title: MDA-MB-231dTOP DOC NEG1

description:
DOCN1
MDA-MB-231dTOP_DOC_NEG1
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: CEM, ATAC-seq

status: Public on Sep 25 2025

type: SRA

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

state: MI

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

country: USA

institute: University of Michigan

library_source: genomic

data_processing:
Data processing was performing using Chipseq ATACseq Pipelines 1.0.1 (https://github.com/russell-ryan-lab/ChIPseq_ATACseq_pipelines).
Paired-end reads were aligned to hg19 using BWA-ALN (v 0.7.17).
Bam files were filtered (samtools view) to retain only paired reads in a proper pair (flags: 0x1, 0x2), and to remove reads flagged as secondary alignments, not passing quality control, PCR or optical duplicates, and supplementary alignments (flags: 0x100, 0x200, 0x400, 0x800).
Reads were filtered to retain only read-pairs mapping to <=2 sites genome-wide (X0 tag <=2 for both reads).
Display files were generated with deeptools bamCoverage (options: "--binSize 25 --normalizeUsing CPM --extendReads")
Assembly: hg19
Supplementary files format and content: bigwig (hg19 fragment coverage, normalized to fragments per million post-filtering)

molecule: genomic DNA

organism: Homo sapiens

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Nuclei were isolated from 50,000 cells for each sample using Nuclei EZ prep-Nuclei Isolation Kit (Sigma-Aldrich, USA).
The transposition reaction mix (25μl of 2X TD buffer, 2.5μl of Tn5 transposase (Illumina, San Diego, CA, USA), 15ul of PBS and 7.5μl of nuclease free water) was added to nuclei and incubated at 37°C for 1hour in an orbital shaker at 300RPM. 50uL Qiagen buffer PB was added to each sample to stop the reaction and DNA was isolated with AMPure XP beads (Beckman Coulter). 15 cycles of PCR were performed with transposed DNA using the dual index primers and NEBNext PCR Master Mix, followed by AMPure XP purification.

tag: tissue

value: T-cell acute lymphoblastic leukemia

tag: cell line

value: CEM/SS


title: smRNAseq_Anthers_b8_rim16_rep1

city: La Jolla

first: Julie

middle: A

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: Plant Molecular and Cellular Biology

institute: Salk Institute for Biological Studies

description: Library name: sample122

library_source: other

data_processing:
For each sample, fastq files were trimmed using cutadapt (v1.18) with the -a AGATCGGAAGAGC option to remove the adapter sequence and the -m 15 option to discard reads shorter than 15 nt. Clean reads were then mapped to the TAIR10 reference genome using ShortStack (v3.8.5) allowing one mismatch (--mismatches 1). The --mmap f option was also included to assign multiple-mapped reads to a specific locus using the fractional-seeded algorithm. The resulting bam files were then filtered to keep perfectly mapped reads or reads with a single mismatch at the 3’ end using bamtools (v2.5.1) together with an in-house script (JSON_findPerfectMatches_and_TerminalMisMatches_v3) to meet the characteristics of Pol-IV transcription. To facilitate downstream analyses, the filtered bam files were used to generate Tag Directories using the makeTagDirectory function of HOMER (v4.10) with the following options: -format sam -mis 1 -keepAll. To quantify the expression of smRNAs with specific sizes, the tag directories were split by size (20nt-25nt) using a custom perl script (splitTagDirectoryByLength.dev2.pl) and all subsequent analyses utilized the Tag Directories corresponding to 24nt siRNAs.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

molecule: other

organism: Arabidopsis thaliana

source_name: anthers (stage9)

growth_protocol: For transgenic lines that required drug selection, seeds were sterilized in sterilization buffer (70% ethanol, 0.05% SDS) for 10 minutes, followed by plating on half strength Linsmaier and Skoog medium (1/2 LS; Caisson Labs, Cat# LSP03) supplemented with 0.6% agar (Phyto Agar, Cat# P1003). The plates were placed in a 4˚C cold room for 4 days before growing in a growth chamber with 16h-light and 8h-dark cycles for 7 days. The seedlings were transplanted and grown under Salk greenhouse conditions. For the HEM EMS lines, the T-DNA insertion lines, and their corresponding control lines, seeds were stratified in 0.1% agar (Phyto Agar, Cat# P1003) at 4˚C for 4 days before sowing directly onto soil and grown under Salk greenhouse conditions. Approximately five weeks after planting, flower buds (stage 12 and younger), ovules (stage 12 unfertilized ovules), and anthers (stage 9) were collected and frozen in liquid nitrogen. Flower development stages were determined according to Smyth et al. Ovule collection was performed using a vacuum pump-based collection device that was engineered at the Salk Institute and was described previously.

extract_protocol:
Total RNA extraction and smRNA enrichment was performed following a previously reported protocol. Briefly, 10 μg of total RNA extracted from flower buds (stage 12 and younger), ovules (stage 12 unfertilized ovules), and anthers (stage 9) were used for each smRNA library prep.
The smRNA-seq libraries were constructed using the NEBNext Small RNA Library Prep Kit (NEB, Cat# E7330L). The smRNA libraries were further purified using an 8% acrylamide gel and size selected (130-160 bp) relative to the O'RangeRuler 10 bp DNA Ladder (Thermo Scientific, Cat# SM1313). The size selected smRNA libraries were pooled for sequencing with single-end 50 bp kit (SE50) on Illumina Nextseq 2000 or Novaseq X plus platforms.

value: anthers (stage9)

tag: ecotype

value: Columbia

tag: genotype

tag: batch

value: experiment batch8


title: IPF4I

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

library_source: transcriptomic

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample.
Cutadapt (v1.18) is used to maintain minimum read length of 25 bp post trimming of adapters as well as trimming of N’s.
Splice-aware alignment of reads using a Hierarchical Graph FM index (HGFM) method is performed using HISAT2 software (v2.1.0) with parameters (--rna-strandness RF –dta) against human reference genome (vGRCh38).
To obtain the abundance of each of these transcripts based only on the known reference genome and transcriptome, StringTie was run again using different parameters (-e -B -G referencetranscripts.gtf) to generate output of Ballgown software as compatible table files.
A script named ‘prepDE.py’ by StringTie software was used to extract the read count information.
Supplementary files format and content: 1 tab-delimited text file includes raw count values for each Sample.

molecule: total RNA

source_name: Lung

growth_protocol: Primary P4 human IPF lung fibroblasts were seeded in 6-well culture dishes at 2 x 10^6 cells in 10% FBS/DMEM for 24 h (5% CO2).

extract_protocol:
Total RNA is extracted from treated IPF cells by standard Trizol method and quantified using the Qubit RNA BR assay (Denovix). Quality of RNA is assessed using the Agilent RNA Nano chips on a Bioanalyzer instrument. For all the samples, RNA integrity number (RIN) was 10.
Total RNA libraries are prepared from 200 ηg total RNA using the TruSeq Stranded total RNA library preparation kit (Illumina Cat# 20020596) as per manufacturer’s recommendations.  Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
Libraries prepared for sequencing (volumetrically pooled, diluted and denatured): 75 paired end read-cycles on an Illumina NextSeq 550 sequencer.

treatment_protocol: One day after seeding, cells were treated for 24 h with either 250 nM of the ephb4 inhibitor NVP-BHG712 or an equivalent volume of DMSO (as control).

tag: cell type

value: primary fibroblasts

tag: treatment

value: 250 nM NVP-BHG712

tag: age (years)

tag: Sex

value: male

tag: diagnosis

value: IPF


title: Day 40, sublibrary 5

city: Singapore

first: John

middle: F

last: Ouyang

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Parse biosciences

library_source: transcriptomic single cell

data_processing:
Sequencing raw reads were demultiplexed and processed using the Parse Biosciences pipeline (v1.0.5), aligned to GrCH38 human genome.
Assembly: GrCH38
Supplementary files format and content: tab separated value files and matrix file

extract_protocol:
Midbrain organoids were dissociated into single cells using Papain-based dissociation. Samples were fixed and stored for scRNA sequencing according to Parse Biosciences Evercode Fixation kit (v2.0.2) and stored at -80°C until library preparation.
Library preparation was conducted using the Parse Biosciences Evercode Whole Transcriptome (WT) kit (v2.0.1). Sequencing sublibraries were quantified with the KAPA Library Quantification Kit (#KK4824). Sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Midbrain organoids


title: MDA-MB-231dTOP UNT POS3

city: Leuven

first: Frederic

last: Lluis

state: Leuven

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

description:
DTOPCP3
MDA-MB-231dTOP_UNT_POS3
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv

data_processing:
Trimming of adapters, polyA/T tails, and low-quality reads was performed using the Trimgalore package with default parameters. Using the Salmon package with default parameters, the reads were aligned to the transcriptome and quantified using release 32 of the human reference transcriptome sequence and gene annotation. Counts were then imported into R using Tximport.
Assembly: Release 32 (GRCh38.p13)
Supplementary files format and content: raw counts per sample
Supplementary files format and content: normalized (VST) counts per sample

molecule: polyA RNA

source_name: MDA-MB-231dTOP cell line without chemotherapy exposure - sorted for WNTHigh cells (GFP +)

extract_protocol:
Total RNA was extracte MDA-MB-231 cells using the GenElute™ Mammalian Total RNA Miniprep Kit according to the Manufacturer's instructions.
RNA sequencing (RNAseq) libraries were prepared from 4 µg of total RNA using the KAPA stranded mRNA-seq kit (Roche, KK8581) according to manufacturer’s specifications. 100 nM KAPA-single index adapters (Roche, KK8700) were added to A-tailed cDNA, and libraries were amplified for 10 cycles. Finally, 1x library cleanup was performed using Agencourt AMPure XP beads (Beckman Coulter, A63881). Library fragment size was assessed using Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent, 5067-4626) and concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854). Each library was diluted to 4 nM and pooled for sequencing on an Illumina Hiseq4000, aiming at 15-20 million SE50 reads per sample (19 million reads on average).

value: Breast tumor-derived

value: Mesenchymal

tag: timepoint


title: smRNAseq_Anthers_b8_pol-iv_rep2

description: Library name: sample119


title: Day 30, sublibrary 7

description: Parse biosciences


title: Day 30, sublibrary 6

description: Parse biosciences


title: IPF4C

value: 0.1% DMSO


title: smRNAseq_Anthers_b8_pol-iv_rep1

description: Library name: sample118


title: IPF3I


title: MDA-MB-231dTOP UNT POS2

description:
DTOPCP2
MDA-MB-231dTOP_UNT_POS2
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: Day 30, sublibrary 4

description: Parse biosciences


title: MDA-MB-231dTOP UNT POS1

description:
DTOPCP1
MDA-MB-231dTOP_UNT_POS1
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: IPF3C


title: smRNAseq_Anthers_b8_clsy3,4_rep2

description: Library name: sample117


title: Day 30, sublibrary 3

description: Parse biosciences


title: IPF2I


title: smRNAseq_Anthers_b8_clsy3,4_rep1

description: Library name: sample116


title: smRNAseq_Anthers_b8_clsy3_rep2

description: Library name: sample115


title: MDA-MB-231dTOP UNT POS4

description:
DTOPCP4
MDA-MB-231dTOP_UNT_POS4
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: Day 30, sublibrary 5

description: Parse biosciences


title: MDA-MB-231dTOP UNT NEG5

description:
DTOPCN5
MDA-MB-231dTOP_UNT_NEG5
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv

source_name: MDA-MB-231dTOP cell line without chemotherapy exposure - sorted for WNTLow cells (GFP -)


title: MDA-MB-231dTOP UNT NEG4

description:
DTOPCN4
MDA-MB-231dTOP_UNT_NEG4
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: Day 30, sublibrary 8

description: Parse biosciences


title: MDA-MB-231dTOP UNT NEG6

description:
DTOPCN6
MDA-MB-231dTOP_UNT_NEG6
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: IPF1I


title: smRNAseq_Anthers_b8_clsy1,2_rep1

description: Library name: sample120


title: smRNAseq_Anthers_b8_clsy3_rep1

description: Library name: sample114


title: Day 30, sublibrary 2

description: Parse biosciences


title: MDA-MB-231dTOP UNT NEG3

description:
DTOPCN3
MDA-MB-231dTOP_UNT_NEG3
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: IPF1C


title: smRNAseq_Anthers_b8_WT_rep3

description: Library name: sample113


title: Day 25, sublibrary 8

description: Parse biosciences


title: MDA-MB-231dTOP UNT NEG2

description:
DTOPCN2
MDA-MB-231dTOP_UNT_NEG2
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: NHA_mRNA-seq_with-dCas9-KRAB

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: High St

department: Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

data_processing:
For the PolyA+ RNA-seq library, reads were mapped to hg38 using STAR v2.5.2b (Dobin et al. 2013) with the following parameters: --outSJfilterOverhangMin 15 15 15 15 --alignSJoverhangMin 15 --alignSJDBoverhangMin 15 --outFilterMultimapNmax 1 --outFilterScoreMin 1 --outFilterMatchNmin 1 --outFilterMismatchNmax 2  --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15. GENCODE v32 (Frankish et al. 2019) was used for gene coordinates.
For ribo-depleted RNA-seq and TT-seq, FASTQs were processed using the nf-core RNA-seq pipeline (https://nf-co.re/rnaseq/3.13.2) (Ewels et al. 2020). Reads were mapped to hg38 using the STAR aligner (2.7.10a) (Dobin et al. 2013), where genomic origin was identified (STable 11). Candidate peak expression was determined using FeatureCounts (Dobin et al. 2013) implemented in the Rsubread package (Liao et al. 2019). The following parameters were set: useMetaFeatures = FALSE, allowMultiOverlap = TRUE, isPairedEnd = TRUE, strandSpecific = 2, minMQS = 10, checkFragLength = FALSE, countChimericFragments = FALSE. Candidate size was set to a standard length of by adjusting start and end coordinates to be ±500bp centred around the midpoint.
Assembly: hg38
Supplementary files format and content: RNA-seq_with_and_without_dCas9-KRAB.tsv - tab separated values with ENSEMBL Gene ID (gene.id), gene symbol (gene_name), and counts for NHA samples with (NHA_dCas9-KRAB) and without (NHA) dCas-KRAB

source_name: Normal Human Astrocytes (Lonza, #CC-2565)

growth_protocol: NHA were grown in DMEM media supplemented with 10% foetal bovine serum and 1% streptomycin/penicillin at 37°C, 5% CO2

extract_protocol:
RNA was extracted using the Qiagen miRNeasy kit, according to manufacturer's instructions
For TT-seq samples, cells were treated with 4sU for 5 mins before RNA extraction as above
For TT-seq samples, RNA was sonicated to ~1.5kb (Schwalb et al. 2016), then 4sU-labeled RNA was biotinylated (Duffy et al 2016) before isolation using streptavidin conjugated magnetic beads (Rädle et al. 2013)
For mRNA-seq samples, libraries were prepared using the Illumina TruSeq Stranded mRNA Prep Kit, according to manufacturer's instructions
For ribo-depleted RNA-seq samples, libraries were prepared using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus, according to manufacturer's instructions

treatment_protocol: NHAs were transduced with lenti-dCas9-KRAB and selected using 10 µg/mL blasticidine S hydrochloride


title: smRNAseq_Anthers_b8_WT_rep2

description: Library name: sample112


title: Day 25, sublibrary 7

description: Parse biosciences


title: smRNAseq_Anthers_b8_WT_rep1

description: Library name: sample111


title: MDA-MB-231dTOP UNT NEG1

description:
DTOPCN1
MDA-MB-231dTOP_UNT_NEG1
Count Matrix (Raw) - Bulk RNA-seq Fig. 2.csv
Count Matrix (Normalized) - Bulk RNA-seq Fig. 2.csv


title: NHA_mRNA-seq_without_dCas9-KRAB

value: Normal Human Astrocytes (Lonza, #CC-2565)


title: Day 25, sublibrary 6

description: Parse biosciences


title: IPF2C


title: MDA-MB-231 CAR D3 3

description:
D3_CAR3
RNA_seq_MDA231_D3_CAR3
Count Matrix (Raw) - Bulk RNA-seq Fig. 1.xlsx
Count Matrix (Normalized) - Bulk RNA-seq Fig. 1.xlsx

source_name: MDA-MB-231 cell line treated with Carboplatin (35uM) for 72 hours and then sorted to exclude DAPI + (dead cells)

value: Chemotherapy (Carboplatin - 35uM)

value: 72 hours


title: Day 25, sublibrary 5

description: Parse biosciences


title: MDA-MB-231 CAR D3 2

description:
D3_CAR2
RNA_seq_MDA231_D3_CAR2
Count Matrix (Raw) - Bulk RNA-seq Fig. 1.xlsx
Count Matrix (Normalized) - Bulk RNA-seq Fig. 1.xlsx


title: smRNAseq_Ovules_b7_cs828917_rep1

description: Library name: sample109

source_name: Unfertilized ovules (stage12)

value: Unfertilized ovules (stage12)

value: experiment batch7


title: Low_rep9

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description: Single Crypt with low methylation

data_processing:
Quality assessment of Fastq files was performed using FastQC v0.11.5.
Subsequently, alignment to the mm9 genome was performed using TopHat v2.1.0 (Trapnell, Roberts et al. 2012) employing the parameters --bowtie1 --no-coverage-search -a 5.
HTSeq-Count 0.11.2 (Anders, Pyl et al. 2015) was then employed to determine the read coverage for each gene, using the parameters -s no -a 0 -t exon -m intersection-nonempty.
Assembly: mm9
Supplementary files format and content: HTSeq count txt files

organism: Mus musculus

source_name: Intestin

growth_protocol: All the mice were group housed and maintained in a Specific Opportunist Pathogen Free (SOPF) animal facility in Fritz Lipmann Institute with 12 h of light/dark cycle and fed with a standard mouse chow.

extract_protocol:
Mouse small intestine was dissected, washed in cold PBS and opened longitudinally. Villi were removed by scraping with a coverslip. The villi-free intestinal pieces (2 cm) were washed four times in cold PBS and transferred to 5 mM EDTA/PBS, followed by two 30-min incubations at 4°C on a rotator. The tissue was transferred to fresh cold PBS and manually shaken for 30 sec. The crypt solution was filtered using a 70 µm cell strainer and centrifuged at 120xg for 5 min at 4°C. The crypts pellet was resuspended in 1 ml of cold PBS and evaluated for purity microscopically. Isolated crypts were aliquoted, snap frozen in liquid nitrogen and stored at -80°C for further experiments.  Genomic DNA and RNA from single crypts were isolated using Quick-DNA/RNA Microprep Plus Kit (Zymo Research) following the manufacturer’s instructions.  We processed around 150 crypts from old mice, analyzed their DNAm level by Pyrosequencing on the 4 gene promoters (Dkk1, Dkk2, Sfrp1 and Sfrp2), calculated the average DNAm level, then we selected the crypts of the top 10% (high 5mC crypts) and the bottom 10% (low 5mC crypts) and performed single-crypt RNAseq.
The RNAseq library preparation of single crypts was performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit (NEB) following the manufactures' instructions.

value: Intestin

value: Intestinal Crypt

value: Wild Type


title: Low_rep8

description: Single Crypt with low methylation


title: Day 30, sublibrary 1

description: Parse biosciences


title: smRNAseq_Ovules_b7_salk_107926_rep2

description: Library name: sample108

value: Columbia


title: MDA-MB-231 CAR D3 1

description:
D3_CAR1
RNA_seq_MDA231_D3_CAR1
Count Matrix (Raw) - Bulk RNA-seq Fig. 1.xlsx
Count Matrix (Normalized) - Bulk RNA-seq Fig. 1.xlsx


title: Low_rep7

description: Single Crypt with low methylation


title: Day 25, sublibrary 3

description: Parse biosciences


title: Day 25, sublibrary 4

description: Parse biosciences


title: MDA-MB-231 DOC D3 3

description:
D3_DOC3
RNA_seq_MDA231_D3_DOC3
Count Matrix (Raw) - Bulk RNA-seq Fig. 1.xlsx
Count Matrix (Normalized) - Bulk RNA-seq Fig. 1.xlsx

source_name: MDA-MB-231 cell line treated with Docetaxel (4.5nM) for 72 hours and then sorted to exclude DAPI + (dead cells)

value: Chemotherapy (Docetaxel - 4.5nM)


title: smRNAseq_Ovules_b7_salk_107926_rep1

description: Library name: sample107


title: smRNAseq_Ovules_b7_cs828917_rep2

description: Library name: sample110


title: Day 25, sublibrary 2

description: Parse biosciences


title: MDA-MB-231 DOC D3 2

description:
D3_DOC2
RNA_seq_MDA231_D3_DOC2
Count Matrix (Raw) - Bulk RNA-seq Fig. 1.xlsx
Count Matrix (Normalized) - Bulk RNA-seq Fig. 1.xlsx


title: Low_rep6

description: Single Crypt with low methylation


title: smRNAseq_Ovules_b7_rim-q_rep2

description: Library name: sample106


title: Day 25, sublibrary 1

description: Parse biosciences


title: MDA-MB-231 DOC D3 1

description:
D3_DOC1
RNA_seq_MDA231_D3_DOC1
Count Matrix (Raw) - Bulk RNA-seq Fig. 1.xlsx
Count Matrix (Normalized) - Bulk RNA-seq Fig. 1.xlsx


title: Low_rep5

description: Single Crypt with low methylation


title: Low_rep4

description: Single Crypt with low methylation


title: MDA-MB-231 UNT 2

description:
CTRL2
RNA_seq_MDA231_CTRL_VEH2
Count Matrix (Raw) - Bulk RNA-seq Fig. 1.xlsx
Count Matrix (Normalized) - Bulk RNA-seq Fig. 1.xlsx

source_name: MDA-MB-231 cell line without chemotherapy exposure


title: smRNAseq_Ovules_b7_rim-q_rep1

description: Library name: sample105


title: smRNAseq_Ovules_b7_rim-cr_rep2

description: Library name: sample104


title: Low_rep3

description: Single Crypt with low methylation


title: Day 20, sublibrary 7

description: Parse biosciences


title: MDA-MB-231 UNT 1

description:
CTRL1
RNA_seq_MDA231_CTRL_VEH1
Count Matrix (Raw) - Bulk RNA-seq Fig. 1.xlsx
Count Matrix (Normalized) - Bulk RNA-seq Fig. 1.xlsx


title: smRNAseq_Ovules_b7_rim-cr_rep1

description: Library name: sample103


title: Low_rep2

description: Single Crypt with low methylation


title: Day 20, sublibrary 6

description: Parse biosciences


title: smRNAseq_Ovules_b7_rim22-2_rep2

description: Library name: sample102


title: Low_rep1

description: Single Crypt with low methylation


title: Day 20, sublibrary 5

description: Parse biosciences


title: Scr3

city: shanghai

first: yue

last: lou

address: No. 393 HuaxiaCentral Road

country: China

institute: Shanghai Jiao Tong University

description: Library name: sample6

data_processing:
RNA-seq
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Rnor_6 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Rnor_6
Supplementary files format and content: tab-delimited text files include count, FPKM values for each Sample

organism: Rattus norvegicus

source_name: vessel

extract_protocol:
RNA was harvested using RNA kit ( Qiagen ).500 ng of total RNA was used for the construction of sequencing libraries
library construction protocol

treatment_protocol: Rat VSMCs treated with siRNAs and ASOs total 50nM for 72 hours to knockdown MIAT

value: vessel

value: Vascular smooth muscle cells

value: WT


title: smRNAseq_Ovules_b7_rim22-2_rep1

description: Library name: sample101


title: Day 20, sublibrary 4

description: Parse biosciences

value: Midbrain organoids


title: Low_rep12

description: Single Crypt with low methylation


title: Low_rep11

description: Single Crypt with low methylation


title: Scr2

description: Library name: sample5


title: Day 20, sublibrary 3

description: Parse biosciences


title: KD_M_3

description: Library name: sample3

value: MIAT knockdown


title: smRNAseq_Ovules_b7_rim16_rep2

description: Library name: sample100


title: smRNAseq_Ovules_b7_rim16_rep1

description: Library name: sample99


title: Scr1

description: Library name: sample4


title: Day 20, sublibrary 8

description: Parse biosciences


title: Low_rep10

description: Single Crypt with low methylation


title: KD_M_2

description: Library name: sample2


title: High_rep9

description: Single Crypt with high methylation


title: Day 20, sublibrary 1

description: Parse biosciences


title: KD_M_1

description: Library name: sample1


title: High_rep8

description: Single Crypt with high methylation


title: smRNAseq_Ovules_b7_clsy1,2_rep1

description: Library name: sample97


title: smRNAseq_Ovules_b7_pol-iv_rep2

description: Library name: sample96


title: High_rep7

description: Single Crypt with high methylation


title: 170366, primary hepatocytes, UTC, 0.00000 nM, rep11

city: Carlsbad

first: Sagar

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

data_processing:
Custom pipeline executed in linux shell
Libraries mapped to human genome using STAR
PCR duplications were removed post-alignment and making use of UMIs introduced during first-strand-synthesis
Read assignment to genes performed in salmon using pseudoalignment mode and default settings
TPM computed by normalizing per-gene read counts by total number of assigned reads
Assembly: Grch39 (ensembl homo-sapiens build 109)
Supplementary files format and content: tab-delimited files containing salmon output (gene counts)

source_name: primary hepatocytes

growth_protocol: Primary Human Hepatocytes (BioIVT, M0095-P, lot ZFW)  were thawed and resuspended in Lonza HCM Hepatocyte Culture Medium. Cells were counted and diluted to 300,000 cells per ml in room temperature growth medium before adding 100 μl of the cell suspension to the wells of collagen I coated 96-well culture plate.

extract_protocol:
After 96 h, the cells were lysed for RNA isolation and analysis.
Libraries constructed using Lexogen 3'QuantSeq (Rev) kit with custom first-strand-synthesis primers containing UMIs for PCR deduplication

treatment_protocol: Immediately after plating the cells, 11 μL of 10X oligonucleotide in water was added to the appropriate wells, cells were treated at 10 doses with a top concentration of 5 uM and 1:5 dilutions . The culture plate was then incubated at 37° C and 5% CO2.

value: primary hepatocytes

tag: treatment concentration

tag: replicate

value: UTC


title: High_rep6

description: Single Crypt with high methylation


title: 170354, primary hepatocytes, UTC, 0.00000 nM, rep10


title: 170369, primary hepatocytes, UTC, 0.00000 nM, rep12


title: High_rep5

description: Single Crypt with high methylation


title: High_rep4

description: Single Crypt with high methylation


title: smRNAseq_Ovules_b7_clsy3,4_rep1

description: Library name: sample93


title: Day 20, sublibrary 2

description: Parse biosciences


title: smRNAseq_Ovules_b7_pol-iv_rep1

description: Library name: sample95


title: High_rep3

description: Single Crypt with high methylation


title: 170339, primary hepatocytes, UTC, 0.00000 nM, rep9


title: smRNAseq_Ovules_b7_clsy3_rep1

description: Library name: sample91


title: High_rep2

description: Single Crypt with high methylation


title: 170330, primary hepatocytes, UTC, 0.00000 nM, rep8


title: smRNAseq_Ovules_b7_clsy1,2_rep2

description: Library name: sample98


title: smRNAseq_Ovules_b7_clsy3_rep2

description: Library name: sample92


title: 170320, primary hepatocytes, UTC, 0.00000 nM, rep7


title: smRNAseq_Ovules_b7_WT_rep4

description: Library name: sample90


title: graft vein 4

city: Shanghai

first: Qingping

last: Yao

address: Dongchuan Road 800#

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: graft 5

growth_protocol: One week after the vein graft operation

extract_protocol:
prefrontal cortex were harvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The left common carotid artery from the carotid artery bifurcation down to 7 mm was mobilized and divided. Cuffs (1.2 ± 0.2 mm) cut from an indwelling needle cannula were placed on both ends of the divided artery. The arterial ends were everted over the cuff and ligated with 6.0 silk sutures. After 1 week, rats were euthanized, and the vein grafts and self-contralateral jugular vein were obtained for further analysis.

tag: strain

value: Sprague Dawley (SD)

value: graft vein


title: graft vein 2

source_name: graft 10


title: control vein 4

source_name: zuo 4

value: control jugular vein


title: control vein 3

source_name: zuo 3


title: control vein 1

source_name: zuo 1


title: control vein 2

source_name: zuo 2


title: graft vein 3

source_name: graft 3


title: High_rep1

description: Single Crypt with high methylation


title: 170317, primary hepatocytes, UTC, 0.00000 nM, rep5


title: smRNAseq_Ovules_b7_WT_rep3

description: Library name: sample89

value: Unfertilized ovules (stage12)


title: smRNAseq_Ovules_b7_clsy3,4_rep2

description: Library name: sample94

value: experiment batch7


title: 170315, primary hepatocytes, UTC, 0.00000 nM, rep4


title: High_rep16

description: Single Crypt with high methylation

value: Intestin


title: High_rep15

description: Single Crypt with high methylation

value: Intestinal Crypt


title: smRNAseq_Ovules_b7_WT_rep2

description: Library name: sample88


title: smRNAseq_Ovules_b7_WT_rep1

description: Library name: sample87


title: 170286, primary hepatocytes, UTC, 0.00000 nM, rep2


title: 170318, primary hepatocytes, UTC, 0.00000 nM, rep6


title: High_rep14

description: Single Crypt with high methylation

value: Wild Type


title: ChIPseq_Flower_b2_CLSY3-3xFLAG_clsy3_delta4-336_IP

description: Library name: sample222

data_processing:
For the RIM12 OE and CLSY3 ChIP-seq datasets generated in this study, reads were trimmed using trim_galore (v0.6.0) and then mapped to the TAIR10 reference genome using bowtie2 (v2.2.8) with default options. The resulting SAM files were converted into BAM files using samtools (v1.6) with default options. Bam files were filtered to retain only unduplicated and uniquely mapped reads using the following samtools (v1.6) steps: sort -n, fixmate -m, markdup, view -b -F 1024, and view -q 20.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

source_name: flower buds (stage12 and younger)

growth_protocol: For transgenic lines that required drug selection, seeds were sterilized in sterilization buffer (70% ethanol, 0.05% SDS) for 10 minutes, followed by plating on half strength Linsmaier and Skoog medium (1/2 LS; Caisson Labs, Cat# LSP03) supplemented with 0.6% agar (Phyto Agar, Cat# P1003). The plates were placed in a 4˚C cold room for 4 days before growing in a growth chamber with 16h-light and 8h-dark cycles for 7 days. The seedlings were transplanted and grown under Salk greenhouse conditions. Approximately five weeks after planting, flower buds (stage 12 and younger) were collected and frozen in liquid nitrogen.

extract_protocol:
Genomic DNA were extracted from flower buds or shoot tissues using CTAB method or using the DNeasy Plant Mini Kit (QIAGEN, Cat# 69014).
1 g of flower buds (stage12 and younger) were collected and ground in liquid nitrogen. ChIP experiment using the anti FLAG antibody (Sigma, Cat# M8823) was perfomed following the protocol described in the Materials and methods. The DNA was isolated using Phenol/Chloroform/IAA (Sigma, Cat# 6805), precipitated by ethanol, and resuspended in 20 μL of H2O. Library preparation was conducted using the NEBNext Ultra II DNA Library prep kit (NEB, Cat# E7645L) for sequencing.

value: flower buds (stage12 and younger)

value: Columbia

value: experiment batch2


title: 170282, primary hepatocytes, UTC, 0.00000 nM, rep1


title: ChIPseq_Flower_b2_CLSY3-3xFLAG_clsy3_delta3-396_IP

description: Library name: sample221


title: High_rep13

description: Single Crypt with high methylation


title: High_rep12

description: Single Crypt with high methylation


title: 170481, primary hepatocytes, UTC, 8.00000 nM, rep2


title: ChIPseq_Flower_b2_CLSY3-3xFLAG_clsy3_IP

description: Library name: sample220


title: 170402, primary hepatocytes, UTC, 8.00000 nM, rep1


title: ChIPseq_Flower_b2_Col-0_IP

description: Library name: sample219


title: 170503, primary hepatocytes, ASO#26, 5000.00000 nM, rep2


title: High_rep10

description: Single Crypt with high methylation


title: graft vein 1

source_name: graft 9


title: PST_6

city: Fuzhou

first: Aling

last: Shen

state: Fujian

address: 1 Qiuyang road, Minhou Shangjie

institute: Fujian university of Traditional Chinese Medicine

description: LOP + JSQ Model group with 21 days treated with loperamide and 19 days treated with PST

data_processing:
Data were filtered using the following specifications fastq software. The filtering standards from raw data to clean reads are: check the sample for contamination and, if there is pollution, remove it if the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window, remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed, if the truncated read length is less than 50 bp, the entire read is removedRemove unmatched reads
Q30, Q20 explanation：
Q30 indicates that the sequencing error rate of the base is 0.1%.
Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

source_name: colon tissue

extract_protocol:
The colon tissues were dissected and stored in RNA later. Total RNA was extracted with TRIzol® Reagent (Invitrogen,Carlsbad, CA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

value: colon tissue

value: LOP +PST

value: loperamide

value: LOP + PST


title: Lgr5_f_O_rep4 (WGBS)

data_processing:
Fastq files quality check was performed with FastQC v0.11.5
Sequencing reads were adapter clipped with fastx_clipper by using the following parameters: -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -Q33 -l 20 -n -v -M 10 .
The fastq files were mapped to the mm9 genome using BSMAP v2.89
Duplicates were removed using a custom script.
The CpG methylation was calculated using methratio.py script in the BSMAP package with -z -g -x CG parameters.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data is the output of the methraio.py indicating the methylation level in each CpG.

source_name: Lgr5 positive cells from small intestine(intestinal stem cells)

growth_protocol: Young (2 months old) and old (18-26 months old) male and female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility in Fritz Lipmann Institute with 12 h of light/dark cycle and fed with a standard mouse chow.

extract_protocol:
For the Lgr5-eGFP ISCs isolation, the villi-free intestinal pieces (2 cm) were incubated in 5mM EDTA/PBS on ice for 45 min. The tissue was then shaken vigorously for 1 min, the crypt solution was filtered through a 100 µm cell strainer and centrifuged at 300xg for 5 min at 4°C. The crypts were dissociated with the mixture of 18 ml TrypLE Express, 2 ml of 10X DNase I Buffer (100 mM Tris HCl pH 7.5, 25 mM MgCl2, 5 mM CaCl2) and 1 ml DNase I (10 mg/ml) for 30 min at 37°C with brief vortexing every 10 min. The single-cell suspension was then passed through a 20 µm cell strainer and centrifuged at 450xg for 5 minutes at 4°C. The pellet was resuspended in 3 ml FSM (2% FBS, 2.5 mM EDTA) containing 10 µM Y27632 and DAPI (1:1000). The single cell suspension was applied to FACS LSRII (BD Biosciences) and the Lgr5-eGFPHi ISCs were sorted for downstream analysis.
For whole genome bisulfite sequencing (WGBS) library preparation, 10 ng of genomic DNA was used as input using Pico Methyl-Seq™ Library Prep Kit (Zymo Research). The bisulfite conversion was performed using the Methylation-Lightning Kit (Zymo Research) following manufacturer’s instructions.


title: ChIPseq_Flower_b2_CLSY3-3xFLAG_clsy3_delta4-336_input

description: Library name: sample218


title: 170307, primary hepatocytes, UTC, 0.00000 nM, rep3

value: primary hepatocytes


title: 170360, primary hepatocytes, ASO#26, 5000.00000 nM, rep1


title: MDA-MB-231,sinc, replicate 3

type: RNA

city: Shijiazhuang

first: Fei

last: Liu

state: China

address: No. 12 Jiankang Road

institute: The Fourth Hospital of Hebei Medical University Cancer Institute

description: Gene expression in MDA-MB-231 cells after siNC transfection.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyzearray images to get raw data. Genespring (version 14.8, Agilent Technologies) were employedto finish the basic analysis with the raw data.

label_protocol: The sample labeling,microarray hybridization and washing were performed based on the manufacturer’s standardprotocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesizedinto cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

growth_protocol: MDA-MB-231 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37°C in a humidified incubator with 5% CO₂.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integritywas assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: MDA-MB-231 cells were transfected with si-hsa_circ_0001910 and siNC. RNA was extracted from the cells 24 hours after transfection.

value: siNC transfection


title: ChIPseq_Flower_b2_CLSY3-3xFLAG_clsy3_delta3-396_input

description: Library name: sample217


title: MDA-MB-231,si-hsa_circ_0001910, replicate 3

description: Gene expression in MDA-MB-231 cells after si-hsa_circ_0001910 transfection.

value: si-hsa_circ_0001910 transfection


title: MDA-MB-231,sinc, replicate 1


title: MDA-MB-231,si-hsa_circ_0001910, replicate 1


title: MDA-MB-231,si-hsa_circ_0001910, replicate 2


title: PST_5

description: LOP + JSQ Model group with 21 days treated with loperamide and 18 days treated with PST

value: WT


title: ChIPseq_Flower_b2_CLSY3-3xFLAG_clsy3_input

description: Library name: sample216


title: 170441, primary hepatocytes, ASO#26, 40.00000 nM, rep2


title: PST_4

description: LOP + JSQ Model group with 21 days treated with loperamide and 17 days treated with PST


title: Lgr5_f_O_rep2 (WGBS)


title: High_rep11

description: Single Crypt with high methylation


title: 170423, primary hepatocytes, ASO#26, 40.00000 nM, rep1


title: MDA-MB-231,sinc, replicate 2


title: 170564, primary hepatocytes, ASO#26, 200.00000 nM, rep2


title: crypt_m_2m_rep4 (RRBS)

description: Reduced representation bisulfite sequencing

data_processing:
Fastq files quality check was performed with FastQC v0.11.5
The fastq files were mapped to the mm9 genome using BSMAP v2.89
The CpG methylation was calculated using methratio.py script in the BSMAP package with -z -g -x CG parameters.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data is the output of the methraio.py indicating the methylation level in each CpG.

growth_protocol: Young (2 months old) and old (18-26 months old) male and female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility in Fritz Lipmann Institute with 12 h of light/dark cycle and fed with a standard mouse chow. For all experiments, four animals per age group were used.

extract_protocol:
Small intestinal crypts were isolated using the established protocol (Sato and Clevers, 2013) with minor modifications. Briefly, mouse small intestine was dissected, washed in cold PBS and opened longitudinally. Villi were removed by scraping with a coverslip. The villi-free intestinal pieces (2 cm) were washed four times in cold PBS and transferred to 5 mM EDTA/PBS, followed by two 30-min incubations at 4°C on a rotator. The tissue was transferred to fresh cold PBS and manually shaken for 30 sec. The crypt solution was filtered using a 70 µm cell strainer and centrifuged at 120xg for 5 min at 4°C. Genomic DNA from crypts was isolated using DNeasy Blood and Tissue kit (Qiagen) following the manufacturer’s instructions.
For reduced representation bisulfite sequencing (RRBS) library preparation, 250 ng of genomic DNA were digested with MspI enzyme (NEB) at 37°C for 12 hours, and purified using Agencourt AMPure XP beads (Beckman Coulter) following manufacturer’s instructions. The MspI-digested genomic DNA was used as input for RRBS library preparation using the NEXTflex™ Bisulfite-Seq Kit (PerkinElmer) following manufacturer’s instructions. The bisulfite conversion was performed using the Methylation-Lightning Kit (Zymo Research) following manufacturer’s instructions.

value: Small intestinal crypts

tag: gender

value: m

tag: age


title: ChIPseq_Flower_b1_CLSY3-3xFLAG_clsy3_IP

description: Library name: sample214

value: experiment batch1


title: ChIPseq_Flower_b1_3xFLAG-RIM12_IP

description: Library name: sample213


title: ChIPseq_Flower_b2_Col-0_input

description: Library name: sample215


title: 170449, primary hepatocytes, ASO#26, 200.00000 nM, rep1


title: crypt_m_2m_rep3 (RRBS)


title: 170611, primary hepatocytes, ASO#26, 1000.00000 nM, rep2


title: PST_3

description: LOP + JSQ Model group with 21 days treated with loperamide and 16 days treated with PST


title: JSQ_6

description: LOP + JSQ Model group with 21 days treated with loperamide and 14 days treated with JSQ

value: LOP +JSQ

value: LOP + JSQ


title: crypt_m_2m_rep2 (RRBS)


title: JSQ_5


title: Lgr5_f_O_rep3 (WGBS)


title: PST_2

description: LOP + JSQ Model group with 21 days treated with loperamide and 15 days treated with PST


title: 170269, primary hepatocytes, ASO#26, 1.60000 nM, rep1


title: JSQ_4


title: ChIPseq_Flower_b1_3xFLAG-RIM12_input

description: Library name: sample210


title: Lgr5_f_O_rep1 (WGBS)


title: 170584, primary hepatocytes, ASO#26, 1000.00000 nM, rep1


title: crypt_m_26m_rep4 (RRBS)


title: ChIPseq_Flower_b1_Col-0_input

description: Library name: sample209


title: 170311, primary hepatocytes, ASO#26, 1.60000 nM, rep2


title: 170495, primary hepatocytes, ASO#26, 0.32000 nM, rep2


title: crypt_m_2m_rep1 (RRBS)


title: JSQ_2


title: ChIPseq_Flower_b1_CLSY3-3xFLAG_clsy3_input

description: Library name: sample211


title: ChIPseq_Flower_b1_Col-0_IP

description: Library name: sample212


title: PST_1

description: LOP + JSQ Model group with 21 days treated with loperamide and 14 days treated with PST


title: crypt_m_26m_rep3 (RRBS)


title: 170393, primary hepatocytes, ASO#26, 0.32000 nM, rep1


title: JSQ_3


title: mRNAseq_Ovules_b5_WTCol-0_rep3

description: Library name: sample185

data_processing:
Reads were mapped to the TAIR10 reference genome using STAR (v2.7.10a) allowing 2 mismatches and only uniquely mapped reads with the following options: --alignIntronMin 20 --alignIntronMax 6000 --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 and --alignMatesGapMax 7500. To facilitate expression quantification, Tag Directories were generated from the resulting bam files using the makeTagDirectory function of HOMER (v4.10) with the following options: -format sam -mis 2 and -unique. mRNA expression was quantified using the analyzeRepeats.pl function of HOMER (v4.10). A custom gtf file containing genes, transposons, and repeats was used for quantification with the option -condenseGenes to report the highest expressed transcript, and -noadj to report raw read count. UCSC format track files were generated using the makeUCSCfile function of HOMER (v4.10) with the following options: -fragLength given -norm 10000000 -style rnaseq and -strand both.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

source_name: ovules (stage12)

extract_protocol:
Total RNA was extracted from flower buds (stage 12 and younger), unfertilized ovules (stage 12), and anthers (stage 9) using the Zymo Quick-RNA Miniprep Kit (R1055).
1 μg of DNase I treated total RNA was used for mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490L). Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit (NEB, Cat# E7770L). Pooled libraries were sequenced using a 50 bp single-end kit (SE50) or paired-end kit (PE50) on the Illumina Nextseq 2000 or Novaseq X plus platforms.

value: ovules (stage12)

value: experiment batch5


title: JSQ_1


title: 170532, primary hepatocytes, ASO#26, 0.06400 nM, rep2


title: mRNAseq_Ovules_b5_WTCol-0_rep2

description: Library name: sample184

value: Columbia


title: LOP_6

description: LOP group with 21 days treated with loperamide

value: LOP


title: crypt_m_26m_rep1 (RRBS)


title: 170511, primary hepatocytes, ASO#26, 0.06400 nM, rep1


title: mRNAseq_Ovules_b5_WTCol-0_rep1

description: Library name: sample183


title: crypt_m_18m_rep4 (RRBS)


title: crypt_m_18m_rep3 (RRBS)


title: LOP_4

value: colon tissue


title: crypt_m_18m_rep2 (RRBS)


title: LOP_3


title: mRNAseq_Anthers_b4_WTCol-0_rep2

description: Library name: sample181

source_name: anther (stage 9)

value: anther (stage 9)

value: experiment batch4


title: crypt_m_18m_rep1 (RRBS)


title: mRNAseq_Anthers_b4_WTCol-0_rep3

description: Library name: sample182


title: LOP_1

value: loperamide


title: 170271, primary hepatocytes, ASO#26, 0.00256 nM, rep1

value: primary hepatocytes


title: 170450, primary hepatocytes, ASO#26, 0.01280 nM, rep1


title: LOP_2


title: 170569, primary hepatocytes, ASO#26, 0.00256 nM, rep2


title: mRNAseq_Ovules_b5_WTCol-0_rep4

description: Library name: sample186


title: mRNAseq_Anthers_b4_WTCol-0_rep1

description: Library name: sample180


title: STm LT2, GlcNAc, 3 h, Sequencing Run 3, Bio Rep 3

city: Cambridge

first: Katharina

last: Ribbeck

state: Massachusetts

address: 21 Ames St

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Reads were analyzed on the Galaxy platform (24.1.2) with the Burrows-Wheeler algorithm for alignment and HTseq-count for read counts. DESeq2 was used for differential expression analysis between the medium alone control and treated cells from the same experiment with the recommended settings. For all analyses of the sequencing data, we considered FDR-adjusted P values < 0.05 as significant.
For paired end reads, the fastq files from the two lanes were concatenated prior to mapping.
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, GCF_000006945.2
Supplementary files format and content: excel workbooks with raw read counts

source_name: Bacterial culture

growth_protocol: S. Typhimurium LT2 overnight cultures were diluted 1:100 in 100 µL of SPI-1-inducing LB.3 medium with or without treatments and then cultured for 3 h at 37 °C under static conditions.

extract_protocol:
RNA was extracted with the MasterPure RNA Purification Kit (Biosearch Technologies), and DNA was eliminated using the Turbo DNA-Free Kit (Ambion). The Agilent 2100 Bioanalyzer (Agilent Technologies) was used to assess RNA integrity.
rRNA was depleted with the NEBNext rRNA Depletion Kit for bacteria (NEB). The Illumina HiSeq platform was used for the sequencing mucin-, glycan-treated, and monosaccharide pool-treated samples with a single-end protocol and read lengths of 40 nucleotides. The Illumina NovaSeq platform was used for sequencing HexNAc-treated samples with a paired-end protocol and read lengths of 50 nucleotides.

treatment_protocol: For treated bacterium, LB.3 contained either 0.1% MUC2, 0.1% MUC2 glycans, 0.2% GalNAc, 0.2% GlcNAc, 0.1% monosaccharide pool containing equal volumes of D-galactose, D-GalNAc, D-GlcNAc, L-fucose, and Neu5AC.

value: Bacterial culture

value: 0.2% D-GlcNAc


title: crypt_m_26m_rep2 (RRBS)


title: crypt_f_2m_rep3 (RRBS)

value: f


title: STm LT2, GlcNAc, 3 h, Sequencing Run 3, Bio Rep 2

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

value: WT


title: CTRL_6

description: Control group with 22 days treated with double distilled water

value: Control

value: double distilled water


title: 170500, primary hepatocytes, ASO#26, 8.00000 nM, rep2


title: crypt_f_2m_rep2 (RRBS)

value: Small intestinal crypts


title: 170389, primary hepatocytes, ASO#26, 8.00000 nM, rep1


title: CTRL_5

description: Control group with 21 days treated with double distilled water


title: LOP_5


title: crypt_f_2m_rep1 (RRBS)


title: 170501, primary hepatocytes, ASO#26, 0.01280 nM, rep2


title: STm LT2, GlcNAc, 3 h, Sequencing Run 3, Bio Rep 1


title: crypt_f_2m_rep4 (RRBS)


title: crypt_f_26m_rep4 (RRBS)


title: 170331, primary hepatocytes, ASO#26, 5000.00000 nM, rep2


title: STm LT2, GalNAc, 3 h, Sequencing Run 3, Bio Rep 3

value: 0.2% D-GalNAc


title: CTRL_4


title: crypt_f_26m_rep3 (RRBS)


title: 170405, primary hepatocytes, ASO#26, 40.00000 nM, rep2


title: STm LT2, GalNAc, 3 h, Sequencing Run 3, Bio Rep 2


title: CTRL_1


title: CTRL_3


title: CTRL_2


title: STm LT2, GalNAc, 3 h, Sequencing Run 3, Bio Rep 1


title: STm LT2, Medium alone, 3 h, Sequencing Run 3, Bio Rep 9

value: Medium alone control


title: HighYoked10Male

city: Bellaterra (Cerdanyola del Vallès)

first: Laura

last: Cutando Ruiz

state: Barcelona

address: Facultat de Medicina, M1/125, Av. de Can Domènech Campus de la UAB · 08193 Bellaterra

department: Department of Cellular Biology, Physiology and Immunology - Institute of Neurosciences

country: Spain

institute: Universitat Autònoma de Barcelona

description: Library name: AJ3589

data_processing:
For the operant behavior experiment, RNA-seq reads were aligned to the Mus musculus GRCm38 genome using STAR v2.5.3a with ENCODE parameters. Gene-level quantification was performed with RSEM v1.3.0 using the GENCODE M21 annotation. Both datasets followed ENCODE RNA-seq processing guidelines to generate gene-level expression estimates from raw FASTQ files.
Assembly: GRCm39 (GENCODE M33, mm39)
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

source_name: Brain, striatum

extract_protocol:
RNA was extracted using the RNeasy micro kit (Qiagen)
RNA sequencing libraries from Pvalb-RiboTag mouse striatal tissue were prepared using a modified SMART-seq2 protocol (Picelli et al., 2014). Total RNA (6–11 ng) was quantified (Qubit RNA BR Assay) and integrity assessed (Agilent Fragment Analyzer). Reverse transcription was performed with SuperScript II, oligo-dT30VN primers, template-switching oligonucleotides, and betaine. The resulting cDNA was amplified by 8 PCR cycles (KAPA HiFi HotStart), purified (AMPure XP beads), and quality-checked (Bioanalyzer HS DNA Kit). Two hundred nanograms of amplified cDNA was tagmented (Nextera XT Kit) and subjected to 12 cycles of indexed PCR amplification. Libraries were further purified, quantified, and sequenced on an Illumina NovaSeq 6000 system (paired-end 2 × 51 bp) with dual indexing, followed by image analysis and quality scoring using RTA v3.4.4.

value: Brain, striatum

value: Parvalbumin-expressing neurons

value: Pvalb-Cre;RiboTag

value: High Palatable Food Yoked


title: 170371, primary hepatocytes, ASO#26, 200.00000 nM, rep2


title: STm LT2, Medium alone, 3 h, Sequencing Run 3, Bio Rep 8


title: 170266, primary hepatocytes, ASO#26, 5000.00000 nM, rep1


title: crypt_f_18m_rep4 (RRBS)


title: HighMaster8Female

description: Library name: AJ3584

value: High Palatable Food Master


title: STm LT2, Medium alone, 3 h, Sequencing Run 3, Bio Rep 7


title: crypt_f_18m_rep3 (RRBS)


title: HighYoked6Female

description: Library name: AJ3581


title: crypt_f_18m_rep2 (RRBS)


title: HighMaster6Female

description: Library name: AJ3575


title: 170420, primary hepatocytes, ASO#26, 1000.00000 nM, rep2


title: 170337, primary hepatocytes, ASO#26, 1000.00000 nM, rep1


title: CRCHUG_169_stroma

city: Geneva

first: MELIVOIA

last: RAPTI

address: Rue du Général-Dufour

department: Medicine

country: Switzerland

institute: University of Geneva

data_processing:
GeoMX transcriptomic data was used to identify genes associated with response to treatment according or independently from their spatial localization (tumor or stroma segments). We fitted a mixed linear model for gene expression looking for association to the response alone or together with localization. Patient IDs were added as random effects to account for patient and batch technical variability. We used the DREAM method from the R package VariancePartition18 to fit the mixed linear model, and to extract the statistical test result table. Reported p-values are adjusted for multiple testing with the Benjamini-Hochberg procedure. The averaged measurements of tumor and stroma segments were calculated to give a pseudo bulk estimate of the data. Expression of the samples that had information on either one or the other segment didn’t change. A log2 transformation was applied afterwards. Genes with low expression were filtered according to the Nanostring guidelines.
Library strategy: GeoMX transcriptomic

source_name: FFPE tissue

growth_protocol: not relevant to this study

extract_protocol:
The FFPE tissue sections were incubated with cocktails of unique DNA probes (18’677 targeted genes). The region of interest (ROI) was selected using up to 4 morphologic antibodies combined with fluorochromes. Compartments were chosen for high-resolution multiplex profiling, and oligonucleotide tags from the selected region were released upon exposure to UV light. Photocleaved oligos were then collected via microcapillary tube inspiration into in microplates and analyzed using Ncounter platform or sequencing. Digital counts were then imported back into the GeoMx DSP instrument for QC and data analyses using the GeoMx DSP analysis suite version (v2.4). All raw data have also been exported for downstream analysis within R statistical language.
DNA oligonucleotide probes were designed to bind mRNA targets. From 5′ to 3′, they are each comprised of a 35- to 50-nucleotide target complementary sequence, a ultraviolet (UV) photocleavable linker and a 66-nucleotide indexing oligonucleotide sequence containing a unique molecular identifier (UMI), RNA ID sequence and primer binding sites. AOIs were exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited in a 96-well plate for subsequent processing. The indexing oligonucleotides were dried down overnight and resuspended in 10 μl of DEPC-treated water. Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences, and unique i5 and i7 sample indices were added.
Pooled libraries were paired-sequenced at 2 × 27 base pairs and with the single-index workflow on an Illumina HiSeq 3000/4000 instrument. FastQ files were converted into Digital Count Conversion (DCC) files according to manufacturer’s pipeline. DCC files are imported back into the GeoMx DSP instrument for QC and data analyses.

treatment_protocol: All patients included into this study received nCRT as a standard of care treatment. Formalin-fiyed and paraffin embedded blocks from these patiens were used to build a next generation TMA (ngTMA).

value: FFPE tissue

value: TMA2 | 071 | stroma

tag: slidename

tag: roilabel

tag: segmentlabel

value: stroma

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: type

value: Biopsy

tag: status

value: Alive

value: TRG 1

tag: code

tag: response

value: Good responders

value: Male


title: crypt_f_26m_rep1 (RRBS)

tag: tissue

value: f


title: 170272, primary hepatocytes, ASO#26, 40.00000 nM, rep1

source_name: primary hepatocytes

value: primary hepatocytes

tag: treatment concentration

tag: treatment


title: CRCHUG_168_stroma

value: TMA2 | 066 | stroma

value: TRG 3-4

value: Non responders

value: Female


title: crypt_f_26m_rep2 (RRBS)

tag: strain

value: Small intestinal crypts


title: NormalYoked5Female

description: Library name: AJ3568

value: Brain, striatum

tag: cell type

value: Parvalbumin-expressing neurons

tag: genotype

value: Pvalb-Cre;RiboTag

value: Normal Food Yoked

tag: batch


title: CRCHUG_168_tumor

value: FFPE tissue

value: TMA2 | 066 | tumor

tag: slidename

tag: roilabel

value: tumor

tag: gender


title: CRCHUG_167_stroma

value: TMA2 | 061 | stroma

tag: segmentlabel

value: stroma

tag: aoisurfacearea

tag: aoinucleicount

value: Biopsy

value: Alive

value: TRG 1


title: NormalYoked3Male

description: Library name: AJ3566


title: 170609, primary hepatocytes, ASO#26, 1.60000 nM, rep2

value: primary hepatocytes

tag: replicate


title: crypt_f_18m_rep1 (RRBS)

value: f

tag: age


title: Jurkat cell stimulated ChIP-seq RNA PoII rep2

city: Guangzhou

first: Mulin Jun

last: Li

state: Guangdong

address: No. 9 Jinsui Road, Guangzhou

institute: Guangzhou Women and Children's Medical Center

description: Library name: Jurkat_stimuated_ChIP-seq_RNA PolII_rep2

data_processing:
For data analysis, sequences with adaptors and low quality were trimmed for all 150-bp paired-end reads.
The clean reads were mapped against the human reference genome (GRCh37/hg19) using BWA (v0.7.17).
All samples were processed separately, and unique mapped reads were retained.
Peaks were called using MACS2 (v2.1.1) with IgG as the control.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig

source_name: Jurkat cell

growth_protocol: Jurkat (Clone E6-1) cell line (ATCC, CRL-9855) was cultured in Iscove’s Modified Eagle’s Medium (IMDM; Thermo Fisher Scientific, 31980030) containing 10% FBS and Penicillin and Streptomycin. All cell lines were authenticated by Short Tandem Repeat (STR) and tested no mycoplasma contamination utilizing the Quantiative PCR mycoplasma detection kit (Sigma-Aldrich, MP0040A).

extract_protocol:
1 × 10^7 Jurkat cells were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) in 10% FBS/phosphate-buffered saline (PBS) for 9 minutes at room temperature and subsequently quenched with 0.125 M glycine (Sigma-Aldrich, 50046). The cells were then collected and lysed twice using ice-cold lysis buffer, which consisted of 20 mM Tris-HCl (pH 7.5) (Thermo Fisher Scientific, 15567027), 2 mM EDTA (Thermo Fisher Scientific, 15575020), 1% Triton X-100 (Sigma-Aldrich, T8787), 0.1% SDS (Thermo Fisher Scientific, 15525017), 0.1% sodium deoxycholate (Sigma-Aldrich, D6750), and 1× protease inhibitors (Thermo Fisher Scientific, 78425) for 15 minutes with slow rotation at 4°C. The nuclear lysates were sonicated to obtain DNA fragments ranging from 200 to 500 bp using a Biorupter system (Diagenode, B01060001) at high energy, with a working time of 30 seconds and a resting time of 30 seconds, for a total of 30 cycles, until the solutions became clear. After removing insoluble debris, the lysates were incubated separately with specific antibodies against Rabbit IgG (1:100, Cell Signaling Technology, 7074), CTCF (1:100, Abcam, ab128873), ZNF384 (1:100, Novus Biologicals, NBP3-30592), H3K27me3 (1:100, Cell Signaling Technology, 9733), Rpb1 NTD (1:100, Cell Signaling Technology, 14958), H3K4me1 (1:100, Cell Signaling Technology, 5326), H3K4me3 (1:100, Cell Signaling Technology, 9751), or H3K27ac (1:100, Abcam, ab4729), and then purified using protein A-agarose beads (Millipore, 16-157). The beads were washed four times with TE buffer (10 mM Tris-HCl pH 8.0 [Thermo Fisher Scientific, 15568025] and 1 mM EDTA), TSE I buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), TSE II buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), and Buffer III (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 0.25 M LiCl [Sigma-Aldrich, L4408], and 1% sodium deoxycholate) before elution (20 mM Tris-HCl pH 7.5, 5 mM EDTA, 50 mM NaCl, and 1% SDS), reverse cross-linking, and subsequent DNA extraction.
ChIP-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions and were sequenced on a HiSeq X Ten platform (Illumina).

treatment_protocol: Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.

tag: cell line

value: Jurkat cell

value: Cells derived from human T cells

value: Rpb1 NTD antibody (CST, #14958)

value: anti-CD3/CD28 stimulated


title: 170560, primary hepatocytes, ASO#26, 0.32000 nM, rep2


title: NormalMaster5Female

description: Library name: AJ3562

value: Brain, striatum

value: Parvalbumin-expressing neurons

value: Normal Food Master


title: CRCHUG_167_tumor

value: FFPE tissue

value: TMA2 | 061 | tumor

tag: roicoordinatex

tag: roicoordinatey

tag: type

tag: status

tag: code

tag: response

value: Good responders

value: Male


title: Jurkat cell stimulated ChIP-seq H3K27me3 rep2

description: Library name: Jurkat_stimulated_ChIP-seq_H3K27me3_rep2

tag: cell type

tag: genotype

value: H3K27me3 antibody (CST, #9733)

tag: treatment


title: 170343, primary hepatocytes, ASO#26, 200.00000 nM, rep1

tag: tissue

tag: treatment concentration


title: CRCHUG_166_stroma

value: TMA2 | 056 | stroma

tag: slidename

tag: roilabel

tag: segmentlabel

value: stroma

value: Biopsy

value: TRG 3-4

value: Non responders

tag: gender

value: Female


title: NormalMaster3Male

description: Library name: AJ3560

value: Pvalb-Cre;RiboTag

tag: batch


title: 170296, primary hepatocytes, ASO#26, 1.60000 nM, rep1

value: primary hepatocytes

tag: replicate


title: Jurkat cell stimulated ChIP-seq H3K4me3 rep2

description: Library name: Jurkat_stimulated_ChIP-seq_H3K4me3_rep2

tag: cell line

value: Jurkat cell

value: Cells derived from human T cells

value: H3K4me3 antibody (CST, #9751)

value: anti-CD3/CD28 stimulated


title: 170325, primary hepatocytes, ASO#26, 0.06400 nM, rep1


title: CRCHUG_166_tumor

value: FFPE tissue

value: TMA2 | 056 | tumor

value: tumor

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

value: Alive


title: CRCHUG_165_tumor

value: TMA2 | 051 | tumor

tag: type

tag: status

value: Dead

value: TRG 1

tag: code

tag: response

value: Good responders

value: Male


title: Jurkat cell stimulated ChIP-seq H3K4me1 rep2

description: Library name: Jurkat_stimulated_ChIP-seq_H3K4me1_rep2

tag: cell type

tag: genotype

value: H3K4me1 antibody (CST, #5236)

tag: treatment


title: TdTom/DTR Control Orthotopic

first: Marina

last: Pasca di Magliano

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

description:
Library name: TdTomDTR_Control
3 male R26tdTomato mice

data_processing:
Raw data were processed and aligned by the University of Michigan Advanced Genomics Core. Cell Ranger count version 6.0.1 or 6.1.2 (10× Genomics, Pleasanton, CA) was used with default settings, with an initial expected cell count of 10,000.
Assembly: mm10-2020-A
Supplementary files format and content: Raw and filtered Cell Ranger outputs

source_name: Pancreas

extract_protocol:
Pancreas tissues/tumors were mechanically minced and enzymatically digested with collagenase V (1 mg/mL in Roswell Park Memorial Institute (RPMI) 1640) at 37°C. Normal Pancreas was incubated in Collagenase V for 15 minutes and orthotopic tumors for 25 minutes. Cell suspensions were filtered through 500 μm, 100 μm, and 40 μm mesh cell strainers. Dead cells were removed using the MACS Dead Cell Removal Kit (Miltenyi Biotec, catalog number 130-090-101). Single-cell complementary DNA libraries were prepared and sequenced at the University of Michigan Advanced Genomics Core using the 10× Genomics Platform
Samples were run using 50-cycle, paired-end reads on the HiSeq 4000 (Illumina, San Diego, CA) to a depth of 100,000 reads.

tag: tissue

value: Pancreas

tag: number of_mice_pooled

tag: cell ranger_version

tag: genome

tag: run date

value: June 2021


title: WT1Cre TdTomDTR Depletion Orthotopic

description:
Library name: WT1Cre_TdTomDTR
2 male R26tdTomato mice

tag: cell line

value: WT1-CreERT2/+; R26tdTomato/DTR


title: Jurkat cell stimulated ChIP-seq CTCF rep2

description: Library name: Jurkat_stimuated_ChIP-seq_CTCF_rep2

value: Jurkat cell

value: CTCF antibody (Abcam, #ab128873)


title: CRCHUG_162_stroma

value: TMA2 | 046 | stroma

tag: slidename

tag: roilabel

tag: segmentlabel

value: stroma

tag: aoisurfacearea

value: Biopsy

value: TRG 5

value: Non responders

tag: gender

value: Female


title: Orthotopic Mouse Pancreas #1

description:
Library name: Orthotopic_Mouse_PANC1
1 female R26tdTomato mouse

value: April 2022


title: Jurkat cell stimulatedChIP-seq H3K27ac rep2

description: Library name: Jurkat_stimulated_ChIP-seq_H3K27ac_rep2

value: Cells derived from human T cells

value: H3K27ac antibody (Abcam, #ab4729)

value: anti-CD3/CD28 stimulated


title: Jurkat cell stimulated ChIP-seq Input rep2

description: Library name: Jurkat_stimulated_ChIP-seq_Input_rep2


title: 170477, primary hepatocytes, ASO#26, 0.01280 nM, rep1

value: primary hepatocytes

tag: treatment concentration

tag: replicate


title: Orthotopic Mouse Pancreas #2

description:
Library name: Orthotopic_Mouse_PANC2
1 female WT1-CreERT2/+; R26tdTomato mouse


title: Jurkat cell resting ChIP-seq CTCF rep2

description: Library name: Jurkat_resting_ChIP-seq_CTCF_rep2

value: resting


title: 170562, primary hepatocytes, ASO#26, 0.01280 nM, rep2


title: Jurkat cell resting ChIP-seq RNA PoII rep2

description: Library name: Jurkat_resting_ChIP-seq_RNA PolII_rep2

value: Rpb1 NTD antibody (CST, #14958)


title: CRCHUG_161_stroma

value: FFPE tissue

value: TMA2 | 041 | stroma

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: type

tag: status

value: Alive

value: TRG 3

tag: code

tag: response

value: Mid responders

value: Male


title: Healthy Mouse Pancreas #2

description:
Library name: Normal_Mouse_PANC2
1 male WT1-CreERT2/+; R26tdTomato mouse

tag: tissue

value: Pancreas

tag: number of_mice_pooled

tag: genotype

value: WT1-CreERT2/+; R26tdTomato/DTR

tag: cell ranger_version

tag: genome


title: 170297, primary hepatocytes, ASO#26, 0.00256 nM, rep1

tag: treatment


title: 170352, primary hepatocytes, ASO#26, 0.00256 nM, rep2


title: CRCHUG_161_tumor

value: TMA2 | 041 | tumor

tag: slidename

tag: roilabel

tag: segmentlabel

value: tumor

tag: aoisurfacearea

value: Biopsy


title: 170516, primary hepatocytes, ASO#26, 0.32000 nM, rep1

tag: treatment concentration

tag: replicate


title: Healthy Mouse Pancreas #1

description:
Library name: Normal_Mouse_PANC1
1 male R26tdTomato mouse

tag: cell line

tag: run date

value: April 2022


title: 170353, primary hepatocytes, ASO#26, 0.06400 nM, rep2


title: Jurkat cell resting ChIP-seq H3K27me3 rep2

description: Library name: Jurkat_resting_ChIP-seq_H3K27me3_rep2

value: Jurkat cell

tag: cell type

value: Cells derived from human T cells

value: H3K27me3 antibody (CST, #9733)


title: CRCHUG_162_tumor

value: TMA2 | 046 | tumor

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: type

tag: status

value: Dead

value: TRG 5

tag: code

value: Non responders

tag: gender

value: Female


title: hPSC-derived 2D cardiac model, D30,CTRL,scRNA-seq

city: Beijing

first: li

last: wang

institute: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital

description: 10x Genomics

data_processing:
Raw reads were processed with the Cell Ranger Single-Cell Software Suite (version 7.0.1, 10x Genomics). The command "cellranger mkfastq" demultiplexed binary base call (BCL) files were generated by Illumina sequencers and converted into FASTQ files. The "cellranger count" command was employed to perform alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting.
We aligned the gene expression libraries to the GRCh38 human genome reference provided by 10x Genomics. Gene counts were calculated by Cell Ranger using the default parameters. The gene-by-cell expression matrices were obtained for downstream analyses.
Cell Ranger raw result tables were merged and analyzed using the R package Seurat (version 3.1.5) to filter out low-quality cells.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HES7 (WiCell Research Institute)

growth_protocol: The hPSC cell lines were maintained with mTeSR1 medium (Stem Cell Technologies) on Matrigel (354277, Corning) coated plates (BD Biosciences).

extract_protocol:
All the samples were washed twice with wash buffer (0.04% BSA in DPBS) before dissociation and scRNA-seq. For each differentiated day 0, 2, 4, and 8 timepoint, cells were dissociated with Accutase (A11105-01, ThermoFisher) for 3 min at 37 °C into single cells, while the day 14 and 30 populations were dissociated with TryPLE (A1217701, ThermoFisher) for 5 and 8 min at 37 °C. The resulting cells were resuspended in 0.04% BSA in DPBS for counting (10,000 cells for each sample).
Cells were processed using the Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns (PN-1000268, 10x Genomics), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120, 10x Genomics), and Dual Index Kit TT Set A, 96 rxns (PN-1000215, 10x Genomics) following 10X Genomic manufacturers’ protocol to generate Gel Beads-in-emulsion (GEMs) and single-cell sequencing libraries.

treatment_protocol: We used a well-established CHIR-based monolayer differentiation protocol and added RA between days 4 and days 6 during cardiac differentiation.

value: HES7 (WiCell Research Institute)

tag: treatment

value: normal condition


title: Activated male, scRNAseq

first: Xueli

last: Zhang

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Omentum

extract_protocol:
For the normal situations, the omentum from 6 male/female mice were pooled for single cell isolation. For the activation stats, the omentum from 2-3 male/female mice were pooled for single cell isolation. Briefly, omemum were chopped into small pieces and digested in collagenase I (Sigma, C0130) for 10 min, 20min, 30min at 37 °C. Cells were collected at  the different time points in order to get all kinds of cells from the omentum. Then the cells were washed in serum-free medium and then passed through a 40 um cell strainer to generate a single cell suspension.
Single cells around 10,000 -15,000 cells from naive and activated omentum were used to generate single cell RNA-seq libraries which was further sequenced and analyzed. Single cells per sample were encapsulated in droplets using 10x Genomics Gemcode Technology and processed following the manufacture’s protocols (#CG00052). cDNA and libraries were checked for quality on Agilent 4200 Tapestation and quantified by KAPA qPCR before sequencing on a single lane of a HiSeq4000 (Illumina).

tag: tissue

value: Omentum

tag: Sex

value: Male

tag: age

value: 8-10 weeks old


title: Jurkat cell resting ChIP-seq H3K4me3 rep2

description: Library name: Jurkat_resting_ChIP-seq_H3K4me3_rep2

tag: genotype

value: H3K4me3 antibody (CST, #9751)

value: resting


title: hPSC-derived 2D cardiac model, D30,PGD model,scRNA-seq

description: 10x Genomics

value: high glucose


title: Activated female, scRNAseq

description: 10x Genomics


title: CRCHUG_158_tumor

value: FFPE tissue

value: TMA2 | 036 | tumor

tag: slidename

tag: roilabel

tag: segmentlabel

value: tumor

tag: aoisurfacearea

value: Biopsy

value: TRG 3

tag: response

value: Mid responders


title: Jurkat cell resting ChIP-seq H3K4me1 rep2

description: Library name: Jurkat_resting_ChIP-seq_H3K4me1_rep2

tag: cell line

value: Jurkat cell

tag: cell type

value: Cells derived from human T cells

value: H3K4me1 antibody (CST, #5236)


title: CRCHUG_155_stroma

value: TMA2 | 031 | stroma

value: stroma

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

value: Dead

value: TRG 1

value: Good responders


title: hPSC-derived 2D cardiac model, D30,2.0 μM RA,scRNA-seq

description: 10x Genomics

value: HES7 (WiCell Research Institute)


title: Jurkat cell resting ChIP-seq H3K27ac rep2

description: Library name: Jurkat_resting_ChIP-seq_H3K27ac_rep2

value: H3K27ac antibody (Abcam, #ab4729)

value: resting


title: CRCHUG_155_tumor

value: FFPE tissue

value: TMA2 | 031 | tumor

tag: type

tag: status

tag: code

value: Male


title: Male, scRNAseq

description: 10x Genomics

tag: tissue

value: Omentum

value: 8-10 weeks old


title: hPSC-derived 2D cardiac model, D30,0.5 μM RA,scRNA-seq

description: 10x Genomics

tag: treatment


title: Jurkat cell resting ChIP-seq Input rep2

description: Library name: Jurkat_resting_ChIP-seq_Input_rep2


title: hPSC-derived 2D cardiac model, D14,0.5 μM RA,scRNA-seq

description: 10x Genomics


title: hPSC-derived 2D cardiac model, D14,2.0 μM RA,scRNA-seq

description: 10x Genomics


title: CRCHUG_151_stroma

value: TMA2 | 026 | stroma

value: Biopsy

value: Alive

value: TRG 4

value: Non responders

tag: gender


title: CRCHUG_150_stroma

value: TMA2 | 021 | stroma

value: stroma


title: hPSC-derived 2D cardiac model, D8,2.0 μM RA,scRNA-seq

description: 10x Genomics


title: CRCHUG_151_tumor

value: TMA2 | 026 | tumor

value: tumor


title: L3 eye-brain, w[1118], Replicate 1, NovaSeq 6000 (input)

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

description: Library name: L3 eye-brain, w[1118], Replicate 1 (input)

data_processing:
ChIP-seq reads were trimmed using Trimmomatic v0.33 with default settings.  ChIP-seq reads were algined to dm6 genome using Burrows-Wheeler Aligner v0.7.16a with default settings. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequnced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format using HOMER 4.11.1.
Peaks were called using MACS v2.1.2 with the significance cut-off q-value <= 0.01 and were annotated with ChIPseeker and motifs identified with HOMER v4.11.1.
Assembly: dm6
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

source_name: L3 eye-brain complex

growth_protocol: Drosophila were reared at 25C on standard fly food.  Embryos were collected and aged at 25C on grape juice agar plates.

extract_protocol:
Embryos were collected for 4 hrs, aged for 16 hrs at 25C, and dechorionated in 50% bleach.  Eye-brain complexes were dissected from 3rd instar larvae in ice-cold PBS.  Tissues were crosslinked in 2 mM EGS for 45 min, followed by paraformaldehyde for 15 min, quenched, washed, flash frozen in liquid nitrogen and stored at -80C until use.  50 ml settled embryos or 100 eye-brain complexes were used per sample.  Crosslinked tissues were homogenized by douncing, followed by nuclear lysis and sonication of the genomic DNA using a Bioruptor or Qsonica Q700 sonicator.  Fragmented chromatin was incubated with anti-GFP or anti-FLAG antibodies and precipitated using MagnaChIP A+G beads or Dynabeads G.
ChIP-seq libraries were prepared from 10 ng DNA.  DNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends.  Size selection was performed with AMPure beads to limit the fragment size to 150-700 bp.  Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags.

value: L3 eye-brain complex

tag: genotype

tag: chip antibody

value: a-FLAG (M2, Sigma F1804)


title: HAInv84_Inv45, H3K27me3 ChIP 2

city: Los Angeles

first: Natalie

middle: Dianna

last: Gehred

address: 650 Charles E Young Dr

department: Anesthesiology & Perioperative Medicine

institute: University of California, Los Angeles

description: Library name: HAInv84_Inv45, H3K27me3 ChIP 2

data_processing:
ChIP-seq reads were aligned to dm3 reference genome using Bowtie2. The PCR duplicates for each dataset were removed using the rmdup function of SAMtools. The bam files were then converted to tdf format by using igvtools for visualization in the Integrative Genomics Viewer.
Assembly: dm3
Supplementary files format and content: TDF coverage files for input and H3K27me3 ChIP-seq libraries.

source_name: Third instar larval wing imaginal discs and brains

extract_protocol:
The protocol for carrying out chromatin immunoprecipitation (ChIP) has been described (De et al. 2019). Anti-H3K27me3 antibody (17–622; Millipore, Bedford, MA) was used at 1:200 dilution.
ChIP-sequencing (ChIP-seq) libraries were made with the TruSeq DNA Sample Prep Kit V2 Library Prep kit and sequenced on the Illumina HiSeq 2500.


title: CRCHUG_158_stroma

value: TMA2 | 036 | stroma

tag: slidename

tag: roilabel

value: Dead

value: TRG 3

value: Mid responders

value: Female


title: CRCHUG_150_tumor

value: FFPE tissue

value: TMA2 | 021 | tumor

tag: segmentlabel

tag: aoisurfacearea

value: TRG 1

value: Good responders

value: Male


title: hPSC-derived 2D cardiac model, D8,0.5 μM RA,scRNA-seq

description: 10x Genomics

tag: cell line

value: HES7 (WiCell Research Institute)


title: HAInv84_Inv45, Input 2

description: Library name: HAInv84_Inv45, Input 2

value: Third instar larval wing imaginal discs and brains


title: L3 eye-brain, w[1118], Replicate 2, NovaSeq 6000 (ChIP)

description: Library name: L3 eye-brain, w[1118], Replicate 2 (ChIP)


title: HAInv84_Inv45, Input 1

description: Library name: HAInv84_Inv45, Input 1


title: HAInv84_Inv45, H3K27me3 ChIP 1

description: Library name: HAInv84_Inv45, H3K27me3 ChIP 1


title: L3 eye-brain, w[1118], Replicate 1, NovaSeq 6000 (ChIP)

description: Library name: L3 eye-brain, w[1118], Replicate 1 (ChIP)


title: CRCHUG_147_stroma

value: TMA2 | 016 | stroma

value: stroma

value: Biopsy

value: Alive

tag: response


title: hPSC-derived 2D cardiac model, D4,replicate2,scRNA-seq

description: 10x Genomics

value: RA


title: Inv45, H3K27me3 ChIP 2

description: Library name: Inv45, H3K27me3 ChIP 2


title: L3 eye-brain, w[1118], Replicate 2, NovaSeq 6000 (input)

description: Library name: L3 eye-brain, w[1118], Replicate 2 (input)

value: L3 eye-brain complex

value: a-FLAG (M2, Sigma F1804)


title: Female, scRNAseq

description: 10x Genomics

value: Omentum

tag: cell type

tag: Sex

tag: age

value: 8-10 weeks old


title: hPSC-derived 2D cardiac model, D2,replicate2,scRNA-seq

description: 10x Genomics


title: Inv45, H3K27me3 ChIP 1

description: Library name: Inv45, H3K27me3 ChIP 1


title: CRCHUG_144_tumor

value: TMA2 | 011 | tumor

value: tumor

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: type

value: Female


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 5, NovaSeq 6000 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 5 (ChIP)

tag: tissue

value: ubi-Gal4; UAS-FtICD-FLAG


title: Inv45, Input 2

description: Library name: Inv45, Input 2


title: hPSC-derived 2D cardiac model, D2,replicate1,scRNA-seq

description: 10x Genomics

tag: treatment


title: Inv45, Input 1

description: Library name: Inv45, Input 1


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 4, NovaSeq 6000 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 4 (input)

tag: genotype


title: CRCHUG_141_tumor

value: FFPE tissue

value: TMA2 | 006 | tumor

tag: status

value: TRG 4

tag: code

value: Non responders

tag: gender


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 3, HiSeq 2500 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 3 (input)

tag: chip antibody


title: CRCHUG_137_tumor

value: TMA1 | 082 | tumor

tag: slidename

tag: roilabel

tag: segmentlabel

tag: aoisurfacearea

value: TRG 1

value: Good responders


title: 16-20 h embryo, w[1118], Replicate 3, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, w[1118], Replicate 3 (Input)

source_name: 16-20 h embryo

value: 16-20 h embryo

value: a-GFP (ab290)


title: CRCHUG_138_tumor

value: TMA2 | 001 | tumor

value: Biopsy

value: Alive

value: TRG 3

tag: response

value: Mid responders

value: Male


title: CRCHUG_137_stroma

value: TMA1 | 082 | stroma

value: stroma

value: Female


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 4, NovaSeq 6000 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 4 (ChIP)

value: L3 eye-brain complex

value: ubi-Gal4; UAS-FtICD-FLAG

value: a-FLAG (M2, Sigma F1804)


title: hPSC-derived 2D cardiac model, D0,replicate2,scRNA-seq

description: 10x Genomics

tag: cell line

value: HES7 (WiCell Research Institute)

value: CHIR


title: CM199_Treated_Rep_3

city: Ann Arbor

first: Mark

last: Chiang

address: 109 Zina Pitcher Place

institute: University of Michigan

description: instrument model: Illumina NovaSeq X

data_processing:
FastQC v0.11.8 on raw and trimmed reads
TrimGalore v0.4.5 and cutadapt v1.15 with --nextera -e 0.1 --stringency 6 --length 20 --nextseq 20
Read deduplication with Picard v2.20.2
Alignment to hg38 with Bowtie2 v2.3.4.1 with -X 2000 --no-mixed --no-discordant
Filter reads with samtools with -q 10 -F 1024
Filter reads out from ENCODE blacklist
Call narrowPeaks with macs2 with -f BAM --nomodel --shift -100 --extsize 200
BigWigs created with deeptools bamCoverage with --normalizeUsing CPM and --binSize 5
Assembly: hg38
Supplementary files format and content: narrowPeak files represent regions of open chromatin
Supplementary files format and content: bw files represent normalized read pile-ups

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: Cells were maintain cells in RPMI  with 10% FBS, penicillin/streptomycine, glutamine, and HEPES.

extract_protocol:
We used the Omni-ATAC-Seq protocol (Corces et al., 2017).
The final libraries were cleaned using Qiagen MinElute columns and AMPure XP beads before quantitation with the Qubit HS dsDNA kit, and quality assessment on a TapeStation HS D1000 kit. The libraries were pooled and quantitated by qPCR using KAPA’s Illumina Library quantitation kit

treatment_protocol: Cells were treated with DMSO (control) or 500nM dTAGV-1 (treated) for 72 hours prior to submission.

value: T-cell acute lymphoblastic leukemia

value: THP-6 with ETS1-FKBP(D36V) fusion

tag: cell type

value: dTAGV-1 (500nM)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 3, HiSeq 2500 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 3 (ChIP)


title: CM199_Treated_Rep_2

description: instrument model: Illumina NovaSeq X


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 5, NovaSeq 6000 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 5 (input)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 2, HiSeq 2500 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 2 (input)


title: 16-20 h embryo, w[1118], Replicate 2, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, w[1118], Replicate 2 (Input)

value: 16-20 h embryo

value: a-GFP (ab290)


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 2, HiSeq 2500 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 2 (ChIP)


title: hPSC-derived 2D cardiac model, D0,replicate1,scRNA-seq

description: 10x Genomics


title: hPSC-derived 2D cardiac model, D4,replicate1,scRNA-seq

description: 10x Genomics

value: RA


title: CRCHUG_136_stroma

value: FFPE tissue

value: TMA3 | 062 | stroma

tag: aoinucleicount

tag: roicoordinatex

value: Biopsy

value: Alive

value: TRG 4

value: Non responders


title: CRCHUG_144_stroma

value: TMA2 | 011 | stroma

value: stroma

tag: roicoordinatey

tag: type

value: TRG 1

value: Good responders

value: Female


title: 16-20 h embryo, w[1118], Replicate 2, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, w[1118], Replicate 2 (ChIP)

tag: tissue


title: 16-20 h embryo, w[1118], Replicate 3, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, w[1118], Replicate 3 (ChIP)

tag: genotype


title: CM199_Treated_Rep_1

description: instrument model: Illumina NovaSeq X

value: T-cell acute lymphoblastic leukemia

tag: treatment


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 1, HiSeq 2500 (input)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 1 (input)

value: L3 eye-brain complex

value: ubi-Gal4; UAS-FtICD-FLAG

value: a-FLAG (M2, Sigma F1804)


title: CRCHUG_136_tumor

value: TMA3 | 062 | tumor

value: tumor

tag: status

tag: code

value: Male


title: CRCHUG_134_stroma

value: FFPE tissue

value: TMA1 | 077 | stroma

value: TRG 3

value: Mid responders

tag: gender


title: 16-20 h embryo, w[1118], Replicate 1, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, w[1118], Replicate 1 (Input)

value: 16-20 h embryo

tag: chip antibody

value: a-GFP (ab290)


title: 16-20 h embryo, w[1118], Replicate 1, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, w[1118], Replicate 1 (ChIP)


title: CRCHUG_134_tumor

value: TMA1 | 077 | tumor

tag: slidename

tag: roilabel

value: Biopsy

value: Alive


title: CM199_Control_Rep_3

description: instrument model: Illumina NovaSeq X

value: THP-6 with ETS1-FKBP(D36V) fusion

value: DMSO


title: L3 eye-brain, ubi>FtICD-FLAG, Replicate 1, HiSeq 2500 (ChIP)

description: Library name: L3 eye-brain, ubi_FtICD-FLAG, Replicate 1 (ChIP)

value: L3 eye-brain complex


title: STm LT2, Monosach. pool, 3 h, Sequencing Run 2, Bio Rep 2

value: Bacterial culture

value: WT

value: 0.1% Monosaccharide pool


title: CRCHUG_127_stroma

value: TMA1 | 072 | stroma

tag: segmentlabel

value: stroma

tag: aoisurfacearea

value: TRG 1

value: Good responders

value: Female


title: CM199_Control_Rep_2

description: instrument model: Illumina NovaSeq X

value: T-cell acute lymphoblastic leukemia

tag: cell line


title: CM199_Control_Rep_1

description: instrument model: Illumina NovaSeq X

tag: cell type


title: STm LT2, MUC2 glycans, 3 h, Sequencing Run 2, Bio Rep 3

value: 0.1% MUC2 glycans


title: 16-20 h embryo, ubi>FtICD-FLAG, Replicate 1, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, ubi_FtICD-FLAG, Replicate 1 (Input)

value: 16-20 h embryo

value: ubi-Gal4; UAS-FtICD-FLAG

value: a-FLAG (M2, Sigma F1804)


title: NHA_mRNA-seq

first: Irina

last: Voineagu

data_processing:
For the PolyA+ RNA-seq library, reads were mapped to hg38 using STAR v2.5.2b (Dobin et al. 2013) with the following parameters: --outSJfilterOverhangMin 15 15 15 15 --alignSJoverhangMin 15 --alignSJDBoverhangMin 15 --outFilterMultimapNmax 1 --outFilterScoreMin 1 --outFilterMatchNmin 1 --outFilterMismatchNmax 2  --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15. GENCODE v32 (Frankish et al. 2019) was used for gene coordinates.
For ribo-depleted RNA-seq and TT-seq, FASTQs were processed using the nf-core RNA-seq pipeline (https://nf-co.re/rnaseq/3.13.2) (Ewels et al. 2020). Reads were mapped to hg38 using the STAR aligner (2.7.10a) (Dobin et al. 2013), where genomic origin was identified (STable 11). Candidate peak expression was determined using FeatureCounts (Dobin et al. 2013) implemented in the Rsubread package (Liao et al. 2019). The following parameters were set: useMetaFeatures = FALSE, allowMultiOverlap = TRUE, isPairedEnd = TRUE, strandSpecific = 2, minMQS = 10, checkFragLength = FALSE, countChimericFragments = FALSE. Candidate size was set to a standard length of by adjusting start and end coordinates to be ±500bp centred around the midpoint.
Assembly: hg38
Supplementary files format and content: PolyA.csv - comma separated values with ENSEMBL Gene ID, gene symbol, counts and CPM for the mRNA-seq sample
Supplementary files format and content: TTseq_RiboDep.csv - comma separated values with enhancer ID from our CRISPRi screen, chromosome, enhancer start and end locations (+-500bp from enhancer midpoint), and postive strand, negative strand and unstranded counts for TT-seq and ribo-depleted RNA-seq

source_name: Normal Human Astrocytes (Lonza, #CC-2565)

extract_protocol:
RNA was extracted using the Qiagen miRNeasy kit, according to manufacturer's instructions
For TT-seq samples, cells were treated with 4sU for 5 mins before RNA extraction as above
For TT-seq samples, RNA was sonicated to ~1.5kb (Schwalb et al. 2016), then 4sU-labeled RNA was biotinylated (Duffy et al 2016) before isolation using streptavidin conjugated magnetic beads (Rädle et al. 2013)
For mRNA-seq samples, libraries were prepared using the Illumina TruSeq Stranded mRNA Prep Kit, according to manufacturer's instructions
For ribo-depleted RNA-seq samples, libraries were prepared using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus, according to manufacturer's instructions


title: CRCHUG_112_stroma

value: FFPE tissue

value: TMA1 | 067 | stroma

tag: aoinucleicount

value: Biopsy

value: Alive

value: TRG 3

tag: response

value: Mid responders

value: Male


title: 16-20 h embryo, ubi>FtICD-FLAG, Replicate 1, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, ubi_FtICD-FLAG, Replicate 1 (ChIP)


title: CRCHUG_127_tumor

value: TMA1 | 072 | tumor

value: tumor

tag: roicoordinatex

tag: roicoordinatey


title: STm LT2, Monosach. pool, 3 h, Sequencing Run 2, Bio Rep 1

value: Bacterial culture

value: WT

value: 0.1% Monosaccharide pool


title: 16-20 h embryo, ft-GFP[int], Replicate 3, NovaSeq 6000 (Input)

description: Library name: 16-20 h embryo, ft-GFP[int], Replicate 3 (Input)

tag: tissue

value: Ft-GFP[int]

value: a-GFP (ab290)


title: NHA_ATAC-seq

description: ATAC-seq

data_processing:
pre-processing and peak calling was performed within the Snakepipes environment (Bhardwaj et al. 2019)
Reads were mapped to hg38 using Bowtie2 (Langmead et al. 2012), keeping only deduplicated reads with a mapping quality score > 10.
Adapters were trimmed using CutAdapt (Martin et al. 2012)
Peaks were called using the MACS2 algorithm (Feng et al 2012), setting maxFragmentSize to 150bp and qval to 0.001.
Assembly: hg38
Supplementary files format and content: BigWigs contain a reads per genome coverage (RPGC) value quantifying the smoothed ATAC-seq signal depth at base-pair resolution. Here, ATAC-seq reads were mapped to hg38 using BowTie2, from which BigWigs were generated using using bamCoverage from the deepTools suite. Parameters included an effective genome size of 3,049,315,783, plus a binLength and stepSize of 25

extract_protocol:
ATAC-seq. Briefly, nuclei were isolated, before DNA transposed at regions of open chromatin using Tn5 enzyme (Corces et al. 2017)
Transposed DNA was PCR amplified to prepare the library for sequencing (Corces et al. 2017)

value: Normal Human Astrocytes (Lonza, #CC-2565)


title: STm LT2, MUC2 glycans, 3 h, Sequencing Run 2, Bio Rep 2

tag: genotype

value: 0.1% MUC2 glycans


title: 16-20 h embryo, ft-GFP[int], Replicate 3, NovaSeq 6000 (ChIP)

description: Library name: 16-20 h embryo, ft-GFP[int], Replicate 3 (ChIP)

value: 16-20 h embryo


title: ATAC-seq_mixed H7 cells,positive,Week 5

city: Macau

first: Ning-Yi

last: Shao

address: University of Macau

department: Faculty of Health Sciences

institute: University of Macau

data_processing:
ATAC-seq Guidelines from Harvard FAS informatics
Quality control, alignment, and format transformation were the same as those mentioned in bulk RNA-seq data
Peaks were called by Genrich v0.6.1, which can set ATAC-seq analysis mode to run all the post-alignment steps (removal of mitochondrial reads, removal of PCR duplicates, analysis of multimapping reads, and analysis of multiple replicates) through peak-calling within one command. The parameter sets like this: -j, -r, -e chrM ,-v,-E human blacklist,-q 0.01. Multiple replicates in the same biological condition were used together to call peaks for the replicates collectively.
Peaks were combined before being quantified by FeatureCounts.
The differential enriched region test was performed by DESeq2 v1.37.4 (pvalue<0.05 & logFC >1 or logFC <-1) and these regions were annotated by CHIPseeker v1.32.0 and enriched functionally by GeneAnswers v1.16.0 (pvalue<0.05) (Yu et al., 2015).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include DApeaks results

growth_protocol: To generate mixed organoids, S6K1 knockout H7 cells were labeled with eGFP through infection with eGFP-expressing AAV2 viral particles (Gene Copoeia, AA001) followed by fluorescence-activated cell sorting (FACS). Dorsal forebrain organoids were generated with 1:1 mixture of eGFP-labeled S6K1 knockout cells and non-labeled wild-type cells.

extract_protocol:
For the ATAC sequencing, the mixed organoids were dissociated into single cells with Papain dissociation kit. Then, the dissociated cells were divided into eGFP-positive and eGFP-negative portions using a BD FACS Aria, and 50,000 of sorted cells were lysed with 50 ul of nuclei isolation buffer (10mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA, 1 mM DTT) for 5 min on ice. The 500 ul of chilled Wash Buffer (10mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT) were added to lysed cells, and cells were centrifuged at 500 x g for 5 min at 4°C. The supernatant was removed, and transposition was performed using Tn5 (illumina).
The fragmented DNA by Tn5 was purified using MinElute reaction Cleanup kit (Qiagen) and amplified with predesigned primers containing adaptors and barcodes. Next, the ATAC-seq libraries were purified using AMPure XP beads and final libraries were sequenced with a paired end read of 150 bp on the NovaSeq 6000 illumina platform.

treatment_protocol: S6K1 knockout H7 cells were generated by targeting exon 9 and 11 of RPS6KB1. The guide RNAs targeting exon 9 (E9-For: TTAAACATAATTGGTTTGGGGG, E9-Rev: GCAGCTTTTAACTGTGCACCTA) & exon 11 (E11-For: AAAAGAAATGCTGCTTCTCGTC, E11-Rev: AGGAAGAAAAGTTGAGGGGACT) of S6K1 were designed using online CRISPR design tool (https://chopchop.cbu.uib.no/) and cloned into the pSpCas9(BB)-2A-Puro (PX459) V2.0 (Addgene, #62988). The 1ug of cloned plasmids were transfected into H7 ESCs using Lipofectamin 3000 reagent. After two days, GPF-expressing transfected cells were sorted with a BD FACS Aria. The sorted cells were seeded on 6 well plates and expanded clonally. To confirm genotype of each clone, genomic DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen), and PCR was conducted using PrimeSTAR GXl DNA Polymerase (TaKaRa).

value: human dorsal forebrain organoids

tag: cell marker

value: GFP-positive

value: S6K1 knockout