT-Saline


title: Neutrophil, WT-LPS, rep2

value: LPS

value: WT-LPS


title: Patient18

tag: diagnosis

tag: age

value: Failure


title: 11-63.Tumour

tag: experiment


title: 14-275.Tumour

tag: disease


title: 13-542.Normal

value: Normal


title: Neutrophil, WT-LPS, rep1

tag: tissue


title: PDAC Propranolol+ICB scRNA

city: La Jolla

first: Susan

middle: M

last: Kaech

address: 10010 N Torrey Pines Rd

department: NOMIS Center for Immunobiology and Microbial Pathogenesis

institute: Salk Institute for Biological Studies

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Assembly: mm10
Supplementary files format and content: h5 containing filtered count data from CellRanger

source_name: PDAC

extract_protocol:
PDAC tumors were dissected out at d21 after tumor implantation and subsequently minced with razor blades in a cell culture dish before being digested with dissociation buffer (10x dissociation buffer: 40ml RPMI/DMEM with 1% Pen/Strep + 1mM NaPyr + 25mM HEPES + 400mg Collagenase  IV + 400mg Soybean Trypsin Inhibitor + 50mg Dispase II + 20mg DNAse) for 30 min at 37°C. Samples were then strained through a 70µM cell strainer, spun down at 420rcf and 4°C for 4 min. 4 tumors each per treatment condition were pooled and stained for sorting. The following cell populations were sorted into RPMI supplemented with 20% fetal bovine serum: Thy1.2+CD45.2+, Thy1.2-CD45.2+, YFP+CD45.2-. Sorted cells were spun down at 420 rcf at 4°C for 4 minutes, resuspended in PBS + 2% fetal bovine serum and mixed at 8k Thy1.2+CD45.2+, 10k Thy1.2-CD45.2+, 2k YFP+CD45.2- for a total of 20k cells per sample.
Single cell RNA libraries were generated following the manufacturer’s instructions of the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics).

value: PDAC

tag: cell line

value: Propranolol+ICB


title: PDAC Propranolol scRNA

description: 10x Genomics

value: Propranolol


title: 15-1420.Tumour


title: Neutrophil, WT-Saline, rep1


title: PDAC ICB scRNA

description: 10x Genomics

value: ICB


title: Patient17

value: cutaneous leishmaniasis

value: CL lesion skin biopsy

value: female

tag: lesion size mm2

tag: lymphadenophathy

value: no

value: Cure

tag: microbiome cluster 16s-seq


title: Neutrophil, WT-Saline, rep2

value: Blood

tag: cell type

value: Neutrophil

tag: genotype

value: WT


title: 14-326.Tumour

value: in situ Hi-C

value: colorectal cancer


title: Patient15

value: yes

tag: dth mm2

value: DOT


title: Patient16

tag: Sex

value: male

value: Failure


title: PDAC IgG scRNA

description: 10x Genomics

value: PDAC

tag: treatment

value: IgG


title: 15-446.Tumour


title: Patient14

tag: treatment outcome

tag: healing time days


title: 15-418.Tumour


title: Patient13


title: 15-1382.Tumour


title: NUP98HOXA9 ES, anti-MLL1C_ChIP

source_name: mouse embryonic stem cells (mESCs)

tag: strain

value: mouse embryonic stem cells (mESCs)

tag: genotype/variation

tag: chip antibody

value: anti-MLL1C (CST, 14197)


title: Patient12

tag: diagnosis

value: cutaneous leishmaniasis

value: CL lesion skin biopsy

tag: age


title: 14-328.Tumour

tag: experiment

tag: disease


title: Patient11

tag: tissue

tag: lesion size mm2


title: NUP98HOXA9 ES, anti-CRM1(CST)_ChIP

value: anti-CRM1 (CST, 46249)


title: Parental ES, anti-MLL1N_ChIP

value: Parental

value: anti-MLL1N (CST, 14689)


title: 13-1483.Tumour


title: Patient9

value: female

tag: lymphadenophathy

tag: microbiome cluster 16s-seq


title: Parental ES, anti-MLL1C_ChIP

tag: cell type


title: Patient8

tag: dth mm2


title: Parental ES, anti-CRM1(CST)_ChIP


title: 11-51.Tumour


title: Patient7

tag: Sex

value: no


title: 11-51.Normal

value: in situ Hi-C

value: Normal


title: S0112

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

data_processing:
FASTQs were generated using cellranger (v6.0.0) mkfastq with default parameters.
Raw counts were generated by aligning FASTQs to a combined custom reference that included mus musculus + C134 oHSV transcripts using cellranger (v6.0.0) count with default parameters.
Assembly: mm10 + C134 (custom) which was made using cellranger mkref with default parameters
Supplementary files format and content: Raw counts are provided in sparse matrices and were generated by aligning FASTQs to a combined custom reference that included mus musculus + C134 oHSV transcripts using cellranger (v6.0.0) count with default parameters.

source_name: murine CMYC medulloblastoma tumor

growth_protocol: Mouse cell lines (CMYC, MYCN, Ptch) were maintained in NeurobasalTM-A medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 2 μM L-glutamine, 1% N-2 supplement, 2% B-27 supplement (Gibco, Thermo Fisher Scientific), 20 ng/ml human epidermal growth factor, 20 ng/ml human basis fibroblast growth factor (Miltenyi Biotec, Auburn, CA), and 20 ng/ml Leukemia inhibitory Factor (Millipore Sigma, St. Louis, MO)

extract_protocol:
To dissociate resected tumors into single cells, a 1 mL pre-warmed Papain solution at 2 mg/mL was added, and samples were incubated for 20 minutes at 37 degrees Celsius on a heating block with gentle shaking. Wide bore pipette tips were used to homogenate the solution with pipetting, and the brain tumor homogenates were subsequently mixed with 5 mL 10X buffer. Samples were passed through 100 micron followed by 70 micron filters and then counted.
10x Genomics Chromium Single Cell 3' v3.1 single-index kit was used according to the manufacturer's protocol.

treatment_protocol: Viable tumor cells previously harvested from tumor-bearing animals were resuspended in Matrigel (5 µl/animal; BD Biosciences, Franklin Lakes, NJ).  Tumor cells were injected into the cerebral cortices of 5-week-old B6(Cg)-Tyrc-2J/J (Jackson Laboratory, Bar Harbor, ME).  The injection coordinates were 1.75 mm caudal from bregma, 1.5 mm to the right of the sagittal suture, and 3 mm ventral from the skull surface.  Cells were injected at 2.5 µl/min using a 26-gauge Hamilton syringe under isoflurane gas anesthesia. Treatment with C134 (1 × 107 pfu/dose) delivered in 5µl total volume or an equivalent volume of vehicle (10% glycerol in phosphate buffered saline (PBS)) was administered five days after tumor implantation by intratumoral injection using the same coordinates on the stereotactic frame as those used for implantation. Tumors were resected 2- or 5- days post treatment for single cell RNA-seq preparation.

value: murine CMYC medulloblastoma tumor

tag: treatment

value: C134 oHSV

tag: timepoint (post-treatment)

value: 6 days


title: NUP98HOXA9 ES, anti-MLL1N_ChIP


title: 16-178.Tumour

value: colorectal cancer


title: S0111

value: vehicle


title: 16-178.Normal


title: Patient5

value: male

value: yes

tag: treatment outcome

value: DOT

tag: healing time days


title: Patient4

value: cutaneous leishmaniasis

value: Failure


title: 14-258.Tumour


title: Patient3

value: CL lesion skin biopsy

value: Cure


title: NUP98HOXA9 ES, INPUT

tag: strain

value: mouse embryonic stem cells (mESCs)

tag: genotype/variation

value: INPUT


title: 14-1251.Tumour


title: Patient2

tag: diagnosis


title: 13-1320.Tumour


title: Patient10

tag: age

value: female


title: 14-1251.Normal

tag: experiment

value: in situ Hi-C


title: S0110

source_name: murine MYCN medulloblastoma tumor

value: murine MYCN medulloblastoma tumor


title: S0109


title: 13-1317.Tumour

tag: disease


title: S0107

tag: tissue

value: 2 days


title: 14-151.Tumour


title: Parental ES, INPUT

value: Parental

tag: chip antibody


title: Patient6

tag: lesion size mm2

tag: lymphadenophathy


title: Patient1

tag: microbiome cluster 16s-seq


title: S0106


title: LRPF62

city: Richardson

first: Zhenyu

last: Xuan

address: 800 West Campbell

institute: UT Dallas

description: P2 100bp

data_processing:
We performed pan-genome analysis of 34 E. coli strains gene annotation by Roary with default parameter setting.
Kallisto was used to estimate the read counts on transcripts for each library by using all transcripts from 34 E. coli strains.
We quantified gene expression at group level by using gene groups defined from Roary and summing estimated read counts from all transcripts clustered into this group.
Assembly: All transcripts from 34 E. coli strains grouped by Roary.
Supplementary files format and content: A matrix of estimated read counts per group per sample.
Supplementary files format and content: A matrix of estimated TPM (transcript per million transcripts) per group per sample.

extract_protocol:
Once grown, cells were collected by centrifugation at maximum speed for 10 minutes at 4 degrees Celsius. Media was decanted and pellets frozen overnight a -80 degrees Celsius. The next day, pellets were thawed on ice and 700 microliters of buffer RLT added. Buffered cells are mechanically lysed using a bead beater set the highest setting for 45 five seconds a cycle for three cycles with a 5 minute rest between cycles. During the rest, the cells are stored on ice. Once lysed, a Qiagen RNeasy mini kit was used to collect RNA. Contaminating DNA was removed though RNase-free DNase digestion of at least 10 micrograms of RNA determined by nanodrop. To remove the DNase and concentrate the RNA, a GeneJet RNA isolation and concentration kit was used.
Lexogen RiboCop rRNA depletion kit for Bacteria followed by Illumina Truseq Stranded mRNA library prep kit.

tag: cell line

tag: cell type

value: UPEC

tag: genotype

value: Group B2


title: 14-151.Normal

value: Normal


title: S0090

value: murine CMYC medulloblastoma tumor

tag: treatment

value: vehicle

tag: timepoint (post-treatment)


title: S0091

value: C134 oHSV


title: imb_koenig_2020_12, RPE1, FUBP1 N-mut, rep3

last: Ebersberger

institute: Institute of Molecular Biology

data_processing:
Trimming: RPE1 samples: Cutadapt (v2.4) with non-default parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -O 1 -m 50
Quality control: FastQC (v0.11.8)
Mapping: STAR (v2.6.1b) with non-default parameters: --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outSJfilterReads Unique --genomeDir Gencode_release31_GRCh38.p12 --sjdbGTFfile gencode.v31.annotation.gtf --sjdbOverhang MAX_READLENGTH-1  --outSAMunmapped Within --runThreadN 4 (in case of RPE1 samples: ERCC spike-ins genes were added to the genome assembly and the GTF file used for mapping)
Filter/remove secondary hits: Samtools (v1.9) with parameters: samtools view -F 256
Counts per gene: Subread (v1.6.2) with non-default parameters: featureCounts --donotsort -s 2 (defaults used for -t exon -g gene_id)
Assembly: GRCh38.p12 (Gencode release 31) (+ ERCC spike-ins in RPE1)
Supplementary files format and content: txt (counts per gene)

extract_protocol:
Rneasy PLUS Mini Kit (Qiagen)
"imb_koenig_2018_18: NGS library prep was performed with Illumina's TruSeq stranded total RNA LT Ribo Zero Gold Sample Prep Kit following Illumina’s standard protocol (Part # 15031048 Rev. E). Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All 4 samples were pooled in equimolar ratio and sequenced on an Illumina NextSeq 500 sequencing machine as 84 nt single-end reads. imb_koenig_2020_12: NGS library prep was performed with Illumina's TruSeq stranded Total RNA LT Sample Prep Kit following Illumina’s standard protocol (Part # 15031048 Rev. E). Libraries were prepared with a starting amount of 200 ng and amplified in 12 PCR cycles. In addition, 1 µl of ERCC spike-ins (1:250 dilution) was added to every sample. Libraries were profiled in a DNA 1000 kit on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All 12 samples were pooled in equimolar ratio and sequenced on an Illumina NextSeq 500 sequencing machine as 159 nt single-end reads.

value: FUBP1 Mutant


title: MEERvvR-3

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5115 Centre Ave.

institute: University of Pittsburgh

data_processing:
CLC Genomics Workbench for adapter trimming, alignment and differential gene expression analysis
R package pheatmap used to make heatmaps
Genome_build: GRCm38 (Ensembl release 80)
Supplementary_files_format_and_content: FASTQ files used to generate reads

source_name: MEERvvR Tumor cells

growth_protocol: MEERvvR or MEERvvS were cultured  in DMEM/F12 supplememented with 10% FBS, epidermal growth factor (10 µg/mL), insulin (10 mg/mL), transferrin (25 µg/mL), hydrocortisone (25µg/mL), cholera toxin (0.25 µg/mL) and tri-iodo-tyronine (0.2 µg/mL) as per Williams et al, 2009 (PMID 19283850) on fibronectin covered plates for 2 days.

extract_protocol:
RNA extaction and cDNA generation was performed using Clontech SMART-seq HT kit as per manufactuerer's instructions.
cDNA libraries were prepared using Illumina Nextera XT kit as per manufacturer's instructions.

value: untreated

value: Vaccinia virus resistant MEER tumor cells


title: MEERvvR-2


title: KE25

description: P2 100bp


title: KE26

description: P2 100bp


title: imb_koenig_2020_12, RPE1, FUBP1 N-mut, rep1


title: imb_koenig_2020_12, RPE1, FUBP1 N-mut, rep4


title: imb_koenig_2020_12, RPE1, FUBP1 N-mut, rep2


title: imb_koenig_2020_12, RPE1, FUBP1 knockout, rep4

value: FUBP1 KO


title: KE24

description: P2 100bp


title: MEERvvR-1


title: MEERvvS-3

source_name: MEERvvS Tumor cells

value: Vaccinia virus sensitive MEER tumor cells


title: imb_koenig_2020_12, RPE1, FUBP1 knockout, rep2


title: MEERvvS-2


title: imb_koenig_2020_12, RPE1, FUBP1 knockout, rep3


title: KE21

description: P2 100bp


title: MEERvvS-1


title: imb_koenig_2020_12, RPE1, FUBP1 knockout, rep1


title: KE4

description: P2 100bp


title: NASH Diet Liver L2aKO rep4

city: Singapore

first: Cheen Fei

last: Chin

address: 8 College Road, Level 8

department: Cardiovascular and Metabolic Disorders

country: Singapore

institute: Duke-NUS Medical School

data_processing:
RNA-seq analysis was performed with Partek Flow (version 10). The RNA-seq reads were mapped against mm10 using STAR-2.7.8a aligner. Differential expression analysis was performed using DESeq2 and a gene is considered significantly differentially expressed when p-value <0.05 and fold change ≥ 1.25.
Genome_build: mm10
Supplementary_files_format_and_content: Deseq2.xlsx

source_name: Liver

extract_protocol:
Mice livers were perfused with Phosphate Buffered Saline and followed by flash frozen in liquid nitrogen. Mouse livers were homogenized in Trizol reagent and RNA were purified using RNeasy Mini kit (Qiagen) according to the manufacturer recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: 10-weeks old

tag: diet

value: NASH diet


title: imb_koenig_2020_12, RPE1, WT, rep3

city: Mainz

first: Stefanie

address: Ackermannweg 4

value: WT


title: LRPF007

description: P2 100bp


title: NASH Diet Liver L2aKO rep2


title: imb_koenig_2020_12, RPE1, WT, rep2


title: NASH Diet Liver L2aKO rep1


title: imb_koenig_2018_18, HeLa, WT, 2018, rep4

source_name: HeLa

value: HeLa


title: imb_koenig_2018_18, HeLa, WT, 2018, rep3


title: imb_koenig_2018_18, HeLa, WT, 2018, rep2


title: imb_koenig_2020_12, RPE1, WT, rep4


title: NASH Diet Liver 2afl/fl rep4


title: NASH Diet Liver 2afl/fl rep2


title: NASH Diet Liver 2afl/fl rep3


title: SSc_5445

status: Public on Jul 26 2023

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the human genome assembly GRCh38.
Assembly: GRCh38
Supplementary files format and content: TSV count matrices

source_name: lung

extract_protocol:
Lung tiusue were grinded in liquid nitrogen and total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: lung

tag: disease state

value: systemic sclerosis


title: SSc_5443


title: SSc_5444


title: imb_koenig_2018_18, HeLa, WT, 2018, rep1


title: NASH Diet Liver L2aKO rep3


title: SSc_5442


title: SSc_5439


title: SSc_5440


title: SSc_5437


title: imb_koenig_2020_12, RPE1, WT, rep1


title: SSc_5436


title: SSc_5438


title: SSc_5435


title: SSc_5434


title: T-ALL cell_3DOICR_biological rep4

city: Madrid

first: Javier

last: Redondo-Muñoz

address: C/ Ramiro de Maeztu 9

country: Spain

institute: Centro de Investigaciones Biológicas Margarita Salas - CSIC

description: Gene expression data from T-ALL cells treated with OICR-9429 and cultured in 3D conditions for 1 hour

hyb_protocol: RNA was hybridized to Clariom™ S Human Array following manufacturer’s instructions in a GeneChip Hybridization Oven 645 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Transcriptome Analysis Console (TAC)

label: Biotin

source_name: OICR-9429 treated CCRF-CEM cells cultured in 3D conditions for 1 hour

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit

growth_protocol: CCRF-CEM cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

extract_protocol: RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.

treatment_protocol: CCRF-CEM cells were pretreated or not with 1µM OICR-9429 for 1 hour and then cultured in 3D conditions for 1 hour. For 3D matrix, type I collagen solution from bovine was reconstituted at 1.7 mg/mL in RPMI and neutralized with 7.5% NaHCO3 and 25 mM Hepes. Cells were added to the collagen solution before polymerization at 37 °C for 1 h.

value: CCRF-CEM

value: T-ALL

value: OICR-9429 treated cells cultured in 3D conditions for 1 hour


title: NASH Diet Liver 2afl/fl rep1


title: SSc_5430


title: SSc_5441


title: T-ALL cell_3DOICR_biological rep2


title: SSc_5431


title: T-ALL cell_3Dunt_biological rep2

description: Gene expression data from T-ALL cells cultured in 3D conditions for 1 hour

source_name: Untreated CCRF-CEM cells cultured in 3D conditions for 1 hour

value: Untreated cells cultured in 3D conditions for 1 hour


title: T-ALL cell_3DOICR_biological rep1


title: SSc_5432


title: T-ALL cell_3DOICR_biological rep3


title: SSc_5428


title: SSc_5429


title: T-ALL cell_3Dunt_biological rep4


title: SSc_5426


title: T-ALL cell_3Dunt_biological rep3


title: Normal_5462

value: normal


title: Normal_5465


title: Normal_5464


title: Normal_5461


title: Normal_5457


title: Normal_5460


title: SSc_5427


title: Normal_5463


title: Normal_5458


title: Normal_5456


title: Normal_5459


title: T-ALL cell_3Dunt_biological rep1


title: SSc_5433


title: Normal_5450


title: Normal_5447


title: IPF_5485

value: idiopathic pulmonary fibrosis


title: Normal_5454


title: Normal_5452


title: Normal_5449


title: Normal_5455


title: IPF_5482


title: IPF_5484


title: Normal_5453


title: Normal_5451


title: Normal_5448


title: IPF_5480


title: Normal_5446


title: IPF_5479


title: IPF_5483


title: IPF_5475


title: IPF_5478


title: IPF_5477


title: IPF_5474


title: IPF_5476


title: IPF_5469


title: IPF_5470


title: IPF_5481


title: IPF_5468


title: IPF_5472


title: IPF_5471


title: IPF_5466


title: SSc_8997

source_name: blood

extract_protocol:
Total RNA was extracted using PAXgene Blood RNA Kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: blood


title: SSc_8996


title: SSc_8994


title: IPF_5467


title: SSc_8993


title: SSc_8995


title: SSc_8802


title: SSc_9003


title: SSc_8796


title: SSc_8797


title: SSc_8998


title: SSc_8801


title: IPF_5473


title: SSc_8786


title: SSc_8795


title: SSc_0683