title: Plk1as_3MB_rep4

city: Madison

first: Zhouyuan

last: Shen

state: Wisconsin

address: 1111 Highland Ave

department: Medicine

institute: University of Wisconsin-Madison

description: Library name: Plk1as_3MB_rep4

data_processing:
Raw sequencing data was processed using Nextflow’s atacseq pipeline, which uses Macs2 for peak calling(https://nf-co.re/atacseq/2.1.2/, https://www.biorxiv.org/content/10.1101/496521v1).
The peaks from control and Plk1 inhibited samples were merged to form consensus peaks.
Differential ATAC signal was quantified over these consensus peaks using DeSeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: hg38
Supplementary files format and content: Tab-delimited bed file containing peaks called by macs2 for each sample

source_name: hTERT RPE-1

growth_protocol: DMEM/F12, 10% Fetal bovine serum, 100 units/ml penicillin–streptomycin. Cells were cultured at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
50,000 cells were resuspended in 50 uL transposition reaction mix containing 25 uL Tagment DNA buffer, 16.5 uL 1x PBS, 0.5 uL 10% Tween-20, 0.5 uL 1% Digitonin, 2.5 uL Tn5 Transposase, and 5 uL nuclease-free water. Reaction mixture was incubated at 37°C for 30 min in a Thermomixer set at 1000 rpm. DNA was isolated using a QIAquick PCR Purification kit according to manufacturer’s protocol, and DNA was eluted in 10uL of the supplied elution buffer.
The entirety of the purified DNA was added to a PCR reaction containing 10 uL nuclease-free water, 2.5 uL each of 25uM NextEra i5 and i7 barcoded primers, and 25 uL NEBNext high-Fidelity 2X PCR Master Mix. Samples were amplified on the following program: 72°C 5 min, 90°C 30 sec, (98°C 10 sec, 63°C 30 sec, 63°C 1 min) with certain number of cycles. 5 uL of the PCR reaction was used to calculate the number of cycles needed for the libraries. Amplified samples were size selected using SPRIselect beads by doing a 0.5x standard bead cleanup followed by a 1.8x standard bead cleanup. Samples were eluted from the beads using 20uL of nuclease-free water.

treatment_protocol: Asynchronous cells were treated with 5 µM STLC containing media for 16 hours to enrich prometaphase population. Mitotic cells were isolated by shakeoff. Cells were treated with DMSO (0.5%) or 10 µM 3MB-PP1 in STLC containing media for 2 hours. Before collection, mitotic index of each sample was measured to ensure >95% are in mitosis.

value: hTERT RPE-1

value: Human epithelial cell line

value: hTERT RPE-1 Plk1-/- EGFP-Plk1as

value: 5 µM STLC + 10 µM 3MB-PP1


title: Plk1as_3MB_rep3

status: Public on Nov 18 2025

type: SRA

country: USA

description: Library name: Plk1as_3MB_rep3

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: X_m_1

city: hangzhou

first: li

last: qi

address: xihu

country: China

institute: zhejiang university

description: Library name: X_m-rep1

library_source: transcriptomic

data_processing:
The clean reads were aligned to the Arabidopsis reference genome using STAR software
Transcripts assembled from three independent biological replicates were included in the analysis, compared using DESeq2 (version 1.30.1) with default settings.
The R package DESeq2 (version 1.30.1) in v4.0.3 was employed to identify differentially expressed genes with at least a 1.5-fold change
Assembly: TAIR10
Supplementary files format and content: text files include genecounts for each files

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: The stratified seeds were germinated in half-strength Murashige and Skoog (MS) medium for 7 d. Plants were grown under cool white light in a long-day condition (16 h light /8 h dark, 22 ºC).

extract_protocol:
Seven-day-old seedlings grown on half-strength MS plates were harvested, flash-frozen in liquid nitrogen, and ground to a fine powder. Total RNA was isolated using the Plant RNA Kit (Omega, R6827). For RT-qPCR, 0.5 μg of total RNA was reverse-transcribed using the M5 Super plus qPCR RT Kit (Mei5bio, MF166-plus-01), and 1 μL of the resulting cDNA was used for qPCR on a Biorad CFX96 Touch system.
RNA sequencing was carried out using the Illumina NovaSeq 6000 with Hiseq-PE150 strategy, conducted by Novogene Corporation (Beijing, China).

tag: tissue

value: leaves

value: Columbia

value: MMS


title: K562 CISTR KO 48h hemin rep1

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
PM_K562_CISTRKO1_48h_hemin_S18_L001
K562_CISTR.GENCODEv32.RPKM.genPos.consensus

data_processing:
We aligned reads to hg38 using STAR aligner, version 2.7.0f. We used FeatureCounts to count reads aligning to genes in GENCODE v32 (human), vM33 (mouse).
Assembly: hg38, mm39
Supplementary files format and content: text files include RPKM values for each sample

extract_protocol:
RNA was harvested and purified using TRIzol (Invitrogen). 1 ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus following manufacturer's protocols.

value: erythropoietic precursors

value: [delta]CISTR

value: K562 ΔCISTR cells treated with 50 µM hemin for 48 hours


title: Translatome BCAA-free plus 5+3 sgOgfod1 AML cells biol rep5

city: Boston

first: Christina

last: Mayerhofer

state: MA

address: 185 Cambridge St.

department: Center for Regenerative Medicine

institute: MGH, Simches building

description: Library name: RFP 24

library_source: other

data_processing:
RiboSeq data was processed according to the recommendation of the manufacturer (diagenode user guide C05030001) and the original RiboLite publication. First, the UMI was copied from the read to the read identifier with fumi tools (https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools) to allow subsequent deduplication. Trimming was performed by cutadapt with parameters --match-read-wildcards -u 16 -n 4 -a AGATCGGAAGAGCACACGTCTG -a AAAAAAAA -a GAACTCCAGTCAC -e 0.166666 --nextseq-trim 20 -m 18. The reads were then aligned to mouse rRNA (https://www.ncbi.nlm.nih.gov/nuccore/BK000964) using bowtie2 with --seedlen=23. Unaligned reads were aligned to GRCm38 release 102 reference genome using STAR with parameters  --sjdbOverhang 36 -outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. Deduplication of reads was performed using samtools and fumi_tools (https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools). Read distribution was calculated using read_distribution.py from RSeQC package, and metaplots were generated by RiboCode. Finally, featureCounts was used to detect exons in single-end forward stranded mode, and reads were summarized per gene.
Transcriptome RNASeq data was processed according to the recommendation of the manufacturer (Smart-Seq v4, Takara Bio USA) and the original RiboLite publication. Reads were trimmed with cutadapt in paired-end read mode with parameters: -j 4 --trim-n --match-read-wildcards -a CTGTCTCTTATACACATCT -a AAAAAAAAAAA -A CTGTCTCTTATACACATCT -A AAAAAAAAAAA --nextseq-trim 20 -m 10. Reads were then aligned using STAR to GRCm38 release 102 reference genome in paired-end read mode with parameters --sjdbOverhang 99. Finally, featureCounts was used to detect exons in paired-end unstranded mode, and reads were summarized per gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

molecule: other

organism: Mus musculus

source_name: bone marrow

growth_protocol: The MLL-AF9 leukemia cells express GFP under the control of the ubiquitin transporter.  Leukemic cells from a terminally ill mouse were harvested and expanded ex vivo in RPMI1640 medium (Lonza) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 U/ml penicillin, 100 μg/ml streptomycin, 2mM L-glutamine (all from Corning), 20 ng/ml recombinant mouse SCF (rmSCF), 10 ng/ml recombinant mouse interleukin 3 (rmIL-3) and 10 ng/ml rmIL-6 (all from R&D Systems).

extract_protocol:
Mice were euthanized at the point of maximum response of chemotherapy and femurs, tibias, pelvis and humeri were isolated and cleaned to remove muscle. Bones were then crushed using a pre-cooled mortar and pestle in ice-cold flow buffer (PBS containing 2% FBS), and the obtained BM cell suspension was passed through a 70 μm cell strainer. Red blood cells were removed by incubating cells for 5 minutes in ACK lysing buffer (Gibco) on ice, the remaining BM cells were washed and resuspended in ice-cold flow buffer. Viable cells (AML cells GFP+) were sorted on a BD FACSAria II (BD Biosciences) with the sample collector cooled to 4°C. After centrifugation, samples were lysed in 20 μl ice-cold lysis buffer (20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX, 1% Triton X-100; 25 U/ml Turbo DNase) for 10 min on ice. For mRNA 2 μl of the lysate was subjected to the Smart-seq2 protocol. Following addition to 300 μl lysis buffer to the lysate, it was clarified for 10 min at 20,000g at 4°C, then treated with RNase 1 Ambion, AM2295, 1 μl for up to 50k cells, 2 μl for up to 200k cells) and incubated at room temperature for 45 min with gentle mixing. The digested extracts were stopped by the addition of 10 μl SUPERaseIn and were overlaid onto a 700 μl sucrose cushion of 1 M sucrose in 20 mM Tris–HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX and 20 U/ml SUPERaseIn for 4 h at 260,000g, 4°C in MLA-150 rotor in Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed, and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris pH 7.5 and 1% SDS). RPFs were extracted from pellet buffer by using 1 ml Trizol and 200 μl chloroform. The aqueous phase was precipitated by adding 750 μl isopropanol and 20 μg glycogen. Precipitation was carried out at −20 °C overnight, and RPFs were then pelleted by centrifugation for 40 min at 12,000 g, 4 °C. RPF was resuspended in 6 μl nuclease-free water and mixed with 6 μl Gel Loading Buffer II. The 15% (wt/vol) polyacrylamide TBE-urea gel was pre-run for 30 min at 200 V. The RNA samples were denatured for 90 s at 80°C. RPFs were separated by electrophoresis for 65 min at 200 V. To minimize contamination, each sample was run in a separate gel and the electrophoresis was run without RNA or DNA markers. The region from 26 to 34 nt for RPFs was excised according to the light-blue loading dye and further determined on the basis of the relative position of RNA oligo markers to the loading dye on a separate and parallel gel. Extract RNA from the polyacrylamide gel slices by adding 400 μl RNA extraction buffer (300 mM sodium acetate pH 5.5, 1 mM EDTA and 0.25% SDS), snap-frozen at −80°C for 20 min and thawed at 37°C for two rounds and then kept overnight at room temperature with gentle mixing. The liquid was transferred to a clean tube, and 500 μl isopropanol and 20 μg glycogen were added and precipitated overnight. The RPF sample was pelleted by centrifugation for 40 min at 12,000 g, 4°C and resuspended in 6 μl nuclease-free water. The sample was then subjected to sequencing library preparation by D-Plex Small RNA-seq Kit and DNA library was purified using AMPure XP. Barcoded libraries were pooled and sequenced on the Illumina platform with 2x 100bp reads.
For mRNA 2 μl of the lysate (10%) was subjected to the Smart-seq2 protocol. The Ribo-lite/RPF sample was then subjected to sequencing library preparation by D-Plex Small RNA-seq Kit and DNA library was purified using AMPure XP.

treatment_protocol: Recipient male mice (age 8-10 weeks) were injected intravenously (retro-orbital) with 1 million leukemia cells in 200 μl PBS.  Mice were treated with 5+3 (cytarabine, 100 mg/kg, once daily for 5 days and doxorubicin, 3 mg/kg, once daily for the first 3 days) or vehicle (PBS) delivered via i.p. injection.

value: bone marrow

value: MLL-AF9 AML

value: Acute myeloid leukemia

value: BCAA-free plus 5+3


title: Col_m_3

description: Library name: Col_m-rep3

value: Col


title: K562 WT 48h hemin rep2

description:
PM_K562_WT2_48h_hemin_S17_L001
K562_CISTR.GENCODEv32.RPKM.genPos.consensus

value: WT

value: K562 WT cells treated with 50 µM hemin for 48 hours


title: Col_m_2

description: Library name: Col_m-rep2


title: K562 WT 48h hemin rep1

description:
PM_K562_WT1_48h_hemin_S16_L001
K562_CISTR.GENCODEv32.RPKM.genPos.consensus


title: Plk1as_3MB_rep1

description: Library name: Plk1as_3MB_rep1

value: hTERT RPE-1


title: Col_m_1

description: Library name: Col_m-rep1


title: Plk1as_DMSO_rep4

description: Library name: Plk1as_DMSO_rep4

value: Human epithelial cell line

value: 5 µM STLC + DMSO (0.5%)


title: Translatome BCAA-free plus 5+3 sgScramble AML cells biol rep5

description: Library name: RFP 19

value: sgScramble


title: tsk_3

description: Library name: tsk-rep3

value: leaves

value: mock


title: K562 CISTR KO rep2

description:
PM_K562_CISTRKO2_0h_hemin_S15_L001
K562_CISTR.GENCODEv32.RPKM.genPos.consensus

value: lymphoblast


title: K562 WT rep2

description:
PM_K562_WT2_0h_hemin_S13_L001
K562_CISTR.GENCODEv32.RPKM.genPos.consensus


title: Plk1as_DMSO_rep2

description: Library name: Plk1as_DMSO_rep2

value: hTERT RPE-1 Plk1-/- EGFP-Plk1as


title: Translatome BCAA-free plus 5+3 sgScramble AML cells biol rep3

description: Library name: RFP 17


title: K562 CISTR KO rep1

description:
PM_K562_CISTRKO1_0h_hemin_S14_L001
K562_CISTR.GENCODEv32.RPKM.genPos.consensus

value: [delta]CISTR


title: Translatome BCAA-free plus 5+3 sgScramble AML cells biol rep2

description: Library name: RFP 12


title: Plk1as_DMSO_rep3

description: Library name: Plk1as_DMSO_rep3


title: Translatome BCAA-free plus 5+3 sgScramble AML cells biol rep1

description: Library name: RFP 11


title: tsk_2

description: Library name: tsk-rep2

value: Columbia


title: tsk_1

description: Library name: tsk-rep1


title: Translatome AA vehicle sgOgfdo1 AML cells biol rep5

description: Library name: RFP 10

value: bone marrow

value: AA vehicle


title: K562 WT rep1

description:
PM_K562_WT1_0h_hemin_S12_L001
K562_CISTR.GENCODEv32.RPKM.genPos.consensus


title: Plk1as_DMSO_rep1

description: Library name: Plk1as_DMSO_rep1


title: XW_3

description: Library name: XW-rep3


title: Translatome AA vehicle sgOgfdo1 AML cells biol rep4

description: Library name: RFP 9

value: MLL-AF9 AML

value: Acute myeloid leukemia


title: RPMI 2650 CISTR KO CRISPR-Display CISTR overexpressed rep2

description:
PM_RPMI2650_CRISPRDisplay_CISTRundirected_CISTRKO_2_S55_L002
CISTRundirected.GENCODEv32.RPKM.genPos.consensus

source_name: RPMI 2650

value: RPMI 2650

value: nasal epithelial

value: transfected with CRISPR-Display machinery to overexpress CISTR without localization


title: Plk1as_3MB_rep2

description: Library name: Plk1as_3MB_rep2

value: hTERT RPE-1

value: 5 µM STLC + 10 µM 3MB-PP1


title: XW_2

description: Library name: XW-rep2


title: Translatome BCAA-free plus 5+3 sgOgfod1 AML cells biol rep4

description: Library name: RFP 22

value: BCAA-free plus 5+3


title: Translatome AA vehicle sgOgfdo1 AML cells biol rep3

description: Library name: RFP 8


title: XW_1

description: Library name: XW-rep1


title: RPMI 2650 CISTR KO CRISPR-Display CISTR overexpressed rep1

description:
PM_RPMI2650_CRISPRDisplay_CISTRundirected_CISTRKO_1_S49_L002
CISTRundirected.GENCODEv32.RPKM.genPos.consensus


title: RPMI 2650 CISTR KO CRISPR-Display CISTR to CISTR locus rep1

description:
PM_RPMI2650_CRISPRDisplay_CISTRtoCISTR_CISTRKO_1_S52_L002
CISTRtoCISTR.GENCODEv32.RPKM.genPos.consensus

value: transfected with CRISPR-Display machinery to recruit CISTR transcript to the CISTR locus


title: W_3

description: Library name: W-rep3

value: leaves


title: Translatome AA vehicle sgScramble AML cells biol rep5

description: Library name: RFP 5

value: sgScramble


title: Transcriptome AA vehicle sgOgfod1 AML cells biol rep2

description: Library name: RNA 7


title: Translatome AA vehicle sgScramble AML cells biol rep3

description: Library name: RFP 3


title: Endocervical 3D organoids_5days post_Chlamydia trachomatis_Infection_Replicate2 Patient-3 Ctr Infected

type: RNA

city: Würzburg

first: Cindrilla

last: Chumduri

address: Am Hubland

department: Chair of Microbiology, Biozentrum

country: Germany

institute: University of Wuerzburg

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data files were background corrected, quantile normalized, and further analyzed for differential gene expression using Rstudio (Rstudio. Inc.). Microarray data from three independent infection experiments were combined.

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Ecto- and Endocervical 3D organoids were grown in defined media using the protocol described in the accompanying manuscript (Materials and Methods)

extract_protocol: RNA was isolated from organoids resuspended in Trizol (Life Technologies) according to the manufacturer's protocol

treatment_protocol: Ecto- and endocervical 3D organoids were either uninfected or infected with Chlamydia trachomatis for 5days.

tag: tissue type

value: Endocervical Columnar

tag: patient number

tag: agent

value: chlamydia trachomatis

tag: cells culture type


title: RPMI 2650 CISTR CasRx rep3 lane2

description:
PM_RPMI2650_CISTRCasRx_3_S37_L002
RPMI2650.GENCODE.RPKM.genPos.consensus

value: WT

value: transfected with CasRx machinery and CISTR gRNA array for CISTR knockdown


title: W_2

description: Library name: W-rep2

value: Columbia

value: mock


title: W_1

description: Library name: W-rep1


title: RPMI 2650 CISTR CasRx rep2 lane2

description:
PM_RPMI2650_CISTRCasRx_2_S35_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: Translatome AA vehicle sgScramble AML cells biol rep2

description: Library name: RFP 2

value: bone marrow

value: MLL-AF9 AML

value: AA vehicle


title: RPMI 2650 CISTR CasRx rep3 lane1

description:
PM_RPMI2650_CISTRCasRx_3_S37_L001
RPMI2650.GENCODE.RPKM.genPos.consensus

value: RPMI 2650

value: nasal epithelial


title: X_3

description: Library name: X-rep3


title: CD8T cells, mCherry,tRBP

city: Shanghai

first: Yunzhu

last: Chen

address: 280 South Chong Qing Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The amplicons generated were analyzed on an Illumina NovaSeq 6000 (Illumina). The identified sgRNA sequences were aligned to the our library, where reads with any mismatches were excluded from analysis. The resulting read count table  was used as input for MAGeCK analysis (V.0.5.9.2)
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include sgRNAs and genes summary
Library strategy: CRISPR

source_name: Spleen

extract_protocol:
Genomic DNA was then extracted using the Blood and Cell Culture DNA Maxi Kit (Qiagen), and two rounds of PCR amplification were performed to amplify the sgRNAs.
Two rounds of PCR amplification were performed to amplify the sgRNAs and add Illumina adaptors, using NEBNext High-Fidelity 2× PCR Master Mix (New England BioLabs).

value: Spleen


title: X_2

description: Library name: X-rep2


title: RPMI 2650 CISTR CasRx rep2 lane1

description:
PM_RPMI2650_CISTRCasRx_2_S35_L001
RPMI2650.GENCODE.RPKM.genPos.consensus


title: CD8T cells, Input, R1400


title: Endocervical 3D organoids_5days post_Uninfected_Replicate2 Patient-3 Uninfected


title: X_1

description: Library name: X-rep1


title: RPMI 2650 CISTR KO CRISPR-Display CISTR to CISTR locus rep2

description:
PM_RPMI2650_CRISPRDisplay_CISTRtoCISTR_CISTRKO_2_S58_L002
CISTRtoCISTR.GENCODEv32.RPKM.genPos.consensus

value: [delta]CISTR


title: RPMI 2650 CISTR CasRx rep1 lane2

description:
PM_RPMI2650_CISTRCasRx_1_S33_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: CD8T cells, Input, tRBP


title: Cnpy1KO, replicate 1, scRNAseq

city: Albany

first: Paolo

middle: Emanuele

last: Forni

state: NY

address: 1400 Washington Avenue

department: Biology

institute: University at Albany

description:
Library name: Sample 1  - Cnpy1KO_P21_VNO
10x genomics

library_source: transcriptomic single cell

data_processing:
scRNA-Seq:
Our lab used cellranger count (version4) to perform alignment, filtering, barcode counting, and UMI counting on the fastq files of 6 separate libraries.
We used filtered processed files as input and Seurat 4.3.0 package in R studio to do quality control and downstream cell clustering analysis. Cells with mitochondrial read rate >5% and expressed < 200 genes were  filtered out from our data set.
Assembly: mm10
Supplementary files format and content: tsv and mtx files containing cell barcodes and gene count matrix

source_name: Whole Postnatal VNO

extract_protocol:
2 Cnpy1 KO VNOs that were harvested at 21 days postnatal were isolated and dissociated into single-cell suspension using neural isolation enzyme/papain (NIE/Papain in Neurobasal Medium with 0.5mg/mL Collagenase A, 1.5mM L-cysteine and 100U/mL DNAse I) incubated at 37ºC. The dissociated cells were then washed with HBSS and reconstituted in cell freezing medium (90% FBS, 10% DMSO). Cells were frozen from room temperature to -80ºC at a -1°C/min freeze rate. The single cell suspension was sent to the Center of Functional Genomics (CFG) , generating datasets and high-throughput single-cell gene expression profiling using the 10x Genomics Chromium Platform.
Single cell library preparation and sequencing were conducted by the Center of Functional Genomics (CFG) (https://www.albany.edu/genomics/ngs.html, Albany, NY) and Singulomics Corporation (https://singulomics.com/, Bronx, NY). Cryopreserved, viable single cell suspensions were thawed, washed, resuspended in cell culture media with 0.04% BSA, and counted. Viable cell suspensions were then loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. We targeted 10,000 cells to be captured per sample for a total of 5 samples. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scentific, Wilmington, DE) and reverse transcription was performed in each GEM (GEM-RT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). Amplified full-length cDNAs from poly-adenylated mRNA were then used to generate 3ʹ Gene Expression library (Chromium Next GEM 3’ Single Cell Reagent kits v3.1, dual index), following the manufacturer’s instructions (10x Genomics, Pleasanton, CA). Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA).

value: Whole Postnatal VNO

value: Postnatal day 21


title: Endocervical 3D organoids_5days post_Chlamydia trachomatis_Infection_Replicate2 Patient-2 Ctr Infected


title: Endocervical 3D organoids_5days post_Uninfected_Replicate1 Patient-3 Uninfected

source_name: Endocervical 3D organoids_5days post_Uninfected_Replicate2


title: Endocervical 3D organoids_5days post_Chlamydia trachomatis_Infection_Replicate1 Patient-3 Ctr Infected

source_name: Endocervical 3D organoids_5days post_Chlamydia trachomatis_Infection_Replicate2


title: Endocervical 3D organoids_5days post_Uninfected_Replicate1 Patient-2 Uninfected


title: CD8T cells, mCherry, R1400


title: RPMI 2650 CISTR CasRx rep1 lane1

description:
PM_RPMI2650_CISTRCasRx_1_S33_L001
RPMI2650.GENCODE.RPKM.genPos.consensus


title: Endocervical 3D organoids_5days post_Chlamydia trachomatis_Infection_Replicate1 Patient-2 Ctr Infected


title: NLNN7

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

country: France

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR v.2.5.3a
Quantification : Gene Expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 102 annotations.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

molecule: polyA RNA

source_name: embryonic stem cells

growth_protocol: Embryonic Stem Cells were grown on 0.1% gelatinized (Sigma-Aldrich, Cat# G1890) tissue-culture plates in DMEM (4.5 g/L glucose) with GlutaMAX-I supplemented with ES-tested 15% foetal calf serum (FCS, ThermoFisher Scientific, Cat# 10270-106), 0.1% β-mercaptoethanol (ThermoFisher Scientific, Cat# 31350-010), 100 U/ml penicillin, 100 μg/ml streptomycin (ThermoFisher Scientific, Cat# 15140-122), 0.1 mM non-essential amino acids (ThermoFisher Scientific, Cat# 11140-035), and 1500 U/ml leukaemia inhibitory factor (produced in-house). 3 μM CHIR99021 (Axon Medchem, Cat# 1386) and 1 μM PD0325901 (Axon Medchem, Cat# 1408) (2i) were added freshly to the medium. ESC numbers were assessed using a Countess II Automated Cell Counter (Invitrogen). Cells were tripsinized and 1*106 cells were reseeded in fresh medium 5h before collection.

extract_protocol:
P3153
Total RNA extraction was performed using TRI Reagent® (Molecular Research Center Inc., Cat# TR 188), following the manufacturer's instructions. DNase I treatment was performed to prevent genomic DNA contamination using the TURBO DNA-free™ Kit (ThermoFisher Scientific, Cat# AM1907) manufacturer's instructions.
P3153, P3161 : RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold and IDT for Illumina - TruSeq RNA UD Indexes (Illumina, San Diego, USA), according to manufacturer's instructions with minor modifications. Following ribodepletion, RNAs were fragmented at 94oC for 2minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: Auxin (IAA, 3-Indoleacetic acid, Sigma-Aldrich I2886) was used at 500 μM for 24h

value: embryonic stem cells


title: AR2-4

city: Guangzhou

first: Xiang

last: Li

state: Guangdong

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Heart

extract_protocol:
Snap frozen heart tissues were ground to powder under liquid nitrogen. Pulverized samples were used for total RNA extraction using TRIzol reagent (Thermo Fisher Scientific, USA), and RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Heart

tag: strain


title: Col_2

description: Library name: Col-rep2

value: leaves

value: Col


title: RPMI 2650 CasRx control rep3 lane2

description:
PM_RPMI2650_ctrlCasRx_3_S24_L002
RPMI2650.GENCODE.RPKM.genPos.consensus

value: WT

value: transfected with CasRx machinery and no sgRNAs


title: AR2-3


title: Endocervical 3D organoids_5days post_Uninfected_Replicate2 Patient-2 Uninfected

value: Endocervical Columnar


title: NLNN6


title: Col_1

description: Library name: Col-rep1

value: Columbia

value: mock


title: Col-1, event 3, rep 3

city: Urbana

first: Gabriel

last: Beuchat

email: beuchat2@illinois.edu, beuchag@uw.edu

state: IL

address: 1201 W Gregory Dr

department: Plant Biology

institute: University of Illinois at Urbana Champaign

data_processing:
Trimmomatic
Aligned to Araport11 gene set with STAR
BAM to counts with featcounts
DESeq2 with adj. pval .01 and log2FC 1 cutoffs
Counts converted to TPM data for heatmaps
Assembly: Araport11
Supplementary files format and content: raw_counts.txt is a tab delimited count data output from featurecounts with the library name as the column and the gene as the row.
Supplementary files format and content: TPM_Values.txt is a tab delimited TPM table with genes as row names and the library as the column names. Outliers were removed from the TPM file but are present in the raw files and in the raw counts.

source_name: Leaf

growth_protocol: controlled condition with a temperature of 22°C, the light intensity of 100~150 µmol m-2 s-1, and a 16-h light / 8-h dark photoperiod.

extract_protocol:
All Arabidopsis leaf samples were collected at 21 days after germination (DPG) unless otherwise specified.
cDNA construction from poly-T primers

treatment_protocol: Transgenic or not transgenic

value: Leaf

tag: line or_event

value: Overexpressing PPT1


title: RPMI 2650 CasRx control rep3 lane1

description:
PM_RPMI2650_ctrlCasRx_3_S24_L001
RPMI2650.GENCODE.RPKM.genPos.consensus

value: RPMI 2650


title: RPMI 2650 CasRx control rep2 lane2

description:
PM_RPMI2650_ctrlCasRx_2_S22_L002
RPMI2650.GENCODE.RPKM.genPos.consensus

value: nasal epithelial


title: NLNN5


title: Col-1, event 3, rep 2


title: AR2-2


title: AR2-1


title: RPMI 2650 CasRx control rep2 lane1

description:
PM_RPMI2650_ctrlCasRx_2_S22_L001
RPMI2650.GENCODE.RPKM.genPos.consensus


title: NLNN2


title: NLNN4


title: oocytes_ko_H3K27me3_9

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

institute: Institut Curie

description:
D655T139
H3K27me3 Cut&Run
D655T139

data_processing:
The mm10 fasta file was masked with CAST/EiJ strain-specific SNPs using SNPsplit. The N-masked mm10 fasta was then concatenated to that of Drosophila dm6 and indexed with Bowtie2 bowtie2-build.
Adapters and low-quality bases were removed with TrimGalore and trimmed reads were then mapped against the N-masked reference genome with Bowtie2.
PCR duplicates were discarded using Picard tools and reads overlapping the mouse genome were assigned to either the maternal or the paternal genomes using SNPsplit.
Bam files were merged according to genotype and, when available, sex using SAMtools merge.
Parental-specific bigwig files were generated using Deeptools bamCoverage. A size factor calculated on Drosophila spike-in reads was passed onto bamCoverage as ‘–scaleFactor’ for both parental genomes.
Assembly: mm10
Supplementary files format and content: Bigwig files for the visual representation of the genome-wide distribution of Cut&Run-Seq reads.
Library strategy: CUT&Run

source_name: oocytes

extract_protocol:
Cut&Run-Seq was done as in Hainer et al. 2019 (PMID: 30955888; DOI: 10.1016/j.cell.2019.03.014) with some modifications.
Library construction was performed using the Accel-NGS 2S Unique Dual Indexing DNA library kit (Swift Biosciences), following manufacturer's instructions.
Low input Cut&Run-Seq

value: oocytes

value: Ezhip matKO

tag: Sex

value: F


title: Col-1, event 3, rep 1


title: RPMI 2650 CasRx control rep1 lane2

description:
PM_RPMI2650_ctrlCasRx_1_S20_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: Col_3

description: Library name: Col-rep3


title: NLNN1

extract_protocol:
P3161
Total RNA extraction was performed using TRI Reagent® (Molecular Research Center Inc., Cat# TR 188), following the manufacturer's instructions. DNase I treatment was performed to prevent genomic DNA contamination using the TURBO DNA-free™ Kit (ThermoFisher Scientific, Cat# AM1907) manufacturer's instructions.
P3153, P3161 : RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold and IDT for Illumina - TruSeq RNA UD Indexes (Illumina, San Diego, USA), according to manufacturer's instructions with minor modifications. Following ribodepletion, RNAs were fragmented at 94oC for 2minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).


title: oocytes_ko_H3K27me3_8

description:
D655T135
H3K27me3 Cut&Run
D655T135


title: RPMI 2650 CasRx control rep1 lane1

description:
PM_RPMI2650_ctrlCasRx_1_S20_L001
RPMI2650.GENCODE.RPKM.genPos.consensus


title: Col-1, event 2, rep 3


title: Mouse liver, SFO_6

city: Athens

first: Chad

middle: M.

last: Paton

state: GA

address: 100 Cedar St #211

institute: University of Georgia

data_processing:
Single-read sequencing was performed on Illumina (Illumina, San Diego, CA) NexSeq 2000.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic with following settings: adapters/TruSeq3-SE.fa:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:30.
Trimmed, filtered reads were then mapped against MM39 using the STAR aligner, ver. 2.7.1a.
HTSeq, ver. 0.9.1 (33) was used to extract raw count data from each BAM file and output files containing gene-to-count information for each sample were concatenated to generate a raw count matrix that was manually filtered to remove rows containing zero counts or rows whose summation of counts was less than 50.
Count matrix normalization, DESeq2
Assembly: mm39
Supplementary files format and content: Excel sheet including DESeq values for each sample

source_name: Liver

growth_protocol: Mice were fed ether a chow diet, a cottonseed oil-enriched diet (CSO), an olive oil-enriched diet (OO), or a safflower oil-enriched diet for 6 weeks.

extract_protocol:
RNA was isolated directly from livers using TRIreagent and total RNA (RIN value >7.0) was submitted.
RNA-Seq libraries were synthesized using a QuantSeq 3’ mRNA-Seq library kit following manufacturer's protocols.

value: Liver

value: Male

tag: treatment (diet)

value: Safflower oil (SFO)

tag: time

value: 6 weeks


title: RPMI 2650 CISTRintron KO rep2

description:
PM_RPMI2650_CISTRintronKO_clone2_S21_L001
CISTRintron.GENCODEv32.RPKM.genPos.consensus

value: [delta]CISTRintron


title: RPMI 2650 CISTRintron KO rep1

description:
PM_RPMI2650_CISTRintronKO_clone1_S20_L001
CISTRintron.GENCODEv32.RPKM.genPos.consensus


title: Col-1, event 2, rep 1

value: WT


title: Mouse liver, SFO_5


title: oocytes_ko_H3K27me3_5

description:
D405C14
H3K27me3 Cut&Run
D405C14


title: oocytes_ko_H3K27me3_6

description:
D655T109
H3K27me3 Cut&Run
D655T109


title: Col-1, event 1, rep 3


title: Col-1, event 1, rep 2


title: RPMI 2650 CISTR KO rep3lane1

description:
PM_RPMI2650_CISTRKO_3_S3_L001
RPMI2650.GENCODE.RPKM.genPos.consensus

value: [delta]CISTR


title: RPMI 2650 CISTR KO rep2lane2

description:
PM_RPMI2650_CISTRKO_2_S2_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: Mouse liver, SFO_3


title: oocytes_ko_H3K27me3_7

description:
D655T129
H3K27me3 Cut&Run
D655T129


title: Col-1, event 1, rep 1


title: oocytes_ko_H3K27me3_2

description:
D405C09
H3K27me3 Cut&Run
D405C09


title: Mouse liver, SFO_1


title: RPMI 2650 CISTR KO rep2lane1

description:
PM_RPMI2650_CISTRKO_2_S2_L001
RPMI2650.GENCODE.RPKM.genPos.consensus


title: oocytes_ko_H3K27me3_4

description:
D405C12
H3K27me3 Cut&Run
D405C12


title: Mouse liver, OO_6

value: Olive oil (OO)


title: sweet11;12;13, event 5, rep 3


title: Mouse liver, SFO_4


title: oocytes_ko_H3K27me3_1

description:
D405C06
H3K27me3 Cut&Run
D405C06


title: Col-1, event 2, rep 2


title: RPMI 2650 CISTR KO rep1 lane2

description:
PM_RPMI2650_CISTRKO_1_S1_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: oocytes_wt_H3K27me3_9

description:
D655T138
H3K27me3 Cut&Run
D655T138


title: sweet11;12;13, event 5, rep 1


title: RPMI 2650 CISTR KO rep3lane2

description:
PM_RPMI2650_CISTRKO_3_S3_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: RPMI 2650 CISTR KO rep1 lane1

description:
PM_RPMI2650_CISTRKO_1_S1_L001
RPMI2650.GENCODE.RPKM.genPos.consensus


title: Mouse liver, SFO_2


title: sweet11;12;13, event 2, rep 3


title: oocytes_ko_H3K27me3_3

description:
D405C10
H3K27me3 Cut&Run
D405C10


title: Mouse liver, OO_3


title: oocytes_wt_H3K27me3_7

description:
D655T114
H3K27me3 Cut&Run
D655T114


title: Mouse liver, OO_2


title: sweet11;12;13, event 2, rep 1


title: Mouse liver, OO_1


title: oocytes_wt_H3K27me3_5

description:
D405C11
H3K27me3 Cut&Run
D405C11


title: RPMI 2650 WT rep2 lane1

description:
PM_RPMI2650_WT_2_S5_L001
RPMI2650.GENCODE.RPKM.genPos.consensus


title: oocytes_wt_H3K27me3_6

description:
D405C15
H3K27me3 Cut&Run
D405C15


title: RPMI 2650 WT rep2 lane2

description:
PM_RPMI2650_WT_2_S5_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: sweet11;12;13, event 5, rep 2


title: sweet11;12;13, event 1, rep 3


title: Mouse liver, CSO_5

value: Cottonseed oil (CSO)


title: RPMI 2650 WT rep1 lane2

description:
PM_RPMI2650_WT_1_S4_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: oocytes_wt_H3K27me3_4

description:
D405C08
H3K27me3 Cut&Run
D405C08


title: oocytes_wt_H3K27me3_3

description:
D405C07
H3K27me3 Cut&Run
D405C07


title: Mouse liver, CSO_6


title: Mouse liver, OO_5


title: sweet11;12;13, event 1, rep 2


title: sweet11;12;13, event 1, rep 1


title: RPMI 2650 WT rep3 lane2

description:
PM_RPMI2650_WT_3_S6_L002
RPMI2650.GENCODE.RPKM.genPos.consensus


title: RPMI 2650 WT rep1 lane1

description:
PM_RPMI2650_WT_1_S4_L001
RPMI2650.GENCODE.RPKM.genPos.consensus


title: Mouse liver, CSO_4


title: oocytes_wt_H3K27me3_8

description:
D655T119
H3K27me3 Cut&Run
D655T119


title: Mouse liver, OO_4


title: C-28/I2 CISTR KO rep3lane2

description:
PM_C28I2_CISTRKO_3_S15_L002
C28I2.GENCODE.RPKM.genPos.consensus

value: chondrocyte


title: Col-1, background, rep 3

value: Leaf

value: Control


title: Mouse liver, CSO_3


title: oocytes_wt_H3K27me3_1

description:
D405C02
H3K27me3 Cut&Run
D405C02


title: RPMI 2650 WT rep3 lane1

description:
PM_RPMI2650_WT_3_S6_L001
RPMI2650.GENCODE.RPKM.genPos.consensus

value: RPMI 2650


title: sweet11;12;13, event 2, rep 2

value: Overexpressing PPT1


title: C-28/I2 CISTR KO rep3lane1

description:
PM_C28I2_CISTRKO_3_S15_L001
C28I2.GENCODE.RPKM.genPos.consensus


title: Col-1, background, rep 2


title: 2C_ko_H3K27me3_10

description:
D939C24
H3K27me3 Cut&Run
D939C24


title: Mouse liver, CSO_2


title: Col-1, background, rep 1


title: C-28/I2 CISTR KO rep2lane1

description:
PM_C28I2_CISTRKO_2_S14_L001
C28I2.GENCODE.RPKM.genPos.consensus


title: sweet11;12;13, background, rep 3


title: 2C_ko_H3K27me3_8

description:
D939C13
H3K27me3 Cut&Run
D939C13


title: 2C_ko_H3K27me3_9

description:
D939C17
H3K27me3 Cut&Run
D939C17


title: sweet11;12;13, background, rep 2


title: C-28/I2 CISTR KO rep1 lane2

description:
PM_C28I2_CISTRKO_1_S13_L002
C28I2.GENCODE.RPKM.genPos.consensus


title: Mouse liver, chow_6

value: Chow


title: Mouse liver, chow_5


title: 2C_ko_H3K27me3_7

description:
D939C10
H3K27me3 Cut&Run
D939C10

value: Ezhip matKO


title: sweet11;12;13, background, rep 1


title: C-28/I2 CISTR KO rep1 lane1

description:
PM_C28I2_CISTRKO_1_S13_L001
C28I2.GENCODE.RPKM.genPos.consensus


title: oocytes_wt_H3K27me3_2

description:
D405C05
H3K27me3 Cut&Run
D405C05

value: oocytes

value: F


title: Mouse liver, chow_4

value: Liver

value: Male


title: Mouse liver, chow_3

value: 6 weeks


title: 2C_ko_H3K27me3_6

description:
D939C05
H3K27me3 Cut&Run
D939C05


title: C-28/I2 WT rep3 lane2

description:
PM_C28I2_WT_3_S18_L002
C28I2.GENCODE.RPKM.genPos.consensus


title: 2C_ko_H3K27me3_5

description:
D939C01
H3K27me3 Cut&Run
D939C01


title: C-28/I2 WT rep3 lane1

description:
PM_C28I2_WT_3_S18_L001
C28I2.GENCODE.RPKM.genPos.consensus


title: H9_DMSO_BR2_IPFMRP

city: Syracuse

first: Wenyi

last: Feng

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

description:
Library name: H9-DMSO-FMRP-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#

data_processing:
alignment by Bowtie2
bamCompare by deepTools to normalize IP to IC (input control) signals
Assembly: hg19
Supplementary files format and content: bw

growth_protocol: HEK293T cells were grown in Dulbecco’s modified Eagle’s medium (Gibco) supplemented with 10% FBS, 1X GlutaMAX, 100 IU/ml penicillin and 100 microgram/ml streptomycin, 1 mM sodium pyruvate (Corning), 10 mM Hepes buffer (Corning) and 1X minimum essential medium nonessential amino acids (Corning) and grown at 30 degree celsius with 5% CO2.

extract_protocol:
Cells were fixed and harvested using the truChIP chromatin shearing kit (Covaris), and IP was conducted according to Richard Myers lab ChIP-seq protocol. Briefly, cells were first washed with room temperature 1X PBS. Then, 5 ml fixing buffer A was added, followed by addition of formaldehyde (methanol-free) to 1%, and then incubated for 10 m at room temperature. To stop the reaction, 300 μl of quenching buffer was added and incubated for 5 m. Cells were collected by scraping (one confluent 150 mm plate per reaction), flash frozen in liquid nitrogen, and stored at −70 °C. Cells were thawed on ice with 1 ml of 1× lysis buffer B and Halt protease inhibitor cocktail (Thermo Fisher Scientific) and incubated with agitation for 10 m. Nuclei were prepared by centrifuging the lysate at 1700g for 5 m. The nuclear pellet was washed with 1× wash buffer C and then once with shearing buffer D3 with Halt protease inhibitor cocktail (Thermo Fisher Scientific). Nuclear pellet was then resuspended in 900 μl shearing buffer D3 and sonicated in Covaris M220 ultrasonicator using the protocol ‘ChIP_10%df_10 min’ (75 W peak power, cycle per burst: 200, duty factor: 10, time: 600 s). The sonicated mixture was centrifuged at 13,500 rpm for 15 m at 4 °C. The supernatant was adjusted to 150 mM NaCl, 10 mM Tris–HCl pH 7.5, 1% NP-40, 0.5% sodium deoxycholate. Approximately 5 to 11% of this nuclear preparation was set aside as “input”. The rest was used for immunoprecipitation. Both aliquots were snap frozen in liquid nitrogen and stored at −70 °C.  A total of 300 μl M280 Dyna beads sheep anti-rabbit IgG (Life technologies) was added to 1 ml freshly prepared PBS with 5 mg/ml BSA (PBS/BSA) and Halt protease inhibitor cocktail (1X). The magnetic beads were washed 3 times in PBS/BSA. Twelve micrograms of monoclonal anti-DHX9 (Bethyl Laboratories) or 5 μg of monoclonal anti-FMRP (Biolegend) was mixed with the beads in 1 ml PBS/BSA and incubated overnight at 4 °C with agitation. The antibody-conjugated beads were washed three times with PBS/BSA, and the nuclear preparation was thawed and added to the beads, followed by incubation at 4 °C with rotation overnight. The beads were washed 5 times with cold LiCl wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate), and once with TE buffer (10 mM Tris-HCl pH 7.5, 0.1 mM EDTA). Two hundred microliters of IP elution buffer (1% SDS, 0.1 M NaHCO3) was added to the beads, mixed, and incubated at 65 °C for 2 h with vortex every 30 m. The “input” was thawed and together with the supernatant from the IP sample was reverse-cross-linked at 65 °C overnight. Samples were then treated with 60 μg of proteinase K for 1 h at 55 °C. DNA was purified using Qiagen PCR purification kit. Approx. 20 million cells were used for each ChIP reaction. Cells were cross-linked by 0.5% formaldehyde, 10 mM NaCl, 0.1 mM EDTA, 0.5 mM EGTA, 5 mM Hepes buffer, pH 8.0 instead of 1% formaldehyde. Cell lysis was performed with 1X lysis buffer B as above, except the lysate was passaged through a 21 g needle 6 times. Additionally, 0.5% SDS and 1% NP-40 was added to the nuclear extract, followed by passaging through a 21 g needle 6 times, before sonication. Sonication was performed with the same protocol above except with 20 m instead of 10 m. The supernatant from the nuclear extract was adjusted to contain 150 mM NaCl before IP. Both input control and IP samples were used for standard Illumina TruSeq library construction, followed by multiplexed sequencing on a HiSeq 2500 platform.
Both input control and IP samples were used for standard Illumina TruSeq library construction, followed by multiplexed sequencing on a HiSeq 2500 platform.

treatment_protocol: Cells were grown to ~70% confluency before chemical treatment.  Equal volumes of APH was added at 0.6 μM and 1 μM final concentration from 5000x stocks, respectively.  Equal volume of DMSO (the vehicle for APH), in addition to no treatment, served as controls.  Cells were harvested after 24 h incubation.

value: DMSO

tag: batch


title: H9_NoTreatment_BR2_IPFMRP

description:
Library name: H9-NT-FMRP-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#

value: no treatment


title: Mouse liver, CSO_1

value: WT


title: C-28/I2 CISTR KO rep2lane2

description:
PM_C28I2_CISTRKO_2_S14_L002
C28I2.GENCODE.RPKM.genPos.consensus

value: [delta]CISTR


title: 2C_ko_H3K27me3_4

description:
D655T152
H3K27me3 Cut&Run
D655T152


title: H9_0.6uM_BR2_IPFMRP

description:
Library name: H9-6-FMRP-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#

value: 0.6 uM APH


title: C-28/I2 WT rep2 lane2

description:
PM_C28I2_WT_2_S17_L002
C28I2.GENCODE.RPKM.genPos.consensus

value: chondrocyte


title: Mouse liver, chow_1


title: 2C_ko_H3K27me3_3

description:
D655T148
H3K27me3 Cut&Run
D655T148


title: Mouse liver, chow_2


title: H9_1uM_BR2_IPFMRP

description:
Library name: H9-1-FMRP-BR2
Strain-DrugTreatme1-ChIPtarget-Replicate#

value: 1 uM APH


title: C-28/I2 WT rep2 lane1

description:
PM_C28I2_WT_2_S17_L001
C28I2.GENCODE.RPKM.genPos.consensus


title: IFNg_3

city: Alessandria

first: Valentina

last: Audrito

address: Viale Teresa Michel 11

department: DIST

country: Italy

institute: University of Eastern Piedmont

description:
Library name: IFNg_3
Colum name in gene_fpkm_all samples.txt

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Workflow of sequencing data filtration: Remove reads with adapter contamination, Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.(Yan et al, 2011).
Perform alignments with HISAT2 ((Mortazavi et al., 2008) to the reference.
Reads Distribution in Reference Genome: Mapped regions can be classified as exons, introns, or intergenic regions.
Assembly: hg38
Supplementary files format and content: Colum name in gene_fpkm_all samples.xls

growth_protocol: Complete medium (DMEM + 10%FBS) with antibiotics

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA (Macherey-Nagel)
RNA librearies for RNA-seq were prepared through polyA capture and reverse transcription into cDNA, followed by quality assessment.  150 bp paired-end sequencing using Illumina PE150 technology and Illumina NovaSeq X Plus system (Novogene service).

treatment_protocol: 501MEL were treated or not for 24h with IFNg 100ng/ml (Peprotech) alone or in combination with NAMPT inhibitor FK866 25nM (Sigma)

value: melanoma cell line

value: 24h IFNg 100ng/ml


title: C-28/I2 WT rep1 lane2

description:
PM_C28I2_WT_1_S16_L002
C28I2.GENCODE.RPKM.genPos.consensus


title: IFNgFK866_3

description:
Library name: IFNgFK866_3
Colum name in gene_fpkm_all samples.txt

value: 24h IFNg 100ng/ml + FK866 25nM


title: 2C_ko_H3K27me3_2

description:
D655T146
H3K27me3 Cut&Run
D655T146


title: H9_NoTreatment_BR1_IPDHX9

description:
Library name: H9-NT-DHX9-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: 2C_ko_H3K27me3_1

description:
D655T134
H3K27me3 Cut&Run
D655T134


title: H9_DMSO_BR1_IPDHX9

description:
Library name: H9-DMSO-DHX9-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: UN_3

description:
Library name: UN_3
Colum name in gene_fpkm_all samples.txt

value: untreated


title: 2C_wt_H3K27me3_9

description:
D939C31
H3K27me3 Cut&Run
D939C31


title: IFNgFK866_2

description:
Library name: IFNgFK866_2
Colum name in gene_fpkm_all samples.txt


title: U87 cells, IDH1mt C269S, rep3

city: Charlestown

first: Lu

last: Hu

state: Massachusetts

address: Building 149, 13th St

department: Dermatology

institute: Massachusetts General Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38/hg38
Supplementary files format and content: excel file includes raw counts for each sample
Supplementary files format and content: excel file includes fpkm value for each sample

source_name: Brain

growth_protocol: U87 cells were maintained in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 100 units/mL penicillin, and 100 µg/mL streptomycin in the presence of 5% CO2 at 37°C .

extract_protocol:
Total RNA from U87 cells was isolated with RNeasy Mini Kit (QIAGEN).
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD ( Sacramento, CA)

treatment_protocol: U87 cells stably overexpressed PCDH (Vector control), IDH1mt, IDH1mt C269S, respectively.

value: Brain

value: glioblastoma cells

value: overexpressing IDH1mt C269S


title: U87 cells, IDH1mt C269S, rep2


title: 2C_wt_H3K27me3_8

description:
D939C28
H3K27me3 Cut&Run
D939C28


title: H9_1uM_BR1_IPDHX9

description:
Library name: H9-1-DHX9-BR1
Strain-DrugTreatme1-ChIPtarget-Replicate#


title: H9_NoTreatment_BR2_INPUT

description:
Library name: H9-NT-W-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#


title: U87 cells, IDH1mt C269S, rep1


title: 2C_wt_H3K27me3_7

description:
D939C16
H3K27me3 Cut&Run
D939C16


title: UN_2

description:
Library name: UN_2
Colum name in gene_fpkm_all samples.txt


title: H9_NoTreatment_BR1_INPUT

description:
Library name: H9-NT-W-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: 2C_wt_H3K27me3_6

description:
D939C12
H3K27me3 Cut&Run
D939C12


title: U87 cells, IDH1mt, rep3

value: overexpressing IDH1mt


title: IFNgFK866_1

description:
Library name: IFNgFK866_1
Colum name in gene_fpkm_all samples.txt


title: 2C_wt_H3K27me3_5

description:
D939C09
H3K27me3 Cut&Run
D939C09


title: H9_DMSO_BR2_INPUT

description:
Library name: H9-DMSO-W-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#


title: U87 cells, IDH1mt, rep2


title: C-28/I2 WT rep1 lane1

description:
PM_C28I2_WT_1_S16_L001
C28I2.GENCODE.RPKM.genPos.consensus


title: IFNg_1

description:
Library name: IFNg_1
Colum name in gene_fpkm_all samples.txt


title: 2C_wt_H3K27me3_4

description:
D939C04
H3K27me3 Cut&Run
D939C04


title: 2C_wt_H3K27me3_3

description:
D655T150
H3K27me3 Cut&Run
D655T150


title: H9_0.6uM_BR1_IPDHX9

description:
Library name: H9-6-DHX9-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: U87 cells, PCDH, rep3

value: overexpressing PCDH (vector control)


title: H9_DMSO_BR1_INPUT

description:
Library name: H9-DMSO-W-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: UN_1

description:
Library name: UN_1
Colum name in gene_fpkm_all samples.txt


title: A2780 cells, A3B knockdown, Olaparib  treated, replicate 3

city: LA JOLLA

first: QINGFEI

last: JIANG

state: CA

address: 2880 TORREY PINES SCENIC DR

institute: UNIVERSITY OF CALIFORNIA SAN DIEGO

description: Library name: A2780 3D_shA3B_Olaparib_3

data_processing:
Raw counts were generated from BAM files together with the provided GTF file in R (version 4.3.1) using FeatureCount from the Rsubread package (version 2.16.1), with the pipeline set to unstranded and paired end reads.
Raw counts were normalized to TPM in R (version 4.3.1).
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
Supplementary files format and content: tab-delimited text file contains TPM values for each sample

source_name: Ovary

growth_protocol: A2780  human cell lines were cultured in 37oC in RPMI 1640 supplemented with 10% FBS, 2 mM L-glutamine and 1X penicillin-streptomycin.

extract_protocol:
RNA extraction was performed using RNeasy mini extraction kits (QIAGEN) following the manufacturer’s protocol.  RNA-sequencing was performed using 100 ng of RNA.
Performed on Novogene on NovaSeq X Plus sequencing system with paired-end 150 reads.

treatment_protocol: 3D tumorspheres were treated with DMSO vehicle and Olaparib (50 nM) for 3 days

value: Ovary

value: A2780, Ovarian Cancer

value: APOBEC3B knockdown

value: Olaparib


title: U87 cells, IDH1mt, rep1


title: H9_0.6uM_BR2_INPUT

description:
Library name: H9-6-W-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#


title: U87 cells, PCDH, rep2


title: 2C_wt_H3K27me3_2

description:
D655T137
H3K27me3 Cut&Run
D655T137

value: WT


title: IFNg_2

description:
Library name: IFNg_2
Colum name in gene_fpkm_all samples.txt


title: 2C_wt_H3K27me3_1

description:
D655T133
H3K27me3 Cut&Run
D655T133


title: A2780 cells, A3B knockdown, Olaparib  treated, replicate 2

description: Library name: A2780 3D_shA3B_Olaparib_2


title: H9_0.6uM_BR1_INPUT

description:
Library name: H9-6-W-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#

value: 0.6 uM APH


title: H9_1uM_BR2_INPUT

description:
Library name: H9-1-W-BR2
Strain-DrugTreatme1-ChIPtarget-Replicate#


title: U87 cells, PCDH, rep1


title: H9_1uM_BR1_INPUT

description:
Library name: H9-1-W-BR1
Strain-DrugTreatme1-ChIPtarget-Replicate#


title: A2780 cells, A3B knockdown, Olaparib  treated, replicate 1

description: Library name: A2780 3D_shA3B_Olaparib_1


title: blastocyst_ko_m_H3K27me3_8

description:
D655T128
H3K27me3 Cut&Run
D655T128

source_name: blastocyst

value: blastocyst

value: Ezhip matKO

value: M


title: PBMCs patient single_indolent_4, indolent stage T-PLL

city: Koeln

first: Linus

last: Wahnschaffe

address: Kerpener Str. 62

department: Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD)

institute: University hospital of Cologne

description: demultiplexed

data_processing:
Sequencing with 29+89bp read length
Demultiplexing, alignment, filtering, and counting, using the 10x Genomics Cell Ranger 6.1.2 pipeline at default parameters.
Assembly: GRCh38-2020-A reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
After sampling, peripheral blood mononuclear cells (PBMCs) were isolated via density gradient centrifugation (Histopaque, Sigma-Aldrich). Cryo-preserved PBMCs were transferred to the Cologne Center for Genomics (CCG, Cologne) and CeMM-Biomedical Sequencing Facility (BSF, Vienna) for sequencing. Removal of dead cells was accomplished using a Dead Cell Removal Kit (Miltenyi Biotec) or by FACS sorting of DAPI-negative cells.
Single-cell suspensions were processed with the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics) with dual indices according to the manufacturer’s instructions, using either one reaction per sample or multiplexing two to three samples with the Cell Multiplexing technology option. In short, cells and the appropriate master mix were loaded on a Chromium Next GEM Chip G and processed on the Chromium Controller to generate Gel Bead-In-Emulsions (GEMs). After the creation of barcoded full-length cDNA by incubation with cell lysate, primers, and a reverse transcription master mix, GEMs were broken, and the pooled fractions were recovered. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post-GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon. Library construction was performed, including end repair, A-tailing, adaptor ligation, and PCR. The final libraries were quantified (Qubit), pooled, and the pool was quantified using the Peqlab KAPA Library Quantification kit and the Applied Biosystems 7900HT Sequence Detection System.

tag: individual

value: patient single_indolent_4

value: peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

tag: disease

value: T-PLL

tag: disease stage

value: indolent stage T-PLL

tag: number of cells detected by cellranger


title: A2780 cells, A3B knockdown, DMSO treated, replicate 3

description: Library name: A2780 3D_shA3B_DMSO_3

tag: cell line

tag: cell type

tag: genotype

value: DMSO


title: F10_NoTreatment_BR2_IPFMRP

description:
Library name: F10-NT-FMRP-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#

tag: treatment

value: no treatment


title: blastocyst_ko_m_H3K27me3_7

description:
D655T121
H3K27me3 Cut&Run
D655T121

tag: tissue


title: A2780 cells, A3B knockdown, DMSO treated, replicate 2

description: Library name: A2780 3D_shA3B_DMSO_2


title: F10_DMSO_BR2_IPFMRP

description:
Library name: F10-DMSO-FMRP-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#


title: blastocyst_ko_m_H3K27me3_6

description:
D655T106
H3K27me3 Cut&Run
D655T106


title: PBMCs patient single_indolent_2, indolent stage T-PLL

description: demultiplexed

value: patient single_indolent_2


title: blastocyst_ko_m_H3K27me3_5

description:
D655T105
H3K27me3 Cut&Run
D655T105


title: A2780 cells, A3B knockdown, DMSO treated, replicate 1

description: Library name: A2780 3D_shA3B_DMSO_1

value: Ovary


title: PBMCs patient single_indolent_1, indolent stage T-PLL

description: demultiplexed

value: patient single_indolent_1


title: F10_0.6uM_BR2_IPFMRP

description:
Library name: F10-6-FMRP-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#


title: blastocyst_ko_m_H3K27me3_4

description:
D655T102
H3K27me3 Cut&Run
D655T102


title: A2780 cells, scramble control, Olaparib  treated, replicate 2

description: Library name: A2780 3D_shControl_Olaparib_2

value: A2780, Ovarian Cancer

value: Backbone control


title: A2780 cells, scramble control, Olaparib  treated, replicate 3

description: Library name: A2780 3D_shControl_Olaparib_3

value: Olaparib


title: blastocyst_ko_m_H3K27me3_3

description:
D655T100
H3K27me3 Cut&Run
D655T100


title: PBMCs patient single_active_1, active stage T-PLL

value: patient single_active_1

value: active stage T-PLL


title: F10_1uM_BR2_IPFMRP

description:
Library name: F10-1-FMRP-BR2
Strain-DrugTreatme1-ChIPtarget-Replicate#

value: 1 uM APH


title: F10_NoTreatment_BR1_IPDHX9

description:
Library name: F10-NT-DHX9-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: A2780 cells, scramble control, Olaparib  treated, replicate 1

description: Library name: A2780 3D_shControl_Olaparib_1


title: PBMCs patient pair_7, active stage T-PLL

description: demultiplexed

value: patient pair_7


title: F10_DMSO_BR1_IPDHX9

description:
Library name: F10-DMSO-DHX9-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: A2780 cells, scramble control, DMSO treated, replicate 3

description: Library name: A2780 3D_shControl_DMSO_3


title: blastocyst_ko_m_H3K27me3_1

description:
D419C54
H3K27me3 Cut&Run
D419C54

value: blastocyst

value: Ezhip matKO

value: M


title: PBMCs patient pair_7, indolent stage T-PLL

description: demultiplexed

value: peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

value: T-PLL


title: blastocyst_ko_m_H3K27me3_2

description:
D419C55
H3K27me3 Cut&Run
D419C55


title: PBMCs patient pair_6, indolent stage T-PLL

value: patient pair_6

value: indolent stage T-PLL


title: blastocyst_ko_f_H3K27me3_16

description:
D655T127
H3K27me3 Cut&Run
D655T127

value: F


title: A2780 cells, scramble control, DMSO treated, replicate 1

description: Library name: A2780 3D_shControl_DMSO_1

value: Ovary

value: DMSO


title: PBMCs patient pair_6, active stage T-PLL


title: F10_1uM_BR1_IPDHX9

description:
Library name: F10-1-DHX9-BR1
Strain-DrugTreatme1-ChIPtarget-Replicate#


title: F10_0.6uM_BR1_IPDHX9

description:
Library name: F10-6-DHX9-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#

value: 0.6 uM APH


title: F10_NoTreatment_BR2_INPUT

description:
Library name: F10-NT-W-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#

value: no treatment


title: A2780 cells, scramble control, DMSO treated, replicate 2

description: Library name: A2780 3D_shControl_DMSO_2

value: A2780, Ovarian Cancer

value: Backbone control


title: PBMCs patient single_indolent_3, indolent stage T-PLL

description: demultiplexed

value: patient single_indolent_3


title: blastocyst_ko_f_H3K27me3_14

description:
D655T125
H3K27me3 Cut&Run
D655T125


title: F10_NoTreatment_BR1_INPUT

description:
Library name: F10-NT-W-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: shJNK_donor3rep2

city: Birmingham

first: Charles

middle: Joseph

last: Kuhlmann

state: AL

address: 845 19th St S

department: Microbiology

institute: University of Alabama at Birmingham

description:
Library name: B6
sample B6 in FPKM file

data_processing:
Data filtering Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read
Mapping using hisat2 with default parameters
Quantification with featureCounts with default parameters
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: csv file contains fpkm values for each sample

source_name: Human peripherial blood

growth_protocol: CAR-T cells generated from human peripherial blood T cells by CD3/CD28 activation and expansion in IL7/IL15. CD8+ T cells isolated by flow cytometry

extract_protocol:
Direct Zol RNA Miniprep Plus kit (Zymogen #R2050)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using  dUTP for strand specific library.

treatment_protocol: 16 hour stimulation by plate-bound HER2-Fc protein

value: Human peripherial blood

value: Primary CAR-T cell

value: CD8+ T cell

value: shJNK

value: HER2-Fc Stimulation


title: shJNK_donor3rep1

description:
Library name: B5
sample B5 in FPKM file


title: PBMCs patient pair_5, active stage T-PLL

value: patient pair_5

value: peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

value: active stage T-PLL


title: blastocyst_ko_f_H3K27me3_13

description:
D655T124
H3K27me3 Cut&Run
D655T124

value: blastocyst

value: Ezhip matKO

value: F


title: shJNK_donor2rep2

description:
Library name: B4
sample B4 in FPKM file


title: PBMCs patient pair_4, indolent stage T-PLL

value: patient pair_4

value: T-PLL

value: indolent stage T-PLL


title: PBMCs patient pair_4, active stage T-PLL


title: shJNK_donor2rep1

description:
Library name: B3
sample B3 in FPKM file


title: F10_0.6uM_BR2_INPUT

description:
Library name: F10-6-W-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#

value: 0.6 uM APH


title: PBMCs patient pair_3, indolent stage T-PLL

description: demultiplexed

value: patient pair_3


title: shJNK_donor1rep2

description:
Library name: B2
sample B2 in FPKM file

value: Human peripherial blood


title: blastocyst_ko_f_H3K27me3_15

description:
D655T126
H3K27me3 Cut&Run
D655T126


title: blastocyst_ko_f_H3K27me3_10

description:
D655T107
H3K27me3 Cut&Run
D655T107


title: F10_0.6uM_BR1_INPUT

description:
Library name: F10-6-W-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: shJNK_donor1rep1

description:
Library name: B1
sample B1 in FPKM file

value: Primary CAR-T cell


title: PBMCs patient pair_3, active stage T-PLL

description: demultiplexed


title: PBMCs patient pair_5, indolent stage T-PLL


title: F10_1uM_BR2_INPUT

description:
Library name: F10-1-W-BR2
Strain-DrugTreatme1-ChIPtarget-Replicate#

value: 1 uM APH


title: blastocyst_ko_f_H3K27me3_9

description:
D655T104
H3K27me3 Cut&Run
D655T104


title: shScramble_donor3rep2

description:
Library name: A6
sample A6 in FPKM file

value: CD8+ T cell

value: shScramble


title: blastocyst_ko_f_H3K27me3_8

description:
D655T103
H3K27me3 Cut&Run
D655T103


title: PBMCs patient pair_2, indolent stage T-PLL

description: demultiplexed

value: patient pair_2


title: F10_1uM_BR1_INPUT

description:
Library name: F10-1-W-BR1
Strain-DrugTreatme1-ChIPtarget-Replicate#


title: PBMCs patient pair_2, active stage T-PLL

description: demultiplexed

value: peripheral blood


title: F10_DMSO_BR2_INPUT

description:
Library name: F10-DMSO-W-BR2
Strain-DrugTreatment-ChIPtarget-Replicate#

value: DMSO


title: blastocyst_ko_f_H3K27me3_7

description:
D655T101
H3K27me3 Cut&Run
D655T101


title: shScramble_donor3rep1

description:
Library name: A5
sample A5 in FPKM file

value: HER2-Fc Stimulation


title: blastocyst_ko_f_H3K27me3_12

description:
D655T123
H3K27me3 Cut&Run
D655T123

value: blastocyst


title: PBMCs patient pair_1, indolent stage T-PLL

value: patient pair_1

value: Peripheral blood mononuclear cells (PBMCs)


title: F10_DMSO_BR1_INPUT

description:
Library name: F10-DMSO-W-BR1
Strain-DrugTreatment-ChIPtarget-Replicate#


title: shScramble_donor2rep2

description:
Library name: A4
sample A4 in FPKM file


title: NSC, wt, RNA, rep1

city: Rotterdam

first: Tahsin Stefan

last: Barakat

state: South Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: The Erasmus University Medical Center

data_processing:
The FASTQ files data were trimmed using Trimmomatic (version 0.39) to remove possible adaptor contamination.
The trimmed data were mapped to the GRCh38/hg38 human genome build using the HISAT2 aligner (version 2.2.1)
The aligned reads were counted for each gene using htseq-count (version 0.12.4)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: neural stem cells

extract_protocol:
RNA was isolated from two independent cultures following TRI reagent (Sigma) manufacturer’s instruction. RNA was further purified using column purification (Qiagen, #74204).
mRNA capture, library prep and barcoding were performed according to standard procedures of the Erasmus MC Biomics facility. Libraries were then single end sequenced, 50bp, on an Illumina HiSeq2500 machine at a depth of approximately 20 million reads per sample.

value: neural stem cells


title: blastocyst_ko_f_H3K27me3_6

description:
D419C65
H3K27me3 Cut&Run
D419C65

value: Ezhip matKO

value: F


title: blastocyst_ko_f_H3K27me3_11

description:
D655T122
H3K27me3 Cut&Run
D655T122


title: NSC, wt, RNA, rep2


title: shScramble_donor2rep1

description:
Library name: A3
sample A3 in FPKM file


title: blastocyst_ko_f_H3K27me3_5

description:
D419C64
H3K27me3 Cut&Run
D419C64


title: Endo-3D Ctr infected FACS-sorted, 36hpi

description: 10x Genomics

data_processing:
Sequencing data were processed using Cell Ranger software (v.6.1.1, 10X Genomics).
Processing of raw sequencing reads, demultiplexing, read mapping and UMI counting were done using the standard ‘cellranger multi’ pipeline with default parameters
Assembly: GRCh38-2020-A
Supplementary files format and content: Supplementary_files_format_and_content: 1) Cell-level data: matrix.mtx.gz, barcodes.tsv.gz and features.tsv.gz  2) csv format: Metadata (sample ID, cluster, Infection condition, CMO tag etc) for each cell contained in the UMI count matrix.  3) csv format: Demultiplexed sample-cell barcode assignment indicating the sample membership for each cell barcode with information on their infection status 4) csv format: Information regarding CMO and Feature Barcode and their corresponding experimental condition, sequence etc. 5) csv format: Reference file mapping information of CMO tags and their respective experimental/sample ID

source_name: Endocervix

extract_protocol:
The uninfected and infected organoids from human ectocervix and endocervix were harvested in (0.04% BSA-PBS ). The organoids were incubated with 2 mL of TrypLE in a shaker (20 min, 37 ̊C, 180 rpm for ecto cervix and 10 min, 37 ̊C, 180 rpm for endo cervix organoids). The uninfected and infected organoids were made into single cells by pipetting up and down 20 times using a 1 mL pipette tip and diluted with 5 mL of 0.04% BSA-PBS solution. After inverting, cells were passed through a 40 μm cell strainer. Single cells were pooled at an equal ratio from biological samples and processed for the CMO labeling using kit 3' CellPlex Kit Set A (10x Genomics, #PN-1000261). CMO-labeled cells were pooled at an equal ratio, made the cell concentration to 2000 cell/µL, and proceeded for the library preparation. Single cells were partitioned into nanolitre-scale Gel-Bead-In-EMulsions (GEMs) using a 10x Chromium Controller.
The library was prepared using Single-Cell 3′ reagent kit v3 for reverse transcription, cDNA amplification, and library construction according to the manufacturer's protocol. Sequencing was performed in paired-end mode with an S1 100-cycles kit using Novaseq 6000 sequencer (Illumina).

value: Columnar epithelia

value: Endocervix

tag: group

value: FACS-sorted infected endocervical organoid sample

tag: age

value: between 35 and 75


title: shScramble_donor1rep2

description:
Library name: A2
sample A2 in FPKM file

value: Human peripherial blood

value: Primary CAR-T cell


title: ESC, ATAC, rep2

data_processing:
The FASTQ files were trimmed using Trimmomatic (version 0.39) to remove possible adaptor contamination.
The trimmed ATAC-seq data were mapped to the GRCh38/hg38 human genome build using the HISAT2 aligner (version 2.2.1) . Aligned reads were counted for each gene using htseq-count (version 0.12.4) and expression level was calculated using edgeR after data normalization.
Only properly and uniquely mapped reads, with mapping quality more than 30 (MAPQ >=30), were kept followed by removing possible duplicated reads (only for ChIP-seq data) using Picard's MarkDuplicates (version 4.0.1.1) (http://broadinstitute.github.io/picard/).
The aligned reads were converted to bigwig format using ”bamCoverage” function with --binSize 10 and --normalizeUsing CPM parameters, the read coverage was then computed using “multiBigwigSummary” and pearson correlation between replicates was calculated using “plotCorrelation” via deepTools (version 3.4.3)
Peak calling was performed using MACS2 (version 2.1.2) (with -q 0.05) for each replicate separately, and took sequencing data of total input as background. Peaks overlapping blacklist regions defined by the ENCODE project (Accession: ENCFF356LFX, Date: 05.05.2020) were removed. The overlapping peaks between replicates were merged as common peaks using intersectBed (version2.30.0).
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Briefly, approximately 50.000 single cells were lysed in Resuspension buffer containing 0,1% IgePal, 0,1% Tween-20 and 0,01% Digitonin. Immediately after lysis, the buffer was washed out by Resuspension buffer with only Tween-20. Nuclei were centrifuged at 500xg for 10 min at 4°C. Nuclei were re-suspended in 25 μl 2x TD buffer (Illumina), 2.5 μl TDE1 (transposase, Illumina), 16.5 μl PBS, 0.5 μl Tween-20, 0.5 μl Digitonin, and incubated for 30 min at 37°C. Afterward, the sample was purified using the MinElute PCR Purification Kit (QIAGEN) according to the manufacturer’s protocol and eluted with 10 μl elution buffer. Samples were amplified using the NEBNext High Fidelity PCR master mix (New England Biolabs) and afterwards purified using a MinElute PCR purification kit (Qiagen) according to the manufacturer’s instructions. One microliter was loaded on an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 assay to determine the library concentration and for quality check.
Cluster generation was performed according to the Illumina TruSeq SR Rapid Cluster kit v2 (cBot) Reagents Preparation Guide (www.illumina.com). Briefly, for sequencing libraries were pooled together to get a stock of 10 nM. One microliter of the 10 nM stock was denaturated with NaOH, diluted to 10 pM and hybridized onto the flowcell. The hybridized products were sequentially amplified, linearized and end-blocked according to the Illumina Single Read Multiplex Sequencing user guide. After hybridization of the sequencing primer, sequencing-by-synthesis was performed using the HiSeq 2500 with paired end 50-cycle protocol followed by dual index sequencing.

value: embryonic stem cells


title: blastocyst_ko_f_H3K27me3_4

description:
D419C56
H3K27me3 Cut&Run
D419C56


title: shScramble_donor1rep1

description:
Library name: A1
sample A1 in FPKM file

value: CD8+ T cell

value: shScramble


title: Endo-3D Ctr infected, 36hpi

description: 10x Genomics

value: Infected endocervical organoid sample


title: blastocyst_ko_f_H3K27me3_3

description:
D419C53
H3K27me3 Cut&Run
D419C53


title: NSC, ATAC, rep2


title: ESC, ATAC, rep1


title: Ecto-3D Ctr infected FACS-sorted, 36hpi

description: 10x Genomics

source_name: Ectocervix

value: Squamous epithelia

value: Ectocervix

value: FACS-sorted infected ectocervical organoid sample


title: Endo-3D uninfected, 36hpi

description: 10x Genomics

value: Uninfected endocervical organoid sample


title: ZR-75-30 cells, 2D monolayers, replicate 2

city: Gothenburg

first: Toshima

middle: Z

last: Parris

address: Sahlgrenska Center for Cancer Research, Medicinaregatan 1G, 6th floor

country: Sweden

institute: University of Gothenburg

description: Library name: ZR75302D_2

data_processing:
The RNA-seq raw counts were mapped to the human reference assembly GRCh38 (hg38) using hisat2 (v2.2.1), followed by featureCounts (v2.0.6) for quantification.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited matrix text file including gene counts
Supplementary files format and content: tab-delimited matrix text file including FPKM values

growth_protocol: Human breast cancer cell lines (BT-474, CAL-148, HCC1806, ZR-75-30) were cultured at 37°C in a humidified 5% CO2 environment in RPMI 1640 (HCC1806 and ZR-75-30) or Dulbecco Modified Eagle’s Medium (DMEM; BT-474 and CAL-148) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions. RNA concentration and integrity were assessed using the QuBit Fluorometer and 4200 TapeStation System, respectively.
Human mRNA-seq was performed at Novogene using the NovaSeq X Plus Series to obtain mRNA libraries (polyA enrichment) containing 150 bp pair-end reads with at least 85% of reads having a quality score of Q30 or higher.

value: breast cancer

value: 2D monolayers


title: blastocyst_ko_f_H3K27me3_2

description:
D419C52
H3K27me3 Cut&Run
D419C52

value: blastocyst

value: Ezhip matKO

value: F


title: NSC, ATAC, rep1

value: neural stem cells


title: ZR-75-30 cells, 2D monolayers, replicate 1

description: Library name: ZR75302D_1


title: blastocyst_ko_f_H3K27me3_1

description:
D419C51
H3K27me3 Cut&Run
D419C51


title: ESC, input, YY1

data_processing:
The FASTQ files were trimmed using Trimmomatic (version 0.39) to remove possible adaptor contamination.
Bowtie2 (version 2.4.2) (with --very-sensitive parameter) was used to align both ChIP- and STARR-seq data against the GRCh38/hg38 human genome build. Only properly and uniquely mapped reads, with mapping quality more than 30 (MAPQ >=30), were kept followed by removing possible duplicated reads (only for ChIP-seq data) using Picard's MarkDuplicates (version 4.0.1.1) (http://broadinstitute.github.io/picard/).
The aligned reads were converted to bigwig format using ”bamCoverage” function with --binSize 10 and --normalizeUsing CPM parameters, the read coverage was then computed using “multiBigwigSummary” and pearson correlation between replicates was calculated using “plotCorrelation” via deepTools (version 3.4.3)
Peak calling was performed using MACS2 (version 2.1.2) (with -q 0.05) for each replicate of ESCs and NSCs separately, and took sequencing data of total input as background. Peaks overlapping blacklist regions defined by the ENCODE project (Accession: ENCFF356LFX, Date: 05.05.2020) were removed. The overlapping peaks between replicates were merged as common peaks using intersectBed (version2.30.0).
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Briefly, 10 ng of ChIP DNA were end-repaired, dA tailed and adaptor ligated using NEBNext ChIP-seq library preparation kit (E6240, NEB), according to manufacturer’s instructions. Adaptor ligated DNA was eluted into 32 µL of 0.1xTE, 25 µL were used for ChIP-seq library preparation and 5 µl were processed for ChIP-STARR-seq plasmid libraries preparation.
ChIP-STARR-seq; For ChIP-seq library preparation, purified adaptor ligated DNA was PCR amplified with Illumina index primers (E7335 and E7500, NEB) according to manufacturer's instructions. ChIP-seq libraries were assessed on an Agilent Tapestation. All sequencing occurred on an Illumina HiSeq 2500 platform, using 50bp single-end sequencing.

tag: chip antibody


title: blastocyst_wt_m_H3K27me3_9

description:
D655T111
H3K27me3 Cut&Run
D655T111

value: WT

value: M


title: Ecto-3D Ctr infected, 36hpi

description: 10x Genomics

value: Infected ectocervical organoid sample

value: between 35 and 75


title: PBMCs patient pair_1, active stage T-PLL

value: patient pair_1

value: peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

value: T-PLL

value: active stage T-PLL


title: ESC, YY1, ChIP, rep2

value: embryonic stem cells


title: blastocyst_wt_m_H3K27me3_8

description:
D419C73
H3K27me3 Cut&Run
D419C73


title: Ecto-3D uninfected, 36hpi

description: 10x Genomics

value: Squamous epithelia

value: Ectocervix

value: Uninfected ectocervical organoid sample


title: CAL148 cells, 2D monolayers, replicate 1

description: Library name: CAL1482D_1

value: breast cancer

value: 2D monolayers


title: BT474 cells, 3D spheroids Day 20, replicate 2

description: Library name: BT474D20_2


title: blastocyst_wt_m_H3K27me3_7

description:
D419C70
H3K27me3 Cut&Run
D419C70

value: blastocyst


title: ESC, YY1, ChIP, rep1


title: ESC, input, SOX2


title: MEC-1 AID-WT Valemetostat-5

city: Boston

first: Roberto

last: Chiarle

state: Ma

address: Longwood 333

institute: Boston Childrens Hospital

description:
Library name: MEC-1 AID-WT Valemetostat-5
PE250

data_processing:
GEAT_docker(https://github.com/alessandriLuca/HTGTS_alignment) default parameters
Assembly: hg38
Supplementary files format and content: bedfiles tab separated

source_name: MEC-1 cells

growth_protocol: Cells were cultured at 37 °C with 5% CO2

extract_protocol:
The library preparation was performed as previously described in Zhang, X. et al, Nature 575, 385-389 (2019).
12-16 samples were pooled and sequenced through Illumina MiSeq (PE250) by the Molecular Biology Core Facilities of the Dana-Farber Cancer Institute.

treatment_protocol: LAM-HTGTS libraries were prepared from MEC-1 cells stimulated with EZH2 and/or PI3Kδ inhibitors

value: MEC-1 cells

value: Human chronic lymphocytic leukemia (CLL) cell line

value: Valemetostat


title: MEC-1 AID-WT Valemetostat-4

description:
Library name: MEC-1 AID-WT Valemetostat-4
PE250


title: blastocyst_wt_m_H3K27me3_6

description:
D419C69
H3K27me3 Cut&Run
D419C69

value: WT

value: M


title: blastocyst_wt_m_H3K27me3_5

description:
D419C67
H3K27me3 Cut&Run
D419C67


title: ESC, SOX2, ChIP, rep2


title: blastocyst_wt_m_H3K27me3_4

description:
D419C63
H3K27me3 Cut&Run
D419C63


title: BT474 cells, 3D spheroids Day 10, replicate 1

description: Library name: BT474D10_1


title: ESC, SOX2, ChIP, rep1


title: MEC-1 AID-WT Valemetostat-2

description:
Library name: MEC-1 AID-WT Valemetostat-2
PE250


title: MEC-1 AID-WT Valemetostat-3

description:
Library name: MEC-1 AID-WT Valemetostat-3
PE250


title: BT474 cells, 3D spheroids Day 10, replicate 2

description: Library name: BT474D10_2


title: MEC-1 AID-WT Valemetostat-1

description:
Library name: MEC-1 AID-WT Valemetostat-1
PE250


title: CAL148 cells, 2D monolayers, replicate 2

description: Library name: CAL1482D_2


title: NSC, input, ChIP, rep2

value: neural stem cells


title: blastocyst_wt_m_H3K27me3_3

description:
D419C60
H3K27me3 Cut&Run
D419C60


title: NSC, input, ChIP, rep1


title: blastocyst_wt_m_H3K27me3_2

description:
D419C59
H3K27me3 Cut&Run
D419C59


title: MEC-1 AID-WT Tazemetostat-5

description:
Library name: MEC-1 AID-WT Tazemetostat-5
PE250

value: Tazemetostat


title: NSC, YY1, ChIP, rep2


title: MEC-1 AID-WT Tazemetostat-4

description:
Library name: MEC-1 AID-WT Tazemetostat-4
PE250


title: blastocyst_wt_m_H3K27me3_1

description:
D419C58
H3K27me3 Cut&Run
D419C58


title: BT474 cells, 2D monolayers, replicate 1

description: Library name: BT4742D_1


title: HCC1806 cells, 3D spheroids Day 20, replicate 2

description: Library name: HCC1806D20_2


title: BT474 cells, 3D spheroids Day 20, replicate 1

description: Library name: BT474D20_1


title: NSC, YY1, ChIP, rep1


title: HCC1806 cells, 3D spheroids Day 20, replicate 1

description: Library name: HCC1806D20_1


title: MEC-1 AID-WT Tazemetostat-3

description:
Library name: MEC-1 AID-WT Tazemetostat-3
PE250


title: NSC, SOX2, ChIP, rep2


title: HCC1806 cells, 3D spheroids Day 10, replicate 2

description: Library name: HCC1806D10_2


title: MEC-1 AID-WT Tazemetostat-2

description:
Library name: MEC-1 AID-WT Tazemetostat-2
PE250


title: blastocyst_wt_f_H3K27me3_6

description:
D655T113
H3K27me3 Cut&Run
D655T113

value: F


title: blastocyst_wt_f_H3K27me3_5

description:
D655T112
H3K27me3 Cut&Run
D655T112


title: NSC, SOX2, ChIP, rep1


title: HCC1806 cells, 3D spheroids Day 10, replicate 1

description: Library name: HCC1806D10_1


title: MEC-1 AID-WT Tazemetostat-1

description:
Library name: MEC-1 AID-WT Tazemetostat-1
PE250


title: BT474 cells, 2D monolayers, replicate 2

description: Library name: BT4742D_2


title: NSC, H3K4me1, ChIP, rep2


title: MEC-1 AID-WT DMSO-5

description:
Library name: MEC-1 AID-WT DMSO-5
PE250

value: DMSO


title: HCC1806 cells, 2D monolayers, replicate 2

description: Library name: HCC18062D_2


title: blastocyst_wt_f_H3K27me3_4

description:
D655T110
H3K27me3 Cut&Run
D655T110


title: MEC-1 AID-WT DMSO-4

description:
Library name: MEC-1 AID-WT DMSO-4
PE250


title: NSC, H3K4me1, ChIP, rep1


title: HCC1806 cells, 2D monolayers, replicate 1

description: Library name: HCC18062D_1


title: blastocyst_wt_f_H3K27me3_3

description:
D419C74
H3K27me3 Cut&Run
D419C74


title: NSC, H3K27ac, ChIP, rep2


title: B017_c_5444

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

description:
Library name: B017_c_5444
Raw_counts_human_n17.csv

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.9
Sequence reads were mapped to the combined reference genome (Gencode human GRCh38 and mouse GRCm38 concatenated) using TopHat2 2.1.1 (parameter: --library-type=fr-unstranded)
The BAM file with mapped reads for each sample was sorted and then used as an input for featureCounts (Subread 2.0.6) in order to generate read count data on gene/feature level (parameters: -p --countReadPairs -t exon -g gene_id -s 0)
Genes/features were annotated using the combined GTF file from Gencode human GRCh38 and mouse GRCm38 references
Only the reads that were mapped to the human genome were kept, whereas the reads mapped to the mouse genome were removed
Assembly: Human GRCh38 and mouse GRCm38
Supplementary files format and content: Raw read count data generated by featureCounts (Subread 2.0.6) for each sample

source_name: patient-derived xenograft

extract_protocol:
Total RNA was isolated from cell lysates using Trizol reagent (Ambion Life Technologies) according to manufacturer's protocol
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc (US) following standard Illumina protocols

value: patient-derived xenograft

value: BLU-222:50 mg/kg; BID, oral; palbociclib:50 mg/kg; QD, oral


title: B017_c_5378

description:
Library name: B017_c_5378
Raw_counts_human_n17.csv


title: blastocyst_wt_f_H3K27me3_2

description:
D419C72
H3K27me3 Cut&Run
D419C72


title: blastocyst_wt_f_H3K27me3_7

description:
D655T116
H3K27me3 Cut&Run
D655T116


title: MEC-1 AID-WT DMSO-2

description:
Library name: MEC-1 AID-WT DMSO-2
PE250


title: NSC, H3K27ac, ChIP, rep1


title: MEC-1 AID-WT DMSO-1

description:
Library name: MEC-1 AID-WT DMSO-1
PE250


title: NSC, TF, DNA, rep2

data_processing:
*library strategy: plasmid DNA-seq
The FASTQ files were trimmed using Trimmomatic (version 0.39) to remove possible adaptor contamination.
Bowtie2 (version 2.4.2) (with --very-sensitive parameter) was used to align both ChIP- and STARR-seq data against the GRCh38/hg38 human genome build. Only properly and uniquely mapped reads, with mapping quality more than 30 (MAPQ >=30), were kept followed by removing possible duplicated reads (only for ChIP-seq data) using Picard's MarkDuplicates (version 4.0.1.1) (http://broadinstitute.github.io/picard/).
The aligned reads were converted to bigwig format using ”bamCoverage” function with --binSize 10 and --normalizeUsing CPM parameters, the read coverage was then computed using “multiBigwigSummary” and pearson correlation between replicates was calculated using “plotCorrelation” via deepTools (version 3.4.3)
Peak calling was performed using MACS2 (version 2.1.2) (with -q 0.05) for each replicate of ESCs and NSCs separately, and took sequencing data of total input as background. Peaks overlapping blacklist regions defined by the ENCODE project (Accession: ENCFF356LFX, Date: 05.05.2020) were removed. The overlapping peaks between replicates were merged as common peaks using intersectBed (version2.30.0).
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Briefly, 10 ng of ChIP DNA were end-repaired, dA tailed and adaptor ligated using NEBNext ChIP-seq library preparation kit (E6240, NEB), according to manufacturer’s instructions. Adaptor ligated DNA was eluted into 32 µL of 0.1xTE, 25 µL were used for ChIP-seq library preparation and 5 µl were processed for ChIP-STARR-seq plasmid libraries preparation.
Briefly, 5 µL of purified adaptor ligated DNA for each replicate were separately amplified with primers 147 STARRseq libr FW and 148 STARRseq libr RV (Arnold et al., 2013), and used in a Gibson assembly reaction with an AgeI-SalI digested STARR-seq plasmid and a home-made Gibson reaction buffer (100mM Tris-HCl, 10mM MgCl2, 0.2 mM dNTP, 0.5U Phusion DNA polymerase (NEB), 0.16U 50 T5 exonuclease (NEB)). Gibson reactions for the ChIP replicates were pooled together, purified by ethanol precipitation and used for electroporation into electrocompetent MegaX DH10b E. coli bacteria (C640003, Invitrogen), according to manufacturer’s instructions. A total of 5 electroporation reactions per library were performed with 2 µl of DNA each. After recovery, bacteria from the 5 reactions were pooled together and 100 µL of a 1:100 and 1:10000 dilution was plated on Ampicillin containing Agar plates to enable estimation of the number of transformants. The remaining 5 mL of bacteria culture were incubated in 1 L of LB-media supplemented with Ampicillin over-night, and the plasmid DNA was isolated using a Maxiprep kit (Macherey-Nagel) according to manufacturer’s instructions.


title: MEC-1 AID-KO Valemetostat-2

description:
Library name: MEC-1 AID-KO Valemetostat-2
PE250


title: B017_c_5361

description:
Library name: B017_c_5361
Raw_counts_human_n17.csv


title: NSC, TF, DNA, rep1


title: E6.5_matKO_m_3

data_processing:
The mm10 fasta file was masked with CAST/EiJ strain-specific SNPs using SNPsplit.
Adapters and low-quality bases were removed with TrimGalore and trimmed reads were mapped against the N-masked reference genome with STAR.
Library size, number of expressed genes, and total amount of RNA were used as criteria to select high-quality samples.
To assess allele-specific expression, reads spanning polymorphic sites were assigned to the maternal or paternal genome with SNPsplit and quantified using SAMtools mpileup.
To assess differential gene expression, exon-overlapping reads were counted using FeatureCounts.
Assembly: mm10
Supplementary files format and content: Tables summarizing raw counts over genes.

source_name: E6.5 extraembryonic ectoderm

extract_protocol:
RNA preparation was done as described in Pérez-Palacios et al. 2021 (PMID: 32944911; DOI: 10.1007/978-1-0716-0958-3_13)
Library construction was performed using the Accel-NGS 2S Unique Dual Indexing DNA library kit (Swift Biosciences), following manufacturer's instructions.
Single embryo RNA-Seq

value: E6.5 extraembryonic ectoderm

value: Ezhip matKO

value: male


title: B017_hi_5387

description:
Library name: B017_hi_5387
Raw_counts_human_n17.csv

value: BLU-222:100 mg/kg; BID, oral


title: E6.5_matKO_m_2


title: NSC, histone, DNA, rep2


title: B017_hi_5363

description:
Library name: B017_hi_5363
Raw_counts_human_n17.csv


title: E6.5_matKO_m_1


title: MEC-1 AID-KO Valemetostat-1

description:
Library name: MEC-1 AID-KO Valemetostat-1
PE250


title: E6.5_matKO_f_5

value: female


title: B017_lo_5425

description:
Library name: B017_lo_5425
Raw_counts_human_n17.csv

value: BLU-222:50 mg/kg; BID, oral


title: NSC, histone, DNA, rep1


title: MEC-1 AID-KO Tazemetostat-2

description:
Library name: MEC-1 AID-KO Tazemetostat-2
PE250

value: MEC-1 cells


title: ESC, TF, RNA, rep4

data_processing:
The FASTQ files data were trimmed using Trimmomatic (version 0.39) to remove possible adaptor contamination.
Bowtie2 (version 2.4.2) (with --very-sensitive parameter) was used to align both ChIP- and STARR-seq data against the GRCh38/hg38 human genome build. Only properly and uniquely mapped reads, with mapping quality more than 30 (MAPQ >=30), were kept followed by removing possible duplicated reads (only for ChIP-seq data) using Picard's MarkDuplicates (version 4.0.1.1) (http://broadinstitute.github.io/picard/).
The aligned reads were converted to bigwig format using ”bamCoverage” function with --binSize 10 and --normalizeUsing CPM parameters, the read coverage was then computed using “multiBigwigSummary” and pearson correlation between replicates was calculated using “plotCorrelation” via deepTools (version 3.4.3)
Peak calling was performed using MACS2 (version 2.1.2) (with -q 0.05) for each replicate of ESCs and NSCs separately, and took sequencing data of total input as background. Peaks overlapping blacklist regions defined by the ENCODE project (Accession: ENCFF356LFX, Date: 05.05.2020) were removed. The overlapping peaks between replicates were merged as common peaks using intersectBed (version2.30.0).
Assembly: hg38
Supplementary files format and content:
bigwig, narrowPeak
Whole_contri_percentile.txt: bed format file, that additionally gives for each nucleotide in a large number of gene regulatory elements a "contribution score". This score obtained from a convolutional neural network that was trained on massively parallel reporter assay data in which the regulatory elements were tested functionally, and this score predicts for each of the nucleotides how important this nucleotide is for the enhancer activity.

extract_protocol:
Briefly, RNA was isolated with Trizol (Sigma), following manufacturer’s instruction and split into two replicates.
The mRNA fraction was captured from each replicate of total RNA using Oligo (dT) 25 beads (61002, Life Technologies), DNaseI treated (18068-015, Life Technologies), and reverse transcribed with a GFP-mRNA specific primer (149 STARRseq rep RNA cDNA synth) following Superscript III protocol (18080-044, Life Technologies). To avoid plasmid DNA contamination, cDNA was PCR amplified in 10 parallel reactions for each replicate using primers spanning a synthetic intron (152 STARR reporter specific primer 2 fw and 153 STARR reporter specific primer 2 rv), as previously described (Arnold et al., 2013). 35 ng of PCR amplified DNA were then used in a second round of PCR to add Illumina index primers (E7335, E7500, NEB). PCR was performed in 5 parallel reactions and using 2 independent index primers for each of the two replicates. In total, we sequenced 4 replicates of STARR-seq RNA for each pooled HIST or TF plasmid library. Corresponding plasmid libraries were similarly amplified using two independent Illumina index primers for each plasmid library. Quantity and quality of generated sequencing libraries was assessed on an Agilent Tapestation. All sequencing occurred on an Illumina HiSeq 2500 platform, using 50bp paired-end sequencing.

value: embryonic stem cells


title: MEC-1 AID-WT DMSO-3

description:
Library name: MEC-1 AID-WT DMSO-3
PE250

value: Human chronic lymphocytic leukemia (CLL) cell line


title: B017_lo_5421

description:
Library name: B017_lo_5421
Raw_counts_human_n17.csv


title: blastocyst_wt_f_H3K27me3_1

description:
D419C71
H3K27me3 Cut&Run
D419C71

data_processing:
The mm10 fasta file was masked with CAST/EiJ strain-specific SNPs using SNPsplit. The N-masked mm10 fasta was then concatenated to that of Drosophila dm6 and indexed with Bowtie2 bowtie2-build.
Adapters and low-quality bases were removed with TrimGalore and trimmed reads were then mapped against the N-masked reference genome with Bowtie2.
PCR duplicates were discarded using Picard tools and reads overlapping the mouse genome were assigned to either the maternal or the paternal genomes using SNPsplit.
Bam files were merged according to genotype and, when available, sex using SAMtools merge.
Parental-specific bigwig files were generated using Deeptools bamCoverage. A size factor calculated on Drosophila spike-in reads was passed onto bamCoverage as ‘–scaleFactor’ for both parental genomes.
Assembly: mm10
Supplementary files format and content: Bigwig files for the visual representation of the genome-wide distribution of Cut&Run-Seq reads.
Library strategy: CUT&Run

extract_protocol:
Cut&Run-Seq was done as in Hainer et al. 2019 (PMID: 30955888; DOI: 10.1016/j.cell.2019.03.014) with some modifications.
Library construction was performed using the Accel-NGS 2S Unique Dual Indexing DNA library kit (Swift Biosciences), following manufacturer's instructions.
Low input Cut&Run-Seq

value: blastocyst

value: WT


title: MEC-1 AID-KO Tazemetostat-1

description:
Library name: MEC-1 AID-KO Tazemetostat-1
PE250


title: MEC-1 AID-KO DMSO-2

description:
Library name: MEC-1 AID-KO DMSO-2
PE250


title: E6.5_matKO_f_4


title: B017_lo_5381

description:
Library name: B017_lo_5381
Raw_counts_human_n17.csv


title: ESC, TF, RNA, rep3


title: E6.5_matKO_f_3


title: ESC, TF, RNA, rep2


title: MEC-1 AID-WT Idelalisib Valemetostat-5

description:
Library name: MEC-1 AID-WT Idelalisib Valemetostat-5
PE250

value: Idelalisib + Valemetostat


title: B017_p_5399

description:
Library name: B017_p_5399
Raw_counts_human_n17.csv

value: Palbociclib:50 mg/kg; QD, oral


title: ESC, TF, RNA, rep1


title: E6.5_matKO_f_1


title: ESC, histone, RNA, rep4


title: B017_p_5391

description:
Library name: B017_p_5391
Raw_counts_human_n17.csv


title: E6.5_wt_m_4


title: MEC-1 AID-WT Idelalisib Valemetostat-4

description:
Library name: MEC-1 AID-WT Idelalisib Valemetostat-4
PE250


title: MEC-1 AID-WT Idelalisib Valemetostat-3

description:
Library name: MEC-1 AID-WT Idelalisib Valemetostat-3
PE250


title: MEC-1 AID-KO DMSO-1

description:
Library name: MEC-1 AID-KO DMSO-1
PE250


title: ESC, histone, RNA, rep3


title: B017_p_5370

description:
Library name: B017_p_5370
Raw_counts_human_n17.csv


title: E6.5_matKO_f_2


title: MEC-1 AID-WT Idelalisib Valemetostat-2

description:
Library name: MEC-1 AID-WT Idelalisib Valemetostat-2
PE250


title: ESC, histone, RNA, rep2


title: B017_lo_5017

description:
Library name: B017_lo_5017
Raw_counts_human_n17.csv


title: B017_p_5364

description:
Library name: B017_p_5364
Raw_counts_human_n17.csv


title: E6.5_wt_m_2


title: ESC, histone, RNA, rep1


title: MEC-1 AID-WT Idelalisib Valemetostat-1

description:
Library name: MEC-1 AID-WT Idelalisib Valemetostat-1
PE250


title: NSC, TF, RNA, rep4

value: neural stem cells


title: B017_v_5443

description:
Library name: B017_v_5443
Raw_counts_human_n17.csv

value: Vehicle:BID, oral


title: MEC-1 AID-WT Idelalisib Tazemetostat-5

description:
Library name: MEC-1 AID-WT Idelalisib Tazemetostat-5
PE250

value: Idelalisib + Tazemetostat


title: MEC-1 AID-WT Idelalisib Tazemetostat-4

description:
Library name: MEC-1 AID-WT Idelalisib Tazemetostat-4
PE250


title: E6.5_wt_m_1