title: a8e4_4c4a-PBMC

description:
Sample a8e4_4c4a, age 7
Measured on EPIC array


title: f972_4900-CBMC

status: Public on Jun 04 2020

type: genomic

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

country: USA

institute: The University of Chicago

description:
Sample f972_4900, birth
Measured on EPIC array

hyb_protocol: Illumina Infinium

scan_protocol: Illumina IScan

data_processing:
1.) Remove probes with SNPs whose MAF is >= 0.05 in Africans, Americans or Europeans. 2.) Remove cross hybridizing probes; remove probes on sex chromosomes; remove probes with a detection pvalue >= 0.01 in more than 25% of the samples. 3.) Samples 7804_4bab-CBMC, a60f_493d-CBMC, f86d_4016-PBMC failed QC and were removed from downstream analysis. 4.) Normalize methylated and unmethylated probe intensities separately with normalize.quantile.450k(<Methylset_Object>, method = "quantile1"); this is from ENmix package, version 1.14.0. 5.) Remove probe-type bias with preprocessSWAN from the minfi package, version 1.24.0. 6.) Calculate M-values as log2(Processed unmethylated intensity + 100) - log2(Processed methylated intensity + 100). M-values were used in all downstream analyses.
Normalized Beta-value, calculated as (Normalized methylated intensity + 100)/{(Normalized methylated intensity + 100) + (Normalized unmethylated intensity + 100)}. The offset of 100 was recommended by Du et al., 2010

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Human cord blood at birth

label_protocol: Illumina Infinium

extract_protocol: DNA for methylation studies was extracted from thawed CBMCs and PBMCs using the Qiagen AllPrep kit (QIAGEN, Valencia, CA)

tag: tissue

value: Cord blood

tag: age

value: birth

tag: methylationplatenumber

tag: selfreportedrace

value: Black

tag: Sex

value: Male

tag: samplecollectionsite

value: St. Louis


title: PDIS9063-278

type: SRA

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
library strategy: RamDA-seq (random displacement amplification sequencing)
129 and CAST genomes by incorporating SNPs and indels into reference genome and transcriptome was created by Seqnature (Munger et al., 2014).
Bowtie (version 1.1.2) was used to align scRamDA-seq reads against the diploid transcriptome with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: ASEcount_G1_129.txt and ASEcount_G1_CAST.txt include read count data derived from 129 and CAST alleles, respectively, for each cell.

molecule: total RNA

organism: Mus musculus

source_name: 129/CAST hybrid mESC

growth_protocol: The hybrid mouse ES cell line F1-21.6 (129Sv-Cast/EiJ, female), a kind gift from Prof. Joost Gribnau, were grown on either Laminin-511 (LN511, BioLamina, Stockholm, Sweden) in  Std medium (15% fetal bovine serum [FBS] [Gibco], 0.1 mM β-mercaptoethanol [Wako Pure Chemicals, Osaka, Japan], 1000U/ml of leukemia inhibitory factor [LIF, Wako Pure Chemicals, Osaka, Japan]). This cell line was previously described in (Jonkers et al., 2009).

extract_protocol:
Single cells were collected in 1 μL of cell lysis buffer (1 U RNasein plus (Promega), 10% RealTime ready Cell Lysis Buffer (Roche), 0.3% NP40 (Thermo Fisher), and RNase-free water (TaKaRa)) in a 96-well PCR plate (BIOplastics). The cell lysates were denatured at 70 °C for 90 s and held at 4 °C until the next step. To eliminate genomic DNA contamination, 1 µL of genomic DNA digestion mix (0.5× PrimeScript Buffer, 0.2 U of DNase I Amplification Grade, 1: 5 000 000 ERCC RNA Spike-In Mix I (Thermo Fisher) in RNase-free water) was added to 1 µL of the denatured sample. The mixtures were agitated for 30 s at 2000 rpm using a ThermoMixer C at 4 °C, incubated in a C1000 thermal cycler at 30 °C for 5 min and held at 4 °C until the next step.
Library preparation for single-cell RamDA-Seq was performed as described previously (Hayashi et al., 2018).

tag: strain background

value: 129/CAST hybrid F1

tag: cell type

value: Embryonic stem cell


title: d902_4698-PBMC

description:
Sample d902_4698, age 7
Measured on EPIC array

source_name: Human PBMCs at age 7

value: PBMCs

value: age 7


title: Abf1 75 min IP Replicate 3

city: Utrecht

first: Wim

middle: J

last: de Jonge

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

description: ChIP of Abf1-aa-V5 cells 75 minutes after induction of nuclear depletion

library_source: genomic

data_processing:
Paired-end reads were aligned to the sacCer3 genome assembly (February 2011) using HISAT2 v2.0.5 (Kim et al, 2015) using the settings “--add-chrname -X 1000 --score-min L,0,-0.2 -k 1 --no-spliced-alignment -5 12 -3 6”
The bam files were filtered to keep only fragments with a unique combination of UMIs using the custom scripts “addumis2bam.sh” and “uniqify-umis.pl” available from https://github.com/wdejonge/DIVORSEQ.
Peaks were called using MACS2 v2.1.1.20160309 (Zhang et al, 2008) with the settings “-f BAMPE -g 1.25e7 --keep-dup all --mfold 5 2000 --call-summits -q 0.001 --fe-cutoff 2” using all three replicate t=0 time points (no depletion) versus their corresponding inputs,
To fit the exponential decay model, the bam files were centred and smoothed with a 101bp window, as described in (de Jonge et al, 2017). Subsequently, all samples were scaled to 1 million reads using genomecov from the bedtools2 suite v2.27 (Quinlan & Hall, 2010) which makes sure that total coverage across the genome is the same for all samples (1.01 x 10e8 bases).
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig files contain the binding of Abf1 (or WT) without depletion or after nuclear depletion for the indicated time. For all read pairs the center of the fragment was taken and extended 50 bp on both sides such that all fragments are 101 bp. The bw files were scaled to 1 million reads such that the genome coverage between all samples is the same (101 million bases).
Supplementary_files_format_and_content: The combined peak calls of all three 0 min samples versus their corresponding inputs are provided, with a fold enrichment cutoff of 2 and a q-value cutoff of 0.001. The broad peaks are provided in narrowPeak format (peaks + summits) and the summits are also provided in bed format.

organism: Saccharomyces cerevisiae

source_name: Cell culture

growth_protocol: Strains were streaked from -80oC stocks onto appropriate selection plates and grown for 3 days. Liquid cultures were inoculated with independent colonies and grown overnight (O/N) in Synthetic Complete (SC) medium: 2 gr/L Drop out mix Complete and 6.71 gr/L Yeast Nitrogen Base without AA, Carbohydrate & w/AS (YNB) from US Biologicals (Swampscott, USA) with 2% D-glucose. The following day O/N cultures were used to inoculate 100 ml cultures of SC media at OD595=0.20 and were grown for two doublings. All growth was done at 30oC.

extract_protocol:
ChIP was carried out a described (de Jonge et al., STAR protocols 2020: https://star-protocols.cell.com/protocols/71). All samples were cross-linked using a final concentration of 2% formaldehyde for 5 minutes and subsequently quenched with a final concentration of 1.5M Tris pH=8.0 for 1 minute.
Sequencing libraries were created from the purified DNA using a combination of the Nextflex Rapid DNA-Seq Kit (Bioo Scientific) and the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific) using a modified protocol.

treatment_protocol: Abf1 was depleted from the nucleus using the anchor-away system by adding rapamycin, dissolved in DMSO, to a final concentration of 7.5 µM for the time indicated. For the t=0 timepoints no rapamycin but the same amount of DMSO was added for 90 minutes.

tag: strain

tag: genotype

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4

value: MATalpha

tag: treatment

value: 75 minutes depletion (7.5µM rapamycin)

tag: chip antibody

value: anti-V5, Life Technologies, #R96025


title: 07ad_4bc0-PBMC

description:
Sample 07ad_4bc0, age 7
Measured on EPIC array

value: Female


title: Abf1 75 min IP Replicate 2


title: PDIS9063-270


title: WT 0 min input Replicate 2

description: Input of WT cells treated with DMSO

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT

value: no rapamycin (90 min DMSO)


title: 07ad_4bc0-CBMC

description:
Sample 07ad_4bc0, birth
Measured on EPIC array


title: d902_4698-CBMC

description:
Sample d902_4698, birth
Measured on EPIC array


title: 75de_4408-PBMC

description:
Sample 75de_4408, age 7
Measured on EPIC array

value: Hispanic


title: Abf1 75 min IP Replicate 1


title: PDIS9063-271


title: PDIS9063-269


title: 75de_4408-CBMC

description:
Sample 75de_4408, birth
Measured on EPIC array

value: Cord blood


title: 42b8_4d34-PBMC

description:
Sample 42b8_4d34, age 7
Measured on EPIC array


title: Abf1 60 min IP Replicate 3

description: ChIP of Abf1-aa-V5 cells 60 minutes after induction of nuclear depletion

value: 60 minutes depletion (7.5µM rapamycin)


title: PDIS9063-268


title: Abf1 60 min IP Replicate 2


title: 42b8_4d34-CBMC

description:
Sample 42b8_4d34, birth
Measured on EPIC array

value: birth

value: Black


title: PDIS9063-267


title: 27b6_49c0-PBMC

description:
Sample 27b6_49c0, age 7
Measured on EPIC array

value: St. Louis


title: 7a4b_4bc0-PBMC

description:
Sample 7a4b_4bc0, age 7
Measured on EPIC array


title: afd9_4a3c-PBMC

description:
Sample afd9_4a3c, age 7
Measured on EPIC array

value: Male


title: afd9_4a3c-CBMC

description:
Sample afd9_4a3c, birth
Measured on EPIC array


title: PDIS9063-265

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: 7a4b_4bc0-CBMC

description:
Sample 7a4b_4bc0, birth
Measured on EPIC array


title: 27b6_49c0-CBMC

description:
Sample 27b6_49c0, birth
Measured on EPIC array


title: PDIS9063-266


title: Abf1 60 min IP Replicate 1


title: Abf1 50 min IP Replicate 2

description: ChIP of Abf1-aa-V5 cells 50 minutes after induction of nuclear depletion

value: 50 minutes depletion (7.5µM rapamycin)


title: PDIS9063-264


title: e519_4818-CBMC

description:
Sample e519_4818, birth
Measured on EPIC array


title: e519_4818-PBMC

description:
Sample e519_4818, age 7
Measured on EPIC array

value: PBMCs

value: age 7


title: Abf1 40 min IP Replicate 2

description: ChIP of Abf1-aa-V5 cells 40 minutes after induction of nuclear depletion

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4

value: MATalpha

value: 40 minutes depletion (7.5µM rapamycin)


title: Abf1 40 min IP Replicate 3

value: anti-V5, Life Technologies, #R96025


title: c513_4773-PBMC

description:
Sample c513_4773, age 7
Measured on EPIC array

value: Female


title: 1066_402d-PBMC

description:
Sample 1066_402d, age 7
Measured on EPIC array


title: Abf1 50 min IP Replicate 1


title: c513_4773-CBMC

description:
Sample c513_4773, birth
Measured on EPIC array


title: 46fa_4aad-PBMC

description:
Sample 46fa_4aad, age 7
Measured on EPIC array


title: PDIS9063-261


title: PDIS9063-263


title: 46fa_4aad-CBMC

description:
Sample 46fa_4aad, birth
Measured on EPIC array


title: 1066_402d-CBMC

description:
Sample 1066_402d, birth
Measured on EPIC array


title: Abf1 40 min IP Replicate 1


title: PDIS9063-262


title: Abf1 50 min IP Replicate 3


title: cbc2_4320-PBMC

description:
Sample cbc2_4320, age 7
Measured on EPIC array


title: PDIS9063-260


title: PDIS9063-259


title: 0a13_43f4-PBMC

description:
Sample 0a13_43f4, age 7
Measured on EPIC array


title: Abf1 30 min IP Replicate 2

description: ChIP of Abf1-aa-V5 cells 30 minutes after induction of nuclear depletion

value: 30 minutes depletion (7.5µM rapamycin)


title: 0a13_43f4-CBMC

description:
Sample 0a13_43f4, birth
Measured on EPIC array

value: Cord blood


title: PDIS9063-258


title: cbc2_4320-CBMC

description:
Sample cbc2_4320, birth
Measured on EPIC array


title: Abf1 30 min IP Replicate 1


title: Abf1 30 min IP Replicate 3


title: a280_4aa3-CBMC

description:
Sample a280_4aa3, birth
Measured on EPIC array


title: PDIS9063-257


title: e0ac_46cc-CBMC

description:
Sample e0ac_46cc, birth
Measured on EPIC array


title: e0ac_46cc-PBMC

description:
Sample e0ac_46cc, age 7
Measured on EPIC array


title: Abf1 20 min IP Replicate 3

description: ChIP of Abf1-aa-V5 cells 20 minutes after induction of nuclear depletion

value: 20 minutes depletion (7.5µM rapamycin)


title: c18f_4818-CBMC

description:
Sample c18f_4818, birth
Measured on EPIC array

value: birth


title: PDIS9063-256


title: PDIS9063-255


title: c18f_4818-PBMC

description:
Sample c18f_4818, age 7
Measured on EPIC array

value: Black


title: Abf1 20 min IP Replicate 2


title: 1c92_4793-CBMC

description:
Sample 1c92_4793, birth
Measured on EPIC array

value: St. Louis


title: cdcd_4d4b-CBMC

description:
Sample cdcd_4d4b, birth
Measured on EPIC array


title: 1c92_4793-PBMC

description:
Sample 1c92_4793, age 7
Measured on EPIC array


title: cdcd_4d4b-PBMC

description:
Sample cdcd_4d4b, age 7
Measured on EPIC array


title: Abf1 20 min IP Replicate 1


title: PDIS9063-254


title: 26f6_4a54-PBMC

description:
Sample 26f6_4a54, age 7
Measured on EPIC array


title: 26f6_4a54-CBMC

description:
Sample 26f6_4a54, birth
Measured on EPIC array


title: PDIS9063-253


title: 12d8_4b2c-PBMC

description:
Sample 12d8_4b2c, age 7
Measured on EPIC array

value: Male


title: Abf1 15 min IP Replicate 3

description: ChIP of Abf1-aa-V5 cells 15 minutes after induction of nuclear depletion

value: 15 minutes depletion (7.5µM rapamycin)


title: a280_4aa3-PBMC

description:
Sample a280_4aa3, age 7
Measured on EPIC array


title: PDIS9063-252

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: 7a8b_490f-PBMC

description:
Sample 7a8b_490f, age 7
Measured on EPIC array

value: PBMCs


title: PDIS9063-251


title: 7a8b_490f-CBMC

description:
Sample 7a8b_490f, birth
Measured on EPIC array


title: Abf1 10 min IP Replicate 3

description: ChIP of Abf1-aa-V5 cells 10 minutes after induction of nuclear depletion

value: 10 minutes depletion (7.5µM rapamycin)


title: 5ef4_459d-PBMC

description:
Sample 5ef4_459d, age 7
Measured on EPIC array

value: age 7


title: Abf1 15 min IP Replicate 2

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4

value: MATalpha


title: PDIS9063-250


title: Abf1 10 min IP Replicate 2

value: anti-V5, Life Technologies, #R96025


title: Abf1 15 min IP Replicate 1


title: 5ef4_459d-CBMC

description:
Sample 5ef4_459d, birth
Measured on EPIC array

value: Female


title: PDIS9063-249


title: 75a1_4e15-CBMC

description:
Sample 75a1_4e15, birth
Measured on EPIC array


title: PDIS9063-246


title: 9069_4602-PBMC

description:
Sample 9069_4602, age 7
Measured on EPIC array

value: Mixed (>1 race)


title: Abf1 5 min IP Replicate 3

description: ChIP of Abf1-aa-V5 cells 5 minutes after induction of nuclear depletion

value: 5 minutes depletion (7.5µM rapamycin)


title: 9069_4602-CBMC

description:
Sample 9069_4602, birth
Measured on EPIC array

value: Cord blood


title: Abf1 5 min IP Replicate 2


title: Abf1 5 min IP Replicate 1


title: 12d8_4b2c-CBMC

description:
Sample 12d8_4b2c, birth
Measured on EPIC array

value: birth


title: 797f_4a4f-CBMC

description:
Sample 797f_4a4f, birth
Measured on EPIC array

value: Black


title: a768_4b98-PBMC

description:
Sample a768_4b98, age 7
Measured on EPIC array

value: St. Louis


title: PDIS9063-243


title: PDIS9063-242


title: Abf1 0 min IP Replicate 3

description: ChIP of Abf1-aa-V5 cells without nuclear depletion

value: no depletion (90 min DMSO)


title: Abf1 0 min IP Replicate 2


title: 94db_415e-PBMC

description:
Sample 94db_415e, age 7
Measured on EPIC array


title: PDIS9063-241


title: 94db_415e-CBMC

description:
Sample 94db_415e, birth
Measured on EPIC array


title: ec22_4e0e-CBMC

description:
Sample ec22_4e0e, birth
Measured on EPIC array

value: Male


title: 7527_417c-CBMC

description:
Sample 7527_417c, birth
Measured on EPIC array


title: ec22_4e0e-PBMC

description:
Sample ec22_4e0e, age 7
Measured on EPIC array


title: 75a1_4e15-PBMC

description:
Sample 75a1_4e15, age 7
Measured on EPIC array


title: PDIS9063-240

value: 129/CAST hybrid F1


title: PDIS9063-239

value: Embryonic stem cell


title: WT 90 min IP Replicate 3

description: ChIP of WT cells treated with rapamycin (90 min)

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT

value: 90 minutes rapamycin (7.5µM rapamycin)


title: PDIS9063-244


title: 995e_43b0-PBMC

description:
Sample 995e_43b0, age 7
Measured on EPIC array

value: PBMCs

value: age 7


title: e2d1_4b37-PBMC

description:
Sample e2d1_4b37, age 7
Measured on EPIC array

value: Hispanic

value: New York


title: 995e_43b0-CBMC

description:
Sample 995e_43b0, birth
Measured on EPIC array


title: WT 90 min IP Replicate 2

value: MATalpha

value: anti-V5, Life Technologies, #R96025


title: 797f_4a4f-PBMC

description:
Sample 797f_4a4f, age 7
Measured on EPIC array


title: d97a_46fb-PBMC

description:
Sample d97a_46fb, age 7
Measured on EPIC array

value: Female


title: a768_4b98-CBMC

description:
Sample a768_4b98, birth
Measured on EPIC array

value: Cord blood


title: d97a_46fb-CBMC

description:
Sample d97a_46fb, birth
Measured on EPIC array

value: birth


title: PDIS9063-237


title: PDIS9063-236


title: Abf1 0 min IP Replicate 1

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4


title: e2d1_4b37-CBMC

description:
Sample e2d1_4b37, birth
Measured on EPIC array


title: 1723_4ac8-PBMC

description:
Sample 1723_4ac8, age 7
Measured on EPIC array

value: Black


title: 1723_4ac8-CBMC

description:
Sample 1723_4ac8, birth
Measured on EPIC array


title: 7527_417c-PBMC

description:
Sample 7527_417c, age 7
Measured on EPIC array

value: St. Louis


title: WT 0 min IP Replicate 3

description: ChIP of WT cells treated with DMSO

value: no rapamycin (90 min DMSO)


title: WT 90 min IP Replicate 1


title: WT 0 min IP Replicate 2

description: ChIP of WT cells treated with DMSO


title: d605_43df-CBMC

description:
Sample d605_43df, birth
Measured on EPIC array

value: Male


title: 090a_4655-CBMC

description:
Sample 090a_4655, birth
Measured on EPIC array

value: Mixed (>1 race)


title: PDIS9063-235

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: d605_43df-PBMC

description:
Sample d605_43df, age 7
Measured on EPIC array

value: PBMCs


title: PDIS9063-234


title: Abf1 90 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 90 minutes after induction of nuclear depletion

data_processing:
Paired-end reads were aligned to the sacCer3 genome assembly (February 2011) using HISAT2 v2.0.5 (Kim et al, 2015) using the settings “--add-chrname -X 1000 --score-min L,0,-0.175 -5 10 -3 10 --dta -max-intronlen 1500 --rna-strandness RF”
The bam files were filtered to keep only fragments with a unique combination of UMIs using the custom scripts “addumis2bam.sh” and “uniqify-umis.pl” available from https://github.com/wdejonge/DIVORSEQ.
The 4tU-seq reads were assigned to genomic features using featureCounts from the subread package v1.6.5 (Liao et al, 2014). As an annotation file, transcription start site annotations from (van Bakel et al, 2013) were merged with the genome annotation from the Saccharomyces genome database (SGD) (Cherry et al, 2012) containing ORFs, tRNAs, rRNAs and snRNAs. The counts from the two independent sequence runs were combined.
Differential expression of the genomic features (genes) was calculated using the DESeq2 package v1.10.1 (Love et al, 2014) in R. Only genes with a fold change of more than 1.5 with an adjusted p-value < 0.01 after 20 minutes as well as 30 minutes of depletion were considered differentially expressed. The fold change in mRNA synthesis was calculated relative to t=0.
Genome_build: sacCer3
Supplementary_files_format_and_content: Raw counts table contains the raw counts of all samples after filtering for UMI duplicates. The ribosomal RNAs were excluded from this table.
Supplementary_files_format_and_content: Differential expression matrix contains log2 Fold Change (lFC) and adjusted p-values (padj) of all time points as obtained using DESeq2.

growth_protocol: Cells were grown for two doublings in synthetic complete (SC) medium containing 2% glucose. Rapamycin was added for the indicated amount of time at a final concentration of 7.5 uM (standard). 4-thiouracil (4tU) was added to a final concentration of 5 mM six minutes before harvesting by spinning at 3952 x g for 1 minute. The supernatant was decanted and the cells were snap-frozen in liquid nitrogen.

extract_protocol:
To isolate total RNA, cells were resuspended in Acid Phenol Chloroform (Sigma #P1944) and immediately mixed with the same volume of TES buffer (10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS). The samples were vortexed hard for 20 seconds, the tubes were covered in aluminium foil to keep the samples dark, and incubated in a 65oC water bath for 10 minutes. Next, the samples were transferred to 1.5 ml tubes and incubated in a thermomixer for 50 minutes at 65oC and 1400 rpm, while covered in aluminium foil. After incubation, samples were centrifuged at 18407g for 20 minutes at 4oC. The water phase was recovered and phenol extraction was repeated once, followed by extraction using chloroform-isoamyl-alcohol (25:1). The RNA was precipitated using sodium acetate (NaAc 3M, pH 5.2) and 100% ethanol (-20oC) by incubating at -20oC for at least 30 min. DTT was also added to a final concentration of 1mM to prevent oxidation of the 4tU. The pellet was washed once with 80% ethanol and resuspended to a final concentration of 1 μg/μl in sterile MQ. To recover nascent transcripts the protocol from (Dölken et al, 2008) was used with minor adaptations. In brief, 100 μg of cleaned RNA was heated to 60oC for 10 minutes and immediately put on ice for 2 minutes. The RNA was biotinylated by adding 200 μl Biotin-HPDP (Thermo Fisher Scientific #21341) dissolved to 1 mg/ml in 30% DMF. Unbound biotin was removed using chloroform extraction. Biotinylated RNA was separated from total RNA using streptavidin-conjugated magnetic beads and μMACs columns (Miltenyi Biotec #130-074-101). The beads were washed 6x using 65oC washing buffer (100 mM Tris pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween-20) and bound RNA was eluted using 200 μl of 100 mM DTT. The nascent RNA was purified using an RNeasy MinElute Cleanup Kit (Qiagen #74204).
Sequencing libraries were created from the 4tU-labelled RNA using the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific) with a slightly modified protocol.

value: 90 minutes depletion (7.5µM rapamycin)


title: WT 0 min IP Replicate 1

description: ChIP of WT cells treated with DMSO

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT


title: af19_4bef-PBMC

description:
Sample af19_4bef, age 7
Measured on EPIC array

value: age 7

value: Hispanic

value: New York


title: PDIS9063-238


title: af19_4bef-CBMC

description:
Sample af19_4bef, birth
Measured on EPIC array


title: 5aeb_466f-CBMC

description:
Sample 5aeb_466f, birth
Measured on EPIC array


title: PDIS9063-233


title: 8dab_416d-CBMC

description:
Sample 8dab_416d, birth
Measured on EPIC array

value: Female


title: Abf1 90 min 4tU-seq Replicate 2

value: MATalpha


title: 81f8_457f-PBMC

description:
Sample 81f8_457f, age 7
Measured on EPIC array


title: Abf1 90 min 4tU-seq Replicate 1


title: PDIS9063-232


title: PDIS9063-231


title: 090a_4655-PBMC

description:
Sample 090a_4655, age 7
Measured on EPIC array


title: Abf1 75 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 75 minutes after induction of nuclear depletion

value: 75 minutes depletion (7.5µM rapamycin)


title: f86d_4016-PBMC

description:
Sample f86d_4016, age 7
Measured on EPIC array


title: 81f8_457f-CBMC

description:
Sample 81f8_457f, birth
Measured on EPIC array

value: Cord blood

value: birth


title: PDIS9063-230


title: Abf1 75 min 4tU-seq Replicate 2

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4


title: f86d_4016-CBMC

description:
Sample f86d_4016, birth
Measured on EPIC array


title: c13f_4191-PBMC

description:
Sample c13f_4191, age 7
Measured on EPIC array

value: Black


title: Abf1 75 min 4tU-seq Replicate 1


title: 852c_401d-PBMC

description:
Sample 852c_401d, age 7
Measured on EPIC array


title: c13f_4191-CBMC

description:
Sample c13f_4191, birth
Measured on EPIC array


title: 852c_401d-CBMC

description:
Sample 852c_401d, birth
Measured on EPIC array


title: PDIS9063-228


title: PDIS9063-227


title: PDIS9063-226


title: db7d_4d13-PBMC

description:
Sample db7d_4d13, age 7
Measured on EPIC array


title: 5aeb_466f-PBMC

description:
Sample 5aeb_466f, age 7
Measured on EPIC array

value: Male


title: Abf1 60 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 60 minutes after induction of nuclear depletion

value: 60 minutes depletion (7.5µM rapamycin)


title: Abf1 60 min 4tU-seq Replicate 2


title: db7d_4d13-CBMC

description:
Sample db7d_4d13, birth
Measured on EPIC array


title: b05d_4f85-PBMC

description:
Sample b05d_4f85, age 7
Measured on EPIC array


title: Abf1 60 min 4tU-seq Replicate 1


title: 42d1_4945-CBMC

description:
Sample 42d1_4945, birth
Measured on EPIC array


title: PDIS9063-224

value: 129/CAST hybrid F1


title: 68f8_4d10-PBMC

description:
Sample 68f8_4d10, age 7
Measured on EPIC array


title: PDIS9063-223

value: Embryonic stem cell


title: 68f8_4d10-CBMC

description:
Sample 68f8_4d10, birth
Measured on EPIC array


title: 42d1_4945-PBMC

description:
Sample 42d1_4945, age 7
Measured on EPIC array

value: PBMCs


title: Abf1 50 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 50 minutes after induction of nuclear depletion

value: 50 minutes depletion (7.5µM rapamycin)


title: 5c27_4ef9-PBMC

description:
Sample 5c27_4ef9, age 7
Measured on EPIC array


title: PDIS9063-222


title: Abf1 50 min 4tU-seq Replicate 2


title: PDIS9063-221


title: 9747_46ec-PBMC

description:
Sample 9747_46ec, age 7
Measured on EPIC array


title: Abf1 50 min 4tU-seq Replicate 1


title: 3c61_4020-PBMC

description:
Sample 3c61_4020, age 7
Measured on EPIC array


title: 3c61_4020-CBMC

description:
Sample 3c61_4020, birth
Measured on EPIC array


title: b05d_4f85-CBMC

description:
Sample b05d_4f85, birth
Measured on EPIC array


title: PDIS9063-219


title: 9747_46ec-CBMC

description:
Sample 9747_46ec, birth
Measured on EPIC array


title: PDIS9063-220


title: ce4e_4ee7-PBMC

description:
Sample ce4e_4ee7, age 7
Measured on EPIC array


title: Abf1 40 min 4tU-seq Replicate 2

description: 4tU-labelled RNA of Abf1 40 minutes after induction of nuclear depletion

value: 40 minutes depletion (7.5µM rapamycin)


title: Abf1 40 min 4tU-seq Replicate 1


title: d9bd_448a-CBMC

description:
Sample d9bd_448a, birth
Measured on EPIC array


title: ce4e_4ee7-CBMC

description:
Sample ce4e_4ee7, birth
Measured on EPIC array


title: 5a30_4238-PBMC

description:
Sample 5a30_4238, age 7
Measured on EPIC array

value: age 7


title: PDIS9063-217


title: PDIS9063-218


title: PDIS9063-216


title: 5a30_4238-CBMC

description:
Sample 5a30_4238, birth
Measured on EPIC array


title: 294a_4d95-PBMC

description:
Sample 294a_4d95, age 7
Measured on EPIC array

value: Hispanic


title: 294a_4d95-CBMC

description:
Sample 294a_4d95, birth
Measured on EPIC array

value: New York


title: PDIS9063-215


title: eca1_4379-PBMC

description:
Sample eca1_4379, age 7
Measured on EPIC array

value: Female


title: Abf1 30 min 4tU-seq Replicate 1

description: 4tU-labelled RNA of Abf1 30 minutes after induction of nuclear depletion

value: MATalpha

value: 30 minutes depletion (7.5µM rapamycin)


title: 5c27_4ef9-CBMC

description:
Sample 5c27_4ef9, birth
Measured on EPIC array

value: Cord blood


title: Abf1 30 min 4tU-seq Replicate 3


title: PDIS9063-214


title: Abf1 40 min 4tU-seq Replicate 3


title: 8fc1_4c8c-PBMC

description:
Sample 8fc1_4c8c, age 7
Measured on EPIC array


title: 8fc1_4c8c-CBMC

description:
Sample 8fc1_4c8c, birth
Measured on EPIC array

value: birth


title: 7292_4b1f-PBMC

description:
Sample 7292_4b1f, age 7
Measured on EPIC array


title: Abf1 20 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 20 minutes after induction of nuclear depletion

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4

value: 20 minutes depletion (7.5µM rapamycin)


title: PDIS9063-211


title: Abf1 20 min 4tU-seq Replicate 2


title: PDIS9063-212


title: d9bd_448a-PBMC

description:
Sample d9bd_448a, age 7
Measured on EPIC array


title: 7292_4b1f-CBMC

description:
Sample 7292_4b1f, birth
Measured on EPIC array

value: Male


title: 925c_4863-CBMC

description:
Sample 925c_4863, birth
Measured on EPIC array


title: 925c_4863-PBMC

description:
Sample 925c_4863, age 7
Measured on EPIC array


title: 8207_47b9-PBMC

description:
Sample 8207_47b9, age 7
Measured on EPIC array


title: Abf1 15 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 15 minutes after induction of nuclear depletion

value: 15 minutes depletion (7.5µM rapamycin)


title: PDIS9063-210

value: 129/CAST hybrid F1


title: 8207_47b9-CBMC

description:
Sample 8207_47b9, birth
Measured on EPIC array


title: PDIS9063-209

value: Embryonic stem cell


title: Abf1 15 min 4tU-seq Replicate 2


title: PDIS9063-208


title: 99e1_41b9-CBMC

description:
Sample 99e1_41b9, birth
Measured on EPIC array

value: Black


title: Abf1 30 min 4tU-seq Replicate 2


title: eca1_4379-CBMC

description:
Sample eca1_4379, birth
Measured on EPIC array


title: e34c_4cbe-PBMC

description:
Sample e34c_4cbe, age 7
Measured on EPIC array

value: PBMCs


title: 9681_4fc0-PBMC

description:
Sample 9681_4fc0, age 7
Measured on EPIC array


title: PDIS9063-207


title: e34c_4cbe-CBMC

description:
Sample e34c_4cbe, birth
Measured on EPIC array


title: Abf1 10 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 10 minutes after induction of nuclear depletion

value: 10 minutes depletion (7.5µM rapamycin)


title: PDIS9063-206


title: Abf1 20 min 4tU-seq Replicate 1


title: 4e16_40e8-PBMC

description:
Sample 4e16_40e8, age 7
Measured on EPIC array

value: age 7


title: 4e16_40e8-CBMC

description:
Sample 4e16_40e8, birth
Measured on EPIC array


title: Abf1 10 min 4tU-seq Replicate 1


title: 30e4_4640-PBMC

description:
Sample 30e4_4640, age 7
Measured on EPIC array

value: Hispanic


title: PDIS9063-205


title: PDIS9063-203


title: 99e1_41b9-PBMC

description:
Sample 99e1_41b9, age 7
Measured on EPIC array

value: New York


title: 30e4_4640-CBMC

description:
Sample 30e4_4640, birth
Measured on EPIC array

value: Female


title: e119_4636-PBMC

description:
Sample e119_4636, age 7
Measured on EPIC array


title: Abf1 5 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 5 minutes after induction of nuclear depletion

value: MATalpha

value: 5 minutes depletion (7.5µM rapamycin)


title: PDIS9063-200


title: e119_4636-CBMC

description:
Sample e119_4636, birth
Measured on EPIC array

value: Cord blood


title: Abf1 5 min 4tU-seq Replicate 2


title: 56bd_4ab6-CBMC

description:
Sample 56bd_4ab6, birth
Measured on EPIC array

value: birth


title: Abf1 15 min 4tU-seq Replicate 1

description: 4tU-labelled RNA of Abf1 15 minutes after induction of nuclear depletion

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4


title: 56bd_4ab6-PBMC

description:
Sample 56bd_4ab6, age 7
Measured on EPIC array


title: PDIS9063-199


title: fd34_4c71-PBMC

description:
Sample fd34_4c71, age 7
Measured on EPIC array


title: Abf1 0 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of Abf1 without nuclear depletion

value: no depletion (90 min DMSO)


title: Abf1 5 min 4tU-seq Replicate 1


title: fd34_4c71-CBMC

description:
Sample fd34_4c71, birth
Measured on EPIC array

value: Male


title: PDIS9063-196


title: 9ce4_4aea-PBMC

description:
Sample 9ce4_4aea, age 7
Measured on EPIC array


title: 9ce4_4aea-CBMC

description:
Sample 9ce4_4aea, birth
Measured on EPIC array


title: PDIS9063-197


title: 9681_4fc0-CBMC

description:
Sample 9681_4fc0, birth
Measured on EPIC array


title: Abf1 0 min 4tU-seq Replicate 2


title: b43a_4247-PBMC

description:
Sample b43a_4247, age 7
Measured on EPIC array


title: PDIS9063-195


title: Abf1 10 min 4tU-seq Replicate 2

description: 4tU-labelled RNA of Abf1 10 minutes after induction of nuclear depletion


title: Abf1 0 min 4tU-seq Replicate 1


title: cd72_4cbe-CBMC

description:
Sample cd72_4cbe, birth
Measured on EPIC array


title: PDIS9063-193


title: cd72_4cbe-PBMC

description:
Sample cd72_4cbe, age 7
Measured on EPIC array


title: WT 90 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of WT cells treated with rapamycin (90 min)

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT

value: 90 minutes rapamycin (7.5µM rapamycin)


title: a706_4f38-PBMC

description:
Sample a706_4f38, age 7
Measured on EPIC array


title: a706_4f38-CBMC

description:
Sample a706_4f38, birth
Measured on EPIC array


title: WT 90 min 4tU-seq Replicate 2


title: PDIS9063-191

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: b74e_49f1-PBMC

description:
Sample b74e_49f1, age 7
Measured on EPIC array

value: PBMCs

value: Black


title: PDIS9063-190


title: b74e_49f1-CBMC

description:
Sample b74e_49f1, birth
Measured on EPIC array


title: a122_483d-PBMC

description:
Sample a122_483d, age 7
Measured on EPIC array

value: age 7


title: PDIS9063-189


title: 3206_422c-PBMC

description:
Sample 3206_422c, age 7
Measured on EPIC array


title: a122_483d-CBMC

description:
Sample a122_483d, birth
Measured on EPIC array


title: WT 0 min 4tU-seq Replicate 3

description: 4tU-labelled RNA of WT cells treated with DMSO

value: no rapamycin (90 min DMSO)


title: 3206_422c-CBMC

description:
Sample 3206_422c, birth
Measured on EPIC array

value: New York


title: 9cb0_48bf-CBMC

description:
Sample 9cb0_48bf, birth
Measured on EPIC array

value: Hispanic


title: WT 90 min 4tU-seq Replicate 1

value: MATalpha


title: 819f_4135-PBMC

description:
Sample 819f_4135, age 7
Measured on EPIC array


title: WT 0 min 4tU-seq Replicate 1


title: PDIS9063-187


title: WT 0 min 4tU-seq Replicate 2


title: b43a_4247-CBMC

description:
Sample b43a_4247, birth
Measured on EPIC array


title: PDIS9063-188


title: PDIS9063-186


title: 819f_4135-CBMC

description:
Sample 819f_4135, birth
Measured on EPIC array


title: D1S1.022017.pool2

city: Boston

first: Fenna

middle: Marie

last: Krienen

state: MA

address: 77 Ave Louis Pasteur, NRB 260

department: Genetics

institute: Harvard Medical School

description:
single-nucleus gene expression data based on 3' transcript counts
adHumInt.raw.dge.txt.gz

data_processing:
Sequencing Reads were aligned against the relevant genome build using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output for GAD1+/GAD2+ interneurons. Columns belong to STAMPs (cells) and transcript counts (rows)
Genome_build: GRCm38.81 (mouse); MusPutFur1.0 (ferret); calJac3 (marmoset); rheMac8 (macaque); hg19 (human)
Supplementary_files_format_and_content: digital gene expression matrix; comma-delimited file with columns = cells and rows = transcript counts

source_name: Human Postmortem Brain

extract_protocol:
dx.doi.org/10.17504/protocols.io.2srged6
Drop-seq (Macosko et al. 2014 Cell)

tag: platform

value: Dropseq

value: Neocortex; PFC


title: PDIS9063-182


title: PDIS9063-181


title: 192f_4945-PBMC

description:
Sample 192f_4945, age 7
Measured on EPIC array

value: Female


title: PDIS9063-180


title: 6979_489c-CBMC

description:
Sample 6979_489c, birth
Measured on EPIC array

value: Cord blood

value: birth


title: 90b0_41d4-PBMC

description:
Sample 90b0_41d4, age 7
Measured on EPIC array


title: 60c3_4cd8-PBMC

description:
Sample 60c3_4cd8, age 7
Measured on EPIC array

value: Male


title: 90b0_41d4-CBMC

description:
Sample 90b0_41d4, birth
Measured on EPIC array


title: c5dd_4ee6-CBMC

description:
Sample c5dd_4ee6, birth
Measured on EPIC array


title: 6979_489c-PBMC

description:
Sample 6979_489c, age 7
Measured on EPIC array


title: 9cb0_48bf-PBMC

description:
Sample 9cb0_48bf, age 7
Measured on EPIC array


title: 192f_4945-CBMC

description:
Sample 192f_4945, birth
Measured on EPIC array


title: PDIS9063-178


title: a68e_4495-PBMC

description:
Sample a68e_4495, age 7
Measured on EPIC array


title: 60c3_4cd8-CBMC

description:
Sample 60c3_4cd8, birth
Measured on EPIC array


title: D2S7.030217.pool2

value: Neocortex; Temporal lobe


title: a68e_4495-CBMC

description:
Sample a68e_4495, birth
Measured on EPIC array


title: PDIS9063-176


title: PDIS9063-177


title: 5340_4c6e-CBMC

description:
Sample 5340_4c6e, birth
Measured on EPIC array


title: c5dd_4ee6-PBMC

description:
Sample c5dd_4ee6, age 7
Measured on EPIC array


title: 5340_4c6e-PBMC

description:
Sample 5340_4c6e, age 7
Measured on EPIC array


title: D1S1.022017.pool1


title: PDIS9063-175


title: 3f3a_408c-PBMC

description:
Sample 3f3a_408c, age 7
Measured on EPIC array


title: 3f3a_408c-CBMC

description:
Sample 3f3a_408c, birth
Measured on EPIC array


title: PDIS9063-184


title: 1f68_4160-PBMC

description:
Sample 1f68_4160, age 7
Measured on EPIC array


title: PDIS9063-174


title: 1f68_4160-CBMC

description:
Sample 1f68_4160, birth
Measured on EPIC array


title: 4554_4bab-PBMC

description:
Sample 4554_4bab, age 7
Measured on EPIC array


title: 4554_4bab-CBMC

description:
Sample 4554_4bab, birth
Measured on EPIC array


title: PDIS9063-173


title: 4081_4b64-PBMC

description:
Sample 4081_4b64, age 7
Measured on EPIC array


title: Expression sample, Doxy conc 0, bio rep 2, tech rep 2

city: Stanford

first: Mark

middle: A

last: Kay

address: 269 Campus Drive

institute: Stanford University

data_processing:
For ligation-mediated PCR, BBMap v.38.60 BBDuk was used to quality trim read 3? ends and filter out low quality reads while error-correcting overlapping regions. UMI-tools v1.0.0 extract was used to trim reads of primer sequence. BBMap BBDuk was used to filter out reads for which there was amplification into the provirus from the 5' LTR and trim overlapping reads of primer read-through. BBMap demuxbyname was used to complete demultiplexing of technical replicates using the Read 1 linker-unique sequences, allowing for a hamming distance of 3. Paired reads were aligned to the GRCh38.p12 genome assembly using the STAR aligner v.2.7.1a with --alignIntronMax 1 --alignMatesGapMax 2500, filtering for uniquely mapped and properly matched read pairs. UMI-tools dedup was used to deduplicate aligned reads using the --ignore-umi flag. For each read pair, we required that they maintain the correct predicted orientation: the LTR junction read is ?upstream? of the breakpoint read if aligned to the + strand, or "downstream" if aligned to the - strand. Read 2 LTR junction positions were clustered within 20bp to generate a set of consensus junctions. Clonal abundance was computed as the depth-normalized number of unique breakpoints for each junction after clustering breakpoint positions within 5bp, scaled to the maximum number of breakpoints in any sample. We required that consensus sites be recovered in both technical replicates associated with a biological replicate and have at least two unique breakpoints to be accepted. A set of population-wide consensus sites was generated by repeating junction clustering across all technical replicates.
For inverse PCR, BBTools v.38.60 BBDuk was used to quality trim read 3? ends and filter out low quality reads while error-correcting overlapping regions. UMI-tools v1.0.0 extract was used to trim reads of primer sequence and extract barcodes. In Read 1, barcodes were extracted while discarding all remaining sequence up to the reconstituted AseI/NdeI restriction site (excluding the last two, non-consensus bases). BBTools BBDuk was then used to filter out reads for which there was amplification into the provirus from the 3' LTR and trim primer read-through. Paired reads were aligned to the GRCh38.p12 genome assembly using the STAR aligner v.2.7.1a with --alignIntronMax 1 --alignMatesGapMax 3850, filtering for uniquely mapped and properly matched read pairs. Consensus sites were generated by clustering Read 2 LTR junction positions within 20bp and technical replicates were subsequently merged. Inverse PCR consensus sites were mapped back to provirus consensus sites, requiring that iPCR and LM-PCR LTR junctions be mapped to opposite strands and overlap at their LTR junction positions by not more than 10bp using bedtools v2.28.0 intersect.
Processing of normalization (DNA barcodes) and expression (RNA barcodes) reads were carried out in an identical manner. Forward and reverse reads were merged using BBTools v38.60 BBMerge while filtering low quality reads and error-correcting overlapping regions. UMI-toolsv1.0.0 extract was used to extract barcodes. Unique barcodes were collapsed and counted.
The set of accepted barcodes were those that had at least five normalization reads in both of a pair of technical replicates, and two mapping reads at a single site by inverse PCR. A barcode was definitively assigned to a site if at least 90% of the total reads for that barcode mapped to the site, with fewer than 2.5% mapping to a secondary locus.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: provirus_sites_w_abundance.txt: Provirus sites and number of unique breakpoints for each from LM-PCR sequencing
Supplementary_files_format_and_content: barcodes_norm_expr_raw_counts.txt: Raw normalization and expression counts for each mapped barcode
Supplementary_files_format_and_content: mapped_barcodes.txt: Genomic locations of mapped barcodes
Supplementary_files_format_and_content: README.txt: Python regex and sequences for genomic DNA extraction, barcode extraction, and demultiplexing of LM-PCR data

source_name: HAP1 cells

growth_protocol: HAP1 cells infected with a lentivirus-encoded dual Tet-ON expression system and targeted with barcoded AAV library were grown in complete IMDM supplemented with 7ug/mL blasticidin S-hydrochloride.

extract_protocol:
Genomic DNA was extracted from frozen cell pellets of 12e6 cells using the GeneJET Genomic DNA Purification Kit in two technical replicates for every biological replicate.   Total RNA was extracted using the Monarch Total RNA MiniPrep kit from samples frozen in 1X Protection Buffer, including in-column DNase I treatment, in two technical replicates for every biological replicate. 2ug of RNA was reverse transcribed with RNase H treatment in a 21ul reaction using the Superscript III First Strand cDNA Synthesis Kit with oligo(dT) primers.
Ligation-mediated PCR (LM-PCR) to map provirus sites was performed as previously described (Sherman et al., Mol Ther Methods Clin Dev, 2016; PMID: 28344990) except that 5 cycles of linear amplification plus 7 cycles of exponential amplification were used in the second round of PCR and primers were adapted to standard Illumina sequencing primers. Samples with different indexes were pooled together and sequenced on an Illumina MiSeq using 2x300bp paired-end reads.
For inverse PCR to map integrated barcodes, 4ug genomic DNA was digested in a 200ul reaction with 1X NEB Buffer 3.1, 134U AseI (NEB), and 134U NdeI (NEB). Digests were purified through a Monarch PCR & DNA Cleanup Kit column. 3 x 600ng purified digested DNA was self-ligated with 2800U high concentration T4 DNA Ligase (NEB) and incubated at 4ºC overnight in a volume of 400ul. Final PCR template was obtained by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. DNA pellets were dissolved in 30ul water and 5ul of each sample was used as template to amplify fragments containing both an integrated barcode and genomic DNA adjacent to the 5? LTR of the corresponding provirus site. iPCR was performed over two rounds in 12 independent reactions, using ExoI/rSAP (NEB) to remove primers between rounds. Equal volumes of second round PCR products were pooled and cleaned up using 0.8X Agencourt AMPure XP beads, then pooled with other samples having different indexes, and sequenced on an Illumina NextSeq 500 using 2x150bp paired-end reads.
PCR to measure normalized barcode expression was performed over two rounds in 10 independent reactions using 100ng genomic DNA or 1.68ul cDNA, using ExoI/rSAP (NEB) to remove primers between rounds. Equal volumes of the second round PCR products were pooled and cleaned up using 1.2X (normalization) or 1X (expression) Agencourt AMPure XP beads, then pooled with other samples having different indexes, and sequenced on an Illumina HiSeq4000 using 2x100bp paired-end reads.

treatment_protocol: Expression samples were treated with either 100ng/mL or 0ng/mL doxycycline prior to extraction.

tag: doxy concentration

tag: target site

value: Doxycycline-inducible provirus


title: D2S7.030217.pool1

description:
single-nucleus gene expression data based on 3' transcript counts
adHumInt.raw.dge.txt.gz


title: 4081_4b64-CBMC

description:
Sample 4081_4b64, birth
Measured on EPIC array


title: Expression sample, Doxy conc 0, bio rep 1, tech rep 2


title: PDIS9063-172

value: 129/CAST hybrid F1


title: PDIS9063-171

value: Embryonic stem cell


title: a887_4f9f-CBMC

description:
Sample a887_4f9f, birth
Measured on EPIC array


title: a887_4f9f-PBMC

description:
Sample a887_4f9f, age 7
Measured on EPIC array

value: PBMCs


title: Expression sample, Doxy conc 0, bio rep 2, tech rep 1


title: 866d_4438-PBMC

description:
Sample 866d_4438, age 7
Measured on EPIC array

value: Black

value: Boston


title: Expression sample, Doxy conc 0, bio rep 1, tech rep 1


title: 866d_4438-CBMC

description:
Sample 866d_4438, birth
Measured on EPIC array


title: eb24_4354-PBMC

description:
Sample eb24_4354, age 7
Measured on EPIC array

value: age 7


title: PDIS9063-170


title: Expression sample, Doxy conc 100, bio rep 2, tech rep 2


title: PDIS9063-169


title: Expression sample, Doxy conc 100, bio rep 2, tech rep 1


title: eb24_4354-CBMC

description:
Sample eb24_4354, birth
Measured on EPIC array


title: a183_4278-PBMC

description:
Sample a183_4278, age 7
Measured on EPIC array


title: PDIS9063-168


title: Expression sample, Doxy conc 100, bio rep 1, tech rep 2


title: a183_4278-CBMC

description:
Sample a183_4278, birth
Measured on EPIC array


title: e013_484e-PBMC

description:
Sample e013_484e, age 7
Measured on EPIC array


title: Expression sample, Doxy conc 100, bio rep 1, tech rep 1


title: e013_484e-CBMC

description:
Sample e013_484e, birth
Measured on EPIC array


title: PDIS9063-167


title: 6d53_43a9-PBMC

description:
Sample 6d53_43a9, age 7
Measured on EPIC array


title: PDIS9063-166


title: Normalization sample, Doxy conc 0, bio rep 2, tech rep 2


title: 6d53_43a9-CBMC

description:
Sample 6d53_43a9, birth
Measured on EPIC array


title: Normalization sample, Doxy conc 0, bio rep 2, tech rep 1


title: 975b_4857-CBMC

description:
Sample 975b_4857, birth
Measured on EPIC array


title: 975b_4857-PBMC

description:
Sample 975b_4857, age 7
Measured on EPIC array


title: PDIS9063-165


title: 90d2_46cd-PBMC

description:
Sample 90d2_46cd, age 7
Measured on EPIC array


title: e32e_430b-PBMC

description:
Sample e32e_430b, age 7
Measured on EPIC array


title: Normalization sample, Doxy conc 0, bio rep 1, tech rep 1


title: PDIS9063-164


title: e32e_430b-CBMC

description:
Sample e32e_430b, birth
Measured on EPIC array


title: PDIS9063-163


title: 90d2_46cd-CBMC

description:
Sample 90d2_46cd, birth
Measured on EPIC array


title: c005_4ed9-PBMC

description:
Sample c005_4ed9, age 7
Measured on EPIC array


title: Normalization sample, Doxy conc 100, bio rep 2, tech rep 2


title: Normalization sample, Doxy conc 100, bio rep 2, tech rep 1


title: c005_4ed9-CBMC

description:
Sample c005_4ed9, birth
Measured on EPIC array


title: PDIS9063-160


title: Normalization sample, Doxy conc 100, bio rep 1, tech rep 2


title: 2a21_497b-PBMC

description:
Sample 2a21_497b, age 7
Measured on EPIC array


title: 8ec0_4175-PBMC

description:
Sample 8ec0_4175, age 7
Measured on EPIC array


title: 2a21_497b-CBMC

description:
Sample 2a21_497b, birth
Measured on EPIC array


title: 8ec0_4175-CBMC

description:
Sample 8ec0_4175, birth
Measured on EPIC array


title: PDIS9063-159


title: 365d_450b-PBMC

description:
Sample 365d_450b, age 7
Measured on EPIC array


title: Normalization sample, Doxy conc 100, bio rep 1, tech rep 1


title: PDIS9063-158


title: 365d_450b-CBMC

description:
Sample 365d_450b, birth
Measured on EPIC array


title: 32fa_4a92-PBMC

description:
Sample 32fa_4a92, age 7
Measured on EPIC array

value: Mixed (>1 race)


title: Normalization sample, Doxy conc 0, bio rep 1, tech rep 2


title: 5450_4370-PBMC

description:
Sample 5450_4370, age 7
Measured on EPIC array


title: PDIS9063-157


title: 32fa_4a92-CBMC

description:
Sample 32fa_4a92, birth
Measured on EPIC array


title: 5450_4370-CBMC

description:
Sample 5450_4370, birth
Measured on EPIC array


title: PDIS9063-156


title: HARPE on SCP1withTATA - replicate 2 in vitro

city: La Jolla

first: Long

last: Vo ngoc

state: California

address: 9500 Gilman Dr

institute: UCSD

description:
HARPE_SCP1withTATA_inVitro_rep2
reporter RNA and plasmid DNA

data_processing:
Single-read sequences (SR75) were screened according to the following criteria: a perfect match to the 10 nt directly upstream of the randomized region followed by the exact nt count within the randomized region and a perfect match to the 10 nt directly downstream of the randomized region. [For the analysis of the TATA-box (long version), the SR75 sequencing reads only allowed for 8 nt following the barcode; thus, the criteria that we employed were as follows: perfect match to the 12 nt directly upstream of the barcode; exact size of randomized barcode; and perfect match to the 8 nt directly downstream of the barcode.] All reads containing a match to the selection pattern were deemed usable and trimmed for sequences outside of the randomized region.
When present, highly abundant reads in the randomized box that correspond to the original promoter sequence or to invariant sequences from other constructs were discarded, as they likely originated from inaccurate indexing of other multiplexed samples.
Read counts for each variant were then computed and yielded a plasmid DNA dataset (DNA dataset) and a cDNA dataset (RNA dataset) for each sample.
For each DNA dataset, we used only sequences with a minimum read count of 0.75 reads per million (RPM) so that low confidence variants would not be included in the analysis. RNA dataset sequences were then matched to the corresponding DNA dataset, which was used as a reference. For each HARPE experiment, transcription strength was then defined as RNA tag count (in RPMs) divided by DNA tag count (in RPMs).
For the analysis of the TATA-box region, conversion tables from barcode to TATA-box variant were built by paired-end sequencing of amplicons from the starting plasmid libraries. Sequencing reads were screened as described above and clusters with both read 1 and read 2 passing the screening criteria were used to compute read counts. A minimum read count threshold was set so that ≥ 98% of barcodes are associated with a single TATA-box variant. Pairs that did not reach the threshold and the remaining 2% of unassigned barcodes were discarded. DNA datasets and RNA datasets for all TATA-box HARPE experiments were matched to their corresponding barcode to TATA conversion tables. All non-matching barcodes were not included.
For low complexity, high confidence HARPE, the randomization of the DPR was limited and associated with a randomized 3-nt tag downstream of the core promoter. The transcription strength for each DPR variant was computed by determining the average of the RNA tag count/DNA tag count values for all of the DPR-tag pairs for that variant.
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing the position of human focused TSSs identified in MCF7 or GM12878 cells, their 5'GRO-seq/GRO-cap signal and DPR score according to SVRb and SVRc.
Supplementary_files_format_and_content: txt files containing the sequence of each variant, the DNA read count, RNA read count, DNA read count in RPM (DNArpm), the RNA read count in RPM (RNArpm), and the measured transcription strength (score)
Supplementary_files_format_and_content: model files containing the SVR models.

molecule: other

source_name: human cervix adenocarcinoma

growth_protocol: HeLa cells were maintained at 37°C and 5% CO2 in DMEM (Gibco) supplemented with 10% FBS (ATCC), 50 U/mL penicillin (Thermo Fisher Scientific), and 50 μg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol:
For HARPE experiments transcribed in vitro, for each sample library, the products from twelve standard in vitro transcription reactions were combined. Standard reactions were performed as follows. DNA template (500 ng) was incubated with HeLa nuclear extract (prepared as described in Dignam et al. 1983) for preinitiation complex assembly at 30 °C for 1 hour in 46 μL of transcription buffer [20 mM HEPES-K+ (pH 7.6), 50 mM KCl, 6 mM MgCl2, 1.25% (w/v) polyvinyl alcohol, 1.25% (w/v) polyethylene glycol, 0.5 mM DTT, 3 mM ATP, 0.02 mM EDTA, and 2% (v/v) glycerol]. rNTPs (4 μL; 0.4 mM final concentration of each rNTP) were added to initiate transcription. [Where indicated, Sarkosyl was added to 0.2% (w/v) final concentration at 20 seconds after the addition of rNTPs.] The reaction was incubated at 30 °C for 20 min and terminated by the addition of 150 μL of Stop Mix [20 mM EDTA, 200 mM NaCl, 1% (w/v) SDS, 0.3 mg/mL glycogen]. Proteinase K (5 μL; 2.5 mg/mL) was added, and the mixture was incubated at 30 °C for 15 min. All in vitro transcription HARPE experiments were performed independently at least two times to ensure reproducibility of the data.
RNA extraction and processing after transcription of HARPE libraries. RNA transcripts from cells or from in vitro transcription reactions were extracted with Trizol™ or Trizol™ LS (Thermo Fisher Scientific), respectively. Total RNA (40 µg for cell transfection experiments or the entire yield for in vitro experiments) was processed as follows. Contaminating plasmid DNA was removed with the TURBO DNA-free™ Kit - rigorous DNase treatment protocol (Thermo Fisher Scientific) as recommended by the manufacturer. The nucleic acids were precipitated with ethanol, and reverse transcription was performed with SuperScript™ III Reverse Transcriptase (Thermo Fisher Scientific) with the RT primer (5’- GTGACTGGAGTTCAGACGTGT) (Table 1) as recommended by the manufacturer. The reaction products were then treated with 30 U RNase H (New England Biolabs) for 20 min at 37°C. The nucleic acids were extracted with phenol-chloroform-isoamyl alcohol and precipitated with ethanol. The resulting cDNAs were then size-selected on a 6% polyacrylamide-8M urea gel by using radiolabeled size markers (Table 1) that enable the purification of cDNAs corresponding to transcription that initiates in the region from -5 to +6 relative to the A+1 in the Inr sequence. Size-selected cDNAs were used as templates to generate DNA amplicons for Illumina sequencing by using custom forward oligonucleotides containing the Illumina P5 and Read1-primer sequences preceding the sequence corresponding to nucleotides +1 to +16 of the promoter analyzed (Table 1). Reverse primers were selected from the NEBNext® Multiplex Oligos for Illumina® kits (NEB). NGS PCR amplicons were then size-selected on native 6% polyacrylamide gels prior to Illumina sequencing.
Processing of plasmid DNA for Illumina sequencing. For in vitro experiments, the starting material used was the HARPE DNA libraries. For cell transfection experiments, post-transfection plasmid DNA extraction was performed as described in van Arensbergen et al. (2017). Briefly, cells were treated with trypsin, washed with PBS, and then incubated in 500 µL nuclear extraction buffer [10 mM NaCl, 2 mM MgCl2, 10 mM Tris-HCl (pH 7.8), 5 mM DTT, 0.5% NP40] on ice for 5 min. Nuclei were pelleted at 7,000 x g and washed twice with 1 mL nuclear extraction buffer. DNA was then extracted with ZymoPURE™ Plasmid Miniprep Kit (Zymo Research). Plasmid DNA samples were used as a template for the generation of DNA amplicons for Illumina sequencing. The forward oligonucleotides contain the Illumina P5 and Read1-primer sequences followed by a promoter-specific sequence (Table 1) that comprises nucleotides +1 through +16 (relative to the +1 TSS) for accurate DNA count assessment. Reverse primers were selected from the NEBNext® Multiplex Oligos for Illumina® kits (New England Biolabs), which match the Illumina Read2-primer sequence present on the HARPE plasmid. NGS PCR amplicons were then size-selected on native 6% polyacrylamide gels prior to Illumina sequencing.
As described above, size-selected cDNAs or plasmid DNAs were used as templates to generate DNA amplicons for Illumina sequencing by using custom forward oligonucleotides containing the Illumina P5 and Read1-primer sequences preceding the sequence corresponding to nucleotides +1 to +16 of the promoter analyzed (Table 1). Reverse primers were selected from the NEBNext® Multiplex Oligos for Illumina® kits (NEB). NGS PCR amplicons were then size-selected on native 6% polyacrylamide gels prior to Illumina sequencing.

treatment_protocol: Cells were transfected with HARPE libraries using Lipofectamine 3000 (Thermo Fisher Scientific) as recommended by the manufacturer.

tag: biosource type

value: HeLa nuclear extract


title: PDIS9063-162


title: 99e1_4d92-CBMC

description:
Sample 99e1_4d92, birth
Measured on EPIC array


title: PDIS9063-155


title: HARPE on SCP1withTATA - replicate 1 in vitro

description:
HARPE_SCP1withTATA_inVitro_rep1
reporter RNA and plasmid DNA


title: e7de_4d41-PBMC

description:
Sample e7de_4d41, age 7
Measured on EPIC array


title: e7de_4d41-CBMC

description:
Sample e7de_4d41, birth
Measured on EPIC array


title: HARPE on SCP1withTATA - replicate 2 in cells

description:
HARPE_SCP1withTATA_inCells_rep2
reporter RNA and plasmid DNA

value: HeLa cells


title: PDIS9063-154


title: e0e9_4dc6-PBMC

description:
Sample e0e9_4dc6, age 7
Measured on EPIC array


title: vOrganoids_d100_rep3

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

data_processing:
Cell Ranger 2.0.1 was used to perform quality control and read counting of Ensembl genes with default parameter (v2.0.1) by mapping to the GRCh38 human genome.
Poor quality cells after the gene-cell data matrix was generated by Cell Ranger software using the Seurat package (v2.1.0) in Bioconductor.
The data were natural log transformed and normalized for scaling the sequencing depth to a total of 1e4 molecules per cell, followed by regressing-out the number of UMI using Seurat package.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.txt: File reports natural log transformed and normalized UMI counts.  1column/1cell.  Column header format:  barcode-Sample#

source_name: hESCs-derived cerebral organoids

growth_protocol: Human embryonic stem cells (hESCs) H9 lines were maintained on Matrigel-coated 6-well plates (Corning) and were cultured with Essential 8™ Medium (Gibco). On day 0, hESCs colonies were pretreated for one hour with 20 µM Y27632 (Tocris Bioscience), and were dissociated into single cell by Accutase (STEMCELL Technologies). HUVECs were cultured in endothelial Cell Growth Medium, and dissociated into single cell by TrpLE. The mixture of approximately 3×106 dissociated hESCs and 3×105 HUVECs were resuspended in KSR medium, and plated into 96-well U shaped polystyrene plates (Thermo Fisher).The size of EBs is determined by the cell numbers that seeding into each well of the plate. The KSR medium was prepared as follows: DMEM/F12 (Gibco) was supplemented with 20% Knockout Serum Replacement (KSR, Gibco), 2 mM Glutamax (Gibco), 0.1mM nonessential amino acids (NEAA, Gibco), 0.1 mM beta-mercaptoethanol (Gibco), 3 μM endo-IWR1 (Tocris Bioscience), 0.1 μM LDN-193189 (STEMGENT) and 10 μM SB431542 (Tocris Bioscience). On day 18, the self-organized floating EBs were transferred to low-cell-adhesion 6-well plates (Corning) and further cultured in the neural induction medium containing DMEM/F12, 1:100 N2 supplement (Gibco), 2 mM Glutamax (Gibco), 0.1 mM nonessential amino acids (NEAA, Gibco), 55 μM beta-mercaptoethanol (Gibco), 1 μg/ml heparin. After day35, the free-floating aggregates were transferred to the neurobasal-type differentiation medium supplemented with 1:50 B27 (Gibco), 2 mM Glutamax and 0.1 mM NEAA, 0. 55 μM beta-mercaptoethanol, 5 μg/ml heparin, 1% matrigel, 10 ng/ml BDNF, 10 ng/ml GDNF, 1 μM cAMP (Sigma).

extract_protocol:
The organoids with and without HUVECs at 65 days and 100 days, respectively, were cut into small pieces and dissociated into single-cell suspensions by using a papain-based dissociation protocol (hibernate E medium with 1 mg/ml papain (Sigma) at 37℃ on a thermo cycler with 500g for 15-20 min). Single cells were suspended in 0.04% BSA/PBS at the proper concentration to generate cDNA libraries with Single Cell 3’ Reagent Kits, according to the manufacturer’s protocol. Briefly, after the cDNA amplification, enzymatic fragmentation and size selection were performed to optimize the cDNA size. P5, P7, an index sample, and R2 (read 2 primer sequence) were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used in Illumina bridge amplification of the cDNA (http://10xgenomics.com). Finally, the library was processed on the Illumina platform for sequencing with 150bp pair-end reads.
Illumina HiSeq4000

tag: cell line

value: hESC stem cell line H9

value: hESCs-derived cerebral organoids

tag: time point

value: day 100


title: HARPE on SCP1withTATA - replicate 1 in cells

description:
HARPE_SCP1withTATA_inCells_rep1
reporter RNA and plasmid DNA


title: e0e9_4dc6-CBMC

description:
Sample e0e9_4dc6, birth
Measured on EPIC array

tag: tissue

value: Cord blood

tag: age

value: Female


title: PDIS9063-153


title: vOrganoids_d100_rep2


title: 56bb_47e9-PBMC

description:
Sample 56bb_47e9, age 7
Measured on EPIC array

tag: methylationplatenumber

tag: selfreportedrace

value: Male


title: PDIS9063-151


title: 56bb_47e9-CBMC

description:
Sample 56bb_47e9, birth
Measured on EPIC array

value: birth

tag: Sex

tag: samplecollectionsite


title: Organoids_d100_rep3


title: fcfc_4b9f-PBMC

description:
Sample fcfc_4b9f, age 7
Measured on EPIC array


title: fcfc_4b9f-CBMC

description:
Sample fcfc_4b9f, birth
Measured on EPIC array


title: 99e1_4d92-PBMC

description:
Sample 99e1_4d92, age 7
Measured on EPIC array


title: vOrganoids_d65_rep3

value: day 65


title: 1f03_445a-PBMC

description:
Sample 1f03_445a, age 7
Measured on EPIC array

value: Hispanic


title: Organoids_d100_rep2


title: 1f03_445a-CBMC

description:
Sample 1f03_445a, birth
Measured on EPIC array


title: 9e45_40b0-CBMC

description:
Sample 9e45_40b0, birth
Measured on EPIC array


title: vOrganoids_d65_rep2


title: PDIS9063-147

tag: strain background

value: 129/CAST hybrid F1

tag: cell type

value: Embryonic stem cell


title: 9e45_40b0-PBMC

description:
Sample 9e45_40b0, age 7
Measured on EPIC array

value: PBMCs

value: Black


title: d084_4cd9-PBMC

description:
Sample d084_4cd9, age 7
Measured on EPIC array

value: age 7

value: Boston


title: d084_4cd9-CBMC

description:
Sample d084_4cd9, birth
Measured on EPIC array


title: PDIS9063-146


title: Organoids_d65_rep3


title: Organoids_d65_rep2


title: 1455_4f52-PBMC

description:
Sample 1455_4f52, age 7
Measured on EPIC array


title: PDIS9063-145


title: 71e3_4eb8-PBMC

description:
Sample 71e3_4eb8, age 7
Measured on EPIC array


title: PDIS9063-144


title: PDIS9063-150


title: 7777_462d-PBMC

description:
Sample 7777_462d, age 7
Measured on EPIC array

value: Baltimore


title: fab1_4ab2-PBMC

description:
Sample fab1_4ab2, age 7
Measured on EPIC array


title: 71e3_4eb8-CBMC

description:
Sample 71e3_4eb8, birth
Measured on EPIC array


title: PDIS9063-149


title: fab1_4ab2-CBMC

description:
Sample fab1_4ab2, birth
Measured on EPIC array


title: 7777_462d-CBMC

description:
Sample 7777_462d, birth
Measured on EPIC array


title: PDIS9063-148


title: ecad_4437-PBMC

description:
Sample ecad_4437, age 7
Measured on EPIC array


title: PDIS9063-143


title: 8131_4ffe-PBMC

description:
Sample 8131_4ffe, age 7
Measured on EPIC array


title: 8131_4ffe-CBMC

description:
Sample 8131_4ffe, birth
Measured on EPIC array


title: 1455_4f52-CBMC

description:
Sample 1455_4f52, birth
Measured on EPIC array


title: PDIS9063-140


title: HARPE on TATAshort - replicate 2 in vitro

description:
HARPE_TATAshort_inVitro_rep2
Reporter RNA and plasmid DNA
processed data file: TATAshort_ConversionTable.txt

data_processing:
Library strategy: HARPE
Single-read sequences (SR75) were screened according to the following criteria: a perfect match to the 10 nt directly upstream of the randomized region followed by the exact nt count within the randomized region and a perfect match to the 10 nt directly downstream of the randomized region. [For the analysis of the TATA-box (long version), the SR75 sequencing reads only allowed for 8 nt following the barcode; thus, the criteria that we employed were as follows: perfect match to the 12 nt directly upstream of the barcode; exact size of randomized barcode; and perfect match to the 8 nt directly downstream of the barcode.] All reads containing a match to the selection pattern were deemed usable and trimmed for sequences outside of the randomized region.
When present, highly abundant reads in the randomized box that correspond to the original promoter sequence or to invariant sequences from other constructs were discarded, as they likely originated from inaccurate indexing of other multiplexed samples.
Read counts for each variant were then computed and yielded a plasmid DNA dataset (DNA dataset) and a cDNA dataset (RNA dataset) for each sample.
For each DNA dataset, we used only sequences with a minimum read count of 0.75 reads per million (RPM) so that low confidence variants would not be included in the analysis. RNA dataset sequences were then matched to the corresponding DNA dataset, which was used as a reference. For each HARPE experiment, transcription strength was then defined as RNA tag count (in RPMs) divided by DNA tag count (in RPMs).
For the analysis of the TATA-box region, conversion tables from barcode to TATA-box variant were built by paired-end sequencing of amplicons from the starting plasmid libraries. Sequencing reads were screened as described above and clusters with both read 1 and read 2 passing the screening criteria were used to compute read counts. A minimum read count threshold was set so that ≥ 98% of barcodes are associated with a single TATA-box variant. Pairs that did not reach the threshold and the remaining 2% of unassigned barcodes were discarded. DNA datasets and RNA datasets for all TATA-box HARPE experiments were matched to their corresponding barcode to TATA conversion tables. All non-matching barcodes were not included.
For low complexity, high confidence HARPE, the randomization of the DPR was limited and associated with a randomized 3-nt tag downstream of the core promoter. The transcription strength for each DPR variant was computed by determining the average of the RNA tag count/DNA tag count values for all of the DPR-tag pairs for that variant.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content:
bed files containing the position of human focused TSSs identified in MCF7 or GM12878 cells, their 5'GRO-seq/GRO-cap signal and DPR score according to SVRb and SVRc and TATA score according to SVRtata.
txt files containing the sequence of each variant, the DNA read count, RNA read count, DNA read count in RPM (DNArpm), the RNA read count in RPM (RNArpm), and the measured transcription strength (score).
Three model files containing the SVR models and Rscript for use of SVR models.

value: HeLa nuclear extract


title: PDIS9063-139


title: HARPE on TATAshort - replicate 1 in vitro

description:
HARPE_TATAshort_inVitro_rep1
Reporter RNA and plasmid DNA
processed data file: TATAshort_ConversionTable.txt


title: HARPE on TATAshort - replicate 2 in cells

description:
HARPE_TATAshort_inCells_rep2
Reporter RNA and plasmid DNA
processed data file: TATAshort_ConversionTable.txt

value: HeLa cells


title: HARPE on TATAlong - replicate 2 in vitro

description:
HARPE_TATAlong_inVitro_rep2
Reporter RNA and plasmid DNA
processed data file: TATAlong_ConversionTable.txt


title: c2ff_4abd-CBMC

description:
Sample c2ff_4abd, birth
Measured on EPIC array


title: c2ff_4abd-PBMC

description:
Sample c2ff_4abd, age 7
Measured on EPIC array


title: HARPE on TATAshort - replicate 1 in cells

description:
HARPE_TATAshort_inCells_rep1
Reporter RNA and plasmid DNA
processed data file: TATAshort_ConversionTable.txt


title: PDIS9063-136


title: 23a4_43bf-PBMC

description:
Sample 23a4_43bf, age 7
Measured on EPIC array


title: d8c8_41e5-CBMC

description:
Sample d8c8_41e5, birth
Measured on EPIC array


title: HARPE on TATAlong - replicate 2 in cells

description:
HARPE_TATAlong_inCells_rep2
Reporter RNA and plasmid DNA
processed data file: TATAlong_ConversionTable.txt


title: HARPE on TATAlong - replicate 1 in vitro

description:
HARPE_TATAlong_inVitro_rep1
Reporter RNA and plasmid DNA
processed data file: TATAlong_ConversionTable.txt


title: PDIS9063-135


title: 23a4_43bf-CBMC

description:
Sample 23a4_43bf, birth
Measured on EPIC array


title: 8ff5_42e6-PBMC

description:
Sample 8ff5_42e6, age 7
Measured on EPIC array


title: HARPE on TATAlong - replicate 1 in cells

description:
HARPE_TATAlong_inCells_rep1
Reporter RNA and plasmid DNA
processed data file: TATAlong_ConversionTable.txt


title: 8ff5_42e6-CBMC

description:
Sample 8ff5_42e6, birth
Measured on EPIC array


title: PDIS9063-134


title: ecad_4437-CBMC

description:
Sample ecad_4437, birth
Measured on EPIC array


title: PDIS9063-141


title: 3812_4d79-PBMC

description:
Sample 3812_4d79, age 7
Measured on EPIC array


title: 3812_4d79-CBMC

description:
Sample 3812_4d79, birth
Measured on EPIC array


title: HARPE on MTE - replicate 2 in vitro

description:
HARPE_MTE_inVitro_rep2
Reporter RNA and plasmid DNA


title: PDIS9063-133


title: 9854_46d3-PBMC

description:
Sample 9854_46d3, age 7
Measured on EPIC array


title: d8c8_41e5-PBMC

description:
Sample d8c8_41e5, age 7
Measured on EPIC array


title: 9854_46d3-CBMC

description:
Sample 9854_46d3, birth
Measured on EPIC array


title: PDIS9063-132


title: e880_4147-PBMC

description:
Sample e880_4147, age 7
Measured on EPIC array

value: Mixed (>1 race)


title: PDIS9063-131


title: e880_4147-CBMC

description:
Sample e880_4147, birth
Measured on EPIC array


title: PDIS9063-130


title: HARPE on MTE - replicate 2 in cells

description:
HARPE_MTE_inCells_rep2
Reporter RNA and plasmid DNA


title: HARPE on MTE - replicate 1 in vitro

description:
HARPE_MTE_inVitro_rep1
Reporter RNA and plasmid DNA


title: HARPE on MTE - replicate 1 in cells

description:
HARPE_MTE_inCells_rep1
Reporter RNA and plasmid DNA


title: HARPE on low complexity DPR library - replicate 2 in vitro

description:
HARPE_LowComp_inVitro_rep2
Reporter RNA and plasmid DNA


title: PDIS9063-129


title: 605e_42d7-PBMC

description:
Sample 605e_42d7, age 7
Measured on EPIC array


title: 6d2c_4b72-CBMC

description:
Sample 6d2c_4b72, birth
Measured on EPIC array


title: PDIS9063-128


title: 605e_42d7-CBMC

description:
Sample 605e_42d7, birth
Measured on EPIC array


title: HARPE on low complexity DPR library - replicate 2 in cells

description:
HARPE_LowComp_inCells_rep2
Reporter RNA and plasmid DNA


title: HARPE on low complexity DPR library - replicate 1 in vitro

description:
HARPE_LowComp_inVitro_rep1
Reporter RNA and plasmid DNA


title: PDIS9063-127


title: HARPE on low complexity DPR library - replicate 1 in cells

description:
HARPE_LowComp_inCells_rep1
Reporter RNA and plasmid DNA


title: bd6b_42e4-PBMC

description:
Sample bd6b_42e4, age 7
Measured on EPIC array


title: PDIS9063-126


title: HARPE on IRF - replicate 2 in vitro

description:
HARPE_IRF_inVitro_rep2
Reporter RNA and plasmid DNA


title: bd6b_42e4-CBMC

description:
Sample bd6b_42e4, birth
Measured on EPIC array


title: 6d2c_4b72-PBMC

description:
Sample 6d2c_4b72, age 7
Measured on EPIC array


title: PDIS9063-125


title: dcb7_4749-PBMC

description:
Sample dcb7_4749, age 7
Measured on EPIC array


title: PDIS9063-124


title: PDIS9063-123


title: Wt:394

type: RNA

city: Cleveland

first: Maryam

last: Zamanian

state: OH

address: 9500 Euclid Avenue

department: Cardiovascular and Metabolic Diseases

institute: Lerner Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Arrays were scanned in an Illumina Bead Station, and the images processed using Illumina Bead Studio software.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: Homograft B16F10L-luciferase tumor 7 days post sub cutaneous inoculation

label_protocol: Total RNA was amplified and biotinylated for hybridization using Illumina TotalPrep RNA Amplification Kit (AMIL1791, Applied Biosystems, Life Technologies) according to the manufacturer’s protocol.

growth_protocol: Eight to ten (8-10) week male and female animals were inoculated subcutaneously on both flanks with 105 B16F10L-luciferase tumor cells per site (2 sites/flank).

extract_protocol: Tumor tissue (30 mg) was homogenized with zircodium oxide beads using the Bullet blender tissue homogenizer (Next Advance, Troy, NY, USA) and total RNA was prepared (RNeasy Mini kit, Qiagen, Valencia, CA) with on column DNase treatment (Cat# 79254, Qiagen).

treatment_protocol: Tumor tissue from one flank was resected on day 7 post inoculation and stored in RNA later.

tag: gender

tag: strain

tag: genotype

value: C57BL/6J WT


title: HARPE on IRF - replicate 1 in vitro

description:
HARPE_IRF_inVitro_rep1
Reporter RNA and plasmid DNA


title: Wt:377


title: Wt:382


title: Wt:378


title: dcb7_4749-CBMC

description:
Sample dcb7_4749, birth
Measured on EPIC array

value: Cord blood


title: Wt:383

value: Female


title: Wt:362

value: Male


title: HARPE on IRF - replicate 2 in cells

description:
HARPE_IRF_inCells_rep2
Reporter RNA and plasmid DNA


title: PDIS9063-122


title: HARPE on IRF - replicate 1 in cells

description:
HARPE_IRF_inCells_rep1
Reporter RNA and plasmid DNA


title: 65d9_411e-PBMC

description:
Sample 65d9_411e, age 7
Measured on EPIC array


title: 65d9_411e-CBMC

description:
Sample 65d9_411e, birth
Measured on EPIC array

value: birth


title: PDIS9063-118


title: 11fb_4a49-PBMC

description:
Sample 11fb_4a49, age 7
Measured on EPIC array


title: 11fb_4a49-CBMC

description:
Sample 11fb_4a49, birth
Measured on EPIC array


title: PDIS9063-117


title: HARPE on DPR - replicate 1 in vitro (with Sarkosyl)

description:
HARPE_DPR_inVitro_Sarkosylrep1
Reporter RNA and plasmid DNA


title: Wt:371


title: HARPE on DPR - replicate 1 in vitro

description:
HARPE_DPRinVitro_rep1
Reporter RNA and plasmid DNA


title: HARPE on DPR - replicate 2 in vitro

description:
HARPE_DPRinVitro_rep2
Reporter RNA and plasmid DNA


title: PDIS9063-119


title: HARPE on DPR - replicate 2 in cells

description:
HARPE_DPR_inCells_rep2
Reporter RNA and plasmid DNA


title: A1Tg:398

value: ApoA-I Tg


title: HARPE on DPR - replicate 2 in vitro (with Sarkosyl)

description:
HARPE_DPR_inVitro_Sarkosylrep2
Reporter RNA and plasmid DNA


title: Wt:361


title: Wt:360


title: e3c7_4cdd-CBMC

description:
Sample e3c7_4cdd, birth
Measured on EPIC array


title: PDIS9063-114


title: PDIS9063-113


title: PDIS9063-116


title: PDIS9063-115


title: PDIS9063-112


title: 64ca_43ec-PBMC

description:
Sample 64ca_43ec, age 7
Measured on EPIC array


title: HARPE on DPE - replicate 2 in vitro

description:
HARPE_DPE_inVitro_rep2
Reporter RNA and plasmid DNA


title: HARPE on DPR - replicate 1 in cells

description:
HARPE_DPR_inCells_rep1
Reporter RNA and plasmid DNA


title: e3c7_4cdd-PBMC

description:
Sample e3c7_4cdd, age 7
Measured on EPIC array


title: 64ca_43ec-CBMC

description:
Sample 64ca_43ec, birth
Measured on EPIC array


title: A1Tg:393


title: A1Tg:395


title: Wt:363


title: A1Tg:384


title: PDIS9063-111


title: A1Tg:385


title: A1Tg:390


title: A1Tg:391


title: a994_46c0-PBMC

description:
Sample a994_46c0, age 7
Measured on EPIC array


title: PDIS9063-110


title: HARPE on DPE - replicate 1 in cells

description:
HARPE_DPE_inCells_rep1
Reporter RNA and plasmid DNA


title: HARPE on DPE - replicate 2 in cells

description:
HARPE_DPE_inCells_rep2
Reporter RNA and plasmid DNA


title: a994_46c0-CBMC

description:
Sample a994_46c0, birth
Measured on EPIC array


title: PDIS9063-109


title: HARPE on DPE - replicate 1 in vitro

description:
HARPE_DPE_inVitro_rep1
Reporter RNA and plasmid DNA


title: A1Tg:381


title: 62a4_487e-PBMC

description:
Sample 62a4_487e, age 7
Measured on EPIC array

value: Other


title: Organoids_d100_rep1

description: Sample 3

data_processing:
Cell ranger 2.0.1 was used to perform quality control and read counting of Ensemble genes with default parameter (v2.0.1) by mapping to the GRCh38 human genome.
Poor quality cells after the gene-cell data matrix was generated by cell ranger software using the Seurat package (v2.1.0) in Bioconductor.
The data were natural log transformed and normalized for scaling the sequencing depth to a total of 1e4 molecules per cell, followed by regressing-out the number of UMI using Seurat package.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.txt: File reports natural log transformed and normalized UMI counts.  1column/1cell.  Column header format:  barcode-Sample#

value: hESC stem cell line H9

value: hESCs-derived cerebral organoids

value: day 100


title: vOrganoids_d65_rep1

description: Sample 2

value: day 65


title: baf5_4b60-CBMC

description:
Sample baf5_4b60, birth
Measured on EPIC array

value: Black


title: PDIS9063-106

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: vOrganoids_d100_rep1

description: Sample 4


title: A1Tg:379


title: PDIS9063-107


title: 62a4_487e-CBMC

description:
Sample 62a4_487e, birth
Measured on EPIC array

value: Baltimore


title: Organoids_d65_rep1

description: Sample 1


title: d8cf_4012-PBMC

description:
Sample d8cf_4012, age 7
Measured on EPIC array

value: PBMCs

value: age 7

value: White


title: baf5_4b60-PBMC

description:
Sample baf5_4b60, age 7
Measured on EPIC array


title: U87EGFRvIII rep3

city: tianjin

first: Kai

last: Huang

address: anshan roud

institute: tianjin medical university

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were mapped to hg19 whole genome by Hisat2 software.
Cuffdiff software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format files include FPKM values

source_name: U87 cell

growth_protocol: The cells were routinely maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS, HyClone, Logan, UT, USA) in a humidified 5% CO2 atmosphere at 37℃.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U87 cells were transduced with lentivirus expressing vector or EGFRvIII.

value: glioblastoma cells

value: U87 cells transduced with lentivirus encoding EGFRvIII


title: U87EGFRvIII rep2


title: A1Tg:380

value: Male


title: PDIS9063-105


title: PDIS9063-104


title: PDIS9063-103


title: d8cf_4012-CBMC

description:
Sample d8cf_4012, birth
Measured on EPIC array

value: Cord blood

value: birth

value: Female


title: 29dc_4e34-PBMC

description:
Sample 29dc_4e34, age 7
Measured on EPIC array


title: U87EGFRvIII rep1


title: A1Tg:359

value: ApoA-I Tg


title: PDIS9063-101


title: 29dc_4e34-CBMC

description:
Sample 29dc_4e34, birth
Measured on EPIC array


title: A1KO:11

value: ApoA-I Null


title: 0229_43b6-PBMC

description:
Sample 0229_43b6, age 7
Measured on EPIC array


title: PDIS9063-100


title: U87ctrl rep2

value: U87 cells transduced with lentivirus encoding vector


title: A1KO:9


title: A1KO:10


title: 0229_43b6-CBMC

description:
Sample 0229_43b6, birth
Measured on EPIC array


title: U87ctrl rep1


title: 5b5b_4c56-PBMC

description:
Sample 5b5b_4c56, age 7
Measured on EPIC array


title: A1KO:12


title: PDIS9063-098


title: A1KO:7


title: 5b5b_4c56-CBMC

description:
Sample 5b5b_4c56, birth
Measured on EPIC array


title: PDIS9063-097


title: Ribo-seq Mettl3-/- mESCs replicate A

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Library strategy: Ribo-seq
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were pre-processed by trimming their linker (sequence CTGTAGGCACCATCAAT) and polyA removal with cutadapt.
Reads were aligned to mouse genome version mm10 with Bowtie aligner (parameters -v -m 16 -p 8 --max), where only uniquely aligned reads where used for further analyses.
Per gene, for translation calculation, reads were counted in the coding region excluding 15 and 6 nucleotides from the beginning and end of each coding sequence (CDS), respectively (Ingolia et al. 2009; McGlincy and Ingolia 2017).
For each gene and sample, Ribo-seq RPKM values were calculated
Genome_build: mm10
Supplementary_files_format_and_content: Ribo-seq RPKM

source_name: mouse embryonic stem cells

growth_protocol: Maintenance of mESCs was conducted in in 500 mL of High-glucose DMEM (ThermoScientific), 15% USDA certified fetal bovine serum (FBS - Biological Industries), 1 mM L-Glutamine (Biological Industries), 1% nonessential amino acids (Biological Industries), 0.1 mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Biological Industries), 1% Sodium-Pyruvate (Biological Industries), 10μg recombinant human LIF (Peprotech).

extract_protocol:
Cells were lysed in lysis buffer (20mM Tris 7.5, 150mM NaCl, 15mM MgCl2, 1mM dithiothreitol) supplemented with 0.5% triton, 30 U/ml Turbo DNase (Ambion) and 100μg/ml cycloheximide. The lysate was cleared by centrifugation, treated with RNase I for 45min and then loaded on a sucrose cushion. Pellet was resuspended in Trizol and then RNA was isolated from cells using chloroform-based separation.
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.

treatment_protocol: For ribosome profiling cells were treated with Cycloheximide as previously described (McGlincy and Ingolia 2017; Ingolia et al. 2009).

value: mouse embryonic stem cells (mESCs)


title: A1KO:6


title: U87ctrl rep3


title: PDIS9063-096


title: e001_49ca-PBMC

description:
Sample e001_49ca, age 7
Measured on EPIC array

value: Black


title: e001_49ca-CBMC

description:
Sample e001_49ca, birth
Measured on EPIC array


title: Ribo-seq Ythdf1/2/3-triple-KO mESCs replicate B


title: Ribo-seq Ythdf1/2/3-triple-KO mESCs replicate A


title: 2ac4_41fa-PBMC

description:
Sample 2ac4_41fa, age 7
Measured on EPIC array


title: PDIS9063-095

value: 129/CAST hybrid F1


title: PDIS9063-099

value: Embryonic stem cell


title: A1KO:4


title: A1KO:3


title: PDIS9063-092


title: 2ac4_41fa-CBMC

description:
Sample 2ac4_41fa, birth
Measured on EPIC array

value: Baltimore


title: PDIS9063-093


title: A1KO:2


title: Ribo-seq Ythdf3-/- mESCs replicate B


title: A1KO:1


title: Ribo-seq Ythdf3-/- mESCs replicate A


title: PDIS9063-091


title: 65f1_447a-PBMC

description:
Sample 65f1_447a, age 7
Measured on EPIC array

value: PBMCs


title: Ribo-seq Ythdf2-/- mESCs replicate B


title: PDIS9063-090


title: 65f1_447a-CBMC

description:
Sample 65f1_447a, birth
Measured on EPIC array


title: PDIS9063-088


title: 1513_4aa0-CBMC

description:
Sample 1513_4aa0, birth
Measured on EPIC array


title: PDIS9063-087


title: spleens_MOG33-35_Pertussis toxin_rep2

city: Nanjing

first: Zhengying

last: Bian

state: Jiangsu Province

address: 24 Tongjia Street

institute: China Pharmaceutical University

description: Gene expression in the EAE mouse-spleen tissue

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: spleens, MOG33-35, Pertussis toxin, replicate 2

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Mice were housed under a constant temperature and humidity and under a 12-hour light/12-hour dark cycle, with the lights on at 7:00 AM. Food and water were available ad libitum.

extract_protocol: Total RNA was extracted from mouse spleen using Trizol reagent (Intrivogen) according to the manufacturer's instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: EAE induction was performed using 2 mg/mL MOG35-55 immunization plus 200 ng pertussis toxin for each female C57BL/6 mouse via tail vein, and equivalent PBS instead of MOG35-55 was used as negative control. Spleen tissues were sepreated from three EAE model mice and three normal mice. Total RNAs were extracted from the spleen tissue of each mouse using TRIzol reagent.

value: female

value: 12 weeks


title: PDIS9063-086


title: Ribo-seq Ythdf1-/- mESCs replicate A


title: f3e1_47fb-PBMC

description:
Sample f3e1_47fb, age 7
Measured on EPIC array

value: age 7


title: MaleMouse_092718_PC_K64_BeadLot032018

description:
single-nucleus gene expression data based on 3' transcript counts
mouse.nuc.cortical_interneurons.raw.dge.txt.gz

source_name: P60-70 Male Mice

tag: platform

value: Dropseq

value: Neocortex; V1


title: Ribo-seq WT mESCs replicate B

value: WT


title: MaleMouse_092718_PC_K64_BeadLot103117


title: PDIS9063-085


title: Ribo-seq WT mESCs replicate A


title: spleens_MOG33-35_Pertussis toxin_rep3

source_name: spleens, MOG33-35, Pertussis toxin, replicate 3


title: FemaleMouse_092818_PC_K64

source_name: P60-70 Female Mice


title: PDIS9063-084


title: 510c_4155-PBMC

description:
Sample 510c_4155, age 7
Measured on EPIC array

value: Male


title: spleens_PBS_rep2

description: Gene expression in the normal mouse-spleen tissue

source_name: spleens, PBS, replicate 2


title: MaleMouse_092718_FC_K64_BeadLot032018

value: Neocortex; PFC


title: spleens_MOG33-35_Pertussis toxin_rep1

source_name: spleens, MOG33-35, Pertussis toxin, replicate 1


title: Ythdf2+/+ round spermatids [Ythdf2_WT_round_8]

description:
Ythdf2_WT_round_8_S8
processed data file: DESeq_Ythdf2_sperm.txt

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were trimmed using cutadapt (Martin 2011) (parameters: -a ADAPTER1 -a “A{10}” -a “T{10}” -A “A{10}” -A “T{10}” –times 2 -q 20 -m 25).
Reads were mapped to genome mm10 using STAR (Dobin et al. 2013) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic).
Sample counting was done using STAR, quantifying mm10 RefSeq annotated genes.
Normalization of the counts and differential expression analysis was performed using DESeq2 (Love et al. 2014) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 output

source_name: Ythdf2+/+ round spermatids

extract_protocol:
Male germ cell populations were isolated using FACS. Total RNA was extracted using Trizol, followed by ethanol precipitation.
Total RNA was purified using rRNA depletion (Ribo-Zero rRna removal Kit, Illumina), followed by library preparation using ScriptSeq V2 RNA-seq Library Preparation Kit (Illumina) according to manufacturer’s instruction.

value: CB6F1 X C57BL/6

value: mouse round spermatids

tag: library strategy

value: Ribo-Zero RNA-seq


title: spleens_PBS_rep3

source_name: spleens, PBS, replicate 3


title: Ribo-seq Ythdf2-/- mESCs replicate A

value: mouse embryonic stem cells (mESCs)


title: 1513_4aa0-PBMC

description:
Sample 1513_4aa0, age 7
Measured on EPIC array

source_name: Human PBMCs at age 7

value: Black


title: 510c_4155-CBMC

description:
Sample 510c_4155, birth
Measured on EPIC array

source_name: Human cord blood at birth

value: Cord blood

value: birth


title: Ribo-seq Ythdf1-/- mESCs replicate B


title: spleens_PBS_rep1

source_name: spleens, PBS, replicate 1


title: PDIS9063-083

source_name: 129/CAST hybrid mESC

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: Ythdf2-/- round spermatids, replicate 2 [Ythdf2_KO_round_5]

description:
Ythdf2_KO_round_5_S5
processed data file: DESeq_Ythdf2_sperm.txt

source_name: Ythdf2-/- round spermatids


title: MaleMouse_092718_FC_K64_BeadLot103117


title: f947_445f-PBMC

description:
Sample f947_445f, age 7
Measured on EPIC array

value: PBMCs

value: Baltimore


title: f3e1_47fb-CBMC

description:
Sample f3e1_47fb, birth
Measured on EPIC array

value: Female


title: f947_445f-CBMC

description:
Sample f947_445f, birth
Measured on EPIC array


title: PDIS9063-082


title: Ythdf2-/- round spermatids, replicate 1 [Ythdf2_KO_round_11]

description:
Ythdf2_KO_round_11_S11
processed data file: DESeq_Ythdf2_sperm.txt


title: PDIS9063-081


title: Ythdf2+/- control post-GV oocytes, replicate 2 [Ythdf2_WT_oocyte_3]

description:
Ythdf2_WT_3
processed data file: DESeq_Ythdf2_oocytes.txt

source_name: Ythdf2+/- control post-GV oocytes

extract_protocol:
Oocytes were lysed using Smart-seq2 lysis buffer.
Library was prepared according to SMART-seq2 protocol as previously described (Simone Picelli et al, 2014), with few changes: oocytes from each mouse were collected in 3 ul M2 and added to 7.9ul lysis buffer. Additional 1.1 ul of DDW was added prior to the library preparation.

value: post-germinal vesicle (GV) stage mouse oocytes


title: Ythdf2+/- control post-GV oocytes, replicate 2 [Ythdf2_WT_oocyte_2]

description:
Ythdf2_WT_2
processed data file: DESeq_Ythdf2_oocytes.txt


title: ce96_4e2b-PBMC

description:
Sample ce96_4e2b, age 7
Measured on EPIC array

value: age 7


title: PDIS9063-080


title: ce96_4e2b-CBMC

description:
Sample ce96_4e2b, birth
Measured on EPIC array


title: Ythdf2+/- control post-GV oocytes, replicate 1 [Ythdf2_WT_oocyte_1]

description:
Ythdf2_WT_1
processed data file: DESeq_Ythdf2_oocytes.txt


title: PDIS9063-078


title: 099a_4799-PBMC

description:
Sample 099a_4799, age 7
Measured on EPIC array


title: Ythdf2-/- post-GV oocytes, replicate 2 [Ythdf2_KO_oocyte_2]

description:
Ythdf2_KO_2
processed data file: DESeq_Ythdf2_oocytes.txt

source_name: Ythdf2-/- post-GV oocytes


title: Ctl.M2

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

data_processing:
Raw single cell RNA-sequencing data were processed using the CellRanger (10x Genomics) analysis pipeline. mkfastq was used to demultiplex the raw Illumina BCL files into fastq format. count was used to align the reads to the mouse reference genome (mm10), filter reads, count barcodes, and count UMIs. The output from count yields digital gene expression (DGE) matrices for each sample that contain the UMI counts per gene, per cell barcode. DGEs were loaded into the single cell transcriptomic data analysis suite Seurat, then normalized.
We excluded droplets with fewer than 1,000 expressed genes and we excluded genes that were measured in fewer than three cells, leaving a total of 5,258 cells and 17,143 genes expressed across the 8 samples.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with gene counts after filtering droplets and genes

source_name: hippocampal cells

extract_protocol:
During sacrifice, mice were perfused with a saline solution. The hippocampal region of the brain was isolated, and then dissociated into a viable single cell suspension using the Adult Mouse and Rat Brain Dissociation kit (Miltenyi) using a gentleMACS Octo Dissociator with Heaters automated tissue dissociation instrument.  Cells were cryopreserved using Recovery Cell Culture Freezing Medium (Thermo Fisher). Viability and cell concentrations were quantified upon thawing for single cell analysis using a Luna FL Automated Cell Counter (Logos) by co-quantification of fluorescence from acridine orange and propidium iodide dyes.
Single cells were processed for high throughput RNA sequencing using the Chromium (10x Genomics) instrument, attempting to capture approximately 3,000-5,000 cells per sample.

treatment_protocol: Post-pubertal virgin a/a females (~5 weeks old) were randomized into exposure groups: control or drinking water containing 32ppm Pb-acetate. This dose and route of exposure was designed to be relevant to human perinatal exposure. After an initial two weeks of exposure, females were mated with a/a males. Exposure through drinking water continued through gestation and lactation. After weaning, 1 male and 1 female wildtype (a/a) offspring per litter were maintained on Pb-free drinking water. At 5 months, mice were sacrificed for experimental analyses. All animals had access to food and water ad libitum throughout the experiment, were housed in polycarbonate-free cages, and were maintained in accordance with the guidelines set by the Institute of Laboratory Animal Resources.

tag: treatment

value: control diet


title: Ctl.F1


title: PDIS9063-079


title: Pb.M2

value: Male

value: Pb


title: Pb.F2


title: PDIS9063-077


title: Ythdf2-/- post-GV oocytes, replicate 1 [Ythdf2_KO_oocyte_1]

description:
Ythdf2_KO_1
processed data file: DESeq_Ythdf2_oocytes.txt

value: CB6F1 X C57BL/6


title: Ctl.M1


title: 099a_4799-CBMC

description:
Sample 099a_4799, birth
Measured on EPIC array


title: 5498_40e4-PBMC

description:
Sample 5498_40e4, age 7
Measured on EPIC array


title: PDIS9063-076


title: Mettl3f/f Zp3-Cre- GV oocytes replicate 4 [Mettl3_control_mature_oocyte_4]

description:
Mettl3_control_mature_4
processed data file: DESeq_Mettl3_oocytes.txt

source_name: Mettl3f/f Zp3-Cre- GV oocytes

value: Mettl3f/f Zp3-Cre-

value: germinal vesicle (GV) stage mouse oocytes


title: Ctl.F2


title: Pb.M1


title: 5498_40e4-CBMC

description:
Sample 5498_40e4, birth
Measured on EPIC array


title: PDIS9063-075


title: Pb.F1


title: Mettl3f/f Zp3-Cre- GV oocytes replicate 3 [Mettl3_control_mature_oocyte_3]

description:
Mettl3_control_mature_3
processed data file: DESeq_Mettl3_oocytes.txt


title: 3f87_454c-PBMC

description:
Sample 3f87_454c, age 7
Measured on EPIC array


title: 3f87_454c-CBMC

description:
Sample 3f87_454c, birth
Measured on EPIC array


title: Mettl3f/f Zp3-Cre- GV oocytes replicate 2 [Mettl3_control_mature_oocyte_2]

description:
Mettl3_control_mature_2
processed data file: DESeq_Mettl3_oocytes.txt


title: PDIS9063-073


title: Mettl3f/f Zp3-Cre- GV oocytes replicate 1 [Mettl3_control_mature_oocyte_1]

description:
Mettl3_control_mature_1
processed data file: DESeq_Mettl3_oocytes.txt


title: cfea_470d-PBMC

description:
Sample cfea_470d, age 7
Measured on EPIC array

value: Other


title: 45a5_4e0f-PBMC

description:
Sample 45a5_4e0f, age 7
Measured on EPIC array

value: Black


title: Mettl3f/f Zp3-Cre+ GV oocytes replicate 3 [Mettl3_KO_mature_oocyte_3]

description:
Mettl3_KO_mature_3
processed data file: DESeq_Mettl3_oocytes.txt

source_name: Mettl3f/f Zp3-Cre+ GV oocytes

value: Mettl3f/f Zp3-Cre+


title: Mettl3f/f Zp3-Cre+ GV oocytes replicate 2 [Mettl3_KO_mature_oocyte_2]

description:
Mettl3_KO_mature_2
processed data file: DESeq_Mettl3_oocytes.txt


title: cfea_470d-CBMC

description:
Sample cfea_470d, birth
Measured on EPIC array

value: Cord blood

value: birth


title: PDIS9063-072

value: 129/CAST hybrid F1

value: Embryonic stem cell


title: PDIS9063-071


title: Mettl3f/f Zp3-Cre+ GV oocytes replicate 1 [Mettl3_KO_mature_oocyte_1]

description:
Mettl3_KO_mature_1
processed data file: DESeq_Mettl3_oocytes.txt


title: 45a5_4e0f-CBMC

description:
Sample 45a5_4e0f, birth
Measured on EPIC array

value: Baltimore


title: PDIS9063-070


title: A1KO:8

source_name: Homograft B16F10L-luciferase tumor 7 days post sub cutaneous inoculation

value: ApoA-I Null


title: eb8a_436e-PBMC

description:
Sample eb8a_436e, age 7
Measured on EPIC array

value: PBMCs


title: PDIS9063-069


title: eb8a_436e-CBMC

description:
Sample eb8a_436e, birth
Measured on EPIC array