title: RNA-seq_Liver_sgNTC_3

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Raw RNA-seq sequencing data were firstly removed adaptors and low-quality bases, and then the clean reads were mapped to the UCSC human hg19 reference genome using Tophat (version: 2.0.12) with default parameters. Reads counts were calculated with HTSeq, and gene expression levels are quantified with RPKM (reads per kilobase million).
Genome_build: UCSC human reference genome hg19 or UCSC mouse refernce mm10
Supplementary_files_format_and_content: RNA_expression.txt files include the read counts and RPKM of RefSeq genes

source_name: CRISPR Screening

extract_protocol: For RNA-seq, total RNA was extracted by TRIzol (Invitrogen) at diffent time points.

value: Wild type

tag: cell type

value: Mouse liver cell

value: Month 20

tag: biological replication


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E6_ad007

status: Public on Oct 09 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male

tag: age

tag: strain


title: dnmt3bb2_cKO_48hpf_RRBS_rep1

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description: CRISPR-Cas9 injected F0 zebrafish with mosaic KO levels

data_processing:
Reads were trimmed Trimmomatic (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 CROP:140 HEADCROP:5) (Bolger et al. 2014), and mapped using WALT (-m 5 -t 20 -N 10000000) (Chen et al. 2016) onto the bisulfite-converted GRCz11 reference (UCSC) containing λ added as separate chromosomes. The resulting alignments in BAM format were processed with CGmapTools (Guo et al. 2018) (convert bam2cgmap) to obtain methylation calls. ATCGmap files were parsed to discard the CH positions that showed evidence of a CG position in the reads discordant with the reference genome CH annotation.
Genome_build: GRCz11
Supplementary_files_format_and_content: bigwig files for visualization with UCSC genome browser containing methylation value as mC/C

organism: Danio rerio

source_name: 48hpf embryos

growth_protocol: Adult wild type (AB-Tubingen) Danio rerio (zebrafish) were bred in a 1 male:1 female ratio. Embryos were collected 0 hours post-fertilisation (hpf) and incubated in 1X E3 medium (0.03% NaCl, 0.005% CaCl2, 0.0013% KCl, 99.9557% H2O, 0.008% H14MgO11S) for 24 hours at 28.5°C.

extract_protocol:
RRBS library construction was performed using the restriction enzyme BccI and SspI (New England BioLabs, Ipswich, MA, USA) and 0.025ng of unmethylated lambda phage DNA (Promega, Madison, WI, USA) was used as a spike-in control to determine the efficiency of bisufite conversion. Briefly, 500ng of zebrafish gDNA was digested for 2 hours with 10U BccI and 10U SspI (New England BioLabs, Ipswich, MA, USA). The 5’ overhangs of the digested DNA were filled in and A-tailed using klenow fragment exo-  (New England BioLabs, Ipswich, MA, USA) before ligation of adapters to DNA overnight using NEXTFLEX Bisulfite-Seq Barcodes (PerkinElmer, Waltham, MA, USA). DNA was bisulfite converted using EZ DNA Methylation Gold Kit (Zymo Research,Irvine,CA,USA ) according to manufacturer instructions. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 13 cycles of amplification. Library concentration was quantified through qPCR using KAPA Library Quantification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to manufacturer instructions. The combined libraries with 15% PhiX spike-in was sequenced on the Illumina HiSeq 10X platform using 150bp paired-end sequencing (high output mode).
embryos/tissues were snap frozen in liquid nitrogen and stored at -80°C prior to DNA extraction. Genomic DNA (gDNA) was extracted using the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, Chadstone, VIC, Australia) according to manufacturer instructions in two biological replicates.

treatment_protocol: KO microinjection mixtures where made by combining 1000 ng of gRNA with 1 μl EnGene CAS9 NLS, S Pyogenes  (New England BioLabs, Ipswich, MA, USA) and 1.5 μl KCl (1M).  500pL of micoinejection mixtures were injected into single cell stage embryos.

tag: tissue

value: whole embryos

value: Mixed AB and Tubingen

tag: genotype

value: dnmt3bb.2 CRIPSR-CAS9 injected F0


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E6_ad008


title: dnmt3bb1_cKO_48hpf_RRBS_rep2

value: dnmt3bb.1 CRIPSR-CAS9 injected F0


title: dnmt3ba_cKO_72hpf_WGBS_rep2

source_name: 72hpf embryos

extract_protocol:
For WGBS, 500ng of zebrafish gDNA and spiked in 0.025ng of unmethylated lambda phage DNA (Promega, Madison, WI, USA) was sonicated to an average insert size of 300bp. Sonicated DNA was end repaired followed by ligation of adapters to DNA overnight using NEXTFLEX Bisulfite-Seq Barcodes (PerkinElmer, Waltham, MA, USA). DNA was bisulfite converted using EZ DNA Methylation Gold Kit (Zymo Research,Irvine,CA,USA ) according to manufacturer instructions. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 8 cycles of amplification. Library concentration was quantified through qPCR using KAPA Library Quantification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to manufacturer instructions. The combined libraries with 15% PhiX spike-in was sequenced on the Illumina HiSeq 10X platform using 150bp paired-end sequencing (high output mode).
embryos/tissues were snap frozen in liquid nitrogen and stored at -80°C prior to DNA extraction. Genomic DNA (gDNA) was extracted using the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, Chadstone, VIC, Australia) according to manufacturer instructions in two biological replicates.

value: dnmt3ba CRIPSR-CAS9 injected F0


title: RNA-seq_Liver_sgNTC_2

country: China

library_source: transcriptomic

molecule: total RNA


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E6_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E6_ad006


title: dnmt3bb1_cKO_48hpf_RRBS_rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E6_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E5_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E6_ad001


title: dnmt3ba_cKO_48hpf_RRBS_rep2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E5_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E5_ad006


title: RNA-seq_Liver_sgKAT7_2

value: KAT7 Knock-down


title: dnmt3bb3_cKO_48hpf_RRBS_rep2

value: dnmt3bb.3 CRIPSR-CAS9 injected F0


title: dnmt3ba_cKO_48hpf_RRBS_rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E5_ad004


title: RNA-seq_Liver_sgKAT7_3


title: dnmt3ba-bb1-2-3_cKO_48hpf_RRBS_rep2

value: dnmt3ba + dnmt3bb.1  + dnmt3bb.2 + dnmt3bb.3 CRIPSR-CAS9 injected F0


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E5_ad001


title: dnmt3ba-bb1-2-3_cKO_48hpf_RRBS_rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E5_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E4_ad010


title: dnmt3bb2_cKO_48hpf_RRBS_rep2


title: dnmt3ab_cKO_48hpf_RRBS_rep2

value: dnmt3ab CRIPSR-CAS9 injected F0


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E4_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E4_ad004


title: RNA-seq_Liver_28m_2

value: Month 28


title: dnmt3ab_cKO_48hpf_RRBS_rep1


title: RNA-seq_Liver_28m_3


title: dnmt3aa_cKO_48hpf_RRBS_rep2

value: dnmt3aa CRIPSR-CAS9 injected F0


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E4_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E4_ad008


title: RNA-seq_Liver_28m_1


title: RNA-seq_Liver_sgNTC_1


title: RNA-seq_Liver_2m_3

value: Month 2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E3_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E3_ad008


title: dnmt3aa_cKO_48hpf_RRBS_rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E3_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E3_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E3_ad004


title: RNA-seq_Liver_2m_1

value: Wild type


title: dnmt3aa-3ab_cKO_48hpf_RRBS_rep2

value: dnmt3aa + dnmt3ab CRIPSR-CAS9 injected F0


title: RNA-seq_Liver_sgKAT7_1

value: Mouse liver cell

value: Month 20


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E3_ad002

value: CA

value: male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E2_ad012


title: RNA-seq_Kidney_sgNTC_3

value: Mouse kidney cell


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E4_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E2_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E2_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E2_ad007


title: dnmt2_cKO_48hpf_RRBS_rep2

value: whole embryos

value: Mixed AB and Tubingen

value: dnmt2 CRIPSR-CAS9 injected F0


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E2_ad006


title: dnmt3aa-3ab_cKO_48hpf_RRBS_rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E2_ad002


title: RNA-seq_Kidney_sgNTC_2


title: dnmt2_cKO_48hpf_RRBS_rep1


title: dnmt1_cKO_48hpf_RRBS_rep1

value: dnmt1 CRIPSR-CAS9 injected F0


title: RNA-seq_Kidney_sgKAT7_3

value: KAT7 Knock-down


title: dnmt1_cKO_48hpf_RRBS_rep2


title: RNA-seq_Kidney_sgNTC_1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E2_ad001


title: RNA-seq_Kidney_sgKAT7_2


title: RNA-seq_Liver_2m_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E2_ad004


title: uhrf1_cKO_48hpf_RRBS_rep2

extract_protocol:
RRBS library construction was performed using the restriction enzyme MspI (New England BioLabs, Ipswich, MA, USA) and 0.025ng of unmethylated lambda phage DNA (Promega, Madison, WI, USA) was used as a spike-in control to determine the efficiency of bisufite conversion. Briefly, 500ng of zebrafish gDNA was digested for 2 hours with 20U MspI (New England BioLabs, Ipswich, MA, USA). The 5’ overhangs of the digested DNA were filled in and A-tailed using klenow fragment exo-  (New England BioLabs, Ipswich, MA, USA) before ligation of adapters to DNA overnight using NEXTFLEX Bisulfite-Seq Barcodes (PerkinElmer, Waltham, MA, USA). DNA was bisulfite converted using EZ DNA Methylation Gold Kit (Zymo Research,Irvine,CA,USA ) according to manufacturer instructions. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 13 cycles of amplification. Library concentration was quantified through qPCR using KAPA Library Quantification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to manufacturer instructions. The combined libraries with 15% PhiX spike-in was sequenced on the Illumina HiSeq 10X platform using 150bp paired-end sequencing (high output mode).
embryos/tissues were snap frozen in liquid nitrogen and stored at -80°C prior to DNA extraction. Genomic DNA (gDNA) was extracted using the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, Chadstone, VIC, Australia) according to manufacturer instructions in two biological replicates.

value: uhrf1 CRIPSR-CAS9 injected F0


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E12_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E12_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E12_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E12_ad001


title: uhrf1_cKO_48hpf_RRBS_rep1


title: RNA-seq_Kidney_28m_3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E12_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E12_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E11_ad012


title: RNA-seq_Kidney_28m_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E11_ad010


title: WT_48hpf_RRBS_rep1

description: control

value: wild type


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E11_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E11_ad007


title: RNA-seq_Kidney_2m_3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E11_ad001


title: RNA-seq_Kidney_2m_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E11_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E12_ad002


title: RNA-seq_Kidney_sgKAT7_1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E11_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E10_ad002


title: Stroma_eMSC_biopsy 3

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

description:
WTCHG_364973_021
WTCHG_367043_021

data_processing:
Transcriptomic maps of paired-end reads were generated using bowtie-2.2.3, samtools-0.1.19, and tophat-2.0.12 against the hg19 reference genome (2014)
Transcript counts were assessed by HTSeq-0.6.1 using the reverse strand setting and intersection-non-empty mode and counts were assigned to gene ids.
Genome_build: hg19
Supplementary_files_format_and_content: TPM

organism: Homo sapiens

source_name: Endometrial stromal cells

growth_protocol: Endometrial biopsies were processed and single-cell suspensions of eMSCs obtained as described previously (Masuba et al. 2012).

extract_protocol:
Total RNA was extracted from whole tissue, uNK, organoids, SUSD2+ CFUs (eMSC), SUSD2- CFUs (TA), SUSD2+ standard (PVC) and SUSD2- standard (EnSC) cultures using the AllPrep DNA/RNA Micro Kit (QIAGEN). RNA concentration was assessed using the Qubit RNA BR assay and RNA quality was analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). Libraries were prepared using the TruSeq RNA Library preparation kit V2 and sequenced on HiSeq 4000 with 75 bp PE reads at the Wellcome Trust Centre for Human Genetics (Oxford, UK).
RNA libraries were sequenced on two flow cells on the Illumina HiSeq 4000.

treatment_protocol: Endometrial samples were finely minced, and enzymatically digested with collagenase type IA and DNase type I for 1 hour at 37 °C. The dissociated cells were filtered through a 40-μm cell strainer. Stromal cells and blood cells, present as a single-cell suspension, passed through the cell strainer, whereas the undigested fragments, mostly comprising glandular clumps, were retained on the strainer. EnSC suspensions were layered over Ficoll-Paque PLUS and centrifuged to remove erythrocytes. A total of 3 x 106 cells were used for SUSD2+/SUSD2− magnetic activated cell sorting (MACS) and remaining cells were plated into a T-25 flask for isolation of uNK cell.  For SUSD2 separation, stromal cell were resuspended in separation buffer (100 μl/ 1 x 106 cells) containing phycoerythrin (PE) conjugated antihuman W5C5 (SUSD2) or MRP4 antibody for 20 minutes at 4 ºC. Cell suspensions were then incubated with anti-PE-magnetic-activated cell sorting microbeads (20 μl/ 1 x 107 cells) for 20 minutes at 4 ºC. Positive (PVC) and negative (EnSC) selected cells were cultured in growth medium: DMEM/F12 medium containing DCC-FBS, L-glutamine, antibiotic-antimycotic solution, insulin and estradiol until 90% confluence. For the in vitro colony forming unit (CFU) assay, freshly isolated SUSD2+ and SUSD2- cells were seeded at a clonal density of 30 cells/cm2 onto fibronectin-coated 6 well plates and cultured in growth medium supplemented with bFGF for 10 days. Following overnight culture, the supernatant of the EnSC fraction was subjected to MACS to isolate uNK cells using a PE-conjugated anti-human CD56 monoclonal antibody. The glandular clumps, retained on the strainer, were centrifuged and resuspended in trypsin for 10 min at 37 °C to disperse clustered cells. EpC were resuspended in ice cold Matrigel (Corning, New York, USA) in order to obtain 1000 cells per 5 μl of Matrigel and cultured for 10 days in expansion medium supplemented with Y-27632.  All samples were snap-frozen before RNA extraction.

tag: patient id

value: Biopsy 3

tag: Stage

value: midluteal

value: endometrium

value: Endometrial stromal cells


title: Barcode-oligonucleotide

city: Jerusalem

first: David

last: Gokhman

address: Givat Ram, Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

description: ProcessedData.xlsx

data_processing:
Library strategy: DNA-seq
Each samples’ R1 and R3 reads (containing the barcode) were mapped with bowtie2 (--very-sensitive) to the barcode-oligo association list
We applied several quality filters on the resulting alignments. We first filtered out read pairs that didn’t map as proper pairs, and then ensured the mapped sequence completely matched the known barcode sequence by requiring that both R1 and R3 reads have CIGAR stings = 15M, MD flags = 15 and a mapping quality of at least 20
We consolidated read abundance per barcode by selecting only reads with unique UMIs, the result being abundance counts for each barcode, across each replicate library of each cell type for both RNA and DNA
Genome_build: Human: GRCh37
Supplementary_files_format_and_content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 4 columns per sample: ref counts (aligned to reference genome), alt counts (aligned to alternative genome), no ASE (no segregating SNPs) and ambiguous (SNPs from both genome); matrix text files are provided for samples mapped on both the human and chimpanzee genomes; text files with sample meta data are also included for each data set

growth_protocol: Human fetal osteoblasts (HObs) were purchased from Cell Applications Inc. (406K-05f) and were maintained in HOb Growth Medium (Cell Applications Inc.). For passaging, cells were washed with 1x PBS, dissociated with Trypsin/EDTA (Cell Applications Inc.), and plated at approximately 5,000 cells/cm2. H1-ESCs (embyronic stem cells, ESCs, WiCell WA-01, RRID:CVCL_9771) were cultured on Matrigel (Corning) in mTeSR1 media (STEMCELL Technologies) and medium was changed daily. For passaging, cells were dissociated using StemPro Accutase (Thermo Fisher Scientific), washed and re-plated on Matrigel-coated dishes at a dilution of 1:5 to 1:10 in mTeSR1 media supplemented with 10 μM Y-27632 (Selleck Chemicals). ESCs were induced into neural progenitor cells (NPCs) by dual-Smad inhibition as previously described (Chambers et al., 2009; Inoue et al., 2019). Briefly, ESCs were cultured in mTeSR1 media until the cells became 80% confluent and then the media was replaced with neural differentiation media consisting of: KnockOut DMEM (Life Technologies) supplemented with KnockOut Serum Replacement (Life Technologies), 2 mM L-glutamine, 1x MEM-NEAA (Life Technologies), 1x beta-mercaptoethanol (Life Technologies), 200 ng/mL Recombinant mouse Noggin (R&D systems), and 10 μM SB431542 (EMD Millipore). On day 4 of differentiation, the neural differentiation media was gradually replaced by N2 media [DMEM/F12 (Thermo Fisher Scientific) supplemented with N2 (Thermo Fisher Scientific)] every 2 days (3:1 ratio on day 6, 1:1 on day 8 and 1:3 on day 10) while maintaining 200 ng/mL Noggin and 10 μM SB431542. On day 12, cells were dissociated into single-cell using TrypLE Express (Thermo Fisher Scientific) and cultured in N2B27 media [1:1 mixture of N2 media and Neurobasal media (Thermo Fisher Scientific) with B27 (Thermo Fisher Scientific)] supplemented with 20 ng/mL bFGF (R&D systems) and 20 ng/mL EGF (Millipore sigma)] on Matrigel-coated dish. NPCs were maintained in N2B27 with bFGF and EGF for a month and used for the following experiments at passage 15.

extract_protocol:
We purified mRNA from the RNA using the Oligotex mRNA prep kit (Qiagen) and synthesized cDNA from the resulting mRNA with SuperScript II RT (Invitrogen), using a barcode specific primer with a unique molecular identifier (UMI) (P7-pLSmp-ass16UMI-gfp)
DNA fragments containing barcodes were amplified from both the isolated DNA and generated cDNA from each replicate of each cell type with 3-cycle PCR using primers targeting the barcoded region (P7-pLSmp-ass16UMI-gfp and P5-pLSmP-5bc-i#). These primers also contained a sample index for demultiplexing and a UMI for consolidating replicate molecules (see later). A second round of PCR was performed to attach the adapters necessary for sequencing (P5, P7). The fragments were purified and further sequenced with six runs of NextSeq 15PE with 10-cycle dual index reads, using custom primers (R1, pLSmP-ass-seq-ind1; R2 (read for UMI), pLSmP-UMI-seq; R3, pLSmP-bc-seq; R4 (read for sample index), pLSmP-5bc-seq-R2).

treatment_protocol: Lentivirus was produced and packaged with the lentiMPRA library in twelve 15cm dishes of HEK293T cells using the Lenti-Pac HIV expression packaging kit, following the manufacturer’s protocol (GeneCopoeia). Additional lentivirus was produced as needed in batches of ten 15cm dishes. Lentivirus containing the lentiMPRA library (referred to hereafter as lentivirus) was filtered through a 0.45m PES filter system (Thermo Scientific) and concentrated with Lenti-X concentrator (Takara Bio). Titration reactions using varying amounts of lentivirus were conducted on each cell type to determine the best volume to add, based on an optimal number of viral particles per cell, as described in Gordon et al., 2020. Lentiviral infection, DNA/RNA extraction, and barcode sequencing were all performed as described in Gordon et al., 2020 [[ref]]. Briefly, in total approximately 9.6 million cells each of ESC and Hob, and 20 million cells of NPC were used. ESC and HOb cells were seeded into four 10cm dishes with approximately 2.4 million cells in each dish, while NPCs were seeded into five 10cm dishes with approximately 4 million cells per dish (additional cells were used for NPCs due decreased efficiency of DNA/RNA extraction in NPCs). Three replicates were performed per cell type, each replicate with X plates of # cells each. Cells were infected with the lentiMPRA library at a multiplicity of infection (MOI) of 50 for NPCs and HObs, and a MOI of 10 for ESCs. Infected cells were grown for three days before combining all the plates comprising each replicate for extraction of RNA and DNA via the Qiagen AllPrep mini kit (Qiagen).

tag: cell line


title: Osteoblast DNA rep3

description: ProcessedData.xlsx

source_name: osteoblasts

value: HObs


title: Osteoblast RNA rep2

description: ProcessedData.xlsx

data_processing:
Each samples’ R1 and R3 reads (containing the barcode) were mapped with bowtie2 (--very-sensitive) to the barcode-oligo association list
We applied several quality filters on the resulting alignments. We first filtered out read pairs that didn’t map as proper pairs, and then ensured the mapped sequence completely matched the known barcode sequence by requiring that both R1 and R3 reads have CIGAR stings = 15M, MD flags = 15 and a mapping quality of at least 20
We consolidated read abundance per barcode by selecting only reads with unique UMIs, the result being abundance counts for each barcode, across each replicate library of each cell type for both RNA and DNA
Genome_build: Human: GRCh37
Supplementary_files_format_and_content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 4 columns per sample: ref counts (aligned to reference genome), alt counts (aligned to alternative genome), no ASE (no segregating SNPs) and ambiguous (SNPs from both genome); matrix text files are provided for samples mapped on both the human and chimpanzee genomes; text files with sample meta data are also included for each data set


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E10_ad008


title: Osteoblast DNA rep2

description: ProcessedData.xlsx


title: Osteoblast RNA rep3

description: ProcessedData.xlsx


title: WT_48hpf_RRBS_rep2

description: control


title: Osteoblast DNA rep1

description: ProcessedData.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E10_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E10_ad007


title: RNA-seq_Kidney_28m_1

value: Wild type

value: Month 28


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E11_ad002

value: CA


title: RNA-seq_Kidney_2m_1

value: Month 2


title: Osteoblast RNA rep1

description: ProcessedData.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E10_ad006

value: male


title: Stroma_PVC_biopsy 3

description:
WTCHG_364973_011
WTCHG_367043_011


title: Stroma_EnSC_biopsy 3

description:
WTCHG_364973_010
WTCHG_367043_010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E10_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E1_ad010


title: Epithelium_biopsy 3

description:
WTCHG_364973_009
WTCHG_367043_009

source_name: Endometrial epithelial cells

value: Endometrial epithelial cells


title: Stroma_TA_biopsy 3

description:
WTCHG_364973_020
WTCHG_367043_020


title: CEMBA190305_11E_1_CEMBA190305_11E_2_F11_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E1_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E1_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E1_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E1_ad004


title: NPC DNA rep2

description: ProcessedData.xlsx

source_name: neural progenitoc cells

value: ESC-derived NPCs


title: NPC RNA rep2

description: ProcessedData.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E1_ad001


title: uNK_biopsy 3

description:
WTCHG_364973_022
WTCHG_367043_022

source_name: Endometrial uNK cells

value: Endometrial uNK cells


title: NPC RNA rep3

description: ProcessedData.xlsx


title: Whole_biopsy 3

description:
WTCHG_364973_008
WTCHG_367043_008

source_name: Endometrial cells

value: whole tissue


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E1_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D9_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D9_ad010


title: NPC DNA rep1

description: ProcessedData.xlsx


title: Stroma_eMSC_biopsy 2

description:
WTCHG_364973_003
WTCHG_367043_003

value: Biopsy 2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E1_ad012


title: Stroma_TA_biopsy 2

description:
WTCHG_364973_001
WTCHG_367043_001


title: NPC RNA rep1

description: ProcessedData.xlsx


title: Stroma_PVC_biopsy 2

description:
WTCHG_364973_019
WTCHG_367043_019


title: NPC DNA rep3

description: ProcessedData.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D9_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D9_ad008


title: Stroma_EnSC_biopsy 2

description:
WTCHG_364973_018
WTCHG_367043_018


title: ESC DNA rep3

description: ProcessedData.xlsx

source_name: embryonic stem cells


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D9_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D9_ad004


title: ESC RNA rep3

description: ProcessedData.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D9_ad002


title: Epithelium_biopsy 2

description:
WTCHG_364973_016
WTCHG_367043_016


title: ESC DNA rep2

description: ProcessedData.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D9_ad001


title: uNK_biopsy 2

description:
WTCHG_364973_004
WTCHG_367043_004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D8_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D8_ad008


title: ESC RNA rep2

description: ProcessedData.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D8_ad007


title: Stroma_eMSC_biopsy 1

description:
WTCHG_364973_013
WTCHG_367043_013

value: Biopsy 1


title: ESC DNA rep1

description: ProcessedData.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D8_ad004


title: Whole_biopsy 2

description:
WTCHG_364973_015
WTCHG_367043_015


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E10_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D7_ad012


title: Stroma_PVC_biopsy 1

description:
WTCHG_364973_007
WTCHG_367043_007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D7_ad007


title: Stroma_EnSC_biopsy 1

description:
WTCHG_364973_006
WTCHG_367043_006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D7_ad006


title: 293FT cells, circFAM120A shRNA1 replicate2

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

description: circFAM120A KD shRNA shRNA1 (10nt + 11nt target sequences spanning BSJ) p(A)+ RNA-seq replicate2

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
RNA-seq sequencing read quality was evaluated by FastQC (v0.11.5), and then mapped by using TopHat (TopHat v2.0.12, parameters: –microexon-search -g 1 -a 6 -m 2) to GRCh37/hg19 human reference genome with the UCSC Genes annotation (Human: hg19 knownGene.txt updated at 2013/06/30). The TopHat2-mapped sam files were transferred to bam format by samtools (version 0.1.19).
Bam to Bedgraph using genomeCoverageBed (v2.28.0)  Bedgraph to bigwig using UCSC bedGraphToBigWig (v4)
bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig file

molecule: polyA RNA

source_name: 293FT cells, circFAM120A shRNA1

growth_protocol: 293FT cells (human fetus origin) were maintained in DMEM, and all supplemented with 10% Fetal Bovine Serum (FBS) and 0.1% penicillin/streptomycin. We maintained cell lines at 37°C in a 5% CO2 cell culture incubator and tested all cell lines routinely to exclude mycoplasma contamination.

extract_protocol:
Total RNAs from NT or circFAM120A KD cells were extracted with Trizol (Life Technologies) according to the manufacturer’s protocol.
For gene expression analysis after circFAM120A KD (poly(A)+ RNA-seq), polyadenylated (poly(A)+) RNA preparation was carried out as following. Briefly, total RNAs (8 μg) were incubated with oligo(dT) magnetic beads to isolate poly(A)+ RNAs, which were bound to beads, selection was performed three times to ensure the purity of poly(A)+ RNA populations. Poly(A)+ RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. All libraries were size-selected with AmpureXP beads (Agencourt) and quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Size-selected libraries were subjected to deep sequencing with Illumina NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: To knock down circFAM120A, DNA oligos of gRNA or shRNA sequences for circFAM120A or scramble were individually cloned into pLKO.1-TRC vector. To infect 293FT cells with lentivirus, cells were incubated with culture medium containing 10 μL concentrated lentivirus and 5 mg/mL polybrene (Sigma). Infected cells were treated with puromycin for several days to increase knockdown efficiency.

value: 293FT cells

tag: treatment

value: circFAM120A shRNA KD


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D8_ad010


title: 293FT cells, shRNA NT replicate2

description: circFAM120A KD shRNA NT p(A)+ RNA-seq replicate2

source_name: 293FT cells, shRNA NT

value: scramble


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D7_ad004


title: Epithelium_biopsy 1

description:
WTCHG_364973_002
WTCHG_367043_002

value: midluteal

value: endometrium


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D8_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D6_ad012


title: uNK_biopsy 1

description:
WTCHG_364973_014
WTCHG_367043_014


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D6_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D8_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D8_ad002


title: Stroma_TA_biopsy 1

description:
WTCHG_364973_012
WTCHG_367043_012

value: Endometrial stromal cells


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D6_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D7_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D7_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D6_ad007


title: ESC RNA rep1

description: ProcessedData.xlsx


title: Whole_biopsy 1

description:
WTCHG_364973_005
WTCHG_367043_005


title: 293FT cells, RfxCas13d circFAM120A gRNA1 replicate1

description: circFAM120A KD RfxCas13d gRNA1 (15nt + 15nt target sequences spanning BSJ) p(A)+ RNA-seq replicate1

value: circFAM120A RfxCas13d/BSJ-gRNA KD


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D6_ad006


title: 293FT cells, circFAM120A shRNA1 replicate1

description: circFAM120A KD shRNA shRNA1 (10nt + 11nt target sequences spanning BSJ) p(A)+ RNA-seq replicate1


title: 293FT cells, RfxCas13d NT replicate2

description: circFAM120A KD RfxCas13d NT p(A)+ RNA-seq replicate2

source_name: 293FT cells, RfxCas13d NT


title: RNA-seq_D9_sgNTC_3

value: Wild type

value: Human liver cell line

value: Gathered at day 9 (cultured)


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D6_ad002

value: CA

value: male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D7_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D6_ad001


title: 293FT cells, RfxCas13d NT replicate1

description: circFAM120A KD RfxCas13d NT p(A)+ RNA-seq replicate1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D5_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D5_ad010


title: RNA-seq_D9_sgNTC_1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D5_ad008


title: WTPELP_veh_3

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Initial QC performed using FastQC v 0.11.2
Tophat v 2.0.13 was used to align samples
Cufflinks v 2.2.1 was used to generate abundances and fpkm values with max-bundle-frans <10000000>
Genome_build: hg19
Supplementary_files_format_and_content: matrix of fpkm values per sample

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq RNA v2; average insert size of 200 selected

treatment_protocol: Cells (in triplicate) were treated with vehicle (ethanol) or E2 (10-9 mol/L) for 6 hours

value: breast cancer

tag: expression

value: wildtype PELP1

value: vehicle


title: RNA-seq_D9_sgNTC_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D5_ad007


title: WTPELP_veh_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D5_ad006


title: RNA-seq_D9_sgKAT7_3

value: KAT7 Knock-down


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D5_ad004


title: RNA-seq_D9_sgKAT7_2


title: WTPELP_veh_1


title: RNA-seq_D9_sgKAT7_1


title: WTPELP_E2_3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D4_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D5_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D5_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D6_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D4_ad010


title: 293FT cells, shRNA NT replicate1

description: circFAM120A KD shRNA NT p(A)+ RNA-seq replicate1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_E10_ad012


title: WTPELP_E2_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D4_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D4_ad007


title: WTPELP_E2_1


title: RNA-seq_D9_WM_2

value: WM-3835 treated


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D4_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D4_ad004


title: RNA-seq_D9_WM_1


title: LXSN_veh_3

value: LXSN


title: RNA-seq_D9_DMSO_3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D4_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D4_ad001


title: RNA-seq_D9_DMSO_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D3_ad010


title: LXSN_veh_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D3_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D3_ad008


title: RNA-seq_D9_WM_3


title: RNA-seq_D9_DMSO_1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D3_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D3_ad006


title: RNA-seq_D4_WM_3

value: Gathered at day 4 (cultured)


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D3_ad002


title: RNA-seq_D4_WM_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D3_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D3_ad001


title: LXSN_E2_1


title: LXSN_E2_3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D2_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D2_ad010


title: CytoPELP_veh_3

value: cytoplasmic PELP1


title: RNA-seq_D4_WM_1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D2_ad008


title: CytoPELP_veh_2


title: LXSN_E2_2


title: LXSN_veh_1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D2_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D2_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D2_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D2_ad007


title: CytoPELP_E2_3


title: CytoPELP_veh_1


title: RNA-seq_D4_DMSO_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D2_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D12_ad012


title: Hi-C_WS-sgNTC-rep2

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Raw Hi-C sequencing data were firstly removed adaptors and low-quality reads, clean Hi-C reads were analyzed using the HiC-Pro pipeline. Reads were aligned to the human reference genome hg19 using bowtie2 with default options. Duplicate reads were removed, assigned to MboI restriction fragments, filtered for valid interactions, and then used to generate binned interaction matrices of both 5-kb, 40-kb, 100-kb, 500-kb and 1M resolution. These raw interaction matrices was normalized using ICE method.
Genome_build: UCSC human reference genome hg19 and UCSC drosophila reference genome dm6
Supplementary_files_format_and_content: abs.bed files include genomic regions (1st, 2nd, 3rd columns) and index number (4th column) which corresponds to matrix files. Matrix files include 3 columns, showing the contact number (3rd column) between region_1 (1st column) and region_2 (2nd column).

growth_protocol: MSCs were maintained in MEM-α medium (invitrogen) with 10% fetal bovine serum (FBS, Gemcell), 1% penicillin/streptomycin (Gibco), 10 ng/ml bFGF (JPC). Media was added and the cultured cells were expanded onto additional plates to keep cells at an appropriate culture density.

extract_protocol: Cells were cross-linked in 20ml of fresh ice-cold nuclear isolation buffer and 1ml of ~36% formaldehyde solution under a vacuum for 40min at room temperature. This reaction was quenched by the addition of 1ml of 2M glycine under vacuum filtration for an additional 5min. The clean samples were ground to powder in liquid nitrogen. The chromatin extraction procedure was similar to that used in the DNase I digestion experiment. The procedures were similar to those described previously. Briefly, chromatin was digested for 16h with 200 U (4  l) of MboI restriction enzyme at 37  C. DNA ends were labeled with biotin and incubated at 37  C for 45min, and the enzyme was inactivated with 20% SDS solution. DNA ligation was performed by the addition of T4 DNA ligase and incubation at 4  C for 1h, followed by 22  C for 4h. After ligation, the samples were incubated with proteinase K at 65  C overnight to reverse the cross-linking. DNA fragments were puri?ed and dissolved in 86  l of water. Unligated ends were then removed. Purified DNA was fragmented to a size of 300-500bp, and DNA ends were then repaired. DNA fragments labeled with biotin were finally separated with streptavidin C1 beads. Libraries were constructed with an Illumina TruSeq DNA Sample Prep Kit according to the manufacturer 's instructions. TA cloning was performed to examine the quality of the Hi-C library.

value: WS hMSCs


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D12_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D12_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D12_ad008


title: RNA-seq_D4_DMSO_1


title: CytoPELP_E2_1


title: CytoPELP_E2_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D12_ad001


title: Hi-C_WS-sgNTC-rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D12_ad007


title: Hi-C_WS-sgKAT7-rep2


title: RNA-seq_D4_DMSO_3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D12_ad006


title: Hi-C_WS-sgKAT7-rep1


title: ChIP-seq WS-NTC-input-rep2

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Raw ChIP-seq sequencing data were firstly removed adaptors with custom scripts, and then the clean reads were mapped to the reference genome (UCSC human hg19 or the custom combined reference) using bowtie2 (version: 2.2.3) with default parameters. For H3K14ac and H3K23ac, we mapped clean reads into the custom combined reference which was concatenated with human (hg19) and drosophila (dm6) genome, as previously reported. To build the combined reference, we labelled the drosophila reference genome chromosome names with ‘_dm6’ suffix so that we can easily separate the reads mapped into the human or drosophila furtherly. A custom alignment library was built for the combined reference with bowtie2. After mapping process, uniquely mapped reads were retained and then only reads mapped against human genome were removed duplicated reads with macs2 (version: 2.1.1.20160309). For H3K4me3 and H3K9me3, we directly mapped these ChIP-seq data into human genome hg19, and normalized ChIP-seq signal with the number of reads uniquely mapped into the human reference genome.
Genome_build: UCSC human reference genome hg19 and UCSC drosophila reference genome dm6
Supplementary_files_format_and_content: bigwig files include ChIP-seq signal value

extract_protocol: One million cells per sample were cross-linked by 1% vol/vol formaldehyde for 8 or 12 minutes at room temperature, if for acetylated ChIP, add additional 20 mM sodium butyrate. Samples were then re-suspended in lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, pH8.0) for 5 min on ice. Subsequently, lysates were sonicated using a Covaris S2 instrument.

value: H3K4me3 and H3K9me3 wild type input


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D11_ad010


title: normal tissue_normal_3

city: Hefei

first: yongwei

last: zhang

state: China

address: anhui medical university

institute: First Affiliated Hospital of Anhui Medical University

description:
12-Normal-6
non-tumor Circular RNA-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: normal tissue_normal_3

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit  (Qiagen).Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent   Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1μg   total RNA with RIN value above 7 was used for following library preparation. Next generation   sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext®   Ultra™ Directional RNA Library Prep Kit for Illumina®).
The rRNA was depleted from total RNA using Ribo-Zero™ rRNA removal Kit (Human/Mouse/Rat)  /(Yeast) /(Bacteria) (Illumina). The ribosomal depleted RNA was then fragmented and reverse-transcribed.   First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase with random primers and   Actinomycin D. The second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix   （include dACG-TP/dUTP）. The purified double-stranded cDNA by AxyPrep Mag PCR Clean-up   (Axygen) was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one   reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA   was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the   approximate insert size of 300 bp) were recovered. The dUTP-marked second strand was digested with  Uracil-Specific Excision Reagent (USER) enzyme (New England Biolabs). Each sample was then   amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can   anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for   multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated   using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit   2.0 Fluorometer (Invitrogen, Carlsbad, CA,USA).
circular RNA-Seq; libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument   according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out  using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the   HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.  The sequences were processed and analyzed by GENEWIZ.

tag: gender

value: Male

value: martched normal liver tissue


title: normal tissue_normal_2

description:
10-Normal-5
non-tumor Circular RNA-2

source_name: normal tissue_normal_2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D11_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D11_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D11_ad006


title: tumor tissue_HCC_2

description:
9-Tumor-5
tumor Circular RNA-2

source_name: tumor tissue,replicate 2

value: Hepatocellular carcinoma tissue


title: tumor tissue_HCC_3

description:
11-Tumor-6
tumor Circular RNA-3

source_name: tumor tissue,replicate 3


title: tumor tissue_HCC_1

description:
7-Tumor-4
tumor Circular RNA-1

source_name: tumor tissue,replicate 1


title: ChIP-seq WS-sgKAT7-input-rep2

source_name: CRISPR Screening

value: H3K4me3 and H3K9me3 KAT7 Knock-down input


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D10_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D10_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D10_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D10_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D10_ad010


title: ChIP-seq WS-sgNTC-H3K4me3-rep2

value: Wild type

tag: antibody

value: Abcam:anti-H3K4me3 (ab8580)


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D11_ad001

value: CA

value: male


title: ChIP-seq WS-NTC-input-rep1

value: H3K14ac and H3K23ac wild type input


title: ChIP-seq WS-sgKAT7-H3K4me3-rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D11_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D12_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D10_ad004


title: ChIP-seq WS-sgKAT7-input-rep1

value: H3K14ac and H3K23ac KAT7 Knock-down input


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D1_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D1_ad010


title: ChIP-seq WS-sgNTC-H3K4me3-rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D11_ad007


title: normal tissue_normal_1

description:
8-Normal-4
non-tumor Circular RNA-1

source_name: normal tissue_normal_1


title: ChIP-seq WS-sgKAT7-H3K4me3-rep2

value: KAT7 Knock-down


title: P16 KO biological rep 4

type: RNA

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

hyb_protocol: according to manufacturer's protocol

scan_protocol: according to manufacturer's protocol

data_processing: Preprocessing was performed in R using the RMA algorithm implemented in the oligo package of bioconductor.

label: biotin

source_name: primary hepatocytes

label_protocol: according to manufacturer's protocol

growth_protocol: Cells were plated and allowed to adhere overnight in Williams E media supplemented with 10% FBS, 100 nM insulin and 25 nM dexamethasone

extract_protocol: Total RNA was extracted by extract-all according to manufacturer's instructions

treatment_protocol: 16 hours after plating, cells were switched to DMEM 1 mM glucose media supplemented with 0.1% BSA and antibiotics (penicillin/streptomycin) for 8 hours.

tag: genotype/variation


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D10_ad002


title: P16 KO biological rep 3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D1_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D1_ad004


title: ChIP-seq WS-sgNTC-H3K23ac-rep2

value: Millipore:anti-H3K23ac (07-355)


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C9_ad012


title: ChIP-seq WS-sgNTC-H3K23ac-rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D1_ad002


title: P16 KO biological rep 2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D1_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C9_ad008


title: RNA-seq_WS-sgNTC-rep2

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Raw RNA-seq sequencing data were firstly removed adaptors and low-quality bases, and then the clean reads were mapped to the UCSC human hg19 reference genome using Tophat (version: 2.0.12) with default parameters. Reads counts were calculated with HTSeq, and gene expression levels are quantified with RPKM (reads per kilobase million).
Genome_build: UCSC human reference genome hg19 and UCSC drosophila reference genome dm6
Supplementary_files_format_and_content: RNA_expression.txt files include the read counts and RPKM of RefSeq genes

extract_protocol: For RNA-seq, total RNA was extracted by TRIzol (Invitrogen) at passage 4 post infection.


title: ChIP-seq WS-sgKAT7-H3K14ac-rep2

value: Millipore:anti-H3K14ac (07-353)


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C9_ad004


title: ChIP-seq WS-sgKAT7-H3K14ac-rep1


title: P16 KO biological rep 1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C9_ad001


title: P16 WT biological rep 3


title: TFEB-KO3

city: Saint John

first: Thomas

last: Pulinilkunnil

state: New Brunswick

address: 100 Tucker park road

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

data_processing:
For read alignment, we used read aligner analysis tools such as STAR and HISAT2. We also  used the pseudo aligners kallisto and Salmon. Quantification was performed directly with STAR, kallisto  and Salmon or with RSEM and StringTie for the pipelines producing real alignments
The mouse reference genome and transcriptome from version GRCm38 were used from the Ensembl web site (http://www.ensembl.org). In-house Perl scripts were used to sum the read counts at the transcript level for each gene and create a matrix comprising the read counts for all of the genes
Differential expression analysis was then performed on the data from that matrix using the R package  DESeq2 and edgeR
Each sample was assessed using the quality-control software RSeQC and the PtR script from the trinity suite
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene Id, gene name and CPM values for each each Sample

source_name: Heart

growth_protocol: Hearts were excised and adult mouse cardiomyocytes were isolated from WT and TFEB-/- mice prior to extract preparation

extract_protocol:
Total RNA from wild-type (WT) and TFEB-/- adult mouse cardiomyocytes were isolated using TRIzol. Sequencing libraries were prepared from 400 ng total RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA)
Samples were assessed for quality using a Bioanalyzer and quantified using a Qubit fluorometer. Libraries were then multiplexed and sequenced over one rapid run lane on the NextSeq 500 Sequencing System (Illumina), collecting a total of 409 million read pairs (2 x 75 bases). The number of read pairs per sample ranged from 14-75 million (median 21).

value: Heart

value: Cardiomyocyte

value: 3 months

value: TFEB-/-


title: P16 WT biological rep 4


title: TFEB-KO2


title: RNA-seq_WS-sgNTC-rep1

value: WS hMSCs


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C8_ad012


title: P16 WT biological rep 2


title: RNA-seq_WS-sgKAT7-rep2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_D1_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C8_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C8_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C9_ad010


title: P16 WT biological rep 1


title: WT3

value: wild type


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C8_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C8_ad004


title: WT2


title: RNA-seq_LUC-rep2

value: H9 hMSCs


title: RNA-seq_WS-sgKAT7-rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C7_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C7_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C9_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C7_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C7_ad002


title: TFEB-KO1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C8_ad001


title: RNA-seq_KAT7-rep2

value: KAT7 Over-expressed


title: RNA-Ovary_E135_MutFgf9_Mm_R2

city: Berlin

first: Francisca

last: Martinez Real

address: Ihnestrasse 73

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
For all samples 50bp paired-end reads were mapped against the respective genome (talOcc4, mm9) using STAR v2.6.1d (Dobin et al., 2013) with the following options: --chimSegmentMin 10   alignIntronMin 20   outFilterMismatchNoverReadLmax 0.05 --outFilterMismatchNmax 10 --outFilterMultimapNmax 5.
Genome_build: talOcc4, mm9

source_name: Ovary

extract_protocol:
RNA was extracted from the gonads using the RNeasy kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Gonads were disected rapidly after the animal was sacrified and then preserved in RNA later until the extraction

value: Mutant

value: Embryonic day 13.5


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C7_ad001

value: CA


title: 293FT cells, RfxCas13d circFAM120A gRNA1 replicate2

description: circFAM120A KD RfxCas13d gRNA1 (15nt + 15nt target sequences spanning BSJ) p(A)+ RNA-seq replicate2

value: 293FT cells

value: circFAM120A RfxCas13d/BSJ-gRNA KD


title: RNA-seq_KAT7-rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C6_ad012

value: male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C6_ad008


title: RNA-Ovary_E135_WtB6_Mm_R2

value: Wild type


title: RNA-Ovary_E135_MutFgf9_Mm_R1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C6_ad010


title: sgRNA HGPS-D45

description: sgRNA

data_processing:
Library strategy: CRISPR screen
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Raw CRISPR-Cas9 sequencing data were firstly removed adaptors and low-quality bases with custom scripts to obtain clean reads, and then sequencing data were analysis with MAGeCK1 (version: 0.5.7). At first, we obtained read counts from individual samples with the count command in MAGeCK, in which process the software fastqc was used to assess the quality of sequencing data, and reads from high quality samples were mapped to the screening library. Then, we identified top positively selected and negative selected sgRNAs with the test command in MAGeCK, and in this process, read counts were normalized based on “total count normalization” to exclude the effect of sequencing depth, and then the robust rank aggregation (α-RRA) algorithm was used to calculate RRA score which reflects the degree of positive or negative selection.
Genome_build: UCSC human reference genome hg19 and UCSC drosophila reference genome dm6
Supplementary_files_format_and_content: count.txt files include the sgRNA counts.

extract_protocol: Enough cells were maintained during the CRISPR-Cas9 screening process in order to prevent loss of constructs with low initial counts, or over-representation of constructs with higher initial counts. Cells were harvested and DNA was extracted 28, 42 days post-infection (day28, day42), as well as at the end of the experiment (day56) using the Qiagen DNeasy Blood and Tissue Kit to evaluate library representation at middle and final time points. And the initial point are represented by plasmid sequencing. PCR on gDNA was performed using PrimeSTAR HS DNA Polymerase following manufacturer’s instructions (Takara). A two-step PCR method was used to amplify inserted sgRNA sequences and append molecular barcodes and Illumina adapter sequences. In the first PCR, primers were designed to target the flanking sgRNA sequences with a biotin in forward primer. Reaction conditions were as follows: 98 °C denature for 2 minutes followed by 14cycles of 98 °C for 10 seconds, 58.0 °C anneal for 30 seconds, 72 °C extension for 40 seconds, and a final single extension step at 72 °C for 5 minutes. Multiple reactions per library were performed to ensure adequate input library coverage, then combined and purified by C1 beads (Invitrogen) and used as a template for the second PCR. The second PCR primers added the Illumina Hi-Seq2500 adapter sequences and barcode sequences. The reaction conditions were the same as the first PCR except only 12 cycles were used.

treatment_protocol: Genome-scale CRISPR Knock-Out (GeCKO) v2.0 was purchased from Addgene for application in all lentiCRISPRv2 library screens. Version A and Version B are pooled in together. Virus was subsequently concentrated and titered. Infection was performed at a calculated MOI=0.3~0.4, with an expected library coverage of 100x for each individual infection.

value: LMNA608G Knock-in heterozygous (day 45)

value: HGPS hMSCs


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C6_ad004


title: sgRNA D56

description: sgRNA

value: WRN Knock-out (day 56)


title: RNA-seq_LUC-rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C6_ad007


title: sgRNA D42

description: sgRNA

value: WRN Knock-out (day 42)


title: RNA-Ovary_E135_WtB6_Mm_R1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C6_ad002


title: WT1

value: Heart

value: Cardiomyocyte

value: 3 months


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C5_ad012


title: sgRNA D28

description: sgRNA

value: WRN Knock-out (day 28)

value: WS hMSCs


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C5_ad010


title: RNA-Testis_10wks_Wt_Mm-R1

source_name: Testis

value: Adult


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C6_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C5_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C5_ad006


title: RNA-Testis_10wks_Wt_Mm-R2


title: RNA-Ovary_10wks_Wt_Mm-R2


title: RNA-Ovary_10wks_Wt_Mm-R1


title: PO_IMVD_023_Control_Pull_Rep5_Purified_orfEnd_5p

city: New York

first: Panos

last: Oikonomou

state: New York

address: 1150 St. Nicholas Ave

department: Biological Sciences

institute: Columbia University

description:
5' ORF Reads
inVivoDisplay_PO_Supplementary_Table_5_CoIP_Controls.xlsx

data_processing:
Library strategy: in vivo mRNA display
clip 3' universal adapter sequence with cutadapt
clip  5' custom index sequence and demultiplex with cutadapt
Reads aligned with bowtie2  version 2.2.6 to the 5’ and 5’ ends of S. Cerevisiae ORFs
Final matrix of log2(Counts) generated with a custom script in python 2.7.15
Genome_build: SGD genome version R64-1-1
Supplementary_files_format_and_content: xlsx

organism: Saccharomyces cerevisiae

source_name: co-Purification: Control Purified Sample Replicate Rep5

growth_protocol: Cell were induced in SC -URA -MET dropout media at OD660 ~0.05-0.1 and grown for 6-8 hours to OD ~0.75

extract_protocol:
RNA was extracted using Trizol
in vivo mRNA display libraries were subjected to RT, 2nd Strand Synthesis with construct specific primers, followed by RE digestion, y-Linker ligation and amplification with flanking illumina sequences

value: Liquid Culture

tag: protocol

value: in vivo mRNA display

tag: growth stage

value: Exponential

tag: fixed

value: No

tag: sequenced molecule

value: cDNA


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C5_ad002

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C4_ad010

tag: age

tag: strain


title: RNA-Testis_P7_Wt_Mm_R2

tag: genotype

value: Wild type

value: Post-partum day 7


title: PO_IMVD_023_Control_Pull_Rep5_Purified_orfEnd_3p

description:
3' ORF Reads
inVivoDisplay_PO_Supplementary_Table_5_CoIP_Controls.xlsx

tag: tissue


title: PO_IMVD_023_Control_Pull_Rep5_Input_Lysate_orfEnd_5p

source_name: co-Purification: Control Input Lysate Replicate Rep5


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C4_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C5_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C4_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C4_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C4_ad004


title: PO_IMVD_022_Control_Pull_Rep4_Purified_orfEnd_5p

source_name: co-Purification: Control Purified Sample Replicate Rep4


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C4_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C4_ad001


title: PO_IMVD_023_Control_Pull_Rep5_Input_Lysate_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C4_ad002


title: RNA-Testis_P7_Wt_Mm_R1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C8_ad010


title: PO_IMVD_022_Control_Pull_Rep4_Purified_orfEnd_3p


title: RNA-Ovary_P7_Wt_Mm_R1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C3_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C3_ad010


title: sgRNA control

description: sgRNA

value: Wild type (day 0)

tag: cell type

value: plasmid only


title: PO_IMVD_022_Control_Pull_Rep4_Input_Lysate_orfEnd_5p

source_name: co-Purification: Control Input Lysate Replicate Rep4


title: RNA-Testis_E135_Wt_Mm_R1

value: Embryonic day 13.5


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C3_ad007


title: RNA-Testis_E135_Wt_Mm_R2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C3_ad008


title: PO_IMVD_022_Control_Pull_Rep4_Input_Lysate_orfEnd_3p


title: RNA-Ovary_E135_Wt_Mm_R2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C3_ad006


title: RNA-Ovary_E135_Wt_Mm_R1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C3_ad002


title: RNA-Ovary_P7_Wt_Mm_R2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C3_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C3_ad001


title: PO_IMVD_021_Control_Pull_Rep3_Purified_orfEnd_3p

source_name: co-Purification: Control Purified Sample Replicate Rep3


title: PO_IMVD_021_Control_Pull_Rep3_Input_Lysate_orfEnd_5p

source_name: co-Purification: Control Input Lysate Replicate Rep3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C2_ad006


title: J_7139_het_sc

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

data_processing:
Basecalling: bcl2fastq2 v. 2.19.1
Read alignment: GSNAP version 2018-07-04 called with args: gsnap.sse42 -D /projects/seq-work/user/pipeline/gmap -d mm10 --gunzip -A sam -t 16 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-92.ss.mm10.iit --read-group-id=L41733_J_7075_hom_sc --read-group-name=J_7075_hom_sc --read-group-library=L41733 --read-group-platform=illumina fastq/L41733_J_7075_hom_sc_R1.fastq.gz
Counts per feature: featureCounts v1.6.3; Command:"featureCounts" "-a" "/projects/seq-work/user/pipeline/annotation/mus_musculus/mm10/EnsemblGene-92.mm10.TR.gt f" "-s" "0" "-o" "genecount/bfx1243.mm10.e92.txt" "-Q" "1" "-T" "8" "--tmpDir" "/tmp/709805.1.ngs.q" "gsnap/L41741_J_7134_het_sc.bam" "gsnap/L41736_J _7100_het_sc.bam" "gsnap/L41742_J_7135_hom_sc.bam" "gsnap/L41733_J_7075_hom_sc.bam" "gsnap/L41735_J_7096_hom_sc.bam" "gsnap/L41743_J_7136_hom_sc.bam"  "gsnap/L41734_J_7079_het_sc.bam" "gsnap/L41744_J_7139_het_sc.bam"
Read count normalization: The raw read counts (absolute number of reads) were normalized with the DESeq2 R package (v. 1.22.2)(Anders and Huber, 2010)
Genome_build: mm10
Supplementary_files_format_and_content: bfx1243.mm10.e92.txt.original.csv: tab delimited file with raw readcounts per gene (rows) and sample (columns) (featureCounts output)
Supplementary_files_format_and_content: bfx1243.normalised_counts.de-expl.csv: tab delimited file with sample size normalized counts (with DESeq2) per gene (rows) and sample (columns)

source_name: intestine

extract_protocol:
At 10 days after the induction of mutagenesis, intestinal crypts were dissociated into single cells with TrypLE Express (Thermo Fisher Scientific) for 30min at 37°C. Dissociated cells were passed through 70µm cell strainer and washed wit 5% FBS/PBS. Cells were stained with APC-conjugated anti-326 (EpCAM) antibody and Alexa-Fluor 700 CD45 antibody for 45min on ice. Stained cells were collected by centrifugation and resuspended in SYTOX blue dead cell stain. FACS sorting was performed on a FACS AriaTM III cell sorter (BD).
Cells are FACsorted into a PCR tube containing 2 ul of nuclease free water with 0.2% Triton-X 100 and 4 U murine RNase Inhibitor (NEB), spun down and frozen at -80°C. After thawing the samples, RNA is denatured for 3 minutes at 72 °C in the presence of 2.4 mM dNTP (Invitrogen), 240 nM dT-primer* and 4 U RNase Inhibitor (NEB). The reverse transcription and addition of the template switch oligo is performed at 42°C for 90 min after filling up to 10 µl with RT buffer mix for a final concentration of 1x superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. The reverse transcriptase is inactivated at 70 °C for 15 min. The single stranded cDNA is subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at a 1x concentration together with 250 nM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 16 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 1x volume of Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5 % (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA quality and concentration is determined with the Fragment Analyzer (Agilent). For library preparation 1.5 ng cDNA was tagmented using 0.5 µl TruePrep Tagment Enzyme V50 and 1x TruePrep Tagment Buffer L (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme), followed by an incubation step at 55 °C for 10 min. Next, Illumina indices are added during PCR (72 °C 3 min, 98 °C 30 sec, 12 cycles [98 °C 10 sec, 63 °C 20 sec, 72 °C 1 min], 72°C 5 min) with 1x concentrated KAPA Hifi HotStart Ready Mix and 300 nM dual indexing primers. After PCR, libraries are purified twice with 1x volume Sera-Mag SpeedBeads and quantified with the Fragment Analyzer, followed by Illumina sequencing on a Nextseq500 with a sample sequencing depth of 30 mio reads on average.
*dT-primer: C6-aminolinker-AAGCAGTGGTATCAACGCAGAGTCGACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN, where N represents a random base and V any base beside thymidine; TSO-primer: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG, where rG stands for ribo-guanosine; UP-primer: AAGCAGTGGTATCAACGCAGAGT

treatment_protocol: Mutagenesis was induced in 4-6 weeks old mice by intraperitoneal injections of tamoxifen (50mg/kg, diluted 1:10 in sunflower oil) on 3 consecutive days.

tag: developmental stage

value: adult

tag: tag

value: beta-cateninGOF; Mll1+/- (control)

value: intestine


title: J_7136_hom_sc

value: beta-cateninGOF; Mll1-/- (knockout)


title: PO_IMVD_021_Control_Pull_Rep3_Input_Lysate_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C2_ad004

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column


title: J_7135_hom_sc


title: PO_IMVD_020_Control_Pull_Rep2_Purified_orfEnd_5p

source_name: co-Purification: Control Purified Sample Replicate Rep2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C2_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C2_ad002


title: J_7134_het_sc


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C12_ad012


title: PO_IMVD_020_Control_Pull_Rep2_Input_Lysate_orfEnd_5p

source_name: co-Purification: Control Input Lysate Replicate Rep2


title: J_7100_het_sc


title: PO_IMVD_020_Control_Pull_Rep2_Purified_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C2_ad012


title: J_7096_hom_sc


title: PO_IMVD_021_Control_Pull_Rep3_Purified_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C12_ad001


title: PO_IMVD_020_Control_Pull_Rep2_Input_Lysate_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C12_ad006


title: J_7079_het_sc


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C12_ad002


title: PO_IMVD_019_Control_Pull_Rep1_Purified_orfEnd_5p

source_name: co-Purification: Control Purified Sample Replicate Rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C12_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C2_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C11_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C11_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C12_ad007


title: input RAD21

city: Fontenay aux Roses

first: Germain

last: Rousselet

address: 18 route du Panorama

department: Cellular and Molecular Radiobiology (IRCM)

institute: CEA

data_processing:
Sequences were trimmed with Cutadapt 1.5
Alignment on the mm9 version of the mouse genome was done with Bowtie 2.
Peak calling was performed with MACS with default settings.
Co-localization of peaks was analyzed with seqMINER.
Genome_build: mm9
Supplementary_files_format_and_content: bw

source_name: RAW264.7 input RAD21

growth_protocol: RAW264.7 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, ThermoFisher) supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37°C, 5% CO2. Mycoplasma contamination was checked every 6 months with the MycoAlert detection kit (Lonza)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature, and chromatin was sonicated to 100-500 bp fragments in 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH8 with a Bioruptor Pico sonication device (Diagenode). Lysates were precleared with Dynabeads (ThermoFisher), and 1% was sampled as the input. They were then incubated overnight at 4°C with antibodies against mouse CTCF (Millipore #07-729) or mouse RAD21 (Abcam ab992) and then 3 h with saturated Dynabeads. After extensive washing, beads were eluted in 1% sodium dodecyl sulfate, 100 mM NaHCO3, and decrosslinked overnight at 65°C. The immunoprecipitated DNA was purified by phenol extraction and precipitation.
Sequencing libraries were prepared from 1 ng DNA using the MicroPlex kit (Diagenode) according to the manufacturer’s protocol. DNA was repaired and end-blunted by enzymatic treatment. Stem-loop adaptors with blocked 5’ ends were ligated to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The 3’ ends of the genomic DNA were extended to complete library synthesis and Illumina-compatible indexes were added through amplification. Libraries were purified using AMPure XP beads (Beckman Coulter) and quantified using Qbit fluorometer. Libraries fragment size distribution was verified using the Bioanalyzer high sensitivity DNA chip (Agilent Technologies). Libraries were pooled and spike-in PhiX Control v3 (Illumina) was added. Clusters were generated and sequenced using a Nextseq 500 instrument (Illumina) in single read mode (75 cycles)

tag: cell line

value: murine myeloid cells


title: PO_IMVD_019_Control_Pull_Rep1_Purified_orfEnd_3p

value: Liquid Culture


title: PO_IMVD_018_SAM2_Pull_Rep4_Purified_orfEnd_5p

description:
5' ORF Reads
inVivoDisplay_PO_Supplementary_Table_6_CoIP_SAM2.xlsx

source_name: co-Purification: SAM2 Purified Sample Replicate Rep4

value: in vivo mRNA display


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C11_ad001

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C2_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C12_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C12_ad008


title: ChIP-seq RAD21

source_name: RAW264.7 ChIP-seq RAD21

tag: chip antibody

value: RAD21 (Abcam ab992)


title: input CTCF

source_name: RAW264.7 input CTCF


title: PO_IMVD_018_SAM2_Pull_Rep4_Purified_orfEnd_3p

description:
3' ORF Reads
inVivoDisplay_PO_Supplementary_Table_6_CoIP_SAM2.xlsx

value: Exponential

value: No


title: PO_IMVD_018_SAM2_Pull_Rep4_Input_Lysate_orfEnd_5p

source_name: co-Purification: SAM2 Input Lysate Replicate Rep4

value: cDNA


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C10_ad010

value: CA

value: male


title: ChIP-seq CTCF

source_name: RAW264.7 ChIP-seq CTCF

value: CTCF (Millipore #07-729)


title: PO_IMVD_018_SAM2_Pull_Rep4_Input_Lysate_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C11_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C11_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C11_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C10_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C10_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C10_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C10_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C11_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C10_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C10_ad004


title: PO_IMVD_017_SAM2_Pull_Rep3_Purified_orfEnd_3p

source_name: co-Purification: SAM2 Purified Sample Replicate Rep3


title: PO_IMVD_017_SAM2_Pull_Rep3_Input_Lysate_orfEnd_5p

source_name: co-Purification: SAM2 Input Lysate Replicate Rep3


title: PO_IMVD_017_SAM2_Pull_Rep3_Purified_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C1_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C1_ad012


title: PO_IMVD_017_SAM2_Pull_Rep3_Input_Lysate_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C1_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C11_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C1_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C1_ad006


title: J_7075_hom_sc


title: PO_IMVD_016_SAM2_Pull_Rep2_Purified_orfEnd_5p

source_name: co-Purification: SAM2 Purified Sample Replicate Rep2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C1_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C1_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_C1_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B9_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B9_ad012


title: PO_IMVD_016_SAM2_Pull_Rep2_Input_Lysate_orfEnd_3p

source_name: co-Purification: SAM2 Input Lysate Replicate Rep2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B9_ad008


title: PO_IMVD_015_SAM2_Pull_Rep1_Purified_orfEnd_5p

source_name: co-Purification: SAM2 Purified Sample Replicate Rep1


title: OVA DOCK8+ CD4_1 (OVA_DOCK8_p_CD4_1)

city: Kato

first: Shunichi

last: Shiozawa

address: 944-25 Fujita

country: Japan

institute: Institute for Rheumatic Diseases

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: splenic DOCK8+ CD4 T cell, mouse immunized 12x with OVA

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: BALB/c

value: spleen

tag: treatment

value: 12x with OVA


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B9_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B8_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B9_ad004


title: HC20

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

data_processing:
Sequencing reads were quality checked and mapped to the hg19 using BWA or Bowtie (for circRNAs) or STAR (for linear RNAs)
CircRNA prediction was performed by find_circ, version 1.0, and CIRI2 adhering to the recommendation by the authors.  For find_circ, an increased stringency threshold was used requiring that both adaptor sequences map with highest possible mapping quality (mapq = 40). Moreover, only circRNAs supported by at least two reads in a given sample and found by both algorithms were used in subsequent analyses. CircRNA expression was based on back-spliced junction (BSJ)-spanning reads according to CIRI2 quantification.
HTSeq was used to quantify expression of genecode annotated genes  (gencode v28) in a strand-specific manner.
Differential expression analysis was performed using DESeq2 in R-studio and specifying a design formula (~condition + sex) that controls the effect of the sex while contrasting the different conditions (MS vs HC or SP-MS vs RR-MS). Sex was not included as a covariable when the analyses were limited to individuals of one sex. Transcripts (both linear or circular) with an absolute fold-change (FC) value higher than 1,5 (FC >|1.5|) and a p-value less than 0.05 (p<0.05) were considered differentially expressed
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table (coma separate value file) with raw gene counts for all detected circRNA and every sample
Supplementary_files_format_and_content: Matrix table (coma separate value file) with raw gene counts for all detected linearRNAs and every sample

source_name: Leukocytes

extract_protocol:
Whole blood was collected, erythrocytes were lysed with Buffer EL (Qiagen) and total RNA was isolated from the leukocytes with the miRNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
After RNA quality control and quantification, rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit and followed by purification and fragmentation steps. To construct the sequencing libraries, a strand-specific cDNA synthesis was performed, the 3’ ends were adenylated and adaptors were ligated. The resulting libraries were subjected to quality control and normalization process. Paired-end sequencing was performed with Illumina HiSeq PE150 and an average of 10Gb of data were obtained per sample

value: Blood

value: Leukocytes

tag: disease state

value: Healthy controls

tag: ms type

value: Female


title: HC19


title: HC18


title: OVA DOCK8- CD4_1 (OVA_DOCK8_m_CD4_1)

source_name: splenic DOCK8- CD4 T cell, mouse immunized 12x with OVA


title: OVA DOCK8+ CD4_2 (OVA_DOCK8_p_CD4_2)


title: PO_IMVD_015_SAM2_Pull_Rep1_Input_Lysate_orfEnd_5p

source_name: co-Purification: SAM2 Input Lysate Replicate Rep1

tag: protocol

tag: growth stage


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B8_ad010


title: PO_IMVD_016_SAM2_Pull_Rep2_Purified_orfEnd_3p

tag: fixed

tag: sequenced molecule


title: PBS CD4_1

source_name: splenic CD4 T cell, control mouse immunized with PBS

value: PBS


title: OVA DOCK8- CD4_2 (OVA_DOCK8_m_CD4_2)


title: HC15

tag: Sex


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B8_ad008

tag: brain region

tag: age


title: PBS CD4_2

tag: strain


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B8_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B9_ad002


title: HC14

tag: tissue


title: PO_IMVD_016_SAM2_Pull_Rep2_Input_Lysate_orfEnd_5p

value: Liquid Culture


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B8_ad006


title: PO_IMVD_014_ARC40_Pull_Rep4_Purified_orfEnd_5p

source_name: co-Purification: ARC40 Purified Sample Replicate Rep4

value: in vivo mRNA display


title: HC13

tag: cell type


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B8_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B8_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B8_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B7_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B7_ad008


title: PO_IMVD_015_SAM2_Pull_Rep1_Input_Lysate_orfEnd_3p


title: HC16


title: HC12


title: PO_IMVD_015_SAM2_Pull_Rep1_Purified_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B7_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B7_ad006


title: HC11


title: PO_IMVD_014_ARC40_Pull_Rep4_Input_Lysate_orfEnd_3p

source_name: co-Purification: ARC40 Input Lysate Replicate Rep4


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B7_ad004

source_name: C57BL/6J Male P56 Mouse Brain


title: HC10


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B7_ad002


title: PO_IMVD_013_ARC40_Pull_Rep3_Purified_orfEnd_5p

source_name: co-Purification: ARC40 Purified Sample Replicate Rep3


title: PO_IMVD_013_ARC40_Pull_Rep3_Purified_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B6_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B7_ad001


title: PO_IMVD_013_ARC40_Pull_Rep3_Input_Lysate_orfEnd_5p

source_name: co-Purification: ARC40 Input Lysate Replicate Rep3


title: HC09


title: HC08


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B6_ad008


title: PO_IMVD_014_ARC40_Pull_Rep4_Input_Lysate_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B6_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B6_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B7_ad012


title: HC17


title: PO_IMVD_013_ARC40_Pull_Rep3_Input_Lysate_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B6_ad007


title: HC06

value: Male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B5_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B6_ad001


title: HC05


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B5_ad008


title: PO_IMVD_012_ARC40_Pull_Rep2_Purified_orfEnd_5p

source_name: co-Purification: ARC40 Purified Sample Replicate Rep2

value: Exponential


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B5_ad010


title: PO_IMVD_012_ARC40_Pull_Rep2_Input_Lysate_orfEnd_5p

source_name: co-Purification: ARC40 Input Lysate Replicate Rep2

value: No


title: PO_IMVD_012_ARC40_Pull_Rep2_Purified_orfEnd_3p

value: cDNA


title: HC04


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B5_ad004

value: CA


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B5_ad001

value: male


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B5_ad006


title: PO_IMVD_012_ARC40_Pull_Rep2_Input_Lysate_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B5_ad002


title: HC02


title: HC07


title: HC01


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B4_ad008


title: PO_IMVD_011_ARC40_Pull_Rep1_Purified_orfEnd_3p

source_name: co-Purification: ARC40 Purified Sample Replicate Rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B4_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B4_ad006


title: PO_IMVD_011_ARC40_Pull_Rep1_Purified_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B4_ad004


title: SPMS09

value: Multiple sclerosis

value: Secondary-progressive MS


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B3_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B4_ad010


title: SPMS10


title: HC03


title: PO_IMVD_011_ARC40_Pull_Rep1_Input_Lysate_orfEnd_3p

source_name: co-Purification: ARC40 Input Lysate Replicate Rep1


title: PO_IMVD_011_ARC40_Pull_Rep1_Input_Lysate_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B3_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B5_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B3_ad004


title: SPMS08


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B3_ad008


title: PO_IMVD_010_CrudeMito_Rep3_Supernatant_orfEnd_3p

description:
3' ORF Reads
inVivoDisplay_PO_Supplementary_Table_4_Crude_Mitochondrial.xlsx

source_name: Crude Mitochondrial Purification: Supernatant Replicate Rep3


title: PO_IMVD_010_CrudeMito_Rep3_Pellet_orfEnd_5p

description:
5' ORF Reads
inVivoDisplay_PO_Supplementary_Table_4_Crude_Mitochondrial.xlsx

source_name: Crude Mitochondrial Purification: Pellet Replicate Rep3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B4_ad001


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B3_ad001


title: PO_IMVD_010_CrudeMito_Rep3_Supernatant_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B3_ad006


title: SPMS05


title: PO_IMVD_010_CrudeMito_Rep3_Pellet_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B3_ad002


title: SPMS07


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B2_ad012


title: SPMS06


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B2_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B2_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B2_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B2_ad004


title: SPMS04


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B2_ad002


title: PO_IMVD_009_CrudeMito_Rep2_Supernatant_orfEnd_3p

source_name: Crude Mitochondrial Purification: Supernatant Replicate Rep2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B12_ad010


title: PO_IMVD_009_CrudeMito_Rep2_Pellet_orfEnd_5p

source_name: Crude Mitochondrial Purification: Pellet Replicate Rep2


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B12_ad012


title: SPMS02

source_name: Leukocytes


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B12_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B12_ad008


title: SPMS01


title: PO_IMVD_009_CrudeMito_Rep2_Pellet_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B12_ad001


title: PO_IMVD_009_CrudeMito_Rep2_Supernatant_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B12_ad004


title: RRMS20

value: Relapsing-remitting MS


title: RRMS19


title: PO_IMVD_008_CrudeMito_Rep1_Supernatant_orfEnd_5p

source_name: Crude Mitochondrial Purification: Supernatant Replicate Rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B12_ad007


title: PO_IMVD_008_CrudeMito_Rep1_Supernatant_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B11_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B11_ad002


title: RRMS18


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B11_ad006


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B11_ad007


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B11_ad012


title: PO_IMVD_008_CrudeMito_Rep1_Pellet_orfEnd_3p

source_name: Crude Mitochondrial Purification: Pellet Replicate Rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B11_ad004


title: PO_IMVD_007_Library_DisplayScore_Rep4_Purified_orfEnd_5p

description:
5' ORF Reads
inVivoDisplay_PO_Supplementary_Table_3_Yeast_InVivo_mRNA_Library.xlsx

source_name: Library Display Score Estimation: Purified Sample Replicate Rep4


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B10_ad006


title: RRMS15


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B10_ad012


title: PO_IMVD_007_Library_DisplayScore_Rep4_Purified_orfEnd_3p

description:
3' ORF Reads
inVivoDisplay_PO_Supplementary_Table_3_Yeast_InVivo_mRNA_Library.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B10_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B10_ad004


title: RRMS14


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B10_ad008


title: SPMS03


title: PO_IMVD_008_CrudeMito_Rep1_Pellet_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B10_ad007


title: RRMS12


title: RRMS17


title: PO_IMVD_006_Library_DisplayScore_Rep3_Purified_orfEnd_5p

source_name: Library Display Score Estimation: Purified Sample Replicate Rep3


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B1_ad010


title: RRMS11


title: RRMS13


title: PO_IMVD_007_Library_DisplayScore_Rep4_Input_Lysate_orfEnd_3p

source_name: Library Display Score Estimation: Input Lysate Replicate Rep4


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B1_ad012

source_name: C57BL/6J Male P56 Mouse Brain


title: RRMS16


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B1_ad006


title: PO_IMVD_006_Library_DisplayScore_Rep3_Purified_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B1_ad008


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B1_ad007


title: RRMS10


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B1_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B1_ad004


title: CEMBA190305_11E_1_CEMBA190305_11E_2_B1_ad001


title: PO_IMVD_006_Library_DisplayScore_Rep3_Input_Lysate_orfEnd_3p

source_name: Library Display Score Estimation: Input Lysate Replicate Rep3


title: PO_IMVD_006_Library_DisplayScore_Rep3_Input_Lysate_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A9_ad007


title: PO_IMVD_005_Library_DisplayScore_Rep2_Purified_orfEnd_5p

source_name: Library Display Score Estimation: Purified Sample Replicate Rep2


title: RRMS09


title: PO_IMVD_007_Library_DisplayScore_Rep4_Input_Lysate_orfEnd_5p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A9_ad006


title: RRMS08


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A9_ad010


title: PO_IMVD_005_Library_DisplayScore_Rep2_Purified_orfEnd_3p


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A9_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A9_ad004


title: RRMS07


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A9_ad001


title: PO_IMVD_005_Library_DisplayScore_Rep2-AND-PO_IMVD_019_Control_Pull_Rep1_Input_Lysate_orfEnd_3p

description:
3' ORF Reads
inVivoDisplay_PO_Supplementary_Table_3_Yeast_InVivo_mRNA_Library.xlsx AND inVivoDisplay_PO_Supplementary_Table_5_CoIP_Controls.xlsx

source_name: Library Display Score Estimation: Input Lysate Replicate Rep2 AND co-Purification: Control Input Lysate Replicate Rep1


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A8_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A8_ad012


title: RRMS06


title: RRMS05


title: RRMS04


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A9_ad012


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A8_ad007


title: RRMS03


title: PO_IMVD_004_Library_DisplayScore_Rep1_Purified_orfEnd_5p

source_name: Library Display Score Estimation: Purified Sample Replicate Rep1


title: PO_IMVD_005_Library_DisplayScore_Rep2-AND-PO_IMVD_019_Control_Pull_Rep1_Input_Lysate_orfEnd_5p

description:
5' ORF Reads
inVivoDisplay_PO_Supplementary_Table_3_Yeast_InVivo_mRNA_Library.xlsx AND inVivoDisplay_PO_Supplementary_Table_5_CoIP_Controls.xlsx


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A8_ad006


title: PO_IMVD_004_Library_DisplayScore_Rep1_Purified_orfEnd_3p


title: RRMS02


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A8_ad004


title: RRMS01


title: PO_IMVD_004_Library_DisplayScore_Rep1_Input_Lysate_orfEnd_5p

source_name: Library Display Score Estimation: Input Lysate Replicate Rep1


title: PO_IMVD_004_Library_DisplayScore_Rep1_Input_Lysate_orfEnd_3p


title: PO_IMVD_003_Precision_antiFLAG_Purified_orfEnd_5p

description:
5' ORF Reads
inVivoDisplay_PO_Supplementary_Table_2_Precision.xlsx

source_name: Precision: antiFLAG Purification: Purified Sample


title: PO_IMVD_014_ARC40_Pull_Rep4_Purified_orfEnd_3p

source_name: co-Purification: ARC40 Purified Sample Replicate Rep4


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A8_ad002


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A7_ad010


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A7_ad012


title: PO_IMVD_003_Precision_antiFLAG_Purified_orfEnd_3p

description:
3' ORF Reads
inVivoDisplay_PO_Supplementary_Table_2_Precision.xlsx


title: PO_IMVD_003_Precision_antiFLAG_Input_Lysate_orfEnd_5p

source_name: Precision: antiFLAG Purification: Input Lysate Sample


title: gRNA library2 HT29 in vivo D30 replicate2

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
gRNA enrichment and deep sequencing datasets were removed adapters by cutadapt (1.16) using the following adapter sequences (R1: -a TTTTTTAAGCTTGGCGTAACTAGATCT -m 15, -g CCCTACCAACTGGTCGGGGTTTGAAAC -m 15; R2: -a GTTTCAAACCCCGACCAGTTGGTAGGG -m 15, -g AGATCTAGTTACGCCAAGCTTAAAAAA -m 15).
After removing adapters at 3' and 5' ends, processed reads were aligned to gRNA library sequences with Bowtie (v1.1.2, parameters: -v 3 -m 1 -k 1), and only uniquely-mapped reads were obtained for gRNA enrichment.
Uniquely-mapped reads for each unique gRNA were normalized to RPM.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt file (RPM of gRNA enrichment and deep sequencing datasets)

source_name: gRNA library2 HT29 in vivo D30

growth_protocol: HT29, HeLa and 293FT cells were purchased from the American Type Culture Collection (ATCC; http://www.atcc.org) or ThermoFisher, respectively, and were originally authenticated using STR profiling. HT29 cells were maintained in RPMI 1640, HeLa (human female origin) and 293FT cells (human fetus origin) were maintained in DMEM, and all supplemented with 10% Fetal Bovine Serum (FBS) and 0.1% penicillin/streptomycin. We maintained cell lines at 37°C in a 5% CO2 cell culture incubator and tested all cell lines routinely to exclude mycoplasma contamination.

extract_protocol:
Genomic DNA of screening cell samples were extracted with DNA EXTRACTION Kit (Tiangen)according to the manufacturer’s protocol.
For gRNA library analysis, genomic DNAs from HT29, 293FT and HeLa cells for screens were extracted. gRNA library was enriched by PCR amplification. Deep sequencing of amplified PCR products containing gRNA sequences was conducted by Illumina NextSeq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: To infect HeLa, 293FT or HT29 cells with lentivirus, cells were incubated with culture medium containing 10 μL concentrated lentivirus and 5 mg/mL polybrene (Sigma). Infected cells were treated with puromycin to increase knockdown efficiency.

value: HT29 cells

value: lentiviral gRNA library infection

tag: time


title: CEMBA190305_11E_1_CEMBA190305_11E_2_A7_ad006


title: PO_IMVD_003_Precision_antiFLAG_Input_Lysate_orfEnd_3p


title: gRNA library2 HT29 in vivo D30 replicate1


title: gRNA library2 HT29 in vivo D1 replicate2

source_name: gRNA library2 HT29 in vivo D1


title: PO_IMVD_002_Precision_antiMYC_Purified_orfEnd_5p

source_name: Precision: antiMYC Purification: Purified Sample


title: gRNA library1 HeLa in vitro D30 replicate2

source_name: gRNA library1 HeLa in vitro D30

value: HeLa cells